Posters
Poster presentations provide an ideal opportunity for the exchange of ideas and expertise within and between the various computational science domains represented at the PASC Conference.
Sixty-two poster presentations have been accepted for PASC18.
CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects
, Venkat Kapil (EPFL, Switzerland)
+ Abstract { "session": {"id":"sess143","title":"Posters in Chemistry and Materials","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Chemistry and Materials"],"slots":[{"id":"post163","type":"poster","title":"CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects","begin_time":"19:30","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Molecules and materials that contain light nuclei exhibit considerable deviations from classical behavior which are most pronounced at cryogenic temperatures, but extend up to room temperature and beyond. Properties such as dissociation of water in bulk phase or on catalytic surfaces, heat capacity, band gaps etc. are influenced by the quantum nature of nuclei. The precise description of quantum nuclear fluctuations in atomistic simulations is possible by employing path integral techniques, which involve a considerable computational overhead due to the need for simulating multiple replicas of the system. Consequently, simulations combined with advanced electronic structure methods are still prohibitive. In this talk, I will present some methodologies based on high order factorizations of the Boltzmann operator and multiple time steps in real and imaginary time, that can practically reduce the computational cost of including nuclear quantum fluctuations down to zero, while keeping interatomic interactions at high levels of electronic structure theory.","filename":"post163s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post168","type":"poster","title":"CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows","begin_time":"19:42","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, there has been a great increase in the performance and capabilities of computers. Materials science has greatly benefited from this computational boom, which is continuously boosting research, the discovery of new materials and the development of simulation codes. The \u0022materials by design\u0022 approach has become very powerful, but requires running large numbers of simulations and building databases of computed properties. A key challenge is the need to automatically prepare, execute and monitor workflows of calculations, and then retrieve and store the results in a format that is easy to browse and query. The AiiDA open-source platform[1] provides researchers with a tool that fulfills those requirements, by implementing the four \u0022ADES\u0022 requirement pillars of Automation, Data, Environment and Sharing. AiiDA is continuously being developed and has matured into an ecosystem with multiple backend options for increased performance and flexibility, a powerful graph querying tool for easy result analysis, a redesigned plugin system to simplify external user contributions, new more powerful and easy to write workflows and a continuous integration system to ensure the stability of the platform. [1]https:\/\/doi.org\/10.1016\/j.commatsci.2015.09.013.","filename":"post168s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post171","type":"poster","title":"CHM03 - Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation","begin_time":"19:54","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Nucleation has many implications in science and technology, including metal casting, the assembly of microtubules in cells, and the formation of water droplets in the atmosphere. Because the experimental investigation of dynamical nucleation processes is very difficult, much attention has been paid to atomistic simulation efforts in the last two decades. However, atomistic simulation studies of nucleation face two major challenges. Firstly, the free energy barrier separating the metastable phase and the stable phase can be very high, making nucleation times much larger than the time scales accessible to molecular dynamics simulations. Secondly, it is highly non-trivial to develop a predictive macroscopic model of nucleation using the microscopic quantities directly obtained from atomistic simulations. In this poster, I aim to address the aforementioned difficulties. I will first briefly introduce state-of-the-art enhanced sampling methods for atomistic simulations, and their applications to studying homogeneous nucleation. I will then discuss our latest thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework to verify and extend classical nucleation theory.","bio":"","contributors":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post143","type":"poster","title":"CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a\u00a0Cobalt-Cubane","begin_time":"20:06","end_time":"20:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Facing a potentially serious energy crisis towards the end of the century, development of renewable energy sources has become one of the \u0022hot\u0022 topics in modern day research. Among many different solutions, artificial water splitting promises to be a valuable source of sustainable and affordable energy in the future. However, the improvement of existing catalysts, as well as the design of novel catalysts, is a perquisite towards the successful implementation of this technology into devices and powerplants. Informed design requires a firm understanding of underlying reaction mechanisms and how certain bottlenecks might be overcome. We employ ab initio molecular dynamics simulations to an explicitly solvated water oxidation catalyst (Co4(dpO(OH))4) in order to elucidate the elementary reaction steps and propose guidelines for the design of novel catalysts. In our studies we do not only study the catalyst itself \u2013 we also pay close attention to the crucial solute-solvent interactions which were found to play a decisive role in intramolecular proton transfer reactions giving access to a large variety of possible intermediates during the water oxidation cycles.","filename":"post143s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post127","type":"poster","title":"CHM05 - Datamining of Magnetic Double Perovskites","begin_time":"20:18","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Double perovskites (DPs) are a class of materials with AB\u0027B\u0027\u0027C perovskite-like structures. Given the element for the A site, the choice of B\u0027 and B\u0027\u0027 lead to different properties (conducting\/insulating\/semiconducting behaviour, different magnetic properties, etc. [1]). Even though a fair number of B\u0027\/B\u0027\u0027 combinations have been studied, there\u0027s still a lot of \u0022uncharted territory\u0022 to explore. [1] We adopt a data-driven approach, generating a database of computed formation energies for more than 1000 A = Sr, Ba, Ca DPs. All the calculations and database generation and management have been done the through AiiDA materials\u0027 informatics infrastructure. [2] Comparison with data available in the Materials Project (MP) database is promising, with formation energy errors less than 50 meV\/atom. We retrieve the structures of all the competing phases from the MP databse, we generate convex hulls and we give stability predictions for all the DPs analyzed in this study. With a specific focus on A = Sr, B\u0027 or B\u0027\u0027 = Ir DPs, we are able to determine the stability of compounds already present in literature, and give stability predictions for compounds for which there isn\u0027t experimental or theoretical data available. [1] S. Vasala et al., Progress in Solid State Chemistry 43 (2015). [2] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016).","filename":"post127s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true}]},{"id":"post182","type":"poster","title":"CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations","begin_time":"20:30","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Non-Bonded Interactions are the heart of every particle simulation program. Over 90% of the time spent in classical MD simulations is on this step of computing forces due to non-bonded interactions. Current methods don\u0027t offer scalability properties usable in the exascale. It is also a huge software engineering overhead to use new \u0027exascale-friendly\u0027 methods on the most popular packages. We also need to expand the realm of the physics which our interactions describe. Particle simulation packages presently restrict their force fields and methods catering to specific domains. We propose an API to bring modularity and enable proliferation of methods, force fields (physics), parallelisation paradigms and hardware optimisations. The vision is to be able to call alternative back-ends to any of these on custom MD programs as well as popular software packages. This separation of concerns of the most resource intensive part from the rest of the MD pipeline is important for focussed development for the emerging exascale platforms. This would also enable particle simulations to be practical for usage in more domains such as astrophysics, fluid mechanics, etc. This poster highlights our vision, current progress and preliminary results.","filename":"post182s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post161","type":"poster","title":"CHM07 - DFT+U Gamma-Surfaces of UO2","begin_time":"20:42","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The nuclear fuel material uranium dioxide, UO2, undergoes severe microstructural changes along its fuel cycle, forming extended defects like dislocations. Experimental characterization of structural deformations in UO2 is difficult due to safety and cost, making computer simulations vital to bridge this gap. We have carried out a systematic DFT+U study on {001}, {110} and {111} oriented gamma-surfaces of UO2, i.e. the potential energy surfaces of displacement of one crystal part with respect to the other. The DFT+U scheme relies on our earlier work on f-orbitals occupations\u0027 control. Using similar strategy, all possible f-orbital occupation patterns were considered both via single point energy calculations and the subsequent structure optimization of UO2. The f-orbital occupations patterns resulting in lowest energy and minimal deformed structures were further used for gamma-surface calculations. This procedure was repeated for the {001}, {110} and {111} oriented planes. The resulting gamma-surfaces calculated at the DFT+U level of theory are both qualitatively and quantitatively different, i.e. the shape and the energies, from those computed previously by us and others using any empirical potential. It is the result of a peculiar bonding interactions imposed by the resulting geometries during the gamma-surface calculation in conjunction with the specific f-orbital occupation pattern.","filename":"post161s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post148","type":"poster","title":"CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems","begin_time":"20:54","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Sparse matrix-matrix multiplication is an essential building block for a wide range of algorithms in various scientific fields. For this task, the sparse matrix library DBCSR (Distributed Block Compressed Sparse Row) has been developed. Its multi-layered structure automatically takes care of and optimizes several computational aspects like parallelism (MPI, OpenMP, CUDA), data (cache) locality and on-the-fly filtering. Here we report on the latest performance optimization we implemented for improving the CUDA and OpenMP parallelization. For the former, a novel algorithm was implemented for the work-scheduling of the multiplication of the matrix blocks. The latter specifically addresses many-core computing systems, namely Intel Xeon Phi, where we implemented an OpenMP task-based parallel algorithm in order to improve the load-balance by means of a more dynamic scheduling of the workload. We report the performance results, in terms of time-to-solution and energy-to-solution,\u00a0of DBCSR\u00a0on systems with Intel Xeon Phi Knights Landing (KNL) processors,\u00a0and\u00a0systems with Intel Xeon CPUs,\u00a0and NVIDIA GPUs. Finally, we analyze the performance of the library when using compilers from different vendors (GNU, Intel, NAG, PGI, FLANG).","filename":"post148s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post165","type":"poster","title":"CHM09 - Materials Cloud: A Platform for Open Materials Science","begin_time":"21:06","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Materials Cloud (www.materialscloud.org) is an Open Science web portal, built to enable seamless sharing and dissemination of resources in computational materials science. It includes educational material and videos, interactive tools, cloud simulation services based on AiiDA[1] and Jupyter, and displays interactively both curated data along with the corresponding raw data. Being powered by AiiDA, all data is accompanied by their full provenance, allowing peers to inspect how the results have been obtained, download individual files or the whole database, and start their research from where the original authors left off. Combined also with the Archive section, where DOIs are assigned to each entry (making them citable), Materials Cloud empowers data-based discovery, while being compliant with data management plans and the FAIR principles. Among the curated data, it features SSSP, a library of pseudopotentials for electronic-structure calculations, tested and optimized for accuracy and efficiency, as well as a large database of novel 2D materials [2] with their materials properties. [1]G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net. [2]N. Mounet et al., Nat. Nanotech. doi:10.1038\/s41565-017-0035-5 (2018)","filename":"post165s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post176","type":"poster","title":"CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors","begin_time":"21:18","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, machine learning has become a popular method to predict atomic-scale properties of molecular and material systems. While perhaps the most popular applications of machine learning in Chemistry and Materials Science have been to the potential energy surface of a system, a full statistical-mechanical description requires not only the potential energy but also tensorial properties such as dipole moments and polarizabilities. A machine-learning model for these properties must give predictions that transform covariantly with rigid-body rotations of the system, which adds an extra layer of complexity. This poster describes a framework for machine-learning of tensor properties of arbitrary ranks, accounting fully for the covariance of these properties. This method is an extension of Gaussian process regression (GPR), and involves a generalization of the similarity function, or kernel, of GPR to a tensorial kernel. This kernel builds upon the smooth overlap of atomic positions\u00a0(SOAP) kernel used for scalar properties. Results for prediction of electric response tensors of several orders, for a number of water oligomers and for bulk water, show that this method is an extremely promising one for machine-learning of these properties.","filename":"post176s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}]}, "slot": {"id":"post163","type":"poster","title":"CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects","begin_time":"19:30","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Molecules and materials that contain light nuclei exhibit considerable deviations from classical behavior which are most pronounced at cryogenic temperatures, but extend up to room temperature and beyond. Properties such as dissociation of water in bulk phase or on catalytic surfaces, heat capacity, band gaps etc. are influenced by the quantum nature of nuclei. The precise description of quantum nuclear fluctuations in atomistic simulations is possible by employing path integral techniques, which involve a considerable computational overhead due to the need for simulating multiple replicas of the system. Consequently, simulations combined with advanced electronic structure methods are still prohibitive. In this talk, I will present some methodologies based on high order factorizations of the Boltzmann operator and multiple time steps in real and imaginary time, that can practically reduce the computational cost of including nuclear quantum fluctuations down to zero, while keeping interatomic interactions at high levels of electronic structure theory.","filename":"post163s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}] } Presentation
CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows
, Spyros Zoupanos (EPFL, Switzerland)
+ Abstract { "session": {"id":"sess143","title":"Posters in Chemistry and Materials","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Chemistry and Materials"],"slots":[{"id":"post163","type":"poster","title":"CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects","begin_time":"19:30","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Molecules and materials that contain light nuclei exhibit considerable deviations from classical behavior which are most pronounced at cryogenic temperatures, but extend up to room temperature and beyond. Properties such as dissociation of water in bulk phase or on catalytic surfaces, heat capacity, band gaps etc. are influenced by the quantum nature of nuclei. The precise description of quantum nuclear fluctuations in atomistic simulations is possible by employing path integral techniques, which involve a considerable computational overhead due to the need for simulating multiple replicas of the system. Consequently, simulations combined with advanced electronic structure methods are still prohibitive. In this talk, I will present some methodologies based on high order factorizations of the Boltzmann operator and multiple time steps in real and imaginary time, that can practically reduce the computational cost of including nuclear quantum fluctuations down to zero, while keeping interatomic interactions at high levels of electronic structure theory.","filename":"post163s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post168","type":"poster","title":"CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows","begin_time":"19:42","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, there has been a great increase in the performance and capabilities of computers. Materials science has greatly benefited from this computational boom, which is continuously boosting research, the discovery of new materials and the development of simulation codes. The \u0022materials by design\u0022 approach has become very powerful, but requires running large numbers of simulations and building databases of computed properties. A key challenge is the need to automatically prepare, execute and monitor workflows of calculations, and then retrieve and store the results in a format that is easy to browse and query. The AiiDA open-source platform[1] provides researchers with a tool that fulfills those requirements, by implementing the four \u0022ADES\u0022 requirement pillars of Automation, Data, Environment and Sharing. AiiDA is continuously being developed and has matured into an ecosystem with multiple backend options for increased performance and flexibility, a powerful graph querying tool for easy result analysis, a redesigned plugin system to simplify external user contributions, new more powerful and easy to write workflows and a continuous integration system to ensure the stability of the platform. [1]https:\/\/doi.org\/10.1016\/j.commatsci.2015.09.013.","filename":"post168s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post171","type":"poster","title":"CHM03 - Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation","begin_time":"19:54","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Nucleation has many implications in science and technology, including metal casting, the assembly of microtubules in cells, and the formation of water droplets in the atmosphere. Because the experimental investigation of dynamical nucleation processes is very difficult, much attention has been paid to atomistic simulation efforts in the last two decades. However, atomistic simulation studies of nucleation face two major challenges. Firstly, the free energy barrier separating the metastable phase and the stable phase can be very high, making nucleation times much larger than the time scales accessible to molecular dynamics simulations. Secondly, it is highly non-trivial to develop a predictive macroscopic model of nucleation using the microscopic quantities directly obtained from atomistic simulations. In this poster, I aim to address the aforementioned difficulties. I will first briefly introduce state-of-the-art enhanced sampling methods for atomistic simulations, and their applications to studying homogeneous nucleation. I will then discuss our latest thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework to verify and extend classical nucleation theory.","bio":"","contributors":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post143","type":"poster","title":"CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a\u00a0Cobalt-Cubane","begin_time":"20:06","end_time":"20:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Facing a potentially serious energy crisis towards the end of the century, development of renewable energy sources has become one of the \u0022hot\u0022 topics in modern day research. Among many different solutions, artificial water splitting promises to be a valuable source of sustainable and affordable energy in the future. However, the improvement of existing catalysts, as well as the design of novel catalysts, is a perquisite towards the successful implementation of this technology into devices and powerplants. Informed design requires a firm understanding of underlying reaction mechanisms and how certain bottlenecks might be overcome. We employ ab initio molecular dynamics simulations to an explicitly solvated water oxidation catalyst (Co4(dpO(OH))4) in order to elucidate the elementary reaction steps and propose guidelines for the design of novel catalysts. In our studies we do not only study the catalyst itself \u2013 we also pay close attention to the crucial solute-solvent interactions which were found to play a decisive role in intramolecular proton transfer reactions giving access to a large variety of possible intermediates during the water oxidation cycles.","filename":"post143s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post127","type":"poster","title":"CHM05 - Datamining of Magnetic Double Perovskites","begin_time":"20:18","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Double perovskites (DPs) are a class of materials with AB\u0027B\u0027\u0027C perovskite-like structures. Given the element for the A site, the choice of B\u0027 and B\u0027\u0027 lead to different properties (conducting\/insulating\/semiconducting behaviour, different magnetic properties, etc. [1]). Even though a fair number of B\u0027\/B\u0027\u0027 combinations have been studied, there\u0027s still a lot of \u0022uncharted territory\u0022 to explore. [1] We adopt a data-driven approach, generating a database of computed formation energies for more than 1000 A = Sr, Ba, Ca DPs. All the calculations and database generation and management have been done the through AiiDA materials\u0027 informatics infrastructure. [2] Comparison with data available in the Materials Project (MP) database is promising, with formation energy errors less than 50 meV\/atom. We retrieve the structures of all the competing phases from the MP databse, we generate convex hulls and we give stability predictions for all the DPs analyzed in this study. With a specific focus on A = Sr, B\u0027 or B\u0027\u0027 = Ir DPs, we are able to determine the stability of compounds already present in literature, and give stability predictions for compounds for which there isn\u0027t experimental or theoretical data available. [1] S. Vasala et al., Progress in Solid State Chemistry 43 (2015). [2] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016).","filename":"post127s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true}]},{"id":"post182","type":"poster","title":"CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations","begin_time":"20:30","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Non-Bonded Interactions are the heart of every particle simulation program. Over 90% of the time spent in classical MD simulations is on this step of computing forces due to non-bonded interactions. Current methods don\u0027t offer scalability properties usable in the exascale. It is also a huge software engineering overhead to use new \u0027exascale-friendly\u0027 methods on the most popular packages. We also need to expand the realm of the physics which our interactions describe. Particle simulation packages presently restrict their force fields and methods catering to specific domains. We propose an API to bring modularity and enable proliferation of methods, force fields (physics), parallelisation paradigms and hardware optimisations. The vision is to be able to call alternative back-ends to any of these on custom MD programs as well as popular software packages. This separation of concerns of the most resource intensive part from the rest of the MD pipeline is important for focussed development for the emerging exascale platforms. This would also enable particle simulations to be practical for usage in more domains such as astrophysics, fluid mechanics, etc. This poster highlights our vision, current progress and preliminary results.","filename":"post182s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post161","type":"poster","title":"CHM07 - DFT+U Gamma-Surfaces of UO2","begin_time":"20:42","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The nuclear fuel material uranium dioxide, UO2, undergoes severe microstructural changes along its fuel cycle, forming extended defects like dislocations. Experimental characterization of structural deformations in UO2 is difficult due to safety and cost, making computer simulations vital to bridge this gap. We have carried out a systematic DFT+U study on {001}, {110} and {111} oriented gamma-surfaces of UO2, i.e. the potential energy surfaces of displacement of one crystal part with respect to the other. The DFT+U scheme relies on our earlier work on f-orbitals occupations\u0027 control. Using similar strategy, all possible f-orbital occupation patterns were considered both via single point energy calculations and the subsequent structure optimization of UO2. The f-orbital occupations patterns resulting in lowest energy and minimal deformed structures were further used for gamma-surface calculations. This procedure was repeated for the {001}, {110} and {111} oriented planes. The resulting gamma-surfaces calculated at the DFT+U level of theory are both qualitatively and quantitatively different, i.e. the shape and the energies, from those computed previously by us and others using any empirical potential. It is the result of a peculiar bonding interactions imposed by the resulting geometries during the gamma-surface calculation in conjunction with the specific f-orbital occupation pattern.","filename":"post161s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post148","type":"poster","title":"CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems","begin_time":"20:54","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Sparse matrix-matrix multiplication is an essential building block for a wide range of algorithms in various scientific fields. For this task, the sparse matrix library DBCSR (Distributed Block Compressed Sparse Row) has been developed. Its multi-layered structure automatically takes care of and optimizes several computational aspects like parallelism (MPI, OpenMP, CUDA), data (cache) locality and on-the-fly filtering. Here we report on the latest performance optimization we implemented for improving the CUDA and OpenMP parallelization. For the former, a novel algorithm was implemented for the work-scheduling of the multiplication of the matrix blocks. The latter specifically addresses many-core computing systems, namely Intel Xeon Phi, where we implemented an OpenMP task-based parallel algorithm in order to improve the load-balance by means of a more dynamic scheduling of the workload. We report the performance results, in terms of time-to-solution and energy-to-solution,\u00a0of DBCSR\u00a0on systems with Intel Xeon Phi Knights Landing (KNL) processors,\u00a0and\u00a0systems with Intel Xeon CPUs,\u00a0and NVIDIA GPUs. Finally, we analyze the performance of the library when using compilers from different vendors (GNU, Intel, NAG, PGI, FLANG).","filename":"post148s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post165","type":"poster","title":"CHM09 - Materials Cloud: A Platform for Open Materials Science","begin_time":"21:06","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Materials Cloud (www.materialscloud.org) is an Open Science web portal, built to enable seamless sharing and dissemination of resources in computational materials science. It includes educational material and videos, interactive tools, cloud simulation services based on AiiDA[1] and Jupyter, and displays interactively both curated data along with the corresponding raw data. Being powered by AiiDA, all data is accompanied by their full provenance, allowing peers to inspect how the results have been obtained, download individual files or the whole database, and start their research from where the original authors left off. Combined also with the Archive section, where DOIs are assigned to each entry (making them citable), Materials Cloud empowers data-based discovery, while being compliant with data management plans and the FAIR principles. Among the curated data, it features SSSP, a library of pseudopotentials for electronic-structure calculations, tested and optimized for accuracy and efficiency, as well as a large database of novel 2D materials [2] with their materials properties. [1]G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net. [2]N. Mounet et al., Nat. Nanotech. doi:10.1038\/s41565-017-0035-5 (2018)","filename":"post165s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post176","type":"poster","title":"CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors","begin_time":"21:18","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, machine learning has become a popular method to predict atomic-scale properties of molecular and material systems. While perhaps the most popular applications of machine learning in Chemistry and Materials Science have been to the potential energy surface of a system, a full statistical-mechanical description requires not only the potential energy but also tensorial properties such as dipole moments and polarizabilities. A machine-learning model for these properties must give predictions that transform covariantly with rigid-body rotations of the system, which adds an extra layer of complexity. This poster describes a framework for machine-learning of tensor properties of arbitrary ranks, accounting fully for the covariance of these properties. This method is an extension of Gaussian process regression (GPR), and involves a generalization of the similarity function, or kernel, of GPR to a tensorial kernel. This kernel builds upon the smooth overlap of atomic positions\u00a0(SOAP) kernel used for scalar properties. Results for prediction of electric response tensors of several orders, for a number of water oligomers and for bulk water, show that this method is an extremely promising one for machine-learning of these properties.","filename":"post176s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}]}, "slot": {"id":"post168","type":"poster","title":"CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows","begin_time":"19:42","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, there has been a great increase in the performance and capabilities of computers. Materials science has greatly benefited from this computational boom, which is continuously boosting research, the discovery of new materials and the development of simulation codes. The \u0022materials by design\u0022 approach has become very powerful, but requires running large numbers of simulations and building databases of computed properties. A key challenge is the need to automatically prepare, execute and monitor workflows of calculations, and then retrieve and store the results in a format that is easy to browse and query. The AiiDA open-source platform[1] provides researchers with a tool that fulfills those requirements, by implementing the four \u0022ADES\u0022 requirement pillars of Automation, Data, Environment and Sharing. AiiDA is continuously being developed and has matured into an ecosystem with multiple backend options for increased performance and flexibility, a powerful graph querying tool for easy result analysis, a redesigned plugin system to simplify external user contributions, new more powerful and easy to write workflows and a continuous integration system to ensure the stability of the platform. [1]https:\/\/doi.org\/10.1016\/j.commatsci.2015.09.013.","filename":"post168s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}] } Presentation
CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a Cobalt-Cubane
, Mauro Schilling (University of Zurich, Switzerland)
+ Abstract { "session": {"id":"sess143","title":"Posters in Chemistry and Materials","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Chemistry and Materials"],"slots":[{"id":"post163","type":"poster","title":"CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects","begin_time":"19:30","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Molecules and materials that contain light nuclei exhibit considerable deviations from classical behavior which are most pronounced at cryogenic temperatures, but extend up to room temperature and beyond. Properties such as dissociation of water in bulk phase or on catalytic surfaces, heat capacity, band gaps etc. are influenced by the quantum nature of nuclei. The precise description of quantum nuclear fluctuations in atomistic simulations is possible by employing path integral techniques, which involve a considerable computational overhead due to the need for simulating multiple replicas of the system. Consequently, simulations combined with advanced electronic structure methods are still prohibitive. In this talk, I will present some methodologies based on high order factorizations of the Boltzmann operator and multiple time steps in real and imaginary time, that can practically reduce the computational cost of including nuclear quantum fluctuations down to zero, while keeping interatomic interactions at high levels of electronic structure theory.","filename":"post163s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post168","type":"poster","title":"CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows","begin_time":"19:42","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, there has been a great increase in the performance and capabilities of computers. Materials science has greatly benefited from this computational boom, which is continuously boosting research, the discovery of new materials and the development of simulation codes. The \u0022materials by design\u0022 approach has become very powerful, but requires running large numbers of simulations and building databases of computed properties. A key challenge is the need to automatically prepare, execute and monitor workflows of calculations, and then retrieve and store the results in a format that is easy to browse and query. The AiiDA open-source platform[1] provides researchers with a tool that fulfills those requirements, by implementing the four \u0022ADES\u0022 requirement pillars of Automation, Data, Environment and Sharing. AiiDA is continuously being developed and has matured into an ecosystem with multiple backend options for increased performance and flexibility, a powerful graph querying tool for easy result analysis, a redesigned plugin system to simplify external user contributions, new more powerful and easy to write workflows and a continuous integration system to ensure the stability of the platform. [1]https:\/\/doi.org\/10.1016\/j.commatsci.2015.09.013.","filename":"post168s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post171","type":"poster","title":"CHM03 - Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation","begin_time":"19:54","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Nucleation has many implications in science and technology, including metal casting, the assembly of microtubules in cells, and the formation of water droplets in the atmosphere. Because the experimental investigation of dynamical nucleation processes is very difficult, much attention has been paid to atomistic simulation efforts in the last two decades. However, atomistic simulation studies of nucleation face two major challenges. Firstly, the free energy barrier separating the metastable phase and the stable phase can be very high, making nucleation times much larger than the time scales accessible to molecular dynamics simulations. Secondly, it is highly non-trivial to develop a predictive macroscopic model of nucleation using the microscopic quantities directly obtained from atomistic simulations. In this poster, I aim to address the aforementioned difficulties. I will first briefly introduce state-of-the-art enhanced sampling methods for atomistic simulations, and their applications to studying homogeneous nucleation. I will then discuss our latest thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework to verify and extend classical nucleation theory.","bio":"","contributors":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post143","type":"poster","title":"CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a\u00a0Cobalt-Cubane","begin_time":"20:06","end_time":"20:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Facing a potentially serious energy crisis towards the end of the century, development of renewable energy sources has become one of the \u0022hot\u0022 topics in modern day research. Among many different solutions, artificial water splitting promises to be a valuable source of sustainable and affordable energy in the future. However, the improvement of existing catalysts, as well as the design of novel catalysts, is a perquisite towards the successful implementation of this technology into devices and powerplants. Informed design requires a firm understanding of underlying reaction mechanisms and how certain bottlenecks might be overcome. We employ ab initio molecular dynamics simulations to an explicitly solvated water oxidation catalyst (Co4(dpO(OH))4) in order to elucidate the elementary reaction steps and propose guidelines for the design of novel catalysts. In our studies we do not only study the catalyst itself \u2013 we also pay close attention to the crucial solute-solvent interactions which were found to play a decisive role in intramolecular proton transfer reactions giving access to a large variety of possible intermediates during the water oxidation cycles.","filename":"post143s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post127","type":"poster","title":"CHM05 - Datamining of Magnetic Double Perovskites","begin_time":"20:18","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Double perovskites (DPs) are a class of materials with AB\u0027B\u0027\u0027C perovskite-like structures. Given the element for the A site, the choice of B\u0027 and B\u0027\u0027 lead to different properties (conducting\/insulating\/semiconducting behaviour, different magnetic properties, etc. [1]). Even though a fair number of B\u0027\/B\u0027\u0027 combinations have been studied, there\u0027s still a lot of \u0022uncharted territory\u0022 to explore. [1] We adopt a data-driven approach, generating a database of computed formation energies for more than 1000 A = Sr, Ba, Ca DPs. All the calculations and database generation and management have been done the through AiiDA materials\u0027 informatics infrastructure. [2] Comparison with data available in the Materials Project (MP) database is promising, with formation energy errors less than 50 meV\/atom. We retrieve the structures of all the competing phases from the MP databse, we generate convex hulls and we give stability predictions for all the DPs analyzed in this study. With a specific focus on A = Sr, B\u0027 or B\u0027\u0027 = Ir DPs, we are able to determine the stability of compounds already present in literature, and give stability predictions for compounds for which there isn\u0027t experimental or theoretical data available. [1] S. Vasala et al., Progress in Solid State Chemistry 43 (2015). [2] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016).","filename":"post127s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true}]},{"id":"post182","type":"poster","title":"CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations","begin_time":"20:30","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Non-Bonded Interactions are the heart of every particle simulation program. Over 90% of the time spent in classical MD simulations is on this step of computing forces due to non-bonded interactions. Current methods don\u0027t offer scalability properties usable in the exascale. It is also a huge software engineering overhead to use new \u0027exascale-friendly\u0027 methods on the most popular packages. We also need to expand the realm of the physics which our interactions describe. Particle simulation packages presently restrict their force fields and methods catering to specific domains. We propose an API to bring modularity and enable proliferation of methods, force fields (physics), parallelisation paradigms and hardware optimisations. The vision is to be able to call alternative back-ends to any of these on custom MD programs as well as popular software packages. This separation of concerns of the most resource intensive part from the rest of the MD pipeline is important for focussed development for the emerging exascale platforms. This would also enable particle simulations to be practical for usage in more domains such as astrophysics, fluid mechanics, etc. This poster highlights our vision, current progress and preliminary results.","filename":"post182s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post161","type":"poster","title":"CHM07 - DFT+U Gamma-Surfaces of UO2","begin_time":"20:42","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The nuclear fuel material uranium dioxide, UO2, undergoes severe microstructural changes along its fuel cycle, forming extended defects like dislocations. Experimental characterization of structural deformations in UO2 is difficult due to safety and cost, making computer simulations vital to bridge this gap. We have carried out a systematic DFT+U study on {001}, {110} and {111} oriented gamma-surfaces of UO2, i.e. the potential energy surfaces of displacement of one crystal part with respect to the other. The DFT+U scheme relies on our earlier work on f-orbitals occupations\u0027 control. Using similar strategy, all possible f-orbital occupation patterns were considered both via single point energy calculations and the subsequent structure optimization of UO2. The f-orbital occupations patterns resulting in lowest energy and minimal deformed structures were further used for gamma-surface calculations. This procedure was repeated for the {001}, {110} and {111} oriented planes. The resulting gamma-surfaces calculated at the DFT+U level of theory are both qualitatively and quantitatively different, i.e. the shape and the energies, from those computed previously by us and others using any empirical potential. It is the result of a peculiar bonding interactions imposed by the resulting geometries during the gamma-surface calculation in conjunction with the specific f-orbital occupation pattern.","filename":"post161s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post148","type":"poster","title":"CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems","begin_time":"20:54","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Sparse matrix-matrix multiplication is an essential building block for a wide range of algorithms in various scientific fields. For this task, the sparse matrix library DBCSR (Distributed Block Compressed Sparse Row) has been developed. Its multi-layered structure automatically takes care of and optimizes several computational aspects like parallelism (MPI, OpenMP, CUDA), data (cache) locality and on-the-fly filtering. Here we report on the latest performance optimization we implemented for improving the CUDA and OpenMP parallelization. For the former, a novel algorithm was implemented for the work-scheduling of the multiplication of the matrix blocks. The latter specifically addresses many-core computing systems, namely Intel Xeon Phi, where we implemented an OpenMP task-based parallel algorithm in order to improve the load-balance by means of a more dynamic scheduling of the workload. We report the performance results, in terms of time-to-solution and energy-to-solution,\u00a0of DBCSR\u00a0on systems with Intel Xeon Phi Knights Landing (KNL) processors,\u00a0and\u00a0systems with Intel Xeon CPUs,\u00a0and NVIDIA GPUs. Finally, we analyze the performance of the library when using compilers from different vendors (GNU, Intel, NAG, PGI, FLANG).","filename":"post148s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post165","type":"poster","title":"CHM09 - Materials Cloud: A Platform for Open Materials Science","begin_time":"21:06","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Materials Cloud (www.materialscloud.org) is an Open Science web portal, built to enable seamless sharing and dissemination of resources in computational materials science. It includes educational material and videos, interactive tools, cloud simulation services based on AiiDA[1] and Jupyter, and displays interactively both curated data along with the corresponding raw data. Being powered by AiiDA, all data is accompanied by their full provenance, allowing peers to inspect how the results have been obtained, download individual files or the whole database, and start their research from where the original authors left off. Combined also with the Archive section, where DOIs are assigned to each entry (making them citable), Materials Cloud empowers data-based discovery, while being compliant with data management plans and the FAIR principles. Among the curated data, it features SSSP, a library of pseudopotentials for electronic-structure calculations, tested and optimized for accuracy and efficiency, as well as a large database of novel 2D materials [2] with their materials properties. [1]G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net. [2]N. Mounet et al., Nat. Nanotech. doi:10.1038\/s41565-017-0035-5 (2018)","filename":"post165s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post176","type":"poster","title":"CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors","begin_time":"21:18","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, machine learning has become a popular method to predict atomic-scale properties of molecular and material systems. While perhaps the most popular applications of machine learning in Chemistry and Materials Science have been to the potential energy surface of a system, a full statistical-mechanical description requires not only the potential energy but also tensorial properties such as dipole moments and polarizabilities. A machine-learning model for these properties must give predictions that transform covariantly with rigid-body rotations of the system, which adds an extra layer of complexity. This poster describes a framework for machine-learning of tensor properties of arbitrary ranks, accounting fully for the covariance of these properties. This method is an extension of Gaussian process regression (GPR), and involves a generalization of the similarity function, or kernel, of GPR to a tensorial kernel. This kernel builds upon the smooth overlap of atomic positions\u00a0(SOAP) kernel used for scalar properties. Results for prediction of electric response tensors of several orders, for a number of water oligomers and for bulk water, show that this method is an extremely promising one for machine-learning of these properties.","filename":"post176s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}]}, "slot": {"id":"post143","type":"poster","title":"CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a\u00a0Cobalt-Cubane","begin_time":"20:06","end_time":"20:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Facing a potentially serious energy crisis towards the end of the century, development of renewable energy sources has become one of the \u0022hot\u0022 topics in modern day research. Among many different solutions, artificial water splitting promises to be a valuable source of sustainable and affordable energy in the future. However, the improvement of existing catalysts, as well as the design of novel catalysts, is a perquisite towards the successful implementation of this technology into devices and powerplants. Informed design requires a firm understanding of underlying reaction mechanisms and how certain bottlenecks might be overcome. We employ ab initio molecular dynamics simulations to an explicitly solvated water oxidation catalyst (Co4(dpO(OH))4) in order to elucidate the elementary reaction steps and propose guidelines for the design of novel catalysts. In our studies we do not only study the catalyst itself \u2013 we also pay close attention to the crucial solute-solvent interactions which were found to play a decisive role in intramolecular proton transfer reactions giving access to a large variety of possible intermediates during the water oxidation cycles.","filename":"post143s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}] } Presentation
CHM05 - Datamining of Magnetic Double Perovskites
, Michele Visciarelli (KTH Royal Institute of Technology, Sweden)
+ Abstract { "session": {"id":"sess143","title":"Posters in Chemistry and Materials","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Chemistry and Materials"],"slots":[{"id":"post163","type":"poster","title":"CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects","begin_time":"19:30","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Molecules and materials that contain light nuclei exhibit considerable deviations from classical behavior which are most pronounced at cryogenic temperatures, but extend up to room temperature and beyond. Properties such as dissociation of water in bulk phase or on catalytic surfaces, heat capacity, band gaps etc. are influenced by the quantum nature of nuclei. The precise description of quantum nuclear fluctuations in atomistic simulations is possible by employing path integral techniques, which involve a considerable computational overhead due to the need for simulating multiple replicas of the system. Consequently, simulations combined with advanced electronic structure methods are still prohibitive. In this talk, I will present some methodologies based on high order factorizations of the Boltzmann operator and multiple time steps in real and imaginary time, that can practically reduce the computational cost of including nuclear quantum fluctuations down to zero, while keeping interatomic interactions at high levels of electronic structure theory.","filename":"post163s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post168","type":"poster","title":"CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows","begin_time":"19:42","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, there has been a great increase in the performance and capabilities of computers. Materials science has greatly benefited from this computational boom, which is continuously boosting research, the discovery of new materials and the development of simulation codes. The \u0022materials by design\u0022 approach has become very powerful, but requires running large numbers of simulations and building databases of computed properties. A key challenge is the need to automatically prepare, execute and monitor workflows of calculations, and then retrieve and store the results in a format that is easy to browse and query. The AiiDA open-source platform[1] provides researchers with a tool that fulfills those requirements, by implementing the four \u0022ADES\u0022 requirement pillars of Automation, Data, Environment and Sharing. AiiDA is continuously being developed and has matured into an ecosystem with multiple backend options for increased performance and flexibility, a powerful graph querying tool for easy result analysis, a redesigned plugin system to simplify external user contributions, new more powerful and easy to write workflows and a continuous integration system to ensure the stability of the platform. [1]https:\/\/doi.org\/10.1016\/j.commatsci.2015.09.013.","filename":"post168s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post171","type":"poster","title":"CHM03 - Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation","begin_time":"19:54","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Nucleation has many implications in science and technology, including metal casting, the assembly of microtubules in cells, and the formation of water droplets in the atmosphere. Because the experimental investigation of dynamical nucleation processes is very difficult, much attention has been paid to atomistic simulation efforts in the last two decades. However, atomistic simulation studies of nucleation face two major challenges. Firstly, the free energy barrier separating the metastable phase and the stable phase can be very high, making nucleation times much larger than the time scales accessible to molecular dynamics simulations. Secondly, it is highly non-trivial to develop a predictive macroscopic model of nucleation using the microscopic quantities directly obtained from atomistic simulations. In this poster, I aim to address the aforementioned difficulties. I will first briefly introduce state-of-the-art enhanced sampling methods for atomistic simulations, and their applications to studying homogeneous nucleation. I will then discuss our latest thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework to verify and extend classical nucleation theory.","bio":"","contributors":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post143","type":"poster","title":"CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a\u00a0Cobalt-Cubane","begin_time":"20:06","end_time":"20:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Facing a potentially serious energy crisis towards the end of the century, development of renewable energy sources has become one of the \u0022hot\u0022 topics in modern day research. Among many different solutions, artificial water splitting promises to be a valuable source of sustainable and affordable energy in the future. However, the improvement of existing catalysts, as well as the design of novel catalysts, is a perquisite towards the successful implementation of this technology into devices and powerplants. Informed design requires a firm understanding of underlying reaction mechanisms and how certain bottlenecks might be overcome. We employ ab initio molecular dynamics simulations to an explicitly solvated water oxidation catalyst (Co4(dpO(OH))4) in order to elucidate the elementary reaction steps and propose guidelines for the design of novel catalysts. In our studies we do not only study the catalyst itself \u2013 we also pay close attention to the crucial solute-solvent interactions which were found to play a decisive role in intramolecular proton transfer reactions giving access to a large variety of possible intermediates during the water oxidation cycles.","filename":"post143s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post127","type":"poster","title":"CHM05 - Datamining of Magnetic Double Perovskites","begin_time":"20:18","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Double perovskites (DPs) are a class of materials with AB\u0027B\u0027\u0027C perovskite-like structures. Given the element for the A site, the choice of B\u0027 and B\u0027\u0027 lead to different properties (conducting\/insulating\/semiconducting behaviour, different magnetic properties, etc. [1]). Even though a fair number of B\u0027\/B\u0027\u0027 combinations have been studied, there\u0027s still a lot of \u0022uncharted territory\u0022 to explore. [1] We adopt a data-driven approach, generating a database of computed formation energies for more than 1000 A = Sr, Ba, Ca DPs. All the calculations and database generation and management have been done the through AiiDA materials\u0027 informatics infrastructure. [2] Comparison with data available in the Materials Project (MP) database is promising, with formation energy errors less than 50 meV\/atom. We retrieve the structures of all the competing phases from the MP databse, we generate convex hulls and we give stability predictions for all the DPs analyzed in this study. With a specific focus on A = Sr, B\u0027 or B\u0027\u0027 = Ir DPs, we are able to determine the stability of compounds already present in literature, and give stability predictions for compounds for which there isn\u0027t experimental or theoretical data available. [1] S. Vasala et al., Progress in Solid State Chemistry 43 (2015). [2] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016).","filename":"post127s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true}]},{"id":"post182","type":"poster","title":"CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations","begin_time":"20:30","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Non-Bonded Interactions are the heart of every particle simulation program. Over 90% of the time spent in classical MD simulations is on this step of computing forces due to non-bonded interactions. Current methods don\u0027t offer scalability properties usable in the exascale. It is also a huge software engineering overhead to use new \u0027exascale-friendly\u0027 methods on the most popular packages. We also need to expand the realm of the physics which our interactions describe. Particle simulation packages presently restrict their force fields and methods catering to specific domains. We propose an API to bring modularity and enable proliferation of methods, force fields (physics), parallelisation paradigms and hardware optimisations. The vision is to be able to call alternative back-ends to any of these on custom MD programs as well as popular software packages. This separation of concerns of the most resource intensive part from the rest of the MD pipeline is important for focussed development for the emerging exascale platforms. This would also enable particle simulations to be practical for usage in more domains such as astrophysics, fluid mechanics, etc. This poster highlights our vision, current progress and preliminary results.","filename":"post182s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post161","type":"poster","title":"CHM07 - DFT+U Gamma-Surfaces of UO2","begin_time":"20:42","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The nuclear fuel material uranium dioxide, UO2, undergoes severe microstructural changes along its fuel cycle, forming extended defects like dislocations. Experimental characterization of structural deformations in UO2 is difficult due to safety and cost, making computer simulations vital to bridge this gap. We have carried out a systematic DFT+U study on {001}, {110} and {111} oriented gamma-surfaces of UO2, i.e. the potential energy surfaces of displacement of one crystal part with respect to the other. The DFT+U scheme relies on our earlier work on f-orbitals occupations\u0027 control. Using similar strategy, all possible f-orbital occupation patterns were considered both via single point energy calculations and the subsequent structure optimization of UO2. The f-orbital occupations patterns resulting in lowest energy and minimal deformed structures were further used for gamma-surface calculations. This procedure was repeated for the {001}, {110} and {111} oriented planes. The resulting gamma-surfaces calculated at the DFT+U level of theory are both qualitatively and quantitatively different, i.e. the shape and the energies, from those computed previously by us and others using any empirical potential. It is the result of a peculiar bonding interactions imposed by the resulting geometries during the gamma-surface calculation in conjunction with the specific f-orbital occupation pattern.","filename":"post161s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post148","type":"poster","title":"CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems","begin_time":"20:54","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Sparse matrix-matrix multiplication is an essential building block for a wide range of algorithms in various scientific fields. For this task, the sparse matrix library DBCSR (Distributed Block Compressed Sparse Row) has been developed. Its multi-layered structure automatically takes care of and optimizes several computational aspects like parallelism (MPI, OpenMP, CUDA), data (cache) locality and on-the-fly filtering. Here we report on the latest performance optimization we implemented for improving the CUDA and OpenMP parallelization. For the former, a novel algorithm was implemented for the work-scheduling of the multiplication of the matrix blocks. The latter specifically addresses many-core computing systems, namely Intel Xeon Phi, where we implemented an OpenMP task-based parallel algorithm in order to improve the load-balance by means of a more dynamic scheduling of the workload. We report the performance results, in terms of time-to-solution and energy-to-solution,\u00a0of DBCSR\u00a0on systems with Intel Xeon Phi Knights Landing (KNL) processors,\u00a0and\u00a0systems with Intel Xeon CPUs,\u00a0and NVIDIA GPUs. Finally, we analyze the performance of the library when using compilers from different vendors (GNU, Intel, NAG, PGI, FLANG).","filename":"post148s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post165","type":"poster","title":"CHM09 - Materials Cloud: A Platform for Open Materials Science","begin_time":"21:06","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Materials Cloud (www.materialscloud.org) is an Open Science web portal, built to enable seamless sharing and dissemination of resources in computational materials science. It includes educational material and videos, interactive tools, cloud simulation services based on AiiDA[1] and Jupyter, and displays interactively both curated data along with the corresponding raw data. Being powered by AiiDA, all data is accompanied by their full provenance, allowing peers to inspect how the results have been obtained, download individual files or the whole database, and start their research from where the original authors left off. Combined also with the Archive section, where DOIs are assigned to each entry (making them citable), Materials Cloud empowers data-based discovery, while being compliant with data management plans and the FAIR principles. Among the curated data, it features SSSP, a library of pseudopotentials for electronic-structure calculations, tested and optimized for accuracy and efficiency, as well as a large database of novel 2D materials [2] with their materials properties. [1]G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net. [2]N. Mounet et al., Nat. Nanotech. doi:10.1038\/s41565-017-0035-5 (2018)","filename":"post165s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post176","type":"poster","title":"CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors","begin_time":"21:18","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, machine learning has become a popular method to predict atomic-scale properties of molecular and material systems. While perhaps the most popular applications of machine learning in Chemistry and Materials Science have been to the potential energy surface of a system, a full statistical-mechanical description requires not only the potential energy but also tensorial properties such as dipole moments and polarizabilities. A machine-learning model for these properties must give predictions that transform covariantly with rigid-body rotations of the system, which adds an extra layer of complexity. This poster describes a framework for machine-learning of tensor properties of arbitrary ranks, accounting fully for the covariance of these properties. This method is an extension of Gaussian process regression (GPR), and involves a generalization of the similarity function, or kernel, of GPR to a tensorial kernel. This kernel builds upon the smooth overlap of atomic positions\u00a0(SOAP) kernel used for scalar properties. Results for prediction of electric response tensors of several orders, for a number of water oligomers and for bulk water, show that this method is an extremely promising one for machine-learning of these properties.","filename":"post176s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}]}, "slot": {"id":"post127","type":"poster","title":"CHM05 - Datamining of Magnetic Double Perovskites","begin_time":"20:18","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Double perovskites (DPs) are a class of materials with AB\u0027B\u0027\u0027C perovskite-like structures. Given the element for the A site, the choice of B\u0027 and B\u0027\u0027 lead to different properties (conducting\/insulating\/semiconducting behaviour, different magnetic properties, etc. [1]). Even though a fair number of B\u0027\/B\u0027\u0027 combinations have been studied, there\u0027s still a lot of \u0022uncharted territory\u0022 to explore. [1] We adopt a data-driven approach, generating a database of computed formation energies for more than 1000 A = Sr, Ba, Ca DPs. All the calculations and database generation and management have been done the through AiiDA materials\u0027 informatics infrastructure. [2] Comparison with data available in the Materials Project (MP) database is promising, with formation energy errors less than 50 meV\/atom. We retrieve the structures of all the competing phases from the MP databse, we generate convex hulls and we give stability predictions for all the DPs analyzed in this study. With a specific focus on A = Sr, B\u0027 or B\u0027\u0027 = Ir DPs, we are able to determine the stability of compounds already present in literature, and give stability predictions for compounds for which there isn\u0027t experimental or theoretical data available. [1] S. Vasala et al., Progress in Solid State Chemistry 43 (2015). [2] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016).","filename":"post127s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}] } Presentation
CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations
, Prashanth Kanduri (ETH Zurich / CSCS, Switzerland)
+ Abstract { "session": {"id":"sess143","title":"Posters in Chemistry and Materials","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Chemistry and Materials"],"slots":[{"id":"post163","type":"poster","title":"CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects","begin_time":"19:30","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Molecules and materials that contain light nuclei exhibit considerable deviations from classical behavior which are most pronounced at cryogenic temperatures, but extend up to room temperature and beyond. Properties such as dissociation of water in bulk phase or on catalytic surfaces, heat capacity, band gaps etc. are influenced by the quantum nature of nuclei. The precise description of quantum nuclear fluctuations in atomistic simulations is possible by employing path integral techniques, which involve a considerable computational overhead due to the need for simulating multiple replicas of the system. Consequently, simulations combined with advanced electronic structure methods are still prohibitive. In this talk, I will present some methodologies based on high order factorizations of the Boltzmann operator and multiple time steps in real and imaginary time, that can practically reduce the computational cost of including nuclear quantum fluctuations down to zero, while keeping interatomic interactions at high levels of electronic structure theory.","filename":"post163s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post168","type":"poster","title":"CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows","begin_time":"19:42","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, there has been a great increase in the performance and capabilities of computers. Materials science has greatly benefited from this computational boom, which is continuously boosting research, the discovery of new materials and the development of simulation codes. The \u0022materials by design\u0022 approach has become very powerful, but requires running large numbers of simulations and building databases of computed properties. A key challenge is the need to automatically prepare, execute and monitor workflows of calculations, and then retrieve and store the results in a format that is easy to browse and query. The AiiDA open-source platform[1] provides researchers with a tool that fulfills those requirements, by implementing the four \u0022ADES\u0022 requirement pillars of Automation, Data, Environment and Sharing. AiiDA is continuously being developed and has matured into an ecosystem with multiple backend options for increased performance and flexibility, a powerful graph querying tool for easy result analysis, a redesigned plugin system to simplify external user contributions, new more powerful and easy to write workflows and a continuous integration system to ensure the stability of the platform. [1]https:\/\/doi.org\/10.1016\/j.commatsci.2015.09.013.","filename":"post168s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post171","type":"poster","title":"CHM03 - Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation","begin_time":"19:54","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Nucleation has many implications in science and technology, including metal casting, the assembly of microtubules in cells, and the formation of water droplets in the atmosphere. Because the experimental investigation of dynamical nucleation processes is very difficult, much attention has been paid to atomistic simulation efforts in the last two decades. However, atomistic simulation studies of nucleation face two major challenges. Firstly, the free energy barrier separating the metastable phase and the stable phase can be very high, making nucleation times much larger than the time scales accessible to molecular dynamics simulations. Secondly, it is highly non-trivial to develop a predictive macroscopic model of nucleation using the microscopic quantities directly obtained from atomistic simulations. In this poster, I aim to address the aforementioned difficulties. I will first briefly introduce state-of-the-art enhanced sampling methods for atomistic simulations, and their applications to studying homogeneous nucleation. I will then discuss our latest thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework to verify and extend classical nucleation theory.","bio":"","contributors":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post143","type":"poster","title":"CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a\u00a0Cobalt-Cubane","begin_time":"20:06","end_time":"20:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Facing a potentially serious energy crisis towards the end of the century, development of renewable energy sources has become one of the \u0022hot\u0022 topics in modern day research. Among many different solutions, artificial water splitting promises to be a valuable source of sustainable and affordable energy in the future. However, the improvement of existing catalysts, as well as the design of novel catalysts, is a perquisite towards the successful implementation of this technology into devices and powerplants. Informed design requires a firm understanding of underlying reaction mechanisms and how certain bottlenecks might be overcome. We employ ab initio molecular dynamics simulations to an explicitly solvated water oxidation catalyst (Co4(dpO(OH))4) in order to elucidate the elementary reaction steps and propose guidelines for the design of novel catalysts. In our studies we do not only study the catalyst itself \u2013 we also pay close attention to the crucial solute-solvent interactions which were found to play a decisive role in intramolecular proton transfer reactions giving access to a large variety of possible intermediates during the water oxidation cycles.","filename":"post143s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post127","type":"poster","title":"CHM05 - Datamining of Magnetic Double Perovskites","begin_time":"20:18","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Double perovskites (DPs) are a class of materials with AB\u0027B\u0027\u0027C perovskite-like structures. Given the element for the A site, the choice of B\u0027 and B\u0027\u0027 lead to different properties (conducting\/insulating\/semiconducting behaviour, different magnetic properties, etc. [1]). Even though a fair number of B\u0027\/B\u0027\u0027 combinations have been studied, there\u0027s still a lot of \u0022uncharted territory\u0022 to explore. [1] We adopt a data-driven approach, generating a database of computed formation energies for more than 1000 A = Sr, Ba, Ca DPs. All the calculations and database generation and management have been done the through AiiDA materials\u0027 informatics infrastructure. [2] Comparison with data available in the Materials Project (MP) database is promising, with formation energy errors less than 50 meV\/atom. We retrieve the structures of all the competing phases from the MP databse, we generate convex hulls and we give stability predictions for all the DPs analyzed in this study. With a specific focus on A = Sr, B\u0027 or B\u0027\u0027 = Ir DPs, we are able to determine the stability of compounds already present in literature, and give stability predictions for compounds for which there isn\u0027t experimental or theoretical data available. [1] S. Vasala et al., Progress in Solid State Chemistry 43 (2015). [2] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016).","filename":"post127s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true}]},{"id":"post182","type":"poster","title":"CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations","begin_time":"20:30","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Non-Bonded Interactions are the heart of every particle simulation program. Over 90% of the time spent in classical MD simulations is on this step of computing forces due to non-bonded interactions. Current methods don\u0027t offer scalability properties usable in the exascale. It is also a huge software engineering overhead to use new \u0027exascale-friendly\u0027 methods on the most popular packages. We also need to expand the realm of the physics which our interactions describe. Particle simulation packages presently restrict their force fields and methods catering to specific domains. We propose an API to bring modularity and enable proliferation of methods, force fields (physics), parallelisation paradigms and hardware optimisations. The vision is to be able to call alternative back-ends to any of these on custom MD programs as well as popular software packages. This separation of concerns of the most resource intensive part from the rest of the MD pipeline is important for focussed development for the emerging exascale platforms. This would also enable particle simulations to be practical for usage in more domains such as astrophysics, fluid mechanics, etc. This poster highlights our vision, current progress and preliminary results.","filename":"post182s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post161","type":"poster","title":"CHM07 - DFT+U Gamma-Surfaces of UO2","begin_time":"20:42","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The nuclear fuel material uranium dioxide, UO2, undergoes severe microstructural changes along its fuel cycle, forming extended defects like dislocations. Experimental characterization of structural deformations in UO2 is difficult due to safety and cost, making computer simulations vital to bridge this gap. We have carried out a systematic DFT+U study on {001}, {110} and {111} oriented gamma-surfaces of UO2, i.e. the potential energy surfaces of displacement of one crystal part with respect to the other. The DFT+U scheme relies on our earlier work on f-orbitals occupations\u0027 control. Using similar strategy, all possible f-orbital occupation patterns were considered both via single point energy calculations and the subsequent structure optimization of UO2. The f-orbital occupations patterns resulting in lowest energy and minimal deformed structures were further used for gamma-surface calculations. This procedure was repeated for the {001}, {110} and {111} oriented planes. The resulting gamma-surfaces calculated at the DFT+U level of theory are both qualitatively and quantitatively different, i.e. the shape and the energies, from those computed previously by us and others using any empirical potential. It is the result of a peculiar bonding interactions imposed by the resulting geometries during the gamma-surface calculation in conjunction with the specific f-orbital occupation pattern.","filename":"post161s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post148","type":"poster","title":"CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems","begin_time":"20:54","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Sparse matrix-matrix multiplication is an essential building block for a wide range of algorithms in various scientific fields. For this task, the sparse matrix library DBCSR (Distributed Block Compressed Sparse Row) has been developed. Its multi-layered structure automatically takes care of and optimizes several computational aspects like parallelism (MPI, OpenMP, CUDA), data (cache) locality and on-the-fly filtering. Here we report on the latest performance optimization we implemented for improving the CUDA and OpenMP parallelization. For the former, a novel algorithm was implemented for the work-scheduling of the multiplication of the matrix blocks. The latter specifically addresses many-core computing systems, namely Intel Xeon Phi, where we implemented an OpenMP task-based parallel algorithm in order to improve the load-balance by means of a more dynamic scheduling of the workload. We report the performance results, in terms of time-to-solution and energy-to-solution,\u00a0of DBCSR\u00a0on systems with Intel Xeon Phi Knights Landing (KNL) processors,\u00a0and\u00a0systems with Intel Xeon CPUs,\u00a0and NVIDIA GPUs. Finally, we analyze the performance of the library when using compilers from different vendors (GNU, Intel, NAG, PGI, FLANG).","filename":"post148s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post165","type":"poster","title":"CHM09 - Materials Cloud: A Platform for Open Materials Science","begin_time":"21:06","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Materials Cloud (www.materialscloud.org) is an Open Science web portal, built to enable seamless sharing and dissemination of resources in computational materials science. It includes educational material and videos, interactive tools, cloud simulation services based on AiiDA[1] and Jupyter, and displays interactively both curated data along with the corresponding raw data. Being powered by AiiDA, all data is accompanied by their full provenance, allowing peers to inspect how the results have been obtained, download individual files or the whole database, and start their research from where the original authors left off. Combined also with the Archive section, where DOIs are assigned to each entry (making them citable), Materials Cloud empowers data-based discovery, while being compliant with data management plans and the FAIR principles. Among the curated data, it features SSSP, a library of pseudopotentials for electronic-structure calculations, tested and optimized for accuracy and efficiency, as well as a large database of novel 2D materials [2] with their materials properties. [1]G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net. [2]N. Mounet et al., Nat. Nanotech. doi:10.1038\/s41565-017-0035-5 (2018)","filename":"post165s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post176","type":"poster","title":"CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors","begin_time":"21:18","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, machine learning has become a popular method to predict atomic-scale properties of molecular and material systems. While perhaps the most popular applications of machine learning in Chemistry and Materials Science have been to the potential energy surface of a system, a full statistical-mechanical description requires not only the potential energy but also tensorial properties such as dipole moments and polarizabilities. A machine-learning model for these properties must give predictions that transform covariantly with rigid-body rotations of the system, which adds an extra layer of complexity. This poster describes a framework for machine-learning of tensor properties of arbitrary ranks, accounting fully for the covariance of these properties. This method is an extension of Gaussian process regression (GPR), and involves a generalization of the similarity function, or kernel, of GPR to a tensorial kernel. This kernel builds upon the smooth overlap of atomic positions\u00a0(SOAP) kernel used for scalar properties. Results for prediction of electric response tensors of several orders, for a number of water oligomers and for bulk water, show that this method is an extremely promising one for machine-learning of these properties.","filename":"post176s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}]}, "slot": {"id":"post182","type":"poster","title":"CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations","begin_time":"20:30","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Non-Bonded Interactions are the heart of every particle simulation program. Over 90% of the time spent in classical MD simulations is on this step of computing forces due to non-bonded interactions. Current methods don\u0027t offer scalability properties usable in the exascale. It is also a huge software engineering overhead to use new \u0027exascale-friendly\u0027 methods on the most popular packages. We also need to expand the realm of the physics which our interactions describe. Particle simulation packages presently restrict their force fields and methods catering to specific domains. We propose an API to bring modularity and enable proliferation of methods, force fields (physics), parallelisation paradigms and hardware optimisations. The vision is to be able to call alternative back-ends to any of these on custom MD programs as well as popular software packages. This separation of concerns of the most resource intensive part from the rest of the MD pipeline is important for focussed development for the emerging exascale platforms. This would also enable particle simulations to be practical for usage in more domains such as astrophysics, fluid mechanics, etc. This poster highlights our vision, current progress and preliminary results.","filename":"post182s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}] } Presentation
CHM07 - DFT+U Gamma-Surfaces of UO2
, Monica Kosa (Paul Scherrer Institute, Switzerland)
+ Abstract { "session": {"id":"sess143","title":"Posters in Chemistry and Materials","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Chemistry and Materials"],"slots":[{"id":"post163","type":"poster","title":"CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects","begin_time":"19:30","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Molecules and materials that contain light nuclei exhibit considerable deviations from classical behavior which are most pronounced at cryogenic temperatures, but extend up to room temperature and beyond. Properties such as dissociation of water in bulk phase or on catalytic surfaces, heat capacity, band gaps etc. are influenced by the quantum nature of nuclei. The precise description of quantum nuclear fluctuations in atomistic simulations is possible by employing path integral techniques, which involve a considerable computational overhead due to the need for simulating multiple replicas of the system. Consequently, simulations combined with advanced electronic structure methods are still prohibitive. In this talk, I will present some methodologies based on high order factorizations of the Boltzmann operator and multiple time steps in real and imaginary time, that can practically reduce the computational cost of including nuclear quantum fluctuations down to zero, while keeping interatomic interactions at high levels of electronic structure theory.","filename":"post163s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post168","type":"poster","title":"CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows","begin_time":"19:42","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, there has been a great increase in the performance and capabilities of computers. Materials science has greatly benefited from this computational boom, which is continuously boosting research, the discovery of new materials and the development of simulation codes. The \u0022materials by design\u0022 approach has become very powerful, but requires running large numbers of simulations and building databases of computed properties. A key challenge is the need to automatically prepare, execute and monitor workflows of calculations, and then retrieve and store the results in a format that is easy to browse and query. The AiiDA open-source platform[1] provides researchers with a tool that fulfills those requirements, by implementing the four \u0022ADES\u0022 requirement pillars of Automation, Data, Environment and Sharing. AiiDA is continuously being developed and has matured into an ecosystem with multiple backend options for increased performance and flexibility, a powerful graph querying tool for easy result analysis, a redesigned plugin system to simplify external user contributions, new more powerful and easy to write workflows and a continuous integration system to ensure the stability of the platform. [1]https:\/\/doi.org\/10.1016\/j.commatsci.2015.09.013.","filename":"post168s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post171","type":"poster","title":"CHM03 - Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation","begin_time":"19:54","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Nucleation has many implications in science and technology, including metal casting, the assembly of microtubules in cells, and the formation of water droplets in the atmosphere. Because the experimental investigation of dynamical nucleation processes is very difficult, much attention has been paid to atomistic simulation efforts in the last two decades. However, atomistic simulation studies of nucleation face two major challenges. Firstly, the free energy barrier separating the metastable phase and the stable phase can be very high, making nucleation times much larger than the time scales accessible to molecular dynamics simulations. Secondly, it is highly non-trivial to develop a predictive macroscopic model of nucleation using the microscopic quantities directly obtained from atomistic simulations. In this poster, I aim to address the aforementioned difficulties. I will first briefly introduce state-of-the-art enhanced sampling methods for atomistic simulations, and their applications to studying homogeneous nucleation. I will then discuss our latest thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework to verify and extend classical nucleation theory.","bio":"","contributors":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post143","type":"poster","title":"CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a\u00a0Cobalt-Cubane","begin_time":"20:06","end_time":"20:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Facing a potentially serious energy crisis towards the end of the century, development of renewable energy sources has become one of the \u0022hot\u0022 topics in modern day research. Among many different solutions, artificial water splitting promises to be a valuable source of sustainable and affordable energy in the future. However, the improvement of existing catalysts, as well as the design of novel catalysts, is a perquisite towards the successful implementation of this technology into devices and powerplants. Informed design requires a firm understanding of underlying reaction mechanisms and how certain bottlenecks might be overcome. We employ ab initio molecular dynamics simulations to an explicitly solvated water oxidation catalyst (Co4(dpO(OH))4) in order to elucidate the elementary reaction steps and propose guidelines for the design of novel catalysts. In our studies we do not only study the catalyst itself \u2013 we also pay close attention to the crucial solute-solvent interactions which were found to play a decisive role in intramolecular proton transfer reactions giving access to a large variety of possible intermediates during the water oxidation cycles.","filename":"post143s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post127","type":"poster","title":"CHM05 - Datamining of Magnetic Double Perovskites","begin_time":"20:18","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Double perovskites (DPs) are a class of materials with AB\u0027B\u0027\u0027C perovskite-like structures. Given the element for the A site, the choice of B\u0027 and B\u0027\u0027 lead to different properties (conducting\/insulating\/semiconducting behaviour, different magnetic properties, etc. [1]). Even though a fair number of B\u0027\/B\u0027\u0027 combinations have been studied, there\u0027s still a lot of \u0022uncharted territory\u0022 to explore. [1] We adopt a data-driven approach, generating a database of computed formation energies for more than 1000 A = Sr, Ba, Ca DPs. All the calculations and database generation and management have been done the through AiiDA materials\u0027 informatics infrastructure. [2] Comparison with data available in the Materials Project (MP) database is promising, with formation energy errors less than 50 meV\/atom. We retrieve the structures of all the competing phases from the MP databse, we generate convex hulls and we give stability predictions for all the DPs analyzed in this study. With a specific focus on A = Sr, B\u0027 or B\u0027\u0027 = Ir DPs, we are able to determine the stability of compounds already present in literature, and give stability predictions for compounds for which there isn\u0027t experimental or theoretical data available. [1] S. Vasala et al., Progress in Solid State Chemistry 43 (2015). [2] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016).","filename":"post127s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true}]},{"id":"post182","type":"poster","title":"CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations","begin_time":"20:30","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Non-Bonded Interactions are the heart of every particle simulation program. Over 90% of the time spent in classical MD simulations is on this step of computing forces due to non-bonded interactions. Current methods don\u0027t offer scalability properties usable in the exascale. It is also a huge software engineering overhead to use new \u0027exascale-friendly\u0027 methods on the most popular packages. We also need to expand the realm of the physics which our interactions describe. Particle simulation packages presently restrict their force fields and methods catering to specific domains. We propose an API to bring modularity and enable proliferation of methods, force fields (physics), parallelisation paradigms and hardware optimisations. The vision is to be able to call alternative back-ends to any of these on custom MD programs as well as popular software packages. This separation of concerns of the most resource intensive part from the rest of the MD pipeline is important for focussed development for the emerging exascale platforms. This would also enable particle simulations to be practical for usage in more domains such as astrophysics, fluid mechanics, etc. This poster highlights our vision, current progress and preliminary results.","filename":"post182s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post161","type":"poster","title":"CHM07 - DFT+U Gamma-Surfaces of UO2","begin_time":"20:42","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The nuclear fuel material uranium dioxide, UO2, undergoes severe microstructural changes along its fuel cycle, forming extended defects like dislocations. Experimental characterization of structural deformations in UO2 is difficult due to safety and cost, making computer simulations vital to bridge this gap. We have carried out a systematic DFT+U study on {001}, {110} and {111} oriented gamma-surfaces of UO2, i.e. the potential energy surfaces of displacement of one crystal part with respect to the other. The DFT+U scheme relies on our earlier work on f-orbitals occupations\u0027 control. Using similar strategy, all possible f-orbital occupation patterns were considered both via single point energy calculations and the subsequent structure optimization of UO2. The f-orbital occupations patterns resulting in lowest energy and minimal deformed structures were further used for gamma-surface calculations. This procedure was repeated for the {001}, {110} and {111} oriented planes. The resulting gamma-surfaces calculated at the DFT+U level of theory are both qualitatively and quantitatively different, i.e. the shape and the energies, from those computed previously by us and others using any empirical potential. It is the result of a peculiar bonding interactions imposed by the resulting geometries during the gamma-surface calculation in conjunction with the specific f-orbital occupation pattern.","filename":"post161s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post148","type":"poster","title":"CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems","begin_time":"20:54","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Sparse matrix-matrix multiplication is an essential building block for a wide range of algorithms in various scientific fields. For this task, the sparse matrix library DBCSR (Distributed Block Compressed Sparse Row) has been developed. Its multi-layered structure automatically takes care of and optimizes several computational aspects like parallelism (MPI, OpenMP, CUDA), data (cache) locality and on-the-fly filtering. Here we report on the latest performance optimization we implemented for improving the CUDA and OpenMP parallelization. For the former, a novel algorithm was implemented for the work-scheduling of the multiplication of the matrix blocks. The latter specifically addresses many-core computing systems, namely Intel Xeon Phi, where we implemented an OpenMP task-based parallel algorithm in order to improve the load-balance by means of a more dynamic scheduling of the workload. We report the performance results, in terms of time-to-solution and energy-to-solution,\u00a0of DBCSR\u00a0on systems with Intel Xeon Phi Knights Landing (KNL) processors,\u00a0and\u00a0systems with Intel Xeon CPUs,\u00a0and NVIDIA GPUs. Finally, we analyze the performance of the library when using compilers from different vendors (GNU, Intel, NAG, PGI, FLANG).","filename":"post148s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post165","type":"poster","title":"CHM09 - Materials Cloud: A Platform for Open Materials Science","begin_time":"21:06","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Materials Cloud (www.materialscloud.org) is an Open Science web portal, built to enable seamless sharing and dissemination of resources in computational materials science. It includes educational material and videos, interactive tools, cloud simulation services based on AiiDA[1] and Jupyter, and displays interactively both curated data along with the corresponding raw data. Being powered by AiiDA, all data is accompanied by their full provenance, allowing peers to inspect how the results have been obtained, download individual files or the whole database, and start their research from where the original authors left off. Combined also with the Archive section, where DOIs are assigned to each entry (making them citable), Materials Cloud empowers data-based discovery, while being compliant with data management plans and the FAIR principles. Among the curated data, it features SSSP, a library of pseudopotentials for electronic-structure calculations, tested and optimized for accuracy and efficiency, as well as a large database of novel 2D materials [2] with their materials properties. [1]G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net. [2]N. Mounet et al., Nat. Nanotech. doi:10.1038\/s41565-017-0035-5 (2018)","filename":"post165s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post176","type":"poster","title":"CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors","begin_time":"21:18","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, machine learning has become a popular method to predict atomic-scale properties of molecular and material systems. While perhaps the most popular applications of machine learning in Chemistry and Materials Science have been to the potential energy surface of a system, a full statistical-mechanical description requires not only the potential energy but also tensorial properties such as dipole moments and polarizabilities. A machine-learning model for these properties must give predictions that transform covariantly with rigid-body rotations of the system, which adds an extra layer of complexity. This poster describes a framework for machine-learning of tensor properties of arbitrary ranks, accounting fully for the covariance of these properties. This method is an extension of Gaussian process regression (GPR), and involves a generalization of the similarity function, or kernel, of GPR to a tensorial kernel. This kernel builds upon the smooth overlap of atomic positions\u00a0(SOAP) kernel used for scalar properties. Results for prediction of electric response tensors of several orders, for a number of water oligomers and for bulk water, show that this method is an extremely promising one for machine-learning of these properties.","filename":"post176s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}]}, "slot": {"id":"post161","type":"poster","title":"CHM07 - DFT+U Gamma-Surfaces of UO2","begin_time":"20:42","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The nuclear fuel material uranium dioxide, UO2, undergoes severe microstructural changes along its fuel cycle, forming extended defects like dislocations. Experimental characterization of structural deformations in UO2 is difficult due to safety and cost, making computer simulations vital to bridge this gap. We have carried out a systematic DFT+U study on {001}, {110} and {111} oriented gamma-surfaces of UO2, i.e. the potential energy surfaces of displacement of one crystal part with respect to the other. The DFT+U scheme relies on our earlier work on f-orbitals occupations\u0027 control. Using similar strategy, all possible f-orbital occupation patterns were considered both via single point energy calculations and the subsequent structure optimization of UO2. The f-orbital occupations patterns resulting in lowest energy and minimal deformed structures were further used for gamma-surface calculations. This procedure was repeated for the {001}, {110} and {111} oriented planes. The resulting gamma-surfaces calculated at the DFT+U level of theory are both qualitatively and quantitatively different, i.e. the shape and the energies, from those computed previously by us and others using any empirical potential. It is the result of a peculiar bonding interactions imposed by the resulting geometries during the gamma-surface calculation in conjunction with the specific f-orbital occupation pattern.","filename":"post161s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}] } Presentation
CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems
, Andreas Gloess (University of Zurich, Switzerland)
+ Abstract { "session": {"id":"sess143","title":"Posters in Chemistry and Materials","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Chemistry and Materials"],"slots":[{"id":"post163","type":"poster","title":"CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects","begin_time":"19:30","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Molecules and materials that contain light nuclei exhibit considerable deviations from classical behavior which are most pronounced at cryogenic temperatures, but extend up to room temperature and beyond. Properties such as dissociation of water in bulk phase or on catalytic surfaces, heat capacity, band gaps etc. are influenced by the quantum nature of nuclei. The precise description of quantum nuclear fluctuations in atomistic simulations is possible by employing path integral techniques, which involve a considerable computational overhead due to the need for simulating multiple replicas of the system. Consequently, simulations combined with advanced electronic structure methods are still prohibitive. In this talk, I will present some methodologies based on high order factorizations of the Boltzmann operator and multiple time steps in real and imaginary time, that can practically reduce the computational cost of including nuclear quantum fluctuations down to zero, while keeping interatomic interactions at high levels of electronic structure theory.","filename":"post163s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post168","type":"poster","title":"CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows","begin_time":"19:42","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, there has been a great increase in the performance and capabilities of computers. Materials science has greatly benefited from this computational boom, which is continuously boosting research, the discovery of new materials and the development of simulation codes. The \u0022materials by design\u0022 approach has become very powerful, but requires running large numbers of simulations and building databases of computed properties. A key challenge is the need to automatically prepare, execute and monitor workflows of calculations, and then retrieve and store the results in a format that is easy to browse and query. The AiiDA open-source platform[1] provides researchers with a tool that fulfills those requirements, by implementing the four \u0022ADES\u0022 requirement pillars of Automation, Data, Environment and Sharing. AiiDA is continuously being developed and has matured into an ecosystem with multiple backend options for increased performance and flexibility, a powerful graph querying tool for easy result analysis, a redesigned plugin system to simplify external user contributions, new more powerful and easy to write workflows and a continuous integration system to ensure the stability of the platform. [1]https:\/\/doi.org\/10.1016\/j.commatsci.2015.09.013.","filename":"post168s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post171","type":"poster","title":"CHM03 - Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation","begin_time":"19:54","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Nucleation has many implications in science and technology, including metal casting, the assembly of microtubules in cells, and the formation of water droplets in the atmosphere. Because the experimental investigation of dynamical nucleation processes is very difficult, much attention has been paid to atomistic simulation efforts in the last two decades. However, atomistic simulation studies of nucleation face two major challenges. Firstly, the free energy barrier separating the metastable phase and the stable phase can be very high, making nucleation times much larger than the time scales accessible to molecular dynamics simulations. Secondly, it is highly non-trivial to develop a predictive macroscopic model of nucleation using the microscopic quantities directly obtained from atomistic simulations. In this poster, I aim to address the aforementioned difficulties. I will first briefly introduce state-of-the-art enhanced sampling methods for atomistic simulations, and their applications to studying homogeneous nucleation. I will then discuss our latest thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework to verify and extend classical nucleation theory.","bio":"","contributors":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post143","type":"poster","title":"CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a\u00a0Cobalt-Cubane","begin_time":"20:06","end_time":"20:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Facing a potentially serious energy crisis towards the end of the century, development of renewable energy sources has become one of the \u0022hot\u0022 topics in modern day research. Among many different solutions, artificial water splitting promises to be a valuable source of sustainable and affordable energy in the future. However, the improvement of existing catalysts, as well as the design of novel catalysts, is a perquisite towards the successful implementation of this technology into devices and powerplants. Informed design requires a firm understanding of underlying reaction mechanisms and how certain bottlenecks might be overcome. We employ ab initio molecular dynamics simulations to an explicitly solvated water oxidation catalyst (Co4(dpO(OH))4) in order to elucidate the elementary reaction steps and propose guidelines for the design of novel catalysts. In our studies we do not only study the catalyst itself \u2013 we also pay close attention to the crucial solute-solvent interactions which were found to play a decisive role in intramolecular proton transfer reactions giving access to a large variety of possible intermediates during the water oxidation cycles.","filename":"post143s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post127","type":"poster","title":"CHM05 - Datamining of Magnetic Double Perovskites","begin_time":"20:18","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Double perovskites (DPs) are a class of materials with AB\u0027B\u0027\u0027C perovskite-like structures. Given the element for the A site, the choice of B\u0027 and B\u0027\u0027 lead to different properties (conducting\/insulating\/semiconducting behaviour, different magnetic properties, etc. [1]). Even though a fair number of B\u0027\/B\u0027\u0027 combinations have been studied, there\u0027s still a lot of \u0022uncharted territory\u0022 to explore. [1] We adopt a data-driven approach, generating a database of computed formation energies for more than 1000 A = Sr, Ba, Ca DPs. All the calculations and database generation and management have been done the through AiiDA materials\u0027 informatics infrastructure. [2] Comparison with data available in the Materials Project (MP) database is promising, with formation energy errors less than 50 meV\/atom. We retrieve the structures of all the competing phases from the MP databse, we generate convex hulls and we give stability predictions for all the DPs analyzed in this study. With a specific focus on A = Sr, B\u0027 or B\u0027\u0027 = Ir DPs, we are able to determine the stability of compounds already present in literature, and give stability predictions for compounds for which there isn\u0027t experimental or theoretical data available. [1] S. Vasala et al., Progress in Solid State Chemistry 43 (2015). [2] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016).","filename":"post127s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true}]},{"id":"post182","type":"poster","title":"CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations","begin_time":"20:30","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Non-Bonded Interactions are the heart of every particle simulation program. Over 90% of the time spent in classical MD simulations is on this step of computing forces due to non-bonded interactions. Current methods don\u0027t offer scalability properties usable in the exascale. It is also a huge software engineering overhead to use new \u0027exascale-friendly\u0027 methods on the most popular packages. We also need to expand the realm of the physics which our interactions describe. Particle simulation packages presently restrict their force fields and methods catering to specific domains. We propose an API to bring modularity and enable proliferation of methods, force fields (physics), parallelisation paradigms and hardware optimisations. The vision is to be able to call alternative back-ends to any of these on custom MD programs as well as popular software packages. This separation of concerns of the most resource intensive part from the rest of the MD pipeline is important for focussed development for the emerging exascale platforms. This would also enable particle simulations to be practical for usage in more domains such as astrophysics, fluid mechanics, etc. This poster highlights our vision, current progress and preliminary results.","filename":"post182s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post161","type":"poster","title":"CHM07 - DFT+U Gamma-Surfaces of UO2","begin_time":"20:42","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The nuclear fuel material uranium dioxide, UO2, undergoes severe microstructural changes along its fuel cycle, forming extended defects like dislocations. Experimental characterization of structural deformations in UO2 is difficult due to safety and cost, making computer simulations vital to bridge this gap. We have carried out a systematic DFT+U study on {001}, {110} and {111} oriented gamma-surfaces of UO2, i.e. the potential energy surfaces of displacement of one crystal part with respect to the other. The DFT+U scheme relies on our earlier work on f-orbitals occupations\u0027 control. Using similar strategy, all possible f-orbital occupation patterns were considered both via single point energy calculations and the subsequent structure optimization of UO2. The f-orbital occupations patterns resulting in lowest energy and minimal deformed structures were further used for gamma-surface calculations. This procedure was repeated for the {001}, {110} and {111} oriented planes. The resulting gamma-surfaces calculated at the DFT+U level of theory are both qualitatively and quantitatively different, i.e. the shape and the energies, from those computed previously by us and others using any empirical potential. It is the result of a peculiar bonding interactions imposed by the resulting geometries during the gamma-surface calculation in conjunction with the specific f-orbital occupation pattern.","filename":"post161s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post148","type":"poster","title":"CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems","begin_time":"20:54","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Sparse matrix-matrix multiplication is an essential building block for a wide range of algorithms in various scientific fields. For this task, the sparse matrix library DBCSR (Distributed Block Compressed Sparse Row) has been developed. Its multi-layered structure automatically takes care of and optimizes several computational aspects like parallelism (MPI, OpenMP, CUDA), data (cache) locality and on-the-fly filtering. Here we report on the latest performance optimization we implemented for improving the CUDA and OpenMP parallelization. For the former, a novel algorithm was implemented for the work-scheduling of the multiplication of the matrix blocks. The latter specifically addresses many-core computing systems, namely Intel Xeon Phi, where we implemented an OpenMP task-based parallel algorithm in order to improve the load-balance by means of a more dynamic scheduling of the workload. We report the performance results, in terms of time-to-solution and energy-to-solution,\u00a0of DBCSR\u00a0on systems with Intel Xeon Phi Knights Landing (KNL) processors,\u00a0and\u00a0systems with Intel Xeon CPUs,\u00a0and NVIDIA GPUs. Finally, we analyze the performance of the library when using compilers from different vendors (GNU, Intel, NAG, PGI, FLANG).","filename":"post148s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post165","type":"poster","title":"CHM09 - Materials Cloud: A Platform for Open Materials Science","begin_time":"21:06","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Materials Cloud (www.materialscloud.org) is an Open Science web portal, built to enable seamless sharing and dissemination of resources in computational materials science. It includes educational material and videos, interactive tools, cloud simulation services based on AiiDA[1] and Jupyter, and displays interactively both curated data along with the corresponding raw data. Being powered by AiiDA, all data is accompanied by their full provenance, allowing peers to inspect how the results have been obtained, download individual files or the whole database, and start their research from where the original authors left off. Combined also with the Archive section, where DOIs are assigned to each entry (making them citable), Materials Cloud empowers data-based discovery, while being compliant with data management plans and the FAIR principles. Among the curated data, it features SSSP, a library of pseudopotentials for electronic-structure calculations, tested and optimized for accuracy and efficiency, as well as a large database of novel 2D materials [2] with their materials properties. [1]G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net. [2]N. Mounet et al., Nat. Nanotech. doi:10.1038\/s41565-017-0035-5 (2018)","filename":"post165s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post176","type":"poster","title":"CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors","begin_time":"21:18","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, machine learning has become a popular method to predict atomic-scale properties of molecular and material systems. While perhaps the most popular applications of machine learning in Chemistry and Materials Science have been to the potential energy surface of a system, a full statistical-mechanical description requires not only the potential energy but also tensorial properties such as dipole moments and polarizabilities. A machine-learning model for these properties must give predictions that transform covariantly with rigid-body rotations of the system, which adds an extra layer of complexity. This poster describes a framework for machine-learning of tensor properties of arbitrary ranks, accounting fully for the covariance of these properties. This method is an extension of Gaussian process regression (GPR), and involves a generalization of the similarity function, or kernel, of GPR to a tensorial kernel. This kernel builds upon the smooth overlap of atomic positions\u00a0(SOAP) kernel used for scalar properties. Results for prediction of electric response tensors of several orders, for a number of water oligomers and for bulk water, show that this method is an extremely promising one for machine-learning of these properties.","filename":"post176s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}]}, "slot": {"id":"post148","type":"poster","title":"CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems","begin_time":"20:54","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Sparse matrix-matrix multiplication is an essential building block for a wide range of algorithms in various scientific fields. For this task, the sparse matrix library DBCSR (Distributed Block Compressed Sparse Row) has been developed. Its multi-layered structure automatically takes care of and optimizes several computational aspects like parallelism (MPI, OpenMP, CUDA), data (cache) locality and on-the-fly filtering. Here we report on the latest performance optimization we implemented for improving the CUDA and OpenMP parallelization. For the former, a novel algorithm was implemented for the work-scheduling of the multiplication of the matrix blocks. The latter specifically addresses many-core computing systems, namely Intel Xeon Phi, where we implemented an OpenMP task-based parallel algorithm in order to improve the load-balance by means of a more dynamic scheduling of the workload. We report the performance results, in terms of time-to-solution and energy-to-solution,\u00a0of DBCSR\u00a0on systems with Intel Xeon Phi Knights Landing (KNL) processors,\u00a0and\u00a0systems with Intel Xeon CPUs,\u00a0and NVIDIA GPUs. Finally, we analyze the performance of the library when using compilers from different vendors (GNU, Intel, NAG, PGI, FLANG).","filename":"post148s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}] } Presentation
CHM09 - Materials Cloud: A Platform for Open Materials Science
, Giovanni Pizzi (EPFL, Switzerland)
+ Abstract { "session": {"id":"sess143","title":"Posters in Chemistry and Materials","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Chemistry and Materials"],"slots":[{"id":"post163","type":"poster","title":"CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects","begin_time":"19:30","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Molecules and materials that contain light nuclei exhibit considerable deviations from classical behavior which are most pronounced at cryogenic temperatures, but extend up to room temperature and beyond. Properties such as dissociation of water in bulk phase or on catalytic surfaces, heat capacity, band gaps etc. are influenced by the quantum nature of nuclei. The precise description of quantum nuclear fluctuations in atomistic simulations is possible by employing path integral techniques, which involve a considerable computational overhead due to the need for simulating multiple replicas of the system. Consequently, simulations combined with advanced electronic structure methods are still prohibitive. In this talk, I will present some methodologies based on high order factorizations of the Boltzmann operator and multiple time steps in real and imaginary time, that can practically reduce the computational cost of including nuclear quantum fluctuations down to zero, while keeping interatomic interactions at high levels of electronic structure theory.","filename":"post163s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post168","type":"poster","title":"CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows","begin_time":"19:42","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, there has been a great increase in the performance and capabilities of computers. Materials science has greatly benefited from this computational boom, which is continuously boosting research, the discovery of new materials and the development of simulation codes. The \u0022materials by design\u0022 approach has become very powerful, but requires running large numbers of simulations and building databases of computed properties. A key challenge is the need to automatically prepare, execute and monitor workflows of calculations, and then retrieve and store the results in a format that is easy to browse and query. The AiiDA open-source platform[1] provides researchers with a tool that fulfills those requirements, by implementing the four \u0022ADES\u0022 requirement pillars of Automation, Data, Environment and Sharing. AiiDA is continuously being developed and has matured into an ecosystem with multiple backend options for increased performance and flexibility, a powerful graph querying tool for easy result analysis, a redesigned plugin system to simplify external user contributions, new more powerful and easy to write workflows and a continuous integration system to ensure the stability of the platform. [1]https:\/\/doi.org\/10.1016\/j.commatsci.2015.09.013.","filename":"post168s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post171","type":"poster","title":"CHM03 - Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation","begin_time":"19:54","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Nucleation has many implications in science and technology, including metal casting, the assembly of microtubules in cells, and the formation of water droplets in the atmosphere. Because the experimental investigation of dynamical nucleation processes is very difficult, much attention has been paid to atomistic simulation efforts in the last two decades. However, atomistic simulation studies of nucleation face two major challenges. Firstly, the free energy barrier separating the metastable phase and the stable phase can be very high, making nucleation times much larger than the time scales accessible to molecular dynamics simulations. Secondly, it is highly non-trivial to develop a predictive macroscopic model of nucleation using the microscopic quantities directly obtained from atomistic simulations. In this poster, I aim to address the aforementioned difficulties. I will first briefly introduce state-of-the-art enhanced sampling methods for atomistic simulations, and their applications to studying homogeneous nucleation. I will then discuss our latest thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework to verify and extend classical nucleation theory.","bio":"","contributors":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post143","type":"poster","title":"CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a\u00a0Cobalt-Cubane","begin_time":"20:06","end_time":"20:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Facing a potentially serious energy crisis towards the end of the century, development of renewable energy sources has become one of the \u0022hot\u0022 topics in modern day research. Among many different solutions, artificial water splitting promises to be a valuable source of sustainable and affordable energy in the future. However, the improvement of existing catalysts, as well as the design of novel catalysts, is a perquisite towards the successful implementation of this technology into devices and powerplants. Informed design requires a firm understanding of underlying reaction mechanisms and how certain bottlenecks might be overcome. We employ ab initio molecular dynamics simulations to an explicitly solvated water oxidation catalyst (Co4(dpO(OH))4) in order to elucidate the elementary reaction steps and propose guidelines for the design of novel catalysts. In our studies we do not only study the catalyst itself \u2013 we also pay close attention to the crucial solute-solvent interactions which were found to play a decisive role in intramolecular proton transfer reactions giving access to a large variety of possible intermediates during the water oxidation cycles.","filename":"post143s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post127","type":"poster","title":"CHM05 - Datamining of Magnetic Double Perovskites","begin_time":"20:18","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Double perovskites (DPs) are a class of materials with AB\u0027B\u0027\u0027C perovskite-like structures. Given the element for the A site, the choice of B\u0027 and B\u0027\u0027 lead to different properties (conducting\/insulating\/semiconducting behaviour, different magnetic properties, etc. [1]). Even though a fair number of B\u0027\/B\u0027\u0027 combinations have been studied, there\u0027s still a lot of \u0022uncharted territory\u0022 to explore. [1] We adopt a data-driven approach, generating a database of computed formation energies for more than 1000 A = Sr, Ba, Ca DPs. All the calculations and database generation and management have been done the through AiiDA materials\u0027 informatics infrastructure. [2] Comparison with data available in the Materials Project (MP) database is promising, with formation energy errors less than 50 meV\/atom. We retrieve the structures of all the competing phases from the MP databse, we generate convex hulls and we give stability predictions for all the DPs analyzed in this study. With a specific focus on A = Sr, B\u0027 or B\u0027\u0027 = Ir DPs, we are able to determine the stability of compounds already present in literature, and give stability predictions for compounds for which there isn\u0027t experimental or theoretical data available. [1] S. Vasala et al., Progress in Solid State Chemistry 43 (2015). [2] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016).","filename":"post127s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true}]},{"id":"post182","type":"poster","title":"CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations","begin_time":"20:30","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Non-Bonded Interactions are the heart of every particle simulation program. Over 90% of the time spent in classical MD simulations is on this step of computing forces due to non-bonded interactions. Current methods don\u0027t offer scalability properties usable in the exascale. It is also a huge software engineering overhead to use new \u0027exascale-friendly\u0027 methods on the most popular packages. We also need to expand the realm of the physics which our interactions describe. Particle simulation packages presently restrict their force fields and methods catering to specific domains. We propose an API to bring modularity and enable proliferation of methods, force fields (physics), parallelisation paradigms and hardware optimisations. The vision is to be able to call alternative back-ends to any of these on custom MD programs as well as popular software packages. This separation of concerns of the most resource intensive part from the rest of the MD pipeline is important for focussed development for the emerging exascale platforms. This would also enable particle simulations to be practical for usage in more domains such as astrophysics, fluid mechanics, etc. This poster highlights our vision, current progress and preliminary results.","filename":"post182s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post161","type":"poster","title":"CHM07 - DFT+U Gamma-Surfaces of UO2","begin_time":"20:42","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The nuclear fuel material uranium dioxide, UO2, undergoes severe microstructural changes along its fuel cycle, forming extended defects like dislocations. Experimental characterization of structural deformations in UO2 is difficult due to safety and cost, making computer simulations vital to bridge this gap. We have carried out a systematic DFT+U study on {001}, {110} and {111} oriented gamma-surfaces of UO2, i.e. the potential energy surfaces of displacement of one crystal part with respect to the other. The DFT+U scheme relies on our earlier work on f-orbitals occupations\u0027 control. Using similar strategy, all possible f-orbital occupation patterns were considered both via single point energy calculations and the subsequent structure optimization of UO2. The f-orbital occupations patterns resulting in lowest energy and minimal deformed structures were further used for gamma-surface calculations. This procedure was repeated for the {001}, {110} and {111} oriented planes. The resulting gamma-surfaces calculated at the DFT+U level of theory are both qualitatively and quantitatively different, i.e. the shape and the energies, from those computed previously by us and others using any empirical potential. It is the result of a peculiar bonding interactions imposed by the resulting geometries during the gamma-surface calculation in conjunction with the specific f-orbital occupation pattern.","filename":"post161s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post148","type":"poster","title":"CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems","begin_time":"20:54","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Sparse matrix-matrix multiplication is an essential building block for a wide range of algorithms in various scientific fields. For this task, the sparse matrix library DBCSR (Distributed Block Compressed Sparse Row) has been developed. Its multi-layered structure automatically takes care of and optimizes several computational aspects like parallelism (MPI, OpenMP, CUDA), data (cache) locality and on-the-fly filtering. Here we report on the latest performance optimization we implemented for improving the CUDA and OpenMP parallelization. For the former, a novel algorithm was implemented for the work-scheduling of the multiplication of the matrix blocks. The latter specifically addresses many-core computing systems, namely Intel Xeon Phi, where we implemented an OpenMP task-based parallel algorithm in order to improve the load-balance by means of a more dynamic scheduling of the workload. We report the performance results, in terms of time-to-solution and energy-to-solution,\u00a0of DBCSR\u00a0on systems with Intel Xeon Phi Knights Landing (KNL) processors,\u00a0and\u00a0systems with Intel Xeon CPUs,\u00a0and NVIDIA GPUs. Finally, we analyze the performance of the library when using compilers from different vendors (GNU, Intel, NAG, PGI, FLANG).","filename":"post148s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post165","type":"poster","title":"CHM09 - Materials Cloud: A Platform for Open Materials Science","begin_time":"21:06","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Materials Cloud (www.materialscloud.org) is an Open Science web portal, built to enable seamless sharing and dissemination of resources in computational materials science. It includes educational material and videos, interactive tools, cloud simulation services based on AiiDA[1] and Jupyter, and displays interactively both curated data along with the corresponding raw data. Being powered by AiiDA, all data is accompanied by their full provenance, allowing peers to inspect how the results have been obtained, download individual files or the whole database, and start their research from where the original authors left off. Combined also with the Archive section, where DOIs are assigned to each entry (making them citable), Materials Cloud empowers data-based discovery, while being compliant with data management plans and the FAIR principles. Among the curated data, it features SSSP, a library of pseudopotentials for electronic-structure calculations, tested and optimized for accuracy and efficiency, as well as a large database of novel 2D materials [2] with their materials properties. [1]G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net. [2]N. Mounet et al., Nat. Nanotech. doi:10.1038\/s41565-017-0035-5 (2018)","filename":"post165s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post176","type":"poster","title":"CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors","begin_time":"21:18","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, machine learning has become a popular method to predict atomic-scale properties of molecular and material systems. While perhaps the most popular applications of machine learning in Chemistry and Materials Science have been to the potential energy surface of a system, a full statistical-mechanical description requires not only the potential energy but also tensorial properties such as dipole moments and polarizabilities. A machine-learning model for these properties must give predictions that transform covariantly with rigid-body rotations of the system, which adds an extra layer of complexity. This poster describes a framework for machine-learning of tensor properties of arbitrary ranks, accounting fully for the covariance of these properties. This method is an extension of Gaussian process regression (GPR), and involves a generalization of the similarity function, or kernel, of GPR to a tensorial kernel. This kernel builds upon the smooth overlap of atomic positions\u00a0(SOAP) kernel used for scalar properties. Results for prediction of electric response tensors of several orders, for a number of water oligomers and for bulk water, show that this method is an extremely promising one for machine-learning of these properties.","filename":"post176s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}]}, "slot": {"id":"post165","type":"poster","title":"CHM09 - Materials Cloud: A Platform for Open Materials Science","begin_time":"21:06","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Materials Cloud (www.materialscloud.org) is an Open Science web portal, built to enable seamless sharing and dissemination of resources in computational materials science. It includes educational material and videos, interactive tools, cloud simulation services based on AiiDA[1] and Jupyter, and displays interactively both curated data along with the corresponding raw data. Being powered by AiiDA, all data is accompanied by their full provenance, allowing peers to inspect how the results have been obtained, download individual files or the whole database, and start their research from where the original authors left off. Combined also with the Archive section, where DOIs are assigned to each entry (making them citable), Materials Cloud empowers data-based discovery, while being compliant with data management plans and the FAIR principles. Among the curated data, it features SSSP, a library of pseudopotentials for electronic-structure calculations, tested and optimized for accuracy and efficiency, as well as a large database of novel 2D materials [2] with their materials properties. [1]G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net. [2]N. Mounet et al., Nat. Nanotech. doi:10.1038\/s41565-017-0035-5 (2018)","filename":"post165s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}] } Presentation
CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors
, David M. Wilkins (EPFL, Switzerland)
+ Abstract { "session": {"id":"sess143","title":"Posters in Chemistry and Materials","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Chemistry and Materials"],"slots":[{"id":"post163","type":"poster","title":"CHM01 - Accurate and Efficient Molecular Dynamics with Nuclear Quantum Effects","begin_time":"19:30","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Molecules and materials that contain light nuclei exhibit considerable deviations from classical behavior which are most pronounced at cryogenic temperatures, but extend up to room temperature and beyond. Properties such as dissociation of water in bulk phase or on catalytic surfaces, heat capacity, band gaps etc. are influenced by the quantum nature of nuclei. The precise description of quantum nuclear fluctuations in atomistic simulations is possible by employing path integral techniques, which involve a considerable computational overhead due to the need for simulating multiple replicas of the system. Consequently, simulations combined with advanced electronic structure methods are still prohibitive. In this talk, I will present some methodologies based on high order factorizations of the Boltzmann operator and multiple time steps in real and imaginary time, that can practically reduce the computational cost of including nuclear quantum fluctuations down to zero, while keeping interatomic interactions at high levels of electronic structure theory.","filename":"post163s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Venkat","last_name":"Kapil","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post168","type":"poster","title":"CHM02 - AiiDA: A Simulation Platform with Full Provenance Support and Flexible Workflows","begin_time":"19:42","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, there has been a great increase in the performance and capabilities of computers. Materials science has greatly benefited from this computational boom, which is continuously boosting research, the discovery of new materials and the development of simulation codes. The \u0022materials by design\u0022 approach has become very powerful, but requires running large numbers of simulations and building databases of computed properties. A key challenge is the need to automatically prepare, execute and monitor workflows of calculations, and then retrieve and store the results in a format that is easy to browse and query. The AiiDA open-source platform[1] provides researchers with a tool that fulfills those requirements, by implementing the four \u0022ADES\u0022 requirement pillars of Automation, Data, Environment and Sharing. AiiDA is continuously being developed and has matured into an ecosystem with multiple backend options for increased performance and flexibility, a powerful graph querying tool for easy result analysis, a redesigned plugin system to simplify external user contributions, new more powerful and easy to write workflows and a continuous integration system to ensure the stability of the platform. [1]https:\/\/doi.org\/10.1016\/j.commatsci.2015.09.013.","filename":"post168s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leonid","last_name":"Kahle","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Sebastiaan","last_name":"Huber","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Martin","last_name":"Uhrin","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Nicolas","last_name":"Mounet","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Rico Andreas","last_name":"H\u00e4uselmann","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Andrea","last_name":"Cepellotti","affiliation":"UC Berkeley","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Andrius","last_name":"Merkys","affiliation":"Vilnius University","country":"Lithuania","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Boris","last_name":"Kozinsky","affiliation":"Harvard University","country":"United States of America","bio":"","order":"12","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"13","is_presenter":false},{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"14","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Spyros","last_name":"Zoupanos","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post171","type":"poster","title":"CHM03 - Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation","begin_time":"19:54","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Nucleation has many implications in science and technology, including metal casting, the assembly of microtubules in cells, and the formation of water droplets in the atmosphere. Because the experimental investigation of dynamical nucleation processes is very difficult, much attention has been paid to atomistic simulation efforts in the last two decades. However, atomistic simulation studies of nucleation face two major challenges. Firstly, the free energy barrier separating the metastable phase and the stable phase can be very high, making nucleation times much larger than the time scales accessible to molecular dynamics simulations. Secondly, it is highly non-trivial to develop a predictive macroscopic model of nucleation using the microscopic quantities directly obtained from atomistic simulations. In this poster, I aim to address the aforementioned difficulties. I will first briefly introduce state-of-the-art enhanced sampling methods for atomistic simulations, and their applications to studying homogeneous nucleation. I will then discuss our latest thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework to verify and extend classical nucleation theory.","bio":"","contributors":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Bingqing","last_name":"Cheng","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post143","type":"poster","title":"CHM04 - The Crucial Role of the Hydrogen Bonding Network in Water Oxidation Catalyzed by a\u00a0Cobalt-Cubane","begin_time":"20:06","end_time":"20:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Facing a potentially serious energy crisis towards the end of the century, development of renewable energy sources has become one of the \u0022hot\u0022 topics in modern day research. Among many different solutions, artificial water splitting promises to be a valuable source of sustainable and affordable energy in the future. However, the improvement of existing catalysts, as well as the design of novel catalysts, is a perquisite towards the successful implementation of this technology into devices and powerplants. Informed design requires a firm understanding of underlying reaction mechanisms and how certain bottlenecks might be overcome. We employ ab initio molecular dynamics simulations to an explicitly solvated water oxidation catalyst (Co4(dpO(OH))4) in order to elucidate the elementary reaction steps and propose guidelines for the design of novel catalysts. In our studies we do not only study the catalyst itself \u2013 we also pay close attention to the crucial solute-solvent interactions which were found to play a decisive role in intramolecular proton transfer reactions giving access to a large variety of possible intermediates during the water oxidation cycles.","filename":"post143s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sandra","last_name":"Luber","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mauro","last_name":"Schilling","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post127","type":"poster","title":"CHM05 - Datamining of Magnetic Double Perovskites","begin_time":"20:18","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Double perovskites (DPs) are a class of materials with AB\u0027B\u0027\u0027C perovskite-like structures. Given the element for the A site, the choice of B\u0027 and B\u0027\u0027 lead to different properties (conducting\/insulating\/semiconducting behaviour, different magnetic properties, etc. [1]). Even though a fair number of B\u0027\/B\u0027\u0027 combinations have been studied, there\u0027s still a lot of \u0022uncharted territory\u0022 to explore. [1] We adopt a data-driven approach, generating a database of computed formation energies for more than 1000 A = Sr, Ba, Ca DPs. All the calculations and database generation and management have been done the through AiiDA materials\u0027 informatics infrastructure. [2] Comparison with data available in the Materials Project (MP) database is promising, with formation energy errors less than 50 meV\/atom. We retrieve the structures of all the competing phases from the MP databse, we generate convex hulls and we give stability predictions for all the DPs analyzed in this study. With a specific focus on A = Sr, B\u0027 or B\u0027\u0027 = Ir DPs, we are able to determine the stability of compounds already present in literature, and give stability predictions for compounds for which there isn\u0027t experimental or theoretical data available. [1] S. Vasala et al., Progress in Solid State Chemistry 43 (2015). [2] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016).","filename":"post127s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thor","last_name":"Wikfeldt","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Anna","last_name":"Delin","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michele","last_name":"Visciarelli","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"1","is_presenter":true}]},{"id":"post182","type":"poster","title":"CHM06 - Development of a Modular API for Computation of Non-Bonded Interactions in Particle Simulations","begin_time":"20:30","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Non-Bonded Interactions are the heart of every particle simulation program. Over 90% of the time spent in classical MD simulations is on this step of computing forces due to non-bonded interactions. Current methods don\u0027t offer scalability properties usable in the exascale. It is also a huge software engineering overhead to use new \u0027exascale-friendly\u0027 methods on the most popular packages. We also need to expand the realm of the physics which our interactions describe. Particle simulation packages presently restrict their force fields and methods catering to specific domains. We propose an API to bring modularity and enable proliferation of methods, force fields (physics), parallelisation paradigms and hardware optimisations. The vision is to be able to call alternative back-ends to any of these on custom MD programs as well as popular software packages. This separation of concerns of the most resource intensive part from the rest of the MD pipeline is important for focussed development for the emerging exascale platforms. This would also enable particle simulations to be practical for usage in more domains such as astrophysics, fluid mechanics, etc. This poster highlights our vision, current progress and preliminary results.","filename":"post182s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Victor","last_name":"Holanda Rusu","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Claudio","last_name":"Gheller","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Prashanth","last_name":"Kanduri","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post161","type":"poster","title":"CHM07 - DFT+U Gamma-Surfaces of UO2","begin_time":"20:42","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The nuclear fuel material uranium dioxide, UO2, undergoes severe microstructural changes along its fuel cycle, forming extended defects like dislocations. Experimental characterization of structural deformations in UO2 is difficult due to safety and cost, making computer simulations vital to bridge this gap. We have carried out a systematic DFT+U study on {001}, {110} and {111} oriented gamma-surfaces of UO2, i.e. the potential energy surfaces of displacement of one crystal part with respect to the other. The DFT+U scheme relies on our earlier work on f-orbitals occupations\u0027 control. Using similar strategy, all possible f-orbital occupation patterns were considered both via single point energy calculations and the subsequent structure optimization of UO2. The f-orbital occupations patterns resulting in lowest energy and minimal deformed structures were further used for gamma-surface calculations. This procedure was repeated for the {001}, {110} and {111} oriented planes. The resulting gamma-surfaces calculated at the DFT+U level of theory are both qualitatively and quantitatively different, i.e. the shape and the energies, from those computed previously by us and others using any empirical potential. It is the result of a peculiar bonding interactions imposed by the resulting geometries during the gamma-surface calculation in conjunction with the specific f-orbital occupation pattern.","filename":"post161s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Raoul","last_name":"Ngayam Happy","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"S\u00e9bastien","last_name":"Groh","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Matthias","last_name":"Krack","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Monica","last_name":"Kosa","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post148","type":"poster","title":"CHM08 - Improving the Performance of the DBCSR Library for Sparse Matrix Multiplication for Many-Core and GPU Computing Systems","begin_time":"20:54","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Sparse matrix-matrix multiplication is an essential building block for a wide range of algorithms in various scientific fields. For this task, the sparse matrix library DBCSR (Distributed Block Compressed Sparse Row) has been developed. Its multi-layered structure automatically takes care of and optimizes several computational aspects like parallelism (MPI, OpenMP, CUDA), data (cache) locality and on-the-fly filtering. Here we report on the latest performance optimization we implemented for improving the CUDA and OpenMP parallelization. For the former, a novel algorithm was implemented for the work-scheduling of the multiplication of the matrix blocks. The latter specifically addresses many-core computing systems, namely Intel Xeon Phi, where we implemented an OpenMP task-based parallel algorithm in order to improve the load-balance by means of a more dynamic scheduling of the workload. We report the performance results, in terms of time-to-solution and energy-to-solution,\u00a0of DBCSR\u00a0on systems with Intel Xeon Phi Knights Landing (KNL) processors,\u00a0and\u00a0systems with Intel Xeon CPUs,\u00a0and NVIDIA GPUs. Finally, we analyze the performance of the library when using compilers from different vendors (GNU, Intel, NAG, PGI, FLANG).","filename":"post148s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alfio","last_name":"Lazzaro","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Juerg","last_name":"Hutter","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Tiziano","last_name":"Mueller","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Seewald","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ilia","last_name":"Sivkov","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Andreas","last_name":"Gloess","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post165","type":"poster","title":"CHM09 - Materials Cloud: A Platform for Open Materials Science","begin_time":"21:06","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Materials Cloud (www.materialscloud.org) is an Open Science web portal, built to enable seamless sharing and dissemination of resources in computational materials science. It includes educational material and videos, interactive tools, cloud simulation services based on AiiDA[1] and Jupyter, and displays interactively both curated data along with the corresponding raw data. Being powered by AiiDA, all data is accompanied by their full provenance, allowing peers to inspect how the results have been obtained, download individual files or the whole database, and start their research from where the original authors left off. Combined also with the Archive section, where DOIs are assigned to each entry (making them citable), Materials Cloud empowers data-based discovery, while being compliant with data management plans and the FAIR principles. Among the curated data, it features SSSP, a library of pseudopotentials for electronic-structure calculations, tested and optimized for accuracy and efficiency, as well as a large database of novel 2D materials [2] with their materials properties. [1]G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net. [2]N. Mounet et al., Nat. Nanotech. doi:10.1038\/s41565-017-0035-5 (2018)","filename":"post165s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Leopold","last_name":"Talirz","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Snehal","last_name":"Kumbhar","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Fernando","last_name":"Gargiulo","affiliation":"EPFL","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marco","last_name":"Borelli","affiliation":"EPFL","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Elsa","last_name":"Passaro","affiliation":"EPFL","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Aliaksandr","last_name":"Yakutovich","affiliation":"EPFL","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Ole","last_name":"Sch\u00fctt","affiliation":"Empa","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Thomas","last_name":"Schulthess","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Nicola","last_name":"Marzari","affiliation":"EPFL","country":"Switzerland","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Giovanni","last_name":"Pizzi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post176","type":"poster","title":"CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors","begin_time":"21:18","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, machine learning has become a popular method to predict atomic-scale properties of molecular and material systems. While perhaps the most popular applications of machine learning in Chemistry and Materials Science have been to the potential energy surface of a system, a full statistical-mechanical description requires not only the potential energy but also tensorial properties such as dipole moments and polarizabilities. A machine-learning model for these properties must give predictions that transform covariantly with rigid-body rotations of the system, which adds an extra layer of complexity. This poster describes a framework for machine-learning of tensor properties of arbitrary ranks, accounting fully for the covariance of these properties. This method is an extension of Gaussian process regression (GPR), and involves a generalization of the similarity function, or kernel, of GPR to a tensorial kernel. This kernel builds upon the smooth overlap of atomic positions\u00a0(SOAP) kernel used for scalar properties. Results for prediction of electric response tensors of several orders, for a number of water oligomers and for bulk water, show that this method is an extremely promising one for machine-learning of these properties.","filename":"post176s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}]}, "slot": {"id":"post176","type":"poster","title":"CHM10 - A Symmetry-Adapted Approach to Machine Learning of Tensors","begin_time":"21:18","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years, machine learning has become a popular method to predict atomic-scale properties of molecular and material systems. While perhaps the most popular applications of machine learning in Chemistry and Materials Science have been to the potential energy surface of a system, a full statistical-mechanical description requires not only the potential energy but also tensorial properties such as dipole moments and polarizabilities. A machine-learning model for these properties must give predictions that transform covariantly with rigid-body rotations of the system, which adds an extra layer of complexity. This poster describes a framework for machine-learning of tensor properties of arbitrary ranks, accounting fully for the covariance of these properties. This method is an extension of Gaussian process regression (GPR), and involves a generalization of the similarity function, or kernel, of GPR to a tensorial kernel. This kernel builds upon the smooth overlap of atomic positions\u00a0(SOAP) kernel used for scalar properties. Results for prediction of electric response tensors of several orders, for a number of water oligomers and for bulk water, show that this method is an extremely promising one for machine-learning of these properties.","filename":"post176s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Andrea","last_name":"Grisafi","affiliation":"EPFL","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David M.","last_name":"Wilkins","affiliation":"EPFL","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Michele","last_name":"Ceriotti","affiliation":"EPFL","country":"Switzerland","bio":"","order":"3","is_presenter":false}] } Presentation
CLW01 - Automatic Optimization of Domain Specific Languages for Weather and Climate Models
, Tobias Wicky (ETH Zurich, Switzerland)
+ Abstract { "session": {"id":"sess144","title":"Posters in Climate and Weather","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Climate and Weather"],"slots":[{"id":"post155","type":"poster","title":"CLW01 - Automatic Optimization of Domain Specific Languages for Weather and Climate Models","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"We present a compiler toolchain for domain-specific languages (DSLs) that allows for easier design of high-level DSLs for weather and climate models. The growing diversity of computing architectures where scientific models need to run is leading to a decrease of productivity due to the necessity to incorporate multiple programming models. DSLs have been proposed to separate the algorithmic implementation from the architecture-specific implementation. However, DSLs are developed for specific domains or individual applications. Therefore, there is little reuse between existing complex tools, leading to high maintenance costs. Our toolchain provides efficient code optimizers and code generation for multiple architectures to any high-level DSL by means of a standard intermediate representation (IR). This significantly reduces development efforts since these parts can be fully reused. Based on that toolchain, we build a high-level DSL that allows for a full implementation of the dynamical core of the COSMO numerical weather predication and regional climate model. This results in a decrease of code size by a factor of about ten compared to the implementation that is currently in production. This is valuable as it increases productivity as well as maintainability. The automatic optimization is able to achieve speedups compared to expert tuned production code.","filename":"post155s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabian","last_name":"Thuering","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlos E.","last_name":"Osuna","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Oliver","last_name":"Fuhrer","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Hoefler","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post121","type":"poster","title":"CLW02 - ESiWACE: Performance Predictions for Storm-Resolving Simulations of the Climate System","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With exascale computing becoming available in the next decade, global weather prediction at the kilometer scale will be enabled. Moreover, the climate community has already begun to contemplate a new generation of high-resolution climate models. High-resolution model development is confronted with several challenges. Scalability of the models needs to be optimal, including all relevant components such as I\/O which easily becomes a bottleneck; both runtime and I\/O will dictate how fine a resolution can be chosen while still being able to run the model at production level, e.g. at 1-30 years\/day depending on the questions to be addressed. Moreover, given various scalability experiments from prototypical runs and additional model data, estimating performance for new simulations can become challenging. I present results achieved in the scope of the Centre of Excellence in Simulation of Weather and Climate in Europe (ESiWACE) using the ICON model for global high-resolution simulations. I give an overview of the project, I show results from multi-week global 5km simulations, and I discuss current features and limits of the simulations. I further link the findings to a new intercomparison initiative DYAMOND for high-resolution predictions. Finally, I discuss performance prediction approaches for existing performance data.","filename":"post121s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Philipp","last_name":"Neumann","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}]},{"id":"post136","type":"poster","title":"CLW03 - Experiments with Containerising a State-of-the-Art Weather and Climate Model for Application in HPC","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Modern weather and climate models have massively parallel complex codes and complex workflow environments. Porting these codes is inherently difficult, as is installing, developing and maintaining the relevant infrastructure - particularly where reproducibility of workflow and output is required. The associated effort is a major drain on resources. Containerisation directly addresses many of the issues; by packaging the entire application software stack and runtime into a portable stand-alone container, much of the repetitive work is removed, as is the scope for \u0022installer error\u0022. In this work we present an ongoing study into the use of containers to package (specific) climate configurations of the Met Office Unified Model - a complete weather and climate model and workflow system. Three different container solutions have been used: Docker, Singularity and Shifter. A single container was developed, compatible with all three container systems, and comprising model build and control infrastructures and executables. Issues addressed include making use of the MPI ABI, to facilitate the use by the containerised executable of local fast interconnects, and access to the local file system. Results are presented from environments which range from exploiting a virtual cluster using SLURM on a laptop through to using a Cray XC30 supercomputer.","filename":"post136s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bryan","last_name":"Lawrence","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post133","type":"poster","title":"CLW04 - Performance Study of Climate and Weather Models: Towards a More Efficiently Scalable Model","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The enhancement of numerical codes is given a lot of attention around Europe. Weather and climate models are improving the accuracy of their simulations with some factors such as the reduction of parametrization or the increase of grid resolution. However, this accuracy improvement will need more computational resources through a new generation of supercomputers. To take advantage of this new generation, performance analysis could help to know in detail the computational behavior of the models and the information obtained could be used to introduce optimizations. The optimizations will improve the energy efficiency of the models when thousands of resources are used for their parallel execution. Similarly to previous works using profiling tools for EC-Earth, NEMO and IFS, in this study we present our methodology and analyse results to know more about the computational behavior of different Weather and Climate models. Additionally, we present how to improve the functionality and performance of some of the bottlenecks.","filename":"post133s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Xavier","last_name":"Yepes","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Oriol","last_name":"Tinto","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kim","last_name":"Serradell","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Miguel","last_name":"Castrillo","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true}]},{"id":"post164","type":"poster","title":"CLW05 - Porting Physical Parameterizations from a Climate Model to Accelerators","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"ICON (ICOsahedral Non-hydrostatic) is a climate and numerical weather prediction model being developed by the Max Planck Institute for Meteorology (MPI-M) and the German Weather Service (DWD). Together with MPI-M and DWD, MeteoSwiss, the Center for Climate Systems Modeling (C2SM\/ETH), and the Swiss National Supercomputing Center (CSCS) are porting ICON to GPUs and many-core architectures. Within the model, physical parameterizations calculate the collective effect of physical phenomena which occur on a sub-grid scale. We suggest multiple directive-based approaches of porting these parameterizations to accelerators, such as using the OpenACC standard or the CLAW source-to-source translator. Allowing the retention of a single Fortran code, directive approach can offer a high degree of performance portability. Using the FortranTestGenerator tool for automatic unit test generation for Fortran subroutines, the turbulence parameterization is isolated in a testbed subset of the model, so that subsequent changes can be easily validated. Tool-based analysis of loop kernels using the Roofline model is used to estimate attainable performance on various platforms, in particular i86-based multi-core CPUs as well as NVIDIA GPUs. The validated turbulence parameterization, running within a testbed framework, can be integrated into the overall ICON model.","filename":"post164s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gerhard","last_name":"Wellein","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"William","last_name":"Sawyer","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Xavier","last_name":"Lapillonne","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post129","type":"poster","title":"CLW06 - Towards More Efficient Adjustment of Free Parameters in a Global Climate Model?","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Several climate relevant processes are not resolved by the spatial discretization of current global climate models (GCMs). Tropical thunderstorms, for example, with their deep convection must be included via some sub-grid-scale parameterization. Associated free parameters must be adjusted to obtain a \u0027physically meaningful climate\u0027. This \u0027model tuning\u0027 is expensive: the number of tuning parameters is significant (several tens), the response of the model climate to changes in these parameters is typically non-linear, and to quantify this response the GCM must be run for some time, at considerable computational costs. We illustrate model tuning with the example of MPI-ESM-HAM (Max Planck Earth System Model, coupled to the Hamburg Aerosol Module), and discuss how the steadily growing number of GCM simulations (data points) during the tuning process may be exploited to arrive at an overall more efficient, more resource friendly tuning procedure.","filename":"post129s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Martin","last_name":"Wild","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post155","type":"poster","title":"CLW01 - Automatic Optimization of Domain Specific Languages for Weather and Climate Models","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"We present a compiler toolchain for domain-specific languages (DSLs) that allows for easier design of high-level DSLs for weather and climate models. The growing diversity of computing architectures where scientific models need to run is leading to a decrease of productivity due to the necessity to incorporate multiple programming models. DSLs have been proposed to separate the algorithmic implementation from the architecture-specific implementation. However, DSLs are developed for specific domains or individual applications. Therefore, there is little reuse between existing complex tools, leading to high maintenance costs. Our toolchain provides efficient code optimizers and code generation for multiple architectures to any high-level DSL by means of a standard intermediate representation (IR). This significantly reduces development efforts since these parts can be fully reused. Based on that toolchain, we build a high-level DSL that allows for a full implementation of the dynamical core of the COSMO numerical weather predication and regional climate model. This results in a decrease of code size by a factor of about ten compared to the implementation that is currently in production. This is valuable as it increases productivity as well as maintainability. The automatic optimization is able to achieve speedups compared to expert tuned production code.","filename":"post155s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabian","last_name":"Thuering","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlos E.","last_name":"Osuna","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Oliver","last_name":"Fuhrer","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Hoefler","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabian","last_name":"Thuering","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlos E.","last_name":"Osuna","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Oliver","last_name":"Fuhrer","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Hoefler","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false}] } Presentation
CLW02 - ESiWACE: Performance Predictions for Storm-Resolving Simulations of the Climate System
, Joachim Biercamp (German Climate Computing Center, Germany)
+ Abstract { "session": {"id":"sess144","title":"Posters in Climate and Weather","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Climate and Weather"],"slots":[{"id":"post155","type":"poster","title":"CLW01 - Automatic Optimization of Domain Specific Languages for Weather and Climate Models","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"We present a compiler toolchain for domain-specific languages (DSLs) that allows for easier design of high-level DSLs for weather and climate models. The growing diversity of computing architectures where scientific models need to run is leading to a decrease of productivity due to the necessity to incorporate multiple programming models. DSLs have been proposed to separate the algorithmic implementation from the architecture-specific implementation. However, DSLs are developed for specific domains or individual applications. Therefore, there is little reuse between existing complex tools, leading to high maintenance costs. Our toolchain provides efficient code optimizers and code generation for multiple architectures to any high-level DSL by means of a standard intermediate representation (IR). This significantly reduces development efforts since these parts can be fully reused. Based on that toolchain, we build a high-level DSL that allows for a full implementation of the dynamical core of the COSMO numerical weather predication and regional climate model. This results in a decrease of code size by a factor of about ten compared to the implementation that is currently in production. This is valuable as it increases productivity as well as maintainability. The automatic optimization is able to achieve speedups compared to expert tuned production code.","filename":"post155s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabian","last_name":"Thuering","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlos E.","last_name":"Osuna","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Oliver","last_name":"Fuhrer","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Hoefler","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post121","type":"poster","title":"CLW02 - ESiWACE: Performance Predictions for Storm-Resolving Simulations of the Climate System","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With exascale computing becoming available in the next decade, global weather prediction at the kilometer scale will be enabled. Moreover, the climate community has already begun to contemplate a new generation of high-resolution climate models. High-resolution model development is confronted with several challenges. Scalability of the models needs to be optimal, including all relevant components such as I\/O which easily becomes a bottleneck; both runtime and I\/O will dictate how fine a resolution can be chosen while still being able to run the model at production level, e.g. at 1-30 years\/day depending on the questions to be addressed. Moreover, given various scalability experiments from prototypical runs and additional model data, estimating performance for new simulations can become challenging. I present results achieved in the scope of the Centre of Excellence in Simulation of Weather and Climate in Europe (ESiWACE) using the ICON model for global high-resolution simulations. I give an overview of the project, I show results from multi-week global 5km simulations, and I discuss current features and limits of the simulations. I further link the findings to a new intercomparison initiative DYAMOND for high-resolution predictions. Finally, I discuss performance prediction approaches for existing performance data.","filename":"post121s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Philipp","last_name":"Neumann","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}]},{"id":"post136","type":"poster","title":"CLW03 - Experiments with Containerising a State-of-the-Art Weather and Climate Model for Application in HPC","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Modern weather and climate models have massively parallel complex codes and complex workflow environments. Porting these codes is inherently difficult, as is installing, developing and maintaining the relevant infrastructure - particularly where reproducibility of workflow and output is required. The associated effort is a major drain on resources. Containerisation directly addresses many of the issues; by packaging the entire application software stack and runtime into a portable stand-alone container, much of the repetitive work is removed, as is the scope for \u0022installer error\u0022. In this work we present an ongoing study into the use of containers to package (specific) climate configurations of the Met Office Unified Model - a complete weather and climate model and workflow system. Three different container solutions have been used: Docker, Singularity and Shifter. A single container was developed, compatible with all three container systems, and comprising model build and control infrastructures and executables. Issues addressed include making use of the MPI ABI, to facilitate the use by the containerised executable of local fast interconnects, and access to the local file system. Results are presented from environments which range from exploiting a virtual cluster using SLURM on a laptop through to using a Cray XC30 supercomputer.","filename":"post136s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bryan","last_name":"Lawrence","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post133","type":"poster","title":"CLW04 - Performance Study of Climate and Weather Models: Towards a More Efficiently Scalable Model","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The enhancement of numerical codes is given a lot of attention around Europe. Weather and climate models are improving the accuracy of their simulations with some factors such as the reduction of parametrization or the increase of grid resolution. However, this accuracy improvement will need more computational resources through a new generation of supercomputers. To take advantage of this new generation, performance analysis could help to know in detail the computational behavior of the models and the information obtained could be used to introduce optimizations. The optimizations will improve the energy efficiency of the models when thousands of resources are used for their parallel execution. Similarly to previous works using profiling tools for EC-Earth, NEMO and IFS, in this study we present our methodology and analyse results to know more about the computational behavior of different Weather and Climate models. Additionally, we present how to improve the functionality and performance of some of the bottlenecks.","filename":"post133s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Xavier","last_name":"Yepes","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Oriol","last_name":"Tinto","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kim","last_name":"Serradell","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Miguel","last_name":"Castrillo","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true}]},{"id":"post164","type":"poster","title":"CLW05 - Porting Physical Parameterizations from a Climate Model to Accelerators","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"ICON (ICOsahedral Non-hydrostatic) is a climate and numerical weather prediction model being developed by the Max Planck Institute for Meteorology (MPI-M) and the German Weather Service (DWD). Together with MPI-M and DWD, MeteoSwiss, the Center for Climate Systems Modeling (C2SM\/ETH), and the Swiss National Supercomputing Center (CSCS) are porting ICON to GPUs and many-core architectures. Within the model, physical parameterizations calculate the collective effect of physical phenomena which occur on a sub-grid scale. We suggest multiple directive-based approaches of porting these parameterizations to accelerators, such as using the OpenACC standard or the CLAW source-to-source translator. Allowing the retention of a single Fortran code, directive approach can offer a high degree of performance portability. Using the FortranTestGenerator tool for automatic unit test generation for Fortran subroutines, the turbulence parameterization is isolated in a testbed subset of the model, so that subsequent changes can be easily validated. Tool-based analysis of loop kernels using the Roofline model is used to estimate attainable performance on various platforms, in particular i86-based multi-core CPUs as well as NVIDIA GPUs. The validated turbulence parameterization, running within a testbed framework, can be integrated into the overall ICON model.","filename":"post164s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gerhard","last_name":"Wellein","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"William","last_name":"Sawyer","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Xavier","last_name":"Lapillonne","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post129","type":"poster","title":"CLW06 - Towards More Efficient Adjustment of Free Parameters in a Global Climate Model?","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Several climate relevant processes are not resolved by the spatial discretization of current global climate models (GCMs). Tropical thunderstorms, for example, with their deep convection must be included via some sub-grid-scale parameterization. Associated free parameters must be adjusted to obtain a \u0027physically meaningful climate\u0027. This \u0027model tuning\u0027 is expensive: the number of tuning parameters is significant (several tens), the response of the model climate to changes in these parameters is typically non-linear, and to quantify this response the GCM must be run for some time, at considerable computational costs. We illustrate model tuning with the example of MPI-ESM-HAM (Max Planck Earth System Model, coupled to the Hamburg Aerosol Module), and discuss how the steadily growing number of GCM simulations (data points) during the tuning process may be exploited to arrive at an overall more efficient, more resource friendly tuning procedure.","filename":"post129s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Martin","last_name":"Wild","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post121","type":"poster","title":"CLW02 - ESiWACE: Performance Predictions for Storm-Resolving Simulations of the Climate System","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With exascale computing becoming available in the next decade, global weather prediction at the kilometer scale will be enabled. Moreover, the climate community has already begun to contemplate a new generation of high-resolution climate models. High-resolution model development is confronted with several challenges. Scalability of the models needs to be optimal, including all relevant components such as I\/O which easily becomes a bottleneck; both runtime and I\/O will dictate how fine a resolution can be chosen while still being able to run the model at production level, e.g. at 1-30 years\/day depending on the questions to be addressed. Moreover, given various scalability experiments from prototypical runs and additional model data, estimating performance for new simulations can become challenging. I present results achieved in the scope of the Centre of Excellence in Simulation of Weather and Climate in Europe (ESiWACE) using the ICON model for global high-resolution simulations. I give an overview of the project, I show results from multi-week global 5km simulations, and I discuss current features and limits of the simulations. I further link the findings to a new intercomparison initiative DYAMOND for high-resolution predictions. Finally, I discuss performance prediction approaches for existing performance data.","filename":"post121s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Philipp","last_name":"Neumann","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Philipp","last_name":"Neumann","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}] } Presentation
CLW03 - Experiments with Containerising a State-of-the-Art Weather and Climate Model for Application in HPC
, Simon Wilson (NCAS-CMS, United Kingdom)
+ Abstract { "session": {"id":"sess144","title":"Posters in Climate and Weather","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Climate and Weather"],"slots":[{"id":"post155","type":"poster","title":"CLW01 - Automatic Optimization of Domain Specific Languages for Weather and Climate Models","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"We present a compiler toolchain for domain-specific languages (DSLs) that allows for easier design of high-level DSLs for weather and climate models. The growing diversity of computing architectures where scientific models need to run is leading to a decrease of productivity due to the necessity to incorporate multiple programming models. DSLs have been proposed to separate the algorithmic implementation from the architecture-specific implementation. However, DSLs are developed for specific domains or individual applications. Therefore, there is little reuse between existing complex tools, leading to high maintenance costs. Our toolchain provides efficient code optimizers and code generation for multiple architectures to any high-level DSL by means of a standard intermediate representation (IR). This significantly reduces development efforts since these parts can be fully reused. Based on that toolchain, we build a high-level DSL that allows for a full implementation of the dynamical core of the COSMO numerical weather predication and regional climate model. This results in a decrease of code size by a factor of about ten compared to the implementation that is currently in production. This is valuable as it increases productivity as well as maintainability. The automatic optimization is able to achieve speedups compared to expert tuned production code.","filename":"post155s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabian","last_name":"Thuering","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlos E.","last_name":"Osuna","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Oliver","last_name":"Fuhrer","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Hoefler","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post121","type":"poster","title":"CLW02 - ESiWACE: Performance Predictions for Storm-Resolving Simulations of the Climate System","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With exascale computing becoming available in the next decade, global weather prediction at the kilometer scale will be enabled. Moreover, the climate community has already begun to contemplate a new generation of high-resolution climate models. High-resolution model development is confronted with several challenges. Scalability of the models needs to be optimal, including all relevant components such as I\/O which easily becomes a bottleneck; both runtime and I\/O will dictate how fine a resolution can be chosen while still being able to run the model at production level, e.g. at 1-30 years\/day depending on the questions to be addressed. Moreover, given various scalability experiments from prototypical runs and additional model data, estimating performance for new simulations can become challenging. I present results achieved in the scope of the Centre of Excellence in Simulation of Weather and Climate in Europe (ESiWACE) using the ICON model for global high-resolution simulations. I give an overview of the project, I show results from multi-week global 5km simulations, and I discuss current features and limits of the simulations. I further link the findings to a new intercomparison initiative DYAMOND for high-resolution predictions. Finally, I discuss performance prediction approaches for existing performance data.","filename":"post121s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Philipp","last_name":"Neumann","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}]},{"id":"post136","type":"poster","title":"CLW03 - Experiments with Containerising a State-of-the-Art Weather and Climate Model for Application in HPC","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Modern weather and climate models have massively parallel complex codes and complex workflow environments. Porting these codes is inherently difficult, as is installing, developing and maintaining the relevant infrastructure - particularly where reproducibility of workflow and output is required. The associated effort is a major drain on resources. Containerisation directly addresses many of the issues; by packaging the entire application software stack and runtime into a portable stand-alone container, much of the repetitive work is removed, as is the scope for \u0022installer error\u0022. In this work we present an ongoing study into the use of containers to package (specific) climate configurations of the Met Office Unified Model - a complete weather and climate model and workflow system. Three different container solutions have been used: Docker, Singularity and Shifter. A single container was developed, compatible with all three container systems, and comprising model build and control infrastructures and executables. Issues addressed include making use of the MPI ABI, to facilitate the use by the containerised executable of local fast interconnects, and access to the local file system. Results are presented from environments which range from exploiting a virtual cluster using SLURM on a laptop through to using a Cray XC30 supercomputer.","filename":"post136s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bryan","last_name":"Lawrence","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post133","type":"poster","title":"CLW04 - Performance Study of Climate and Weather Models: Towards a More Efficiently Scalable Model","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The enhancement of numerical codes is given a lot of attention around Europe. Weather and climate models are improving the accuracy of their simulations with some factors such as the reduction of parametrization or the increase of grid resolution. However, this accuracy improvement will need more computational resources through a new generation of supercomputers. To take advantage of this new generation, performance analysis could help to know in detail the computational behavior of the models and the information obtained could be used to introduce optimizations. The optimizations will improve the energy efficiency of the models when thousands of resources are used for their parallel execution. Similarly to previous works using profiling tools for EC-Earth, NEMO and IFS, in this study we present our methodology and analyse results to know more about the computational behavior of different Weather and Climate models. Additionally, we present how to improve the functionality and performance of some of the bottlenecks.","filename":"post133s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Xavier","last_name":"Yepes","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Oriol","last_name":"Tinto","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kim","last_name":"Serradell","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Miguel","last_name":"Castrillo","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true}]},{"id":"post164","type":"poster","title":"CLW05 - Porting Physical Parameterizations from a Climate Model to Accelerators","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"ICON (ICOsahedral Non-hydrostatic) is a climate and numerical weather prediction model being developed by the Max Planck Institute for Meteorology (MPI-M) and the German Weather Service (DWD). Together with MPI-M and DWD, MeteoSwiss, the Center for Climate Systems Modeling (C2SM\/ETH), and the Swiss National Supercomputing Center (CSCS) are porting ICON to GPUs and many-core architectures. Within the model, physical parameterizations calculate the collective effect of physical phenomena which occur on a sub-grid scale. We suggest multiple directive-based approaches of porting these parameterizations to accelerators, such as using the OpenACC standard or the CLAW source-to-source translator. Allowing the retention of a single Fortran code, directive approach can offer a high degree of performance portability. Using the FortranTestGenerator tool for automatic unit test generation for Fortran subroutines, the turbulence parameterization is isolated in a testbed subset of the model, so that subsequent changes can be easily validated. Tool-based analysis of loop kernels using the Roofline model is used to estimate attainable performance on various platforms, in particular i86-based multi-core CPUs as well as NVIDIA GPUs. The validated turbulence parameterization, running within a testbed framework, can be integrated into the overall ICON model.","filename":"post164s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gerhard","last_name":"Wellein","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"William","last_name":"Sawyer","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Xavier","last_name":"Lapillonne","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post129","type":"poster","title":"CLW06 - Towards More Efficient Adjustment of Free Parameters in a Global Climate Model?","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Several climate relevant processes are not resolved by the spatial discretization of current global climate models (GCMs). Tropical thunderstorms, for example, with their deep convection must be included via some sub-grid-scale parameterization. Associated free parameters must be adjusted to obtain a \u0027physically meaningful climate\u0027. This \u0027model tuning\u0027 is expensive: the number of tuning parameters is significant (several tens), the response of the model climate to changes in these parameters is typically non-linear, and to quantify this response the GCM must be run for some time, at considerable computational costs. We illustrate model tuning with the example of MPI-ESM-HAM (Max Planck Earth System Model, coupled to the Hamburg Aerosol Module), and discuss how the steadily growing number of GCM simulations (data points) during the tuning process may be exploited to arrive at an overall more efficient, more resource friendly tuning procedure.","filename":"post129s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Martin","last_name":"Wild","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post136","type":"poster","title":"CLW03 - Experiments with Containerising a State-of-the-Art Weather and Climate Model for Application in HPC","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Modern weather and climate models have massively parallel complex codes and complex workflow environments. Porting these codes is inherently difficult, as is installing, developing and maintaining the relevant infrastructure - particularly where reproducibility of workflow and output is required. The associated effort is a major drain on resources. Containerisation directly addresses many of the issues; by packaging the entire application software stack and runtime into a portable stand-alone container, much of the repetitive work is removed, as is the scope for \u0022installer error\u0022. In this work we present an ongoing study into the use of containers to package (specific) climate configurations of the Met Office Unified Model - a complete weather and climate model and workflow system. Three different container solutions have been used: Docker, Singularity and Shifter. A single container was developed, compatible with all three container systems, and comprising model build and control infrastructures and executables. Issues addressed include making use of the MPI ABI, to facilitate the use by the containerised executable of local fast interconnects, and access to the local file system. Results are presented from environments which range from exploiting a virtual cluster using SLURM on a laptop through to using a Cray XC30 supercomputer.","filename":"post136s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bryan","last_name":"Lawrence","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bryan","last_name":"Lawrence","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"2","is_presenter":false}] } Presentation
CLW04 - Performance Study of Climate and Weather Models: Towards a More Efficiently Scalable Model
, Mario Acosta (Barcelona Supercomputing Center, Spain)
+ Abstract { "session": {"id":"sess144","title":"Posters in Climate and Weather","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Climate and Weather"],"slots":[{"id":"post155","type":"poster","title":"CLW01 - Automatic Optimization of Domain Specific Languages for Weather and Climate Models","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"We present a compiler toolchain for domain-specific languages (DSLs) that allows for easier design of high-level DSLs for weather and climate models. The growing diversity of computing architectures where scientific models need to run is leading to a decrease of productivity due to the necessity to incorporate multiple programming models. DSLs have been proposed to separate the algorithmic implementation from the architecture-specific implementation. However, DSLs are developed for specific domains or individual applications. Therefore, there is little reuse between existing complex tools, leading to high maintenance costs. Our toolchain provides efficient code optimizers and code generation for multiple architectures to any high-level DSL by means of a standard intermediate representation (IR). This significantly reduces development efforts since these parts can be fully reused. Based on that toolchain, we build a high-level DSL that allows for a full implementation of the dynamical core of the COSMO numerical weather predication and regional climate model. This results in a decrease of code size by a factor of about ten compared to the implementation that is currently in production. This is valuable as it increases productivity as well as maintainability. The automatic optimization is able to achieve speedups compared to expert tuned production code.","filename":"post155s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabian","last_name":"Thuering","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlos E.","last_name":"Osuna","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Oliver","last_name":"Fuhrer","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Hoefler","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post121","type":"poster","title":"CLW02 - ESiWACE: Performance Predictions for Storm-Resolving Simulations of the Climate System","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With exascale computing becoming available in the next decade, global weather prediction at the kilometer scale will be enabled. Moreover, the climate community has already begun to contemplate a new generation of high-resolution climate models. High-resolution model development is confronted with several challenges. Scalability of the models needs to be optimal, including all relevant components such as I\/O which easily becomes a bottleneck; both runtime and I\/O will dictate how fine a resolution can be chosen while still being able to run the model at production level, e.g. at 1-30 years\/day depending on the questions to be addressed. Moreover, given various scalability experiments from prototypical runs and additional model data, estimating performance for new simulations can become challenging. I present results achieved in the scope of the Centre of Excellence in Simulation of Weather and Climate in Europe (ESiWACE) using the ICON model for global high-resolution simulations. I give an overview of the project, I show results from multi-week global 5km simulations, and I discuss current features and limits of the simulations. I further link the findings to a new intercomparison initiative DYAMOND for high-resolution predictions. Finally, I discuss performance prediction approaches for existing performance data.","filename":"post121s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Philipp","last_name":"Neumann","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}]},{"id":"post136","type":"poster","title":"CLW03 - Experiments with Containerising a State-of-the-Art Weather and Climate Model for Application in HPC","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Modern weather and climate models have massively parallel complex codes and complex workflow environments. Porting these codes is inherently difficult, as is installing, developing and maintaining the relevant infrastructure - particularly where reproducibility of workflow and output is required. The associated effort is a major drain on resources. Containerisation directly addresses many of the issues; by packaging the entire application software stack and runtime into a portable stand-alone container, much of the repetitive work is removed, as is the scope for \u0022installer error\u0022. In this work we present an ongoing study into the use of containers to package (specific) climate configurations of the Met Office Unified Model - a complete weather and climate model and workflow system. Three different container solutions have been used: Docker, Singularity and Shifter. A single container was developed, compatible with all three container systems, and comprising model build and control infrastructures and executables. Issues addressed include making use of the MPI ABI, to facilitate the use by the containerised executable of local fast interconnects, and access to the local file system. Results are presented from environments which range from exploiting a virtual cluster using SLURM on a laptop through to using a Cray XC30 supercomputer.","filename":"post136s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bryan","last_name":"Lawrence","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post133","type":"poster","title":"CLW04 - Performance Study of Climate and Weather Models: Towards a More Efficiently Scalable Model","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The enhancement of numerical codes is given a lot of attention around Europe. Weather and climate models are improving the accuracy of their simulations with some factors such as the reduction of parametrization or the increase of grid resolution. However, this accuracy improvement will need more computational resources through a new generation of supercomputers. To take advantage of this new generation, performance analysis could help to know in detail the computational behavior of the models and the information obtained could be used to introduce optimizations. The optimizations will improve the energy efficiency of the models when thousands of resources are used for their parallel execution. Similarly to previous works using profiling tools for EC-Earth, NEMO and IFS, in this study we present our methodology and analyse results to know more about the computational behavior of different Weather and Climate models. Additionally, we present how to improve the functionality and performance of some of the bottlenecks.","filename":"post133s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Xavier","last_name":"Yepes","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Oriol","last_name":"Tinto","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kim","last_name":"Serradell","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Miguel","last_name":"Castrillo","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true}]},{"id":"post164","type":"poster","title":"CLW05 - Porting Physical Parameterizations from a Climate Model to Accelerators","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"ICON (ICOsahedral Non-hydrostatic) is a climate and numerical weather prediction model being developed by the Max Planck Institute for Meteorology (MPI-M) and the German Weather Service (DWD). Together with MPI-M and DWD, MeteoSwiss, the Center for Climate Systems Modeling (C2SM\/ETH), and the Swiss National Supercomputing Center (CSCS) are porting ICON to GPUs and many-core architectures. Within the model, physical parameterizations calculate the collective effect of physical phenomena which occur on a sub-grid scale. We suggest multiple directive-based approaches of porting these parameterizations to accelerators, such as using the OpenACC standard or the CLAW source-to-source translator. Allowing the retention of a single Fortran code, directive approach can offer a high degree of performance portability. Using the FortranTestGenerator tool for automatic unit test generation for Fortran subroutines, the turbulence parameterization is isolated in a testbed subset of the model, so that subsequent changes can be easily validated. Tool-based analysis of loop kernels using the Roofline model is used to estimate attainable performance on various platforms, in particular i86-based multi-core CPUs as well as NVIDIA GPUs. The validated turbulence parameterization, running within a testbed framework, can be integrated into the overall ICON model.","filename":"post164s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gerhard","last_name":"Wellein","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"William","last_name":"Sawyer","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Xavier","last_name":"Lapillonne","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post129","type":"poster","title":"CLW06 - Towards More Efficient Adjustment of Free Parameters in a Global Climate Model?","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Several climate relevant processes are not resolved by the spatial discretization of current global climate models (GCMs). Tropical thunderstorms, for example, with their deep convection must be included via some sub-grid-scale parameterization. Associated free parameters must be adjusted to obtain a \u0027physically meaningful climate\u0027. This \u0027model tuning\u0027 is expensive: the number of tuning parameters is significant (several tens), the response of the model climate to changes in these parameters is typically non-linear, and to quantify this response the GCM must be run for some time, at considerable computational costs. We illustrate model tuning with the example of MPI-ESM-HAM (Max Planck Earth System Model, coupled to the Hamburg Aerosol Module), and discuss how the steadily growing number of GCM simulations (data points) during the tuning process may be exploited to arrive at an overall more efficient, more resource friendly tuning procedure.","filename":"post129s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Martin","last_name":"Wild","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post133","type":"poster","title":"CLW04 - Performance Study of Climate and Weather Models: Towards a More Efficiently Scalable Model","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The enhancement of numerical codes is given a lot of attention around Europe. Weather and climate models are improving the accuracy of their simulations with some factors such as the reduction of parametrization or the increase of grid resolution. However, this accuracy improvement will need more computational resources through a new generation of supercomputers. To take advantage of this new generation, performance analysis could help to know in detail the computational behavior of the models and the information obtained could be used to introduce optimizations. The optimizations will improve the energy efficiency of the models when thousands of resources are used for their parallel execution. Similarly to previous works using profiling tools for EC-Earth, NEMO and IFS, in this study we present our methodology and analyse results to know more about the computational behavior of different Weather and Climate models. Additionally, we present how to improve the functionality and performance of some of the bottlenecks.","filename":"post133s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Xavier","last_name":"Yepes","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Oriol","last_name":"Tinto","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kim","last_name":"Serradell","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Miguel","last_name":"Castrillo","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Xavier","last_name":"Yepes","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Oriol","last_name":"Tinto","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kim","last_name":"Serradell","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Miguel","last_name":"Castrillo","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false}] } Presentation
CLW05 - Porting Physical Parameterizations from a Climate Model to Accelerators
, Thomas Köster (Università della Svizzera italiana, Switzerland)
+ Abstract { "session": {"id":"sess144","title":"Posters in Climate and Weather","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Climate and Weather"],"slots":[{"id":"post155","type":"poster","title":"CLW01 - Automatic Optimization of Domain Specific Languages for Weather and Climate Models","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"We present a compiler toolchain for domain-specific languages (DSLs) that allows for easier design of high-level DSLs for weather and climate models. The growing diversity of computing architectures where scientific models need to run is leading to a decrease of productivity due to the necessity to incorporate multiple programming models. DSLs have been proposed to separate the algorithmic implementation from the architecture-specific implementation. However, DSLs are developed for specific domains or individual applications. Therefore, there is little reuse between existing complex tools, leading to high maintenance costs. Our toolchain provides efficient code optimizers and code generation for multiple architectures to any high-level DSL by means of a standard intermediate representation (IR). This significantly reduces development efforts since these parts can be fully reused. Based on that toolchain, we build a high-level DSL that allows for a full implementation of the dynamical core of the COSMO numerical weather predication and regional climate model. This results in a decrease of code size by a factor of about ten compared to the implementation that is currently in production. This is valuable as it increases productivity as well as maintainability. The automatic optimization is able to achieve speedups compared to expert tuned production code.","filename":"post155s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabian","last_name":"Thuering","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlos E.","last_name":"Osuna","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Oliver","last_name":"Fuhrer","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Hoefler","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post121","type":"poster","title":"CLW02 - ESiWACE: Performance Predictions for Storm-Resolving Simulations of the Climate System","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With exascale computing becoming available in the next decade, global weather prediction at the kilometer scale will be enabled. Moreover, the climate community has already begun to contemplate a new generation of high-resolution climate models. High-resolution model development is confronted with several challenges. Scalability of the models needs to be optimal, including all relevant components such as I\/O which easily becomes a bottleneck; both runtime and I\/O will dictate how fine a resolution can be chosen while still being able to run the model at production level, e.g. at 1-30 years\/day depending on the questions to be addressed. Moreover, given various scalability experiments from prototypical runs and additional model data, estimating performance for new simulations can become challenging. I present results achieved in the scope of the Centre of Excellence in Simulation of Weather and Climate in Europe (ESiWACE) using the ICON model for global high-resolution simulations. I give an overview of the project, I show results from multi-week global 5km simulations, and I discuss current features and limits of the simulations. I further link the findings to a new intercomparison initiative DYAMOND for high-resolution predictions. Finally, I discuss performance prediction approaches for existing performance data.","filename":"post121s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Philipp","last_name":"Neumann","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}]},{"id":"post136","type":"poster","title":"CLW03 - Experiments with Containerising a State-of-the-Art Weather and Climate Model for Application in HPC","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Modern weather and climate models have massively parallel complex codes and complex workflow environments. Porting these codes is inherently difficult, as is installing, developing and maintaining the relevant infrastructure - particularly where reproducibility of workflow and output is required. The associated effort is a major drain on resources. Containerisation directly addresses many of the issues; by packaging the entire application software stack and runtime into a portable stand-alone container, much of the repetitive work is removed, as is the scope for \u0022installer error\u0022. In this work we present an ongoing study into the use of containers to package (specific) climate configurations of the Met Office Unified Model - a complete weather and climate model and workflow system. Three different container solutions have been used: Docker, Singularity and Shifter. A single container was developed, compatible with all three container systems, and comprising model build and control infrastructures and executables. Issues addressed include making use of the MPI ABI, to facilitate the use by the containerised executable of local fast interconnects, and access to the local file system. Results are presented from environments which range from exploiting a virtual cluster using SLURM on a laptop through to using a Cray XC30 supercomputer.","filename":"post136s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bryan","last_name":"Lawrence","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post133","type":"poster","title":"CLW04 - Performance Study of Climate and Weather Models: Towards a More Efficiently Scalable Model","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The enhancement of numerical codes is given a lot of attention around Europe. Weather and climate models are improving the accuracy of their simulations with some factors such as the reduction of parametrization or the increase of grid resolution. However, this accuracy improvement will need more computational resources through a new generation of supercomputers. To take advantage of this new generation, performance analysis could help to know in detail the computational behavior of the models and the information obtained could be used to introduce optimizations. The optimizations will improve the energy efficiency of the models when thousands of resources are used for their parallel execution. Similarly to previous works using profiling tools for EC-Earth, NEMO and IFS, in this study we present our methodology and analyse results to know more about the computational behavior of different Weather and Climate models. Additionally, we present how to improve the functionality and performance of some of the bottlenecks.","filename":"post133s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Xavier","last_name":"Yepes","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Oriol","last_name":"Tinto","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kim","last_name":"Serradell","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Miguel","last_name":"Castrillo","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true}]},{"id":"post164","type":"poster","title":"CLW05 - Porting Physical Parameterizations from a Climate Model to Accelerators","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"ICON (ICOsahedral Non-hydrostatic) is a climate and numerical weather prediction model being developed by the Max Planck Institute for Meteorology (MPI-M) and the German Weather Service (DWD). Together with MPI-M and DWD, MeteoSwiss, the Center for Climate Systems Modeling (C2SM\/ETH), and the Swiss National Supercomputing Center (CSCS) are porting ICON to GPUs and many-core architectures. Within the model, physical parameterizations calculate the collective effect of physical phenomena which occur on a sub-grid scale. We suggest multiple directive-based approaches of porting these parameterizations to accelerators, such as using the OpenACC standard or the CLAW source-to-source translator. Allowing the retention of a single Fortran code, directive approach can offer a high degree of performance portability. Using the FortranTestGenerator tool for automatic unit test generation for Fortran subroutines, the turbulence parameterization is isolated in a testbed subset of the model, so that subsequent changes can be easily validated. Tool-based analysis of loop kernels using the Roofline model is used to estimate attainable performance on various platforms, in particular i86-based multi-core CPUs as well as NVIDIA GPUs. The validated turbulence parameterization, running within a testbed framework, can be integrated into the overall ICON model.","filename":"post164s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gerhard","last_name":"Wellein","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"William","last_name":"Sawyer","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Xavier","last_name":"Lapillonne","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post129","type":"poster","title":"CLW06 - Towards More Efficient Adjustment of Free Parameters in a Global Climate Model?","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Several climate relevant processes are not resolved by the spatial discretization of current global climate models (GCMs). Tropical thunderstorms, for example, with their deep convection must be included via some sub-grid-scale parameterization. Associated free parameters must be adjusted to obtain a \u0027physically meaningful climate\u0027. This \u0027model tuning\u0027 is expensive: the number of tuning parameters is significant (several tens), the response of the model climate to changes in these parameters is typically non-linear, and to quantify this response the GCM must be run for some time, at considerable computational costs. We illustrate model tuning with the example of MPI-ESM-HAM (Max Planck Earth System Model, coupled to the Hamburg Aerosol Module), and discuss how the steadily growing number of GCM simulations (data points) during the tuning process may be exploited to arrive at an overall more efficient, more resource friendly tuning procedure.","filename":"post129s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Martin","last_name":"Wild","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post164","type":"poster","title":"CLW05 - Porting Physical Parameterizations from a Climate Model to Accelerators","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"ICON (ICOsahedral Non-hydrostatic) is a climate and numerical weather prediction model being developed by the Max Planck Institute for Meteorology (MPI-M) and the German Weather Service (DWD). Together with MPI-M and DWD, MeteoSwiss, the Center for Climate Systems Modeling (C2SM\/ETH), and the Swiss National Supercomputing Center (CSCS) are porting ICON to GPUs and many-core architectures. Within the model, physical parameterizations calculate the collective effect of physical phenomena which occur on a sub-grid scale. We suggest multiple directive-based approaches of porting these parameterizations to accelerators, such as using the OpenACC standard or the CLAW source-to-source translator. Allowing the retention of a single Fortran code, directive approach can offer a high degree of performance portability. Using the FortranTestGenerator tool for automatic unit test generation for Fortran subroutines, the turbulence parameterization is isolated in a testbed subset of the model, so that subsequent changes can be easily validated. Tool-based analysis of loop kernels using the Roofline model is used to estimate attainable performance on various platforms, in particular i86-based multi-core CPUs as well as NVIDIA GPUs. The validated turbulence parameterization, running within a testbed framework, can be integrated into the overall ICON model.","filename":"post164s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gerhard","last_name":"Wellein","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"William","last_name":"Sawyer","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Xavier","last_name":"Lapillonne","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gerhard","last_name":"Wellein","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"William","last_name":"Sawyer","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Xavier","last_name":"Lapillonne","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"5","is_presenter":false}] } Presentation
CLW06 - Towards More Efficient Adjustment of Free Parameters in a Global Climate Model?
, Doris Folini (ETH Zurich, Switzerland)
+ Abstract { "session": {"id":"sess144","title":"Posters in Climate and Weather","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Climate and Weather"],"slots":[{"id":"post155","type":"poster","title":"CLW01 - Automatic Optimization of Domain Specific Languages for Weather and Climate Models","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"We present a compiler toolchain for domain-specific languages (DSLs) that allows for easier design of high-level DSLs for weather and climate models. The growing diversity of computing architectures where scientific models need to run is leading to a decrease of productivity due to the necessity to incorporate multiple programming models. DSLs have been proposed to separate the algorithmic implementation from the architecture-specific implementation. However, DSLs are developed for specific domains or individual applications. Therefore, there is little reuse between existing complex tools, leading to high maintenance costs. Our toolchain provides efficient code optimizers and code generation for multiple architectures to any high-level DSL by means of a standard intermediate representation (IR). This significantly reduces development efforts since these parts can be fully reused. Based on that toolchain, we build a high-level DSL that allows for a full implementation of the dynamical core of the COSMO numerical weather predication and regional climate model. This results in a decrease of code size by a factor of about ten compared to the implementation that is currently in production. This is valuable as it increases productivity as well as maintainability. The automatic optimization is able to achieve speedups compared to expert tuned production code.","filename":"post155s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabian","last_name":"Thuering","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlos E.","last_name":"Osuna","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Oliver","last_name":"Fuhrer","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Hoefler","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Tobias","last_name":"Wicky","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post121","type":"poster","title":"CLW02 - ESiWACE: Performance Predictions for Storm-Resolving Simulations of the Climate System","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With exascale computing becoming available in the next decade, global weather prediction at the kilometer scale will be enabled. Moreover, the climate community has already begun to contemplate a new generation of high-resolution climate models. High-resolution model development is confronted with several challenges. Scalability of the models needs to be optimal, including all relevant components such as I\/O which easily becomes a bottleneck; both runtime and I\/O will dictate how fine a resolution can be chosen while still being able to run the model at production level, e.g. at 1-30 years\/day depending on the questions to be addressed. Moreover, given various scalability experiments from prototypical runs and additional model data, estimating performance for new simulations can become challenging. I present results achieved in the scope of the Centre of Excellence in Simulation of Weather and Climate in Europe (ESiWACE) using the ICON model for global high-resolution simulations. I give an overview of the project, I show results from multi-week global 5km simulations, and I discuss current features and limits of the simulations. I further link the findings to a new intercomparison initiative DYAMOND for high-resolution predictions. Finally, I discuss performance prediction approaches for existing performance data.","filename":"post121s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Philipp","last_name":"Neumann","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Joachim","last_name":"Biercamp","affiliation":"German Climate Computing Center","country":"Germany","bio":"","order":"2","is_presenter":true}]},{"id":"post136","type":"poster","title":"CLW03 - Experiments with Containerising a State-of-the-Art Weather and Climate Model for Application in HPC","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Modern weather and climate models have massively parallel complex codes and complex workflow environments. Porting these codes is inherently difficult, as is installing, developing and maintaining the relevant infrastructure - particularly where reproducibility of workflow and output is required. The associated effort is a major drain on resources. Containerisation directly addresses many of the issues; by packaging the entire application software stack and runtime into a portable stand-alone container, much of the repetitive work is removed, as is the scope for \u0022installer error\u0022. In this work we present an ongoing study into the use of containers to package (specific) climate configurations of the Met Office Unified Model - a complete weather and climate model and workflow system. Three different container solutions have been used: Docker, Singularity and Shifter. A single container was developed, compatible with all three container systems, and comprising model build and control infrastructures and executables. Issues addressed include making use of the MPI ABI, to facilitate the use by the containerised executable of local fast interconnects, and access to the local file system. Results are presented from environments which range from exploiting a virtual cluster using SLURM on a laptop through to using a Cray XC30 supercomputer.","filename":"post136s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bryan","last_name":"Lawrence","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simon","last_name":"Wilson","affiliation":"NCAS-CMS","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post133","type":"poster","title":"CLW04 - Performance Study of Climate and Weather Models: Towards a More Efficiently Scalable Model","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The enhancement of numerical codes is given a lot of attention around Europe. Weather and climate models are improving the accuracy of their simulations with some factors such as the reduction of parametrization or the increase of grid resolution. However, this accuracy improvement will need more computational resources through a new generation of supercomputers. To take advantage of this new generation, performance analysis could help to know in detail the computational behavior of the models and the information obtained could be used to introduce optimizations. The optimizations will improve the energy efficiency of the models when thousands of resources are used for their parallel execution. Similarly to previous works using profiling tools for EC-Earth, NEMO and IFS, in this study we present our methodology and analyse results to know more about the computational behavior of different Weather and Climate models. Additionally, we present how to improve the functionality and performance of some of the bottlenecks.","filename":"post133s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Xavier","last_name":"Yepes","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Oriol","last_name":"Tinto","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kim","last_name":"Serradell","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Miguel","last_name":"Castrillo","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Mario","last_name":"Acosta","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"1","is_presenter":true}]},{"id":"post164","type":"poster","title":"CLW05 - Porting Physical Parameterizations from a Climate Model to Accelerators","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"ICON (ICOsahedral Non-hydrostatic) is a climate and numerical weather prediction model being developed by the Max Planck Institute for Meteorology (MPI-M) and the German Weather Service (DWD). Together with MPI-M and DWD, MeteoSwiss, the Center for Climate Systems Modeling (C2SM\/ETH), and the Swiss National Supercomputing Center (CSCS) are porting ICON to GPUs and many-core architectures. Within the model, physical parameterizations calculate the collective effect of physical phenomena which occur on a sub-grid scale. We suggest multiple directive-based approaches of porting these parameterizations to accelerators, such as using the OpenACC standard or the CLAW source-to-source translator. Allowing the retention of a single Fortran code, directive approach can offer a high degree of performance portability. Using the FortranTestGenerator tool for automatic unit test generation for Fortran subroutines, the turbulence parameterization is isolated in a testbed subset of the model, so that subsequent changes can be easily validated. Tool-based analysis of loop kernels using the Roofline model is used to estimate attainable performance on various platforms, in particular i86-based multi-core CPUs as well as NVIDIA GPUs. The validated turbulence parameterization, running within a testbed framework, can be integrated into the overall ICON model.","filename":"post164s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gerhard","last_name":"Wellein","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"William","last_name":"Sawyer","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Xavier","last_name":"Lapillonne","affiliation":"MeteoSwiss","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Thomas","last_name":"K\u00f6ster","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post129","type":"poster","title":"CLW06 - Towards More Efficient Adjustment of Free Parameters in a Global Climate Model?","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Several climate relevant processes are not resolved by the spatial discretization of current global climate models (GCMs). Tropical thunderstorms, for example, with their deep convection must be included via some sub-grid-scale parameterization. Associated free parameters must be adjusted to obtain a \u0027physically meaningful climate\u0027. This \u0027model tuning\u0027 is expensive: the number of tuning parameters is significant (several tens), the response of the model climate to changes in these parameters is typically non-linear, and to quantify this response the GCM must be run for some time, at considerable computational costs. We illustrate model tuning with the example of MPI-ESM-HAM (Max Planck Earth System Model, coupled to the Hamburg Aerosol Module), and discuss how the steadily growing number of GCM simulations (data points) during the tuning process may be exploited to arrive at an overall more efficient, more resource friendly tuning procedure.","filename":"post129s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Martin","last_name":"Wild","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post129","type":"poster","title":"CLW06 - Towards More Efficient Adjustment of Free Parameters in a Global Climate Model?","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Several climate relevant processes are not resolved by the spatial discretization of current global climate models (GCMs). Tropical thunderstorms, for example, with their deep convection must be included via some sub-grid-scale parameterization. Associated free parameters must be adjusted to obtain a \u0027physically meaningful climate\u0027. This \u0027model tuning\u0027 is expensive: the number of tuning parameters is significant (several tens), the response of the model climate to changes in these parameters is typically non-linear, and to quantify this response the GCM must be run for some time, at considerable computational costs. We illustrate model tuning with the example of MPI-ESM-HAM (Max Planck Earth System Model, coupled to the Hamburg Aerosol Module), and discuss how the steadily growing number of GCM simulations (data points) during the tuning process may be exploited to arrive at an overall more efficient, more resource friendly tuning procedure.","filename":"post129s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Martin","last_name":"Wild","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Doris","last_name":"Folini","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Martin","last_name":"Wild","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false}] } Presentation
CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases
, Antonio Maffia (University of Basel, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}] } Presentation
CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method
, Christoph Rettinger (Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}] } Presentation
CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?
, Aurélien Cavelan (University of Basel, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}] } Presentation
CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian
, Dimosthenis Pasadakis (Università della Svizzera italiana, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}] } Presentation
CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis
, Jaroslaw Surkont (University of Basel, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}] } Presentation
CSM06 - A Distributed Parallel Approach for Large Scale Optimal Power Flow with Security Constraints
, Juraj Kardos (Università della Svizzera italiana, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}] } Presentation
CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation
, Samuel Adolfo Cruz Alegría (Università della Svizzera italiana, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}] } Presentation
CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems
, Manav Choudhary (Università della Svizzera italiana, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}] } Presentation
CSM09 - High Performance Topology Optimization
, Ezekiel Barnett (Università della Svizzera italiana, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}] } Presentation
CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery
, Vaclav Svaton (IT4Innovations National Supercomputing Center, Czech Republic)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}] } Presentation
CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms
, Aniello Esposito (Cray Inc., United Kingdom)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}] } Presentation
CSM13 - Neuronal Network Simulation Code for the Exascale Era
, Susanne Kunkel (Norwegian University of Life Sciences, Norway)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}] } Presentation
CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange
, Anshu Dubey (Argonne National Laboratory, United States of America)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}] } Presentation
CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases
, Michael Chan (University of Missouri - St. Louis, United States of America)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}] } Presentation
CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos
, Matthias Frey (Paul Scherrer Institute, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}] } Presentation
CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems
, Ahmed Eleliemy (University of Basel, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}] } Presentation
CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication
, Marko Kabic (ETH Zurich / CSCS, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}] } Presentation
CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software
, Heike Jagode (University of Tennessee, United States of America)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}] } Presentation
CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment
, James W. D. Hobro (Schlumberger, United Kingdom)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}] } Presentation
CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance
, Anthony Danalis (University of Tennessee, United States of America)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}] } Presentation
CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations
, Ali Mohammed (University of Basel, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}] } Presentation
CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics
, Danilo Guerrera (University of Basel, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}] } Presentation
CSM26 - Towards Whole Program Generation for Ocean Modeling
, Sebastian Kuckuk (Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}] } Presentation
CSM27 - Using Data Analysis Techniques to Detect Ransomware
, Sushma Yellapragada (The Northcap University, India)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}] } Presentation
CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing
, Nur Aiman Fadel (ETH Zurich / CSCS, Switzerland)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}] } Presentation
CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator
, Vit Ptosek (IT4Innovations National Supercomputing Center, Czech Republic)
+ Abstract { "session": {"id":"sess145","title":"Posters in Computer Science and Applied Mathematics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Computer Science and Applied Mathematics"],"slots":[{"id":"post149","type":"poster","title":"CSM01 - Accelerating Life Science Notebook Applications: Architectural Issues and Use Cases","begin_time":"19:30","end_time":"19:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"For quite some time, life science researchers have increasing demands in using high-performance computing systems. The de-facto HPC programming standards (OpenMP and MPI) are however not appropriate for the majority of this community. These users prefer more wide-spread, high-level approaches, such as given by Python and R environments. Our HPC and web computing project builds a bridge between these two worlds. Computational pharmacists are enabled to specify their problems in a Jupyter Notebook environment (jupyter.org). Depending on the computational load, a notebook can be executed either locally on a user workstation or remotely on an HPC system. Users are freed from knowing HPC system-specific details because remote calls will be assisted by HPC container support (e.g. Docker). Our prototype implementation is a distributed architecture which consists of two subsystems: an extended Jupyter Notebook for supporting Python\/R programming and Prova! (prova.io) for handling user sessions and interfacing with remote HPC systems (computational experiment server). As drug design will more and more depend on simulation, computational reproducibility will be a mandatory requirement, which our system fully supports. During the poster session we explain the architecture and demonstrate sample use cases such as lung cancer image detection and stochastic optimization.","filename":"post149s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Helmar","last_name":"Burkhart","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Gang","last_name":"Mu","affiliation":"Roche","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Antonio","last_name":"Maffia","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post130","type":"poster","title":"CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method","begin_time":"19:34","end_time":"19:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Particulate flows are encountered in various application fields, examples being fluidized beds in chemical engineering and sediment transport in riverbeds relevant in environmental engineering. Here, simulations that feature geometrically fully resolved particles are desired since they enable accurate predictions from first principles. The high computational costs, however, usually impose a strong limitation on the system size. In many cases, the flow structures in the vicinity of the particles are of special interest since they influence the particle motion and thus need to be appropriately numerically resolved. On the other hand, regions without particles have less restrictive resolution requirements and allow for coarser grids. With adaptive grid refinement, we can significantly improve the efficiency of such simulations since the overall workload is reduced. We present and evaluate different refinement approaches for particulate flows by comparing their accuracy and performance to simulations with uniform grids. Furthermore, we discuss load balancing strategies to distribute the workload evenly among the available computing resources. This is essential for efficient massively parallel simulations and requires accurate predictors for the local workload generated by the coupled simulation. Illustrating examples from the aforementioned application fields will be presented to demonstrate the generality and flexibility of our approach.","filename":"post130s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Christoph","last_name":"Rettinger","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post154","type":"poster","title":"CSM03 - Are Smooth Particle Hydrodynamics Applications Inherently Resilient to Faults?","begin_time":"19:38","end_time":"19:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Increasing the number of system components is the most viable path towards increasing the computational power of current and future computing systems. Unfortunately, this also contributes to increasing the number of faults, errors, and failures in high performance computing (HPC) applications. Silent data corruptions (SDC) typically result from bit-flips in the HPC system memory and pose a major threat to the correctness of the results. Current error detection techniques for hydrodynamics applications rely on global invariants: properties that hold in the simulated physical model, such as total mass, momentum, and energy conservation. Yet, state-of-the-art methods to resolve conservations laws are based on approximations, which result in imperfect preservation of the invariant properties. As a result, SDC detection during simulation is only possible when an error causes a significant variation in the quantities of one of these properties. This poster considers smooth particle hydrodynamics applications that tend to conserve such physical properties more accurately than classical hydrodynamics techniques. Initially, the impact and propagation of SDC through the data is investigated. Subsequently, the error detection range of this technique is experimentally quantified in terms of recall and precision for different test cases and problem sizes.","filename":"post154s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post162","type":"poster","title":"CSM04 - Balanced Graph Partition Refinement Using the Graph p-Laplacian","begin_time":"19:42","end_time":"19:46","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A continuous formulation of the optimal 2-way graph partitioning based on the p-norm minimization of the graph Laplacian Rayleigh quotient is presented, which provides a sharp approximation to the balanced graph partitioning problem, the optimality of which is known to be NP-hard. The minimization is initialized from a cut provided by a state-of-the-art multilevel recursive bisection algorithm, and then a continuation approach\u00a0reduces the p-norm from a 2-norm towards a 1-norm, employing for each value of p a feasibility-preserving steepest-descent method that converges on the p-Laplacian eigenvector. A filter favors iterates advancing towards minimum edge-cut and partition load imbalance. The complexity of the suggested approach is linear in graph edges. The simplicity of the steepest-descent algorithm renders the overall approach highly scalable and efficient in parallel distributed architectures. Parallel implementation of recursive bisection on multi-core CPUs and GPUs are presented for large-scale graphs with up to 1.9 billion tetrahedra. The suggested approach exhibits improvements of up to 52.8% over METIS for graphs originating from triangular Delaunay meshes, 34.7% over METIS and 21.9% over KaHIP for power network graphs, 40.8% over METIS and 20.6% over KaHIP for sparse matrix graphs, and finally 93.2% over METIS for graphs emerging from social networks.","filename":"post162s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Toby","last_name":"Simpson","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Kohei","last_name":"Fujita","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Takuma","last_name":"Yamaguchi","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Tsuyoshi","last_name":"Ichimura","affiliation":"The University of Tokyo","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post137","type":"poster","title":"CSM05 - BioMedIT: Enabling Interoperable Biomedical Analysis","begin_time":"19:46","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Personalized medicine will enable more efficient treatment of patients with custom tailored intervention. This will require not only changes in how biomedical research is performed, but also to the associated IT infrastructure utilized. The datasets required to gain insight into complex diseases are often spread across institutions with limits on access, transfer, and software. To address these challenges the BioMedIT, a federation of national IT centers, is developing an interoperable infrastructure for the biomedical research being performed by the Swiss Personalized Health Network (SPHN). This infrastructure will enable researchers to develop new analysis workflows on their local computing environment and then seamlessly execute them on larger, possibly distant, computing resources while ensuring patient privacy and security. The initial phase of this project has looked at approaches for providing software interoperability between sites. This work provides an overview of the technologies assessed to enable proof-of-concept multi-site workflow execution including workflow engines, containerization, and HPC strategies.","filename":"post137s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Kevin","last_name":"Sayers","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Thierry","last_name":"Sengstag","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ioannis","last_name":"Xenarios","affiliation":"Swiss Institute of Bioinformatics","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Bernd","last_name":"Rinn","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Marcel","last_name":"Riedi","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Torsten","last_name":"Schwede","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jaroslaw","last_name":"Surkont","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post160","type":"poster","title":"CSM06 - A Distributed Parallel Approach for Large\u00a0Scale Optimal Power Flow with Security Constraints","begin_time":"19:50","end_time":"19:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The electrical power grid is a critical infrastructure, and in addition to economic dispatch, the grid should operate with strict security measures and\u00a0be resilient to failures of its components. Increased penetration of the renewable energy sources is placing greater stress on the grid, shifting operation of the power grid equipment towards their operational limits. Thus, any unexpected contingency could be critical to the overall operation. Security constrained optimal power flow (SCOPF) imposes additional security constraints, such that in the event of any contingency, the power\u00a0grid\u00a0will remain secure and within operational\u00a0limits. For a realistic power network with numerous contingencies considered, the overall problem size becomes intractable for single-core optimization tools in short time frames for industrial operations, such as real-time electricity market responses to electricity prices.\u00a0We propose an efficient distributed interior-point framework exploiting the block-structured KKT linear system arising from the optimality conditions of the augmented Lagrangian of the SCOPF problem. In order to utilize a node-level parallelism, an incomplete augmented multicore sparse factorization is used, which further exploits the sparse structure of the problem. Numerical experiments on Pan-European power grid with large number of contingency scenarios demonstrate that the problem\u00a0can be efficiently solved.","filename":"post160s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Drosos","last_name":"Kourounis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post185","type":"poster","title":"CSM07 - Evaluating OpenACC on a Large Scale Particle Simulation","begin_time":"19:54","end_time":"19:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The simulation of particle systems has become essential for visualizing the behaviour of relevant physical systems, ranging from simulations of molecular dynamics to simulations of colliding galaxies. Performing realistic simulations require considering a large number of particles, leading to immense computational costs. Simulating such systems thus require increasingly long time frames and performing increasingly complex simulations may become intractable for single-core simulation tools. Thus, it is essential to develop simulation tools which scale with the number of bodies used in a simulation. A possible approach for scalable simulation tools is to distribute the workload among different parallel threads available in currently available accelerators. This poster aims to explore the efficiency and scalability of parallelization based on the OpenACC programming standard, which is a directive based standard for parallel computing that offloads the computational kernels to a GPU accelerator. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post185s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Alessandra Martha","last_name":"De Felice","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hrishikesh","last_name":"Gupta","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Juraj","last_name":"Kardos","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Samuel Adolfo","last_name":"Cruz Alegr\u00eda","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post186","type":"poster","title":"CSM08 - Evaluating TensorFlow Optimization Techniques for Solving Elliptic Boundary Control Problems","begin_time":"19:58","end_time":"20:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"TensorFlow is a software library which uses data flow graphs for numerical computations. The graph contains nodes representing mathematical operations and edges represent data tensors. In this work, we investigate the potential of using TensorFlow for solving large scale optimal control problems constrained by elliptic partial differential equations. We use finite difference discretization techniques to formulate the optimal control problem as a general non linear programming problem, which may contain up to tens of thousands of control and state variables. We compare the performance and accuracy of TensorFlow against state-of-the-art interior point optimization package IPOPT frequently used for solving such problems. This work is done as a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026 Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post186s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Olaf","last_name":"Schenk","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Manav","last_name":"Choudhary","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post184","type":"poster","title":"CSM09 - High Performance Topology Optimization","begin_time":"20:02","end_time":"20:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Topology Optimization (TO) is one state-of-the-art method for solving\u00a0constrained optimization problems that arise in structural engineering.\u00a0TO formulates the material design problem as an optimization procedure, which incurs significant computational costs that grow rapidly with the mesh resolution. Each iteration includes a Finite Element (FE) analysis and an optimization procedure, and most problems are\u00a0regarded as highly\u00a0computationally expensive. In this poster we consider a minimum compliance TO procedure for a maximum stiffness problem in 2 dimensions on an arbitrary domain, with Dirichlet boundary conditions (i.e. static load). Our implementation of this canonical TO problem improves both the speed and accuracy on high resolution meshes. The improvements are primarily achieved through the parallelization of the FE procedure, which is implemented through FEniCS and DOLFIN. The poster is based on a master student project within the course \u0022Software Atelier: Simulation, Data Science \u0026amp; Supercomputing\u0022 at Universit\u00e0 della Svizzera italiana.","filename":"post184s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sameer","last_name":"Rawat","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true},{"type":"Author","first_name":"Sumeet","last_name":"Gyanchandani","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimosthenis","last_name":"Pasadakis","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ezekiel","last_name":"Barnett","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":true}]},{"id":"post180","type":"poster","title":"CSM10 - HPC-as-a-Service for Driving Artificial Intelligence for Drug Discovery","begin_time":"20:06","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"HPC-as-a-Service further lowers the entry barrier for users who are interested in utilizing massive parallel computers for modelling. Real-world pharma industry applications often encompass end-to-end data processing pipelines composed of a large number of interconnected tasks of various granularity. Most of the common tasks in the prediction of activity and toxicity of chemical compounds consist of several typical steps, such as compiling, cleaning and combining datasets, feature calculation, feature selection, model training and validation and applying models to predict properties of new compounds. Building and executing such pipelines on HPC systems can be challenging tasks for domain specialists who do not have sufficient level of experience in distributed computing. Therefore, we introduce a drug discovery web platform that enables large-scale machine learning applications being executed on supercomputing facilities via HPC as a Service Middleware. The middleware provides functionality for remote execution and ensures authentication and authorization to provided functions, necessary security for data management, monitoring and reporting of executed HPC jobs and their progress and provides current information about the state of the cluster. The ability of HPC job execution through a web platform provides users intuitive and straightforward access to HPC resources without necessary HPC knowledge.","filename":"post180s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Vojtech","last_name":"Cima","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Nina","last_name":"Jeliazkova","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Vedrin","last_name":"Jeliazkov","affiliation":"Ideaconsult Ltd.","country":"Bulgaria","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Vladimir","last_name":"Chupakhin","affiliation":"Janssen Pharmaceutica NV","country":"Belgium","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vaclav","last_name":"Svaton","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"5","is_presenter":true}]},{"id":"post150","type":"poster","title":"CSM11 - Importance of Rank Reordering for Advanced Polar Decomposition Algorithms","begin_time":"20:10","end_time":"20:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A major goal of reordering the processing elements of a distributed-memory application is to maximize the on-node point-to-point communication and therefore reduce the corresponding off-node traffic in order to improve the total communication time and load balance especially in network-bound codes. We demonstrate the importance of MPI rank reordering in the context of advanced dense linear algebra (DLA) applications, which are naturally assumed to be computation-bound. However, applications composed of successive calls to high-level DLA matrix operations of irregular workloads may also suffer from process misplacement especially in strong scaling mode of operations. In particular, we focus on two advanced polar decomposition (PD) algorithms, i.e. the QR-based Dynamically Weighted Halley method (QDWH) and the Zolotarev rational functions (ZOLOPD). PD is the first computational step toward solving symmetric eigenvalue problems and the singular value decomposition. We consider an extensive combination of grid topologies and rank reorderings for different matrix sizes and number of nodes. Performance profiling reveals an improvement of up to 54%, thanks to a careful process placement. Simulation have been performed on Cray XC systems using rank reordering features of the cray-mpich library. Results presented here are part of a paper submitted to the Cray User Group 2018.","filename":"post150s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"David","last_name":"Keyes","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Hatem","last_name":"Ltaief","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dalal","last_name":"Sukkari","affiliation":"King Abdullah University of Science and Technology","country":"Saudi Arabia","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Aniello","last_name":"Esposito","affiliation":"Cray Inc.","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post175","type":"poster","title":"CSM13 - Neuronal Network Simulation Code for the Exascale Era","begin_time":"20:18","end_time":"20:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Numerical simulation of neuronal networks has become an important part of modern neuroscience, next to experimental and theoretical approaches. Simulation software for spiking neuronal networks, such as the open-source simulator NEST (www.nest-simulator.org), is based on the hypothesis that the main processes of brain function can be captured at the level of individual neurons, their connections, and their interactions through electric pulses, called spikes. As neurons have on average a few thousand incoming connections, connectivity is very sparse in large-scale network models of a billion neurons, which is approximately one percent of the human brain. Today simulating such networks is possible on petascale computers as, for example, the K computer. To manage memory usage and runtime, neuronal simulators ultimately targeting brain-scale simulations on the next generation of supercomputers need to fully exploit the even sparser connectivity of these networks. To this end, we have developed a two-tier connection infrastructure and a framework for directed communication among compute nodes. We show that the new technology implemented in NEST achieves perfect weak scaling with respect to memory usage and good weak scaling with respect to runtime, which is a breakthrough on the way to brain-scale simulations in the exascale era.","filename":"post175s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jakob","last_name":"Jordan","affiliation":"University of Bern","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Tammo","last_name":"Ippen","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Moritz","last_name":"Helias","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Itaru","last_name":"Kitayama","affiliation":"RIKEN","country":"Japan","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Mitsuhisa","last_name":"Sato","affiliation":"RIKEN","country":"Japan","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Jun","last_name":"Igarashi","affiliation":"RIKEN","country":"Japan","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Diesmann","affiliation":"Forschungszentrum J\u00fclich","country":"Germany","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Susanne","last_name":"Kunkel","affiliation":"Norwegian University of Life Sciences","country":"Norway","bio":"","order":"8","is_presenter":true}]},{"id":"post174","type":"poster","title":"CSM14 - A New Community-Driven Resource for Scientific Software Improvement Exchange","begin_time":"20:22","end_time":"20:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Better Scientific Software is an organization dedicated to improving developer productivity and software sustainability for computational science and engineering (CSE). This poster introduces the BSSw website (https:\/\/bssw.io), a new community-based resource for scientific software improvement exchange. We\u0027re creating a central hub for sharing information on practices, techniques, experiences, and tools to improve developer productivity and software sustainability for CSE. The site aims to raise awareness of the importance of good software practices to scientific productivity and to the quality and reliability of computationally-based scientific results. Additional goals are to raise awareness of the increasing challenges facing CSE software developers as high-end computing heads to extreme scales, and to facilitate CSE collaboration via software in order to advance scientific discoveries. Site users can find information on scientific software topics and can propose to curate or create new content based on their own experiences. Communities can also create content tailored to the unique needs and perspectives of a focused scientific domain. The backend enables collaborative content development using standard GitHub tools and processes. We need community contributions to build the BSSw site into a vibrant resource, with content and editorial processes provided by volunteers throughout the international CSE community. Join us!","filename":"post174s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Lois C.","last_name":"McInnes","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"David E.","last_name":"Bernholdt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michael A.","last_name":"Heroux","affiliation":"Sandia National Laboratories","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anshu","last_name":"Dubey","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":true}]},{"id":"post146","type":"poster","title":"CSM15 - ORCA and Cut-and-Solve: A Potential High-Performance Solution to Learning Genetic Causes of Complex Diseases","begin_time":"20:26","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as Alzheimer\u0027s disease, but it has been a challenge to find useful information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases involves patterns of genetic markers rather than single markers working alone. To combat this, we propose an integer programming model called ORCA which finds the pattern with the absolute maximum percentage difference between cases and controls. However, this optimization problem requires massive computations and conventional methods, such as branch-and-cut, are not suitable for large-scale parallelization. We present a novel implementation that utilizes an alternative search strategy, cut-and-solve. Cut-and-solve employs a linear search path where chunks of the solution space are \u0027cut\u0027 away and treated as separate problems. Leveraging this structure, we are in the process of massively parallelizing cut-and-solve to find candidate genetic patterns highly associated with Alzheimer\u0027s disease.","filename":"post146s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Sharlee","last_name":"Climer","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Sanjiv K.","last_name":"Bhatia","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Carlos","last_name":"Cruchaga","affiliation":"Washington University School of Medicine","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michael","last_name":"Chan","affiliation":"University of Missouri - St. Louis","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post131","type":"poster","title":"CSM16 - Parallelization of the Boundary Element Method","begin_time":"20:30","end_time":"20:34","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The main advantage of the boundary element method (BEM) is a reduction of the problem to the boundary of the computational domain. This makes it well suited for problems stated on unbounded domains, such as sound or electromagnetic wave scattering. We present the BEM4I library of parallel BEM-based solvers for problems modeled by the Laplace, Lame, Helmholtz, and wave equation. The library has been parallelized and optimized on multiple levels. OpenMP 4.5 directives have been used for the shared memory parallelization and SIMD vectorization of the computationally most intensive kernels. Two approaches have been implemented for the distributed memory parallelization;\u00a0the first one is based on the parallelization of the adaptive cross approximation method (ACA) while the second uses the boundary element tearing and interconnecting (BETI) domain decomposition method. In the poster, we present the structure of the library and approaches for the vectorization and parallelization as well as the results of the scalability experiments performed on Xeon and Xeon Phi based clusters.","bio":"","contributors":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jan","last_name":"Zapletal","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Michal","last_name":"Kravcenko","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Michal","last_name":"Merta","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":true}]},{"id":"post126","type":"poster","title":"CSM17 - Performance and Implementation of a Geometric Multigrid Solver with Trilinos","begin_time":"20:34","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The accurate and efficient simulation of neighbouring bunch effects in high intensity cyclotrons requires one to solve large-scale \u003Cem\u003EN\u003C\/em\u003E-body problems of \u003Cem\u003EO\u003C\/em\u003E(10^9...10^10) particles coupled with Maxwell\u0027s equations. In order to capture those effects with standard particle-in-cell models an extremely fine mesh with \u003Cem\u003EO\u003C\/em\u003E(10^8...10^9) grid points is necessary to meet the condition of high resolution. This requirement represents a waste of memory in regions of void, therefore, the usage of block-structured adaptive mesh refinement algorithms is more suitable. The \u003Cem\u003EN\u003C\/em\u003E-body problem is then solved on a hierarchy of levels and grids using geometric multigrid algorithms. We show benchmarks of a new implementation of a geometric multigrid algorithm using Trilinos that ran on Piz Daint with \u003Cem\u003EO\u003C\/em\u003E(10^4...10^5) cores.","filename":"post126s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Adelmann","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Matthias","last_name":"Frey","affiliation":"Paul Scherrer Institute","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post153","type":"poster","title":"CSM18 - Performance Evaluation of Dynamic Loop Scheduling Techniques Using MPI Passive RDMA on Distributed Memory Systems","begin_time":"20:38","end_time":"20:42","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Large parallel loops are present in many scientific applications. Static and dynamic loop scheduling (DLS) techniques aim to achieve load balanced executions of applications. The use of DLS techniques in scientific applications, such as the self-scheduling-based techniques, showed significant performance advantages compared to static techniques. On distributed-memory systems, DLS techniques have been implemented using the message-passing interface (MPI). Existing implementations of MPI-based DLS libraries do not consider the novel features of the latest MPI standards, such as one-sided communication, shared-memory window creation, and atomic read-modify-write operations. This poster considers these features and proposes an MPI-based DLS library written in the C language. Unlike existing libraries, the proposed DLS library does not employ a master-worker execution model. Moreover, it contains implementations of five well-known DLS techniques, namely self-scheduling, fixed-size chunking, guided self-scheduling, trapezoid self-scheduling, and factoring. An application from the computer vision is used to assess and compare the performance of the proposed library against the performance of existing solutions. The evaluation results show improved performance and highlight the need to revise and upgrade existing solutions in light of the significant advancements in the MPI standards.","filename":"post153s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ahmed","last_name":"Eleliemy","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post172","type":"poster","title":"CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication","begin_time":"20:46","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Available memory can be traded for reducing expensive communication. The optimal strategy depends on the precise workload and the available memory. CARMA (Demmel et al., 2013) is the first matrix-matrix multiplication algorithm that is communication-optimal for all memory ranges and all matrix shapes.\u00a0The algorithm recursively splits the largest matrix dimension creating smaller subproblems which are then recursively solved sequentially or in parallel, depending on the available memory. While appealing and simple at first sight, the implementation details are tricky and the distributed version requires the data layout very different from any layout used in existing linear-algebra libraries.\u00a0Here, we present results from an implementation of CARMA that provides functionality not present in earlier published prototypes, namely the ability to deal with matrix dimensions and processor numbers that are not powers of two, and do not necessarily share common divisors. Furthermore, we derive a relatively simple data layout, which preserves communication-optimality, but requires fewer intermediate copies during execution, has improved memory access patterns and is potentially more compatible with existing linear algebra libraries.\u00a0Additional validation and verification, benchmarking and a compatibility layer to the established SCALAPACK library, leads to a matrix-matrix multiplication software package that can be used in other applications.","filename":"post172s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Thibault","last_name":"Notargiacomo","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Joost","last_name":"VandeVondele","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Marko","last_name":"Kabic","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post140","type":"poster","title":"CSM21 - Practical Experience with Task-Based Programming Techniques for Quantum Chemistry Software","begin_time":"20:50","end_time":"20:54","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"With the increase in scale, complexity, and heterogeneity of modern high-performance computing (HPC) platforms, one of the grim challenges for traditional programming models is sustaining the expected performance at scale. The main objective of this work is to move away from traditional programming models that force scientific applications to be developed for specific architectures or platforms. Instead, we use dataflow programming models to represent the algorithms in a way that enables us to observe and capture data dependencies, which is the most essential property of an algorithm. We discuss dataflow programming models for computational chemistry applications, because they comprise one of the driving forces of HPC, and compare different dataflow executions in terms of programmability, resource utilization, and scalability. In particular, we evaluate two programming paradigms: (1) explicit dataflow, where the dataflow is specified explicitly by the developer; and (2) implicit dataflow, where a task scheduling runtime derives the dataflow using per-task, data-access information embedded in a serial program. We use the state-of-the-art NWChem chemistry application as our science driver, and we present our findings using three different task-based runtimes PaRSEC, StarPU, and OpenMP, which enable the different forms of dataflow execution.","filename":"post140s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post173","type":"poster","title":"CSM22 - Redesigning Numerical Modelling Algorithms for Efficient, Large-Scale Cloud Deployment","begin_time":"20:54","end_time":"20:58","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The ready availability of cloud computing resources presents an opportunity for rapid turnaround and increased flexibility for large-scale numerical modelling, opening up new possibilities for interactive applications. However, achieving linear scaling and efficient data handling for complex, coupled numerical modelling problems on standard high-latency cloud virtual machines is still challenging. We explore the improvements in scalability and data transfer hiding that are achievable for elastic wave equation modelling by moving away from a sequential programming approach as conventionally used with the Message Passing Interface (MPI), in which it is difficult to avoid synchronization across a parallel system. Instead, we use the concepts of actor-based and reactive programming to remove all unnecessary synchronization within and between virtual machines. We do this by introducing flexibility into the order of computation and data exchange, and by making extensive use of task and data prioritization. This is effective in eliminating wait time and spreads communication out evenly, reducing network contention. We use a theoretical model to examine the scalability characteristics of the new system in comparisons with an optimized traditional MPI implementation. The new system scales linearly to within measurable errors in tests on commodity cloud clusters of up to 2000 cores.","filename":"post173s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Anindya","last_name":"Sharma","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"James W. D.","last_name":"Hobro","affiliation":"Schlumberger","country":"United Kingdom","bio":"","order":"1","is_presenter":true}]},{"id":"post141","type":"poster","title":"CSM23 - Software-Defined Events through PAPI for In-Depth Analysis of Application Performance","begin_time":"20:58","end_time":"21:02","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"One of the most recent developments of the Performance API (PAPI) is the addition of Software-Defined Events (SDE). PAPI has successfully served the role of the abstraction and unification layer for hardware performance counters for over a decade. This poster presents our effort to extend this role to encompass performance critical information that does not originate in hardware, but rather in critical software layers, such as libraries and runtime systems. Our overall objective is to enable monitoring of both types of performance events, hardware- and software-related events, in a uniform way, through one consistent PAPI interface. Performance analysts will be able to form a complete picture of the entire application performance without learning new instrumentation primitives. The goal of the poster is threefold. First, we outline PAPI\u0027s new SDE API and describe the semantics. Second, we showcase the usefulness of SDE through its employment in software layers as diverse as the compiler\/library tool ByFL, and the state-of-the-art chemistry application NWChem. We outline the process of instrumenting these software packages and highlight the performance information that can be acquired with SDEs. Third, we present our vision for future, more advanced features and discuss the benefits and the caveats associated with them.","filename":"post141s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Heike","last_name":"Jagode","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Jack","last_name":"Dongarra","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Anthony","last_name":"Danalis","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post152","type":"poster","title":"CSM24 - A Study of the Performance of Scientific Applications with Dynamic Loop Scheduling under Perturbations","begin_time":"21:02","end_time":"21:06","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scientific applications, such as N-body, Monte Carlo, and computational fluid dynamics consist of large loops. These loops contain computationally-intensive operations, resulting in heavy loop bodies. Loop scheduling techniques are used to parallelize such applications. Dynamic loop scheduling (DLS) techniques are used to mitigate variations in loop iterations execution times caused by problem, algorithmic, or systemic characteristics and, therefore, achieve a balanced load execution of scientific applications on high performance computing systems. Such variations are referred to as perturbations and include, decreased delivered computational speed, reduced available network bandwidth, or larger network latencies. The perturbations can also be caused by other applications or processes that share the same resources, or a temporary system fault or malfunction. In this poster, the performance of a computer vision application scheduled using DLS is studied under nine different perturbation scenarios. The application execution is simulated and its performance is analyzed. The evaluation of the simulation results suggests that no single scheduling technique achieves the best overall performance in all the considered scenarios. This work reveals the need for a mechanism to select the best performing scheduling technique based on the system state during execution to achieve improved application performance.","filename":"post152s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ali","last_name":"Mohammed","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post144","type":"poster","title":"CSM25 - Towards an Exascale-Ready Mini-App for Smooth Particle Hydrodynamics","begin_time":"21:06","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The smooth particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations represent computationally demanding calculations. Therefore, trade-offs are made between temporal and spatial scales, resolution, dimensionality (2-D or 3-D), and approximate versions of the physics involved. The parallelization of SPH codes is not trivial due to the absence of a structured particle grid. This poster presents insights into the current performance and functionalities of three SPH implementations of the SPH-EXA PASC project[1]: SPHYNX[2], ChaNGa[3], and SPH-flow[4]. The insights are obtained by the implementation (configuration and extension of the original code base), execution, evaluation, and analysis on two modern HPC systems, for a common test case: 3D rotating square patch[5] with 1 million particles. The performance of these codes is negatively impacted by factors, such as multiple time-stepping, gravity, or boundary conditions. Therefore, the goal is to extrapolate their common basic SPH features, with the aim of consolidating them into a pure-SPH, Exascale-ready, MPI+X, optimized, mini-app. The SPH mini-app will integrate further specific physics models. [1]https:\/\/www.pasc-ch.org\/projects\/2017-2020\/sph-exa\/. [2]http:\/\/astro.physik.unibas.ch\/sphynx. [3]http:\/\/faculty.washington.edu\/trq\/hpcc\/tools\/changa.html. [4]http:\/\/www.sph-flow.com. [5]http:\/\/padis.uniroma1.it\/handle\/10805\/688 (2D version).","filename":"post144s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Florina","last_name":"Ciorba","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Lucio","last_name":"Mayer","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Rub\u00e9n","last_name":"Cabezon","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"David","last_name":"Imbert","affiliation":"NEXTFLOW Software","country":"France","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true},{"type":"Author","first_name":"Aur\u00e9lien","last_name":"Cavelan","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Darren S.","last_name":"Reed","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Jean-Guillaume","last_name":"Piccinali","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Ioana","last_name":"Banicescu","affiliation":"Mississippi State University","country":"United States of America","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Domingo","last_name":"Garci\u00e1-Senz","affiliation":"Universitat Polit\u00e8cnica de Catalunya","country":"Spain","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Thomas R.","last_name":"Quinn","affiliation":"University of Washington","country":"United States of America","bio":"","order":"11","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Danilo","last_name":"Guerrera","affiliation":"University of Basel","country":"Switzerland","bio":"","order":"5","is_presenter":true}]},{"id":"post138","type":"poster","title":"CSM26 - Towards Whole Program Generation for Ocean Modeling","begin_time":"21:10","end_time":"21:14","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"(Numerical) ocean modeling provides a crucial tool for researching effects such as tsunamis and flooding. However, creating efficient implementations can be challenging, especially when covering a wide range of methods and target hardware. One possible remedy is employing domain-specific languages (DSLs) in conjunction with code generation techniques. ExaStencils and its multi-layered external DSL ExaSlang (ExaStencils language) provides such a framework. In this poster presentation, we present our advances towards developing and adapting code generation techniques for ocean modeling applications. For this, we implement a prototype solver for the shallow water equations (SWE) in ExaSlang. Its base is a finite volume discretization and the Lax-Friedrichs method. We showcase DSL code examples as well as performance results obtained on Piz Daint. Additionally, a roadmap for future extensions is sketched: We aim at adding support for real-world geometries such as coastlines and islands. Here, a patch-based approach allows us to combine the flexibility of an unstructured coarse-grid mesh and the performance benefits of topological structure within patches. Moreover, code generation allows specializing generated applications to varying aspects of the chosen discretization as well as the target hardware. This becomes especially important when switching to more sophisticated discretization techniques such as Discontinuous Galerkin (DG).","filename":"post138s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Harald","last_name":"K\u00f6stler","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sebastian","last_name":"Kuckuk","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post183","type":"poster","title":"CSM27 - Using Data Analysis Techniques to Detect Ransomware","begin_time":"21:14","end_time":"21:18","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A ransomware infection typically disables entire infrastructure by encrypting sensitive files on a system\/network and demands for huge amounts of ransom to unlock these files. Several attempts at protecting vital data from such fatal attacks have been made, but many of the newly developed ransomware variants bypass the existing anti-malware detection systems. In this work, we deployed more robust and efficient techniques on large system and user files that could immediately detect malicious activities and alert the user before a significant amount of information is lost. We monitored four indicators which include file system analysis for malicious contents using Hadoop, checking data integrity by generating hash codes using C#, using machine learning algorithms to predict ransomware prone files, and monitoring the file system log to keep a check on suspicious file activities. Further, we studied how using data processing platforms like Hadoop and R helped improve the computational speed and how these indicators can be deployed on a computer network or HDFS clusters. Various classification tree models were studied for their computational efficiency and scalability. Our ultimate aim is to utilize these techniques in protecting large sets of real-time data that all big research labs and organizations work with.","filename":"post183s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Upasna","last_name":"Sharma","affiliation":"The Northcap University","country":"India","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Abhishek","last_name":"Barry","affiliation":"The Northcap University","country":"India","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Sushma","last_name":"Yellapragada","affiliation":"The Northcap University","country":"India","bio":"","order":"1","is_presenter":true}]},{"id":"post166","type":"poster","title":"CSM28 - Utopia: A High Performance C++ Embedded Domain Specific Language for Scientific Computing","begin_time":"21:18","end_time":"21:22","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The rise of new technologies is a driver for changes in scientific-computing software libraries. However, such changes affect the whole simulation software, inducing unwanted modifications to high-level code in the application. To avoid modifications, state-of-the-art software mainly rely on high-level programming interfaces or scripting languages. This is achieved separating the model from the computation, thus allowing one to keep the implementation details hidden from the application code. We achieve this separation by using C++ meta-programming and particular evaluation strategies. We present the open source project Utopia, a common application programming interface to the best established parallel linear algebra libraries as a possible candidate of \u0022write once, run everywhere\u0022 while maintaining performance portability. We focus on the Utopia back-end implementation based on Trilinos and show how to provide both basic functionalities and extensions targeting backend-specific performance in a simple way. Furthermore, we consider one application to the end-user software FASTER showing the ease of porting and its improved performance.","filename":"post166s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Andreas","last_name":"Fink","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Patrick","last_name":"Zulian","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Dimitrios","last_name":"Karvounis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Krause","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Nur Aiman","last_name":"Fadel","affiliation":"ETH Zurich \/ CSCS","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}]}, "slot": {"id":"post181","type":"poster","title":"CSM29 - Validation of the Self-Adaptive Navigation System by Enhanced HPC Traffic Simulator","begin_time":"21:22","end_time":"21:26","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The navigation challenges for smart cities are the solutions envisioning a central and knowledgeable routing server, which collects and fuses all useful data sources and controls overall traffic in an intelligent way. The self-adaptive navigation system developed within the FET-HPC project ANTAREX implements the traffic flow optimization service coordinated with external client-side navigation applications and heterogeneous data sources. We have developed the enhanced Traffic simulator on HPC infrastructure for testing an efficiency and usability of the navigation system. Building blocks of the simulator include server-side navigation system, virtual Smart City world, benchmark settings, and navigation test bed, which contains industrial Sygic client-side navigation and simplified simulation of vehicles. The important feature of the simulator is the ability to evaluate the traffic flow control strategy in the Smart City world, with and without enabled global view calculation of traffic network, and for a given percentage of vehicles connected to the server-side service. The integration of the Sygic navigation to the large-scale traffic simulator enables to perform compliance test of real navigation applications to the developed central navigation system.","filename":"post181s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Jan","last_name":"Martinovi\u010d","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Jiri","last_name":"Sevcik","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vit","last_name":"Ptosek","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"3","is_presenter":true},{"type":"Author","first_name":"Katerina","last_name":"Slaninova","affiliation":"IT4Innovations National Supercomputing Center","country":"Czech Republic","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Radim","last_name":"Cmar","affiliation":"Sygic","country":"Slovakia","bio":"","order":"5","is_presenter":false}] } Presentation
EAD01 - On the Solution of Macroeconomic Models with Distributional Channels and Default Risk
, Luca Mazzone (University of Zurich, Switzerland)
+ Abstract { "session": {"id":"sess146","title":"Posters in Emerging Application Domains","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Emerging Application Domains"],"slots":[{"id":"post158","type":"poster","title":"EAD01 - On the Solution of Macroeconomic Models with Distributional Channels and Default Risk","begin_time":"19:30","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The importance of distributional channels in macroeconomic dynamics has been object of considerable attention from empirical studies. Despite considerable amount of effort aimed at incorporating heterogeneity into macroeconomics, however, their explicit inclusion in the standard policy toolbox is far from widespread. A relevant obstacle, in such cases, is the computation of equilibria. I propose a global solution method for solving infinite-horizon, heterogeneous agent macroeconomic models with aggregate uncertainty. Details of the algorithm are illustrated by presenting its application in an example model: in it, aggregate dynamics depends explicitly on firm entry and exit, and individual choices are often constrained by a form of market incompleteness. Existing computational strategies are either unfeasible or provide inaccurate solutions. Moreover, global solutions are computationally expensive because the minimal representation of the aggregate state space - and thus the aggregate law of motion - faces the curse of dimensionality. In my example model, the approximate law of motion is still a five-dimensional object, making it already too expensive to evaluate using Cartesian grids. The proposed strategy thus combines adaptive sparse grids with a cross-sectional density approximation, and introduces a framework for solving the more general class of dynamic models with firm or household heterogeneity accurately.","filename":"post158s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Luca","last_name":"Mazzone","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Luca","last_name":"Mazzone","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post158","type":"poster","title":"EAD01 - On the Solution of Macroeconomic Models with Distributional Channels and Default Risk","begin_time":"19:30","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The importance of distributional channels in macroeconomic dynamics has been object of considerable attention from empirical studies. Despite considerable amount of effort aimed at incorporating heterogeneity into macroeconomics, however, their explicit inclusion in the standard policy toolbox is far from widespread. A relevant obstacle, in such cases, is the computation of equilibria. I propose a global solution method for solving infinite-horizon, heterogeneous agent macroeconomic models with aggregate uncertainty. Details of the algorithm are illustrated by presenting its application in an example model: in it, aggregate dynamics depends explicitly on firm entry and exit, and individual choices are often constrained by a form of market incompleteness. Existing computational strategies are either unfeasible or provide inaccurate solutions. Moreover, global solutions are computationally expensive because the minimal representation of the aggregate state space - and thus the aggregate law of motion - faces the curse of dimensionality. In my example model, the approximate law of motion is still a five-dimensional object, making it already too expensive to evaluate using Cartesian grids. The proposed strategy thus combines adaptive sparse grids with a cross-sectional density approximation, and introduces a framework for solving the more general class of dynamic models with firm or household heterogeneity accurately.","filename":"post158s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Luca","last_name":"Mazzone","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Luca","last_name":"Mazzone","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Luca","last_name":"Mazzone","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}] } Presentation
ENG01 - Adaptive Particle Representation: A Novel Framework for Adaptive-Resolution Simulations
, Suryanarayana Maddu (Max Planck Institute for Molecular Cell Biology and Genetics, Germany)
+ Abstract { "session": {"id":"sess147","title":"Posters in Engineering","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Engineering"],"slots":[{"id":"post135","type":"poster","title":"ENG01 - Adaptive Particle Representation: A Novel Framework for Adaptive-Resolution Simulations","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"As progress in HPC hardware and software enables the numerical solution of increasingly complex non-linear models, adaptive-resolution and multi-resolution methods continue to gain importance. Models of this sort can only be efficiently simulated using self-adaptive discretization schemes like AMR and wavelets. However, these schemes are poorly suited for distributed-memory HPC systems, as they rely on global data tree structures and global mappings. We\u00a0therefore\u00a0present the Adaptive Particle Representation (APR), a novel and efficient method for adaptive-resolution simulation. The APR is based on local information only and is designed for scalability. It is based on a linear-time algorithm to construct an optimal resolution function for each point in the domain. It also provides point-wise error bounds for the function value and any derivative approximation. Differential operators can then be consistently evaluated on the evolving APR using discretization-corrected operators. While the APR combines ideas from wavelets and AMR, it effectively avoids\u00a0their performance issues. We benchmark this in numerical experiments and test the consistency and convergence of differential operators approximated on APR discretizations. These include the numerical solution of advection-diffusion of a Gaussian pulse, the two-dimensional unsteady Burgers equation, and adaptive three-dimensional Taylor-Green vortex simulation and\u00a0scaling experiments for testing performance.","filename":"post135s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bevan L.","last_name":"Cheeseman","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post147","type":"poster","title":"ENG02 - Assessment of Detached Eddy Simulation in Predicting Separated Flow over Airfoils at a Moderate Reynolds Number","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A highly scalable stabilized finite element flow solver is employed in the current study to simulate the flow around the NACA-4412 wing at a moderate chord Reynolds number (\u003Cem\u003ERe_c\u003C\/em\u003E = 400,000) with an angle of attack of 5 degrees. The flow under investigation involves a wide range of scales and complicated flow physics induced by the geometry, such as wall-bounded turbulence, flow separation, and turbulent wake flows. Previous DNS investigations have already revealed these complex flow patterns at similar Reynolds numbers. However, industry applications nowadays, targeting higher Reynolds number flows, still heavily depend on RANS or hybrid RANS\/LES approach in aircraft designs. The accurate prediction of separated flows is a cornerstone in successful CFD estimations. A delayed detached eddy simulation (DDES) turbulence model is utilized herein. The RANS model is primarily applied in near wall regions, while it gives way to LES in regions where flow is separated. To assess the readiness of this DDES approach, the obtained simulation results are to be compared with the DNS study conducted at KTH with the same flow configurations. The present research will better inform researchers the strengths and possible limitations of DDES in predicting complicated flow separation phenomenon.","filename":"post147s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jun","last_name":"Fang","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Kenneth","last_name":"Jansen","affiliation":"University of Colorado Boulder","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Philipp","last_name":"Schlatter","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ricardo","last_name":"Vinuesa","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Michel","last_name":"Rasquin","affiliation":"Cenaero","country":"Belgium","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}]},{"id":"post157","type":"poster","title":"ENG03 - Large Eddy Simulation of Tsunami Triggered Coastal Inundation in the Presence of Mitigation Parks","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years we have observed a paradigm shift from 2D shallow water models to models based on the 3D incompressible Navier-Stokes equations to simulate tsunami triggered inundation. The shift is due to the limitations of shallow water models for the simulation of onshore turbulent flows. The fully three-dimensional nature of turbulence and entrainment at the scales of coastal flooding requires massive parallel computing and the ability to have properly designed sub-grid scale models for large eddy simulation. In this poster, numerical mathematics, computational fluid dynamics, and tsunami physics are linked to understand the mechanisms that govern the coastal hydrodynamics as tsunami propagates inland. We look at what geometrical features of the coast line most affect the extension and propagation of flooding, in particular so when artificial, mitigation hills are installed at the shore line. Our numerical simulations rely on a massively parallel (hybrid MPI\/OpenMP) finite element solver of the incompressible 3D Navier-Stokes equations. Turbulence is modeled via dynamic Large Eddy Simulation.","filename":"post157s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jenny","last_name":"Suckale","affiliation":"Stanford University","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Yilang","last_name":"Xu","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Beatriz","last_name":"Eguzkitza","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Guillaume","last_name":"Houzeaux","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Mariano","last_name":"V\u00e1zquez","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post139","type":"poster","title":"ENG04 - A Low-Mach Simulation of Flow and Heat Transfer in a Motored Internal Combustion Engine Using the Spectral Element Method","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In this work, a proof-of-concept, wall-resolved implicit large eddy simulation (LES) campaign was performed to capture in-cylinder flow and heat transfer within an internal combustion engine (ICE). Over 20 cycles of the gas-exchange process was simulated, revealing variations in the intake jet impingement angle on the wall and piston surfaces from cycle-to-cycle. This calculation confirms a rising level of turbulent intensity during the compression stroke which is crucial to efficient engine operation. This work marks a milestone achievement in using Nek5000, a highly-scalable computational fluid dynamics (CFD) solver, to capture turbulent flow and thermal fields inside realistic engine geometries. In the context of an arbitrary Lagrangian-Eulerian (ALE) framework, several algorithms have been developed and integrated into Nek5000 in order overcome the computational challenges associated with moving boundaries (i.e. valves and pistons). In particular, this simulation makes use of a characteristic-based, time-stepping scheme to overcome Courant (CFL) conditions associated with standard, semi-implicit schemes. In addition, a grid-to-grid algorithm is employed to interpolate field variables from one mesh to another in order maintain spatial resolution requirements. The potential impact of this work is an unmatched, accurate, and highly-scalable tool for researchers to facilitate the efficient design of ICEs with short turn-around time.","filename":"post139s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Georgios","last_name":"Giannakopoulos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ananias","last_name":"Tomboulides","affiliation":"Aristotle University of Thessaloniki","country":"Greece","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Paul","last_name":"Fischer","affiliation":"University of Illinois Urbana-Champaign","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Christos","last_name":"Frouzakis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Misun","last_name":"Min","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Konstantinos","last_name":"Boulouchos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post134","type":"poster","title":"ENG05 - OpenFPM for Scalable Particle-Mesh Simulations on Distributed-Memory Computers","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scalable and efficient numerical simulations are of increasing importance in all areas of science and technology. This is fueled by a steady growth in the performance of computing hardware and increasing heterogeneous parallelism. However, efficiently implementing scalable simulation codes on heterogeneous, distributed hardware systems is the current bottleneck. This bottleneck can be relaxed by intermediate software layers that provide abstractions closer to the problem domain, allowing the computational scientist to focus on the simulation algorithm. Here, we present OpenFPM, an open and scalable framework that provides an abstraction layer for numerical simulations using particles and\/or meshes. OpenFPM provides transparent and scalable infrastructure for shared-memory and distributed-memory implementations of hybrid particle-mesh simulations of both discrete and continuous models. This infrastructure is complemented with portable implementations of frequently used numerical routines, as well as interfaces to third-party libraries. We present the architecture and design of OpenFPM, detail the underlying abstractions, and benchmark the framework in applications ranging from Smoothed Particle Hydrodynamics (SPH) to Molecular Dynamics (MD), Discrete Element Methods (DEM), high-dimensional Monte Carlo sampling (CMA-ES), and Reaction-Diffusion solvers, comparing it to the current state of the art and existing simulation software frameworks.","filename":"post134s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post167","type":"poster","title":"ENG06 - Wavelet Based Data Compression Strategies for Exascale CFD Simulations","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The steady increase of available computer resources has enabled engineers and scientists to use progressively more complex models to simulate a myriad of fluid flow problems. Yet, whereas modern high performance computers have seen a steady growth in computing power, the same trend has not been mirrored by a significant gain in data transfer rates. Current systems are capable of producing and processing high amounts of data quickly, while the overall performance is often limited by their ability to transfer and store the computed data. Considering that researchers invariably seek to study simulations with increasingly higher spatial and temporal resolution, the imminent move to exascale computing will consequently only exacerbate this problem. One of the major pitfalls of storing \u0027raw\u0027 simulation data lies in the implicit and redundant manner in which it represents the flow physics. Thus, using image compression algorithms to transform a large \u0027raw\u0027 into a compact data format could help to overcome the I\/O bottleneck. We therefore propose to adapt the wavelet-based JPEG-2000 compression standard for volumetric floating-point arrays.","filename":"post167s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"Rist","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post135","type":"poster","title":"ENG01 - Adaptive Particle Representation: A Novel Framework for Adaptive-Resolution Simulations","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"As progress in HPC hardware and software enables the numerical solution of increasingly complex non-linear models, adaptive-resolution and multi-resolution methods continue to gain importance. Models of this sort can only be efficiently simulated using self-adaptive discretization schemes like AMR and wavelets. However, these schemes are poorly suited for distributed-memory HPC systems, as they rely on global data tree structures and global mappings. We\u00a0therefore\u00a0present the Adaptive Particle Representation (APR), a novel and efficient method for adaptive-resolution simulation. The APR is based on local information only and is designed for scalability. It is based on a linear-time algorithm to construct an optimal resolution function for each point in the domain. It also provides point-wise error bounds for the function value and any derivative approximation. Differential operators can then be consistently evaluated on the evolving APR using discretization-corrected operators. While the APR combines ideas from wavelets and AMR, it effectively avoids\u00a0their performance issues. We benchmark this in numerical experiments and test the consistency and convergence of differential operators approximated on APR discretizations. These include the numerical solution of advection-diffusion of a Gaussian pulse, the two-dimensional unsteady Burgers equation, and adaptive three-dimensional Taylor-Green vortex simulation and\u00a0scaling experiments for testing performance.","filename":"post135s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bevan L.","last_name":"Cheeseman","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bevan L.","last_name":"Cheeseman","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"4","is_presenter":false}] } Presentation
ENG02 - Assessment of Detached Eddy Simulation in Predicting Separated Flow over Airfoils at a Moderate Reynolds Number
, Ramesh Balakrishnan (Argonne National Laboratory, United States of America)
+ Abstract { "session": {"id":"sess147","title":"Posters in Engineering","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Engineering"],"slots":[{"id":"post135","type":"poster","title":"ENG01 - Adaptive Particle Representation: A Novel Framework for Adaptive-Resolution Simulations","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"As progress in HPC hardware and software enables the numerical solution of increasingly complex non-linear models, adaptive-resolution and multi-resolution methods continue to gain importance. Models of this sort can only be efficiently simulated using self-adaptive discretization schemes like AMR and wavelets. However, these schemes are poorly suited for distributed-memory HPC systems, as they rely on global data tree structures and global mappings. We\u00a0therefore\u00a0present the Adaptive Particle Representation (APR), a novel and efficient method for adaptive-resolution simulation. The APR is based on local information only and is designed for scalability. It is based on a linear-time algorithm to construct an optimal resolution function for each point in the domain. It also provides point-wise error bounds for the function value and any derivative approximation. Differential operators can then be consistently evaluated on the evolving APR using discretization-corrected operators. While the APR combines ideas from wavelets and AMR, it effectively avoids\u00a0their performance issues. We benchmark this in numerical experiments and test the consistency and convergence of differential operators approximated on APR discretizations. These include the numerical solution of advection-diffusion of a Gaussian pulse, the two-dimensional unsteady Burgers equation, and adaptive three-dimensional Taylor-Green vortex simulation and\u00a0scaling experiments for testing performance.","filename":"post135s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bevan L.","last_name":"Cheeseman","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post147","type":"poster","title":"ENG02 - Assessment of Detached Eddy Simulation in Predicting Separated Flow over Airfoils at a Moderate Reynolds Number","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A highly scalable stabilized finite element flow solver is employed in the current study to simulate the flow around the NACA-4412 wing at a moderate chord Reynolds number (\u003Cem\u003ERe_c\u003C\/em\u003E = 400,000) with an angle of attack of 5 degrees. The flow under investigation involves a wide range of scales and complicated flow physics induced by the geometry, such as wall-bounded turbulence, flow separation, and turbulent wake flows. Previous DNS investigations have already revealed these complex flow patterns at similar Reynolds numbers. However, industry applications nowadays, targeting higher Reynolds number flows, still heavily depend on RANS or hybrid RANS\/LES approach in aircraft designs. The accurate prediction of separated flows is a cornerstone in successful CFD estimations. A delayed detached eddy simulation (DDES) turbulence model is utilized herein. The RANS model is primarily applied in near wall regions, while it gives way to LES in regions where flow is separated. To assess the readiness of this DDES approach, the obtained simulation results are to be compared with the DNS study conducted at KTH with the same flow configurations. The present research will better inform researchers the strengths and possible limitations of DDES in predicting complicated flow separation phenomenon.","filename":"post147s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jun","last_name":"Fang","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Kenneth","last_name":"Jansen","affiliation":"University of Colorado Boulder","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Philipp","last_name":"Schlatter","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ricardo","last_name":"Vinuesa","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Michel","last_name":"Rasquin","affiliation":"Cenaero","country":"Belgium","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}]},{"id":"post157","type":"poster","title":"ENG03 - Large Eddy Simulation of Tsunami Triggered Coastal Inundation in the Presence of Mitigation Parks","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years we have observed a paradigm shift from 2D shallow water models to models based on the 3D incompressible Navier-Stokes equations to simulate tsunami triggered inundation. The shift is due to the limitations of shallow water models for the simulation of onshore turbulent flows. The fully three-dimensional nature of turbulence and entrainment at the scales of coastal flooding requires massive parallel computing and the ability to have properly designed sub-grid scale models for large eddy simulation. In this poster, numerical mathematics, computational fluid dynamics, and tsunami physics are linked to understand the mechanisms that govern the coastal hydrodynamics as tsunami propagates inland. We look at what geometrical features of the coast line most affect the extension and propagation of flooding, in particular so when artificial, mitigation hills are installed at the shore line. Our numerical simulations rely on a massively parallel (hybrid MPI\/OpenMP) finite element solver of the incompressible 3D Navier-Stokes equations. Turbulence is modeled via dynamic Large Eddy Simulation.","filename":"post157s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jenny","last_name":"Suckale","affiliation":"Stanford University","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Yilang","last_name":"Xu","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Beatriz","last_name":"Eguzkitza","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Guillaume","last_name":"Houzeaux","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Mariano","last_name":"V\u00e1zquez","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post139","type":"poster","title":"ENG04 - A Low-Mach Simulation of Flow and Heat Transfer in a Motored Internal Combustion Engine Using the Spectral Element Method","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In this work, a proof-of-concept, wall-resolved implicit large eddy simulation (LES) campaign was performed to capture in-cylinder flow and heat transfer within an internal combustion engine (ICE). Over 20 cycles of the gas-exchange process was simulated, revealing variations in the intake jet impingement angle on the wall and piston surfaces from cycle-to-cycle. This calculation confirms a rising level of turbulent intensity during the compression stroke which is crucial to efficient engine operation. This work marks a milestone achievement in using Nek5000, a highly-scalable computational fluid dynamics (CFD) solver, to capture turbulent flow and thermal fields inside realistic engine geometries. In the context of an arbitrary Lagrangian-Eulerian (ALE) framework, several algorithms have been developed and integrated into Nek5000 in order overcome the computational challenges associated with moving boundaries (i.e. valves and pistons). In particular, this simulation makes use of a characteristic-based, time-stepping scheme to overcome Courant (CFL) conditions associated with standard, semi-implicit schemes. In addition, a grid-to-grid algorithm is employed to interpolate field variables from one mesh to another in order maintain spatial resolution requirements. The potential impact of this work is an unmatched, accurate, and highly-scalable tool for researchers to facilitate the efficient design of ICEs with short turn-around time.","filename":"post139s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Georgios","last_name":"Giannakopoulos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ananias","last_name":"Tomboulides","affiliation":"Aristotle University of Thessaloniki","country":"Greece","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Paul","last_name":"Fischer","affiliation":"University of Illinois Urbana-Champaign","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Christos","last_name":"Frouzakis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Misun","last_name":"Min","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Konstantinos","last_name":"Boulouchos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post134","type":"poster","title":"ENG05 - OpenFPM for Scalable Particle-Mesh Simulations on Distributed-Memory Computers","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scalable and efficient numerical simulations are of increasing importance in all areas of science and technology. This is fueled by a steady growth in the performance of computing hardware and increasing heterogeneous parallelism. However, efficiently implementing scalable simulation codes on heterogeneous, distributed hardware systems is the current bottleneck. This bottleneck can be relaxed by intermediate software layers that provide abstractions closer to the problem domain, allowing the computational scientist to focus on the simulation algorithm. Here, we present OpenFPM, an open and scalable framework that provides an abstraction layer for numerical simulations using particles and\/or meshes. OpenFPM provides transparent and scalable infrastructure for shared-memory and distributed-memory implementations of hybrid particle-mesh simulations of both discrete and continuous models. This infrastructure is complemented with portable implementations of frequently used numerical routines, as well as interfaces to third-party libraries. We present the architecture and design of OpenFPM, detail the underlying abstractions, and benchmark the framework in applications ranging from Smoothed Particle Hydrodynamics (SPH) to Molecular Dynamics (MD), Discrete Element Methods (DEM), high-dimensional Monte Carlo sampling (CMA-ES), and Reaction-Diffusion solvers, comparing it to the current state of the art and existing simulation software frameworks.","filename":"post134s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post167","type":"poster","title":"ENG06 - Wavelet Based Data Compression Strategies for Exascale CFD Simulations","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The steady increase of available computer resources has enabled engineers and scientists to use progressively more complex models to simulate a myriad of fluid flow problems. Yet, whereas modern high performance computers have seen a steady growth in computing power, the same trend has not been mirrored by a significant gain in data transfer rates. Current systems are capable of producing and processing high amounts of data quickly, while the overall performance is often limited by their ability to transfer and store the computed data. Considering that researchers invariably seek to study simulations with increasingly higher spatial and temporal resolution, the imminent move to exascale computing will consequently only exacerbate this problem. One of the major pitfalls of storing \u0027raw\u0027 simulation data lies in the implicit and redundant manner in which it represents the flow physics. Thus, using image compression algorithms to transform a large \u0027raw\u0027 into a compact data format could help to overcome the I\/O bottleneck. We therefore propose to adapt the wavelet-based JPEG-2000 compression standard for volumetric floating-point arrays.","filename":"post167s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"Rist","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post147","type":"poster","title":"ENG02 - Assessment of Detached Eddy Simulation in Predicting Separated Flow over Airfoils at a Moderate Reynolds Number","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A highly scalable stabilized finite element flow solver is employed in the current study to simulate the flow around the NACA-4412 wing at a moderate chord Reynolds number (\u003Cem\u003ERe_c\u003C\/em\u003E = 400,000) with an angle of attack of 5 degrees. The flow under investigation involves a wide range of scales and complicated flow physics induced by the geometry, such as wall-bounded turbulence, flow separation, and turbulent wake flows. Previous DNS investigations have already revealed these complex flow patterns at similar Reynolds numbers. However, industry applications nowadays, targeting higher Reynolds number flows, still heavily depend on RANS or hybrid RANS\/LES approach in aircraft designs. The accurate prediction of separated flows is a cornerstone in successful CFD estimations. A delayed detached eddy simulation (DDES) turbulence model is utilized herein. The RANS model is primarily applied in near wall regions, while it gives way to LES in regions where flow is separated. To assess the readiness of this DDES approach, the obtained simulation results are to be compared with the DNS study conducted at KTH with the same flow configurations. The present research will better inform researchers the strengths and possible limitations of DDES in predicting complicated flow separation phenomenon.","filename":"post147s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jun","last_name":"Fang","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Kenneth","last_name":"Jansen","affiliation":"University of Colorado Boulder","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Philipp","last_name":"Schlatter","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ricardo","last_name":"Vinuesa","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Michel","last_name":"Rasquin","affiliation":"Cenaero","country":"Belgium","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Jun","last_name":"Fang","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Kenneth","last_name":"Jansen","affiliation":"University of Colorado Boulder","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Philipp","last_name":"Schlatter","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ricardo","last_name":"Vinuesa","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Michel","last_name":"Rasquin","affiliation":"Cenaero","country":"Belgium","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}] } Presentation
ENG03 - Large Eddy Simulation of Tsunami Triggered Coastal Inundation in the Presence of Mitigation Parks
, Simone Marras (New Jersey Institute of Technology, United States of America)
+ Abstract { "session": {"id":"sess147","title":"Posters in Engineering","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Engineering"],"slots":[{"id":"post135","type":"poster","title":"ENG01 - Adaptive Particle Representation: A Novel Framework for Adaptive-Resolution Simulations","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"As progress in HPC hardware and software enables the numerical solution of increasingly complex non-linear models, adaptive-resolution and multi-resolution methods continue to gain importance. Models of this sort can only be efficiently simulated using self-adaptive discretization schemes like AMR and wavelets. However, these schemes are poorly suited for distributed-memory HPC systems, as they rely on global data tree structures and global mappings. We\u00a0therefore\u00a0present the Adaptive Particle Representation (APR), a novel and efficient method for adaptive-resolution simulation. The APR is based on local information only and is designed for scalability. It is based on a linear-time algorithm to construct an optimal resolution function for each point in the domain. It also provides point-wise error bounds for the function value and any derivative approximation. Differential operators can then be consistently evaluated on the evolving APR using discretization-corrected operators. While the APR combines ideas from wavelets and AMR, it effectively avoids\u00a0their performance issues. We benchmark this in numerical experiments and test the consistency and convergence of differential operators approximated on APR discretizations. These include the numerical solution of advection-diffusion of a Gaussian pulse, the two-dimensional unsteady Burgers equation, and adaptive three-dimensional Taylor-Green vortex simulation and\u00a0scaling experiments for testing performance.","filename":"post135s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bevan L.","last_name":"Cheeseman","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post147","type":"poster","title":"ENG02 - Assessment of Detached Eddy Simulation in Predicting Separated Flow over Airfoils at a Moderate Reynolds Number","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A highly scalable stabilized finite element flow solver is employed in the current study to simulate the flow around the NACA-4412 wing at a moderate chord Reynolds number (\u003Cem\u003ERe_c\u003C\/em\u003E = 400,000) with an angle of attack of 5 degrees. The flow under investigation involves a wide range of scales and complicated flow physics induced by the geometry, such as wall-bounded turbulence, flow separation, and turbulent wake flows. Previous DNS investigations have already revealed these complex flow patterns at similar Reynolds numbers. However, industry applications nowadays, targeting higher Reynolds number flows, still heavily depend on RANS or hybrid RANS\/LES approach in aircraft designs. The accurate prediction of separated flows is a cornerstone in successful CFD estimations. A delayed detached eddy simulation (DDES) turbulence model is utilized herein. The RANS model is primarily applied in near wall regions, while it gives way to LES in regions where flow is separated. To assess the readiness of this DDES approach, the obtained simulation results are to be compared with the DNS study conducted at KTH with the same flow configurations. The present research will better inform researchers the strengths and possible limitations of DDES in predicting complicated flow separation phenomenon.","filename":"post147s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jun","last_name":"Fang","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Kenneth","last_name":"Jansen","affiliation":"University of Colorado Boulder","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Philipp","last_name":"Schlatter","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ricardo","last_name":"Vinuesa","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Michel","last_name":"Rasquin","affiliation":"Cenaero","country":"Belgium","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}]},{"id":"post157","type":"poster","title":"ENG03 - Large Eddy Simulation of Tsunami Triggered Coastal Inundation in the Presence of Mitigation Parks","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years we have observed a paradigm shift from 2D shallow water models to models based on the 3D incompressible Navier-Stokes equations to simulate tsunami triggered inundation. The shift is due to the limitations of shallow water models for the simulation of onshore turbulent flows. The fully three-dimensional nature of turbulence and entrainment at the scales of coastal flooding requires massive parallel computing and the ability to have properly designed sub-grid scale models for large eddy simulation. In this poster, numerical mathematics, computational fluid dynamics, and tsunami physics are linked to understand the mechanisms that govern the coastal hydrodynamics as tsunami propagates inland. We look at what geometrical features of the coast line most affect the extension and propagation of flooding, in particular so when artificial, mitigation hills are installed at the shore line. Our numerical simulations rely on a massively parallel (hybrid MPI\/OpenMP) finite element solver of the incompressible 3D Navier-Stokes equations. Turbulence is modeled via dynamic Large Eddy Simulation.","filename":"post157s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jenny","last_name":"Suckale","affiliation":"Stanford University","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Yilang","last_name":"Xu","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Beatriz","last_name":"Eguzkitza","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Guillaume","last_name":"Houzeaux","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Mariano","last_name":"V\u00e1zquez","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post139","type":"poster","title":"ENG04 - A Low-Mach Simulation of Flow and Heat Transfer in a Motored Internal Combustion Engine Using the Spectral Element Method","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In this work, a proof-of-concept, wall-resolved implicit large eddy simulation (LES) campaign was performed to capture in-cylinder flow and heat transfer within an internal combustion engine (ICE). Over 20 cycles of the gas-exchange process was simulated, revealing variations in the intake jet impingement angle on the wall and piston surfaces from cycle-to-cycle. This calculation confirms a rising level of turbulent intensity during the compression stroke which is crucial to efficient engine operation. This work marks a milestone achievement in using Nek5000, a highly-scalable computational fluid dynamics (CFD) solver, to capture turbulent flow and thermal fields inside realistic engine geometries. In the context of an arbitrary Lagrangian-Eulerian (ALE) framework, several algorithms have been developed and integrated into Nek5000 in order overcome the computational challenges associated with moving boundaries (i.e. valves and pistons). In particular, this simulation makes use of a characteristic-based, time-stepping scheme to overcome Courant (CFL) conditions associated with standard, semi-implicit schemes. In addition, a grid-to-grid algorithm is employed to interpolate field variables from one mesh to another in order maintain spatial resolution requirements. The potential impact of this work is an unmatched, accurate, and highly-scalable tool for researchers to facilitate the efficient design of ICEs with short turn-around time.","filename":"post139s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Georgios","last_name":"Giannakopoulos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ananias","last_name":"Tomboulides","affiliation":"Aristotle University of Thessaloniki","country":"Greece","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Paul","last_name":"Fischer","affiliation":"University of Illinois Urbana-Champaign","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Christos","last_name":"Frouzakis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Misun","last_name":"Min","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Konstantinos","last_name":"Boulouchos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post134","type":"poster","title":"ENG05 - OpenFPM for Scalable Particle-Mesh Simulations on Distributed-Memory Computers","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scalable and efficient numerical simulations are of increasing importance in all areas of science and technology. This is fueled by a steady growth in the performance of computing hardware and increasing heterogeneous parallelism. However, efficiently implementing scalable simulation codes on heterogeneous, distributed hardware systems is the current bottleneck. This bottleneck can be relaxed by intermediate software layers that provide abstractions closer to the problem domain, allowing the computational scientist to focus on the simulation algorithm. Here, we present OpenFPM, an open and scalable framework that provides an abstraction layer for numerical simulations using particles and\/or meshes. OpenFPM provides transparent and scalable infrastructure for shared-memory and distributed-memory implementations of hybrid particle-mesh simulations of both discrete and continuous models. This infrastructure is complemented with portable implementations of frequently used numerical routines, as well as interfaces to third-party libraries. We present the architecture and design of OpenFPM, detail the underlying abstractions, and benchmark the framework in applications ranging from Smoothed Particle Hydrodynamics (SPH) to Molecular Dynamics (MD), Discrete Element Methods (DEM), high-dimensional Monte Carlo sampling (CMA-ES), and Reaction-Diffusion solvers, comparing it to the current state of the art and existing simulation software frameworks.","filename":"post134s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post167","type":"poster","title":"ENG06 - Wavelet Based Data Compression Strategies for Exascale CFD Simulations","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The steady increase of available computer resources has enabled engineers and scientists to use progressively more complex models to simulate a myriad of fluid flow problems. Yet, whereas modern high performance computers have seen a steady growth in computing power, the same trend has not been mirrored by a significant gain in data transfer rates. Current systems are capable of producing and processing high amounts of data quickly, while the overall performance is often limited by their ability to transfer and store the computed data. Considering that researchers invariably seek to study simulations with increasingly higher spatial and temporal resolution, the imminent move to exascale computing will consequently only exacerbate this problem. One of the major pitfalls of storing \u0027raw\u0027 simulation data lies in the implicit and redundant manner in which it represents the flow physics. Thus, using image compression algorithms to transform a large \u0027raw\u0027 into a compact data format could help to overcome the I\/O bottleneck. We therefore propose to adapt the wavelet-based JPEG-2000 compression standard for volumetric floating-point arrays.","filename":"post167s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"Rist","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post157","type":"poster","title":"ENG03 - Large Eddy Simulation of Tsunami Triggered Coastal Inundation in the Presence of Mitigation Parks","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years we have observed a paradigm shift from 2D shallow water models to models based on the 3D incompressible Navier-Stokes equations to simulate tsunami triggered inundation. The shift is due to the limitations of shallow water models for the simulation of onshore turbulent flows. The fully three-dimensional nature of turbulence and entrainment at the scales of coastal flooding requires massive parallel computing and the ability to have properly designed sub-grid scale models for large eddy simulation. In this poster, numerical mathematics, computational fluid dynamics, and tsunami physics are linked to understand the mechanisms that govern the coastal hydrodynamics as tsunami propagates inland. We look at what geometrical features of the coast line most affect the extension and propagation of flooding, in particular so when artificial, mitigation hills are installed at the shore line. Our numerical simulations rely on a massively parallel (hybrid MPI\/OpenMP) finite element solver of the incompressible 3D Navier-Stokes equations. Turbulence is modeled via dynamic Large Eddy Simulation.","filename":"post157s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jenny","last_name":"Suckale","affiliation":"Stanford University","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Yilang","last_name":"Xu","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Beatriz","last_name":"Eguzkitza","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Guillaume","last_name":"Houzeaux","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Mariano","last_name":"V\u00e1zquez","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jenny","last_name":"Suckale","affiliation":"Stanford University","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Yilang","last_name":"Xu","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Beatriz","last_name":"Eguzkitza","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Guillaume","last_name":"Houzeaux","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Mariano","last_name":"V\u00e1zquez","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"6","is_presenter":false}] } Presentation
ENG04 - A Low-Mach Simulation of Flow and Heat Transfer in a Motored Internal Combustion Engine Using the Spectral Element Method
, Saumil Patel (Argonne National Laboratory, United States of America)
+ Abstract { "session": {"id":"sess147","title":"Posters in Engineering","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Engineering"],"slots":[{"id":"post135","type":"poster","title":"ENG01 - Adaptive Particle Representation: A Novel Framework for Adaptive-Resolution Simulations","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"As progress in HPC hardware and software enables the numerical solution of increasingly complex non-linear models, adaptive-resolution and multi-resolution methods continue to gain importance. Models of this sort can only be efficiently simulated using self-adaptive discretization schemes like AMR and wavelets. However, these schemes are poorly suited for distributed-memory HPC systems, as they rely on global data tree structures and global mappings. We\u00a0therefore\u00a0present the Adaptive Particle Representation (APR), a novel and efficient method for adaptive-resolution simulation. The APR is based on local information only and is designed for scalability. It is based on a linear-time algorithm to construct an optimal resolution function for each point in the domain. It also provides point-wise error bounds for the function value and any derivative approximation. Differential operators can then be consistently evaluated on the evolving APR using discretization-corrected operators. While the APR combines ideas from wavelets and AMR, it effectively avoids\u00a0their performance issues. We benchmark this in numerical experiments and test the consistency and convergence of differential operators approximated on APR discretizations. These include the numerical solution of advection-diffusion of a Gaussian pulse, the two-dimensional unsteady Burgers equation, and adaptive three-dimensional Taylor-Green vortex simulation and\u00a0scaling experiments for testing performance.","filename":"post135s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bevan L.","last_name":"Cheeseman","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post147","type":"poster","title":"ENG02 - Assessment of Detached Eddy Simulation in Predicting Separated Flow over Airfoils at a Moderate Reynolds Number","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A highly scalable stabilized finite element flow solver is employed in the current study to simulate the flow around the NACA-4412 wing at a moderate chord Reynolds number (\u003Cem\u003ERe_c\u003C\/em\u003E = 400,000) with an angle of attack of 5 degrees. The flow under investigation involves a wide range of scales and complicated flow physics induced by the geometry, such as wall-bounded turbulence, flow separation, and turbulent wake flows. Previous DNS investigations have already revealed these complex flow patterns at similar Reynolds numbers. However, industry applications nowadays, targeting higher Reynolds number flows, still heavily depend on RANS or hybrid RANS\/LES approach in aircraft designs. The accurate prediction of separated flows is a cornerstone in successful CFD estimations. A delayed detached eddy simulation (DDES) turbulence model is utilized herein. The RANS model is primarily applied in near wall regions, while it gives way to LES in regions where flow is separated. To assess the readiness of this DDES approach, the obtained simulation results are to be compared with the DNS study conducted at KTH with the same flow configurations. The present research will better inform researchers the strengths and possible limitations of DDES in predicting complicated flow separation phenomenon.","filename":"post147s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jun","last_name":"Fang","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Kenneth","last_name":"Jansen","affiliation":"University of Colorado Boulder","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Philipp","last_name":"Schlatter","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ricardo","last_name":"Vinuesa","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Michel","last_name":"Rasquin","affiliation":"Cenaero","country":"Belgium","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}]},{"id":"post157","type":"poster","title":"ENG03 - Large Eddy Simulation of Tsunami Triggered Coastal Inundation in the Presence of Mitigation Parks","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years we have observed a paradigm shift from 2D shallow water models to models based on the 3D incompressible Navier-Stokes equations to simulate tsunami triggered inundation. The shift is due to the limitations of shallow water models for the simulation of onshore turbulent flows. The fully three-dimensional nature of turbulence and entrainment at the scales of coastal flooding requires massive parallel computing and the ability to have properly designed sub-grid scale models for large eddy simulation. In this poster, numerical mathematics, computational fluid dynamics, and tsunami physics are linked to understand the mechanisms that govern the coastal hydrodynamics as tsunami propagates inland. We look at what geometrical features of the coast line most affect the extension and propagation of flooding, in particular so when artificial, mitigation hills are installed at the shore line. Our numerical simulations rely on a massively parallel (hybrid MPI\/OpenMP) finite element solver of the incompressible 3D Navier-Stokes equations. Turbulence is modeled via dynamic Large Eddy Simulation.","filename":"post157s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jenny","last_name":"Suckale","affiliation":"Stanford University","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Yilang","last_name":"Xu","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Beatriz","last_name":"Eguzkitza","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Guillaume","last_name":"Houzeaux","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Mariano","last_name":"V\u00e1zquez","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post139","type":"poster","title":"ENG04 - A Low-Mach Simulation of Flow and Heat Transfer in a Motored Internal Combustion Engine Using the Spectral Element Method","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In this work, a proof-of-concept, wall-resolved implicit large eddy simulation (LES) campaign was performed to capture in-cylinder flow and heat transfer within an internal combustion engine (ICE). Over 20 cycles of the gas-exchange process was simulated, revealing variations in the intake jet impingement angle on the wall and piston surfaces from cycle-to-cycle. This calculation confirms a rising level of turbulent intensity during the compression stroke which is crucial to efficient engine operation. This work marks a milestone achievement in using Nek5000, a highly-scalable computational fluid dynamics (CFD) solver, to capture turbulent flow and thermal fields inside realistic engine geometries. In the context of an arbitrary Lagrangian-Eulerian (ALE) framework, several algorithms have been developed and integrated into Nek5000 in order overcome the computational challenges associated with moving boundaries (i.e. valves and pistons). In particular, this simulation makes use of a characteristic-based, time-stepping scheme to overcome Courant (CFL) conditions associated with standard, semi-implicit schemes. In addition, a grid-to-grid algorithm is employed to interpolate field variables from one mesh to another in order maintain spatial resolution requirements. The potential impact of this work is an unmatched, accurate, and highly-scalable tool for researchers to facilitate the efficient design of ICEs with short turn-around time.","filename":"post139s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Georgios","last_name":"Giannakopoulos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ananias","last_name":"Tomboulides","affiliation":"Aristotle University of Thessaloniki","country":"Greece","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Paul","last_name":"Fischer","affiliation":"University of Illinois Urbana-Champaign","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Christos","last_name":"Frouzakis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Misun","last_name":"Min","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Konstantinos","last_name":"Boulouchos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post134","type":"poster","title":"ENG05 - OpenFPM for Scalable Particle-Mesh Simulations on Distributed-Memory Computers","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scalable and efficient numerical simulations are of increasing importance in all areas of science and technology. This is fueled by a steady growth in the performance of computing hardware and increasing heterogeneous parallelism. However, efficiently implementing scalable simulation codes on heterogeneous, distributed hardware systems is the current bottleneck. This bottleneck can be relaxed by intermediate software layers that provide abstractions closer to the problem domain, allowing the computational scientist to focus on the simulation algorithm. Here, we present OpenFPM, an open and scalable framework that provides an abstraction layer for numerical simulations using particles and\/or meshes. OpenFPM provides transparent and scalable infrastructure for shared-memory and distributed-memory implementations of hybrid particle-mesh simulations of both discrete and continuous models. This infrastructure is complemented with portable implementations of frequently used numerical routines, as well as interfaces to third-party libraries. We present the architecture and design of OpenFPM, detail the underlying abstractions, and benchmark the framework in applications ranging from Smoothed Particle Hydrodynamics (SPH) to Molecular Dynamics (MD), Discrete Element Methods (DEM), high-dimensional Monte Carlo sampling (CMA-ES), and Reaction-Diffusion solvers, comparing it to the current state of the art and existing simulation software frameworks.","filename":"post134s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post167","type":"poster","title":"ENG06 - Wavelet Based Data Compression Strategies for Exascale CFD Simulations","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The steady increase of available computer resources has enabled engineers and scientists to use progressively more complex models to simulate a myriad of fluid flow problems. Yet, whereas modern high performance computers have seen a steady growth in computing power, the same trend has not been mirrored by a significant gain in data transfer rates. Current systems are capable of producing and processing high amounts of data quickly, while the overall performance is often limited by their ability to transfer and store the computed data. Considering that researchers invariably seek to study simulations with increasingly higher spatial and temporal resolution, the imminent move to exascale computing will consequently only exacerbate this problem. One of the major pitfalls of storing \u0027raw\u0027 simulation data lies in the implicit and redundant manner in which it represents the flow physics. Thus, using image compression algorithms to transform a large \u0027raw\u0027 into a compact data format could help to overcome the I\/O bottleneck. We therefore propose to adapt the wavelet-based JPEG-2000 compression standard for volumetric floating-point arrays.","filename":"post167s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"Rist","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post139","type":"poster","title":"ENG04 - A Low-Mach Simulation of Flow and Heat Transfer in a Motored Internal Combustion Engine Using the Spectral Element Method","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In this work, a proof-of-concept, wall-resolved implicit large eddy simulation (LES) campaign was performed to capture in-cylinder flow and heat transfer within an internal combustion engine (ICE). Over 20 cycles of the gas-exchange process was simulated, revealing variations in the intake jet impingement angle on the wall and piston surfaces from cycle-to-cycle. This calculation confirms a rising level of turbulent intensity during the compression stroke which is crucial to efficient engine operation. This work marks a milestone achievement in using Nek5000, a highly-scalable computational fluid dynamics (CFD) solver, to capture turbulent flow and thermal fields inside realistic engine geometries. In the context of an arbitrary Lagrangian-Eulerian (ALE) framework, several algorithms have been developed and integrated into Nek5000 in order overcome the computational challenges associated with moving boundaries (i.e. valves and pistons). In particular, this simulation makes use of a characteristic-based, time-stepping scheme to overcome Courant (CFL) conditions associated with standard, semi-implicit schemes. In addition, a grid-to-grid algorithm is employed to interpolate field variables from one mesh to another in order maintain spatial resolution requirements. The potential impact of this work is an unmatched, accurate, and highly-scalable tool for researchers to facilitate the efficient design of ICEs with short turn-around time.","filename":"post139s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Georgios","last_name":"Giannakopoulos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ananias","last_name":"Tomboulides","affiliation":"Aristotle University of Thessaloniki","country":"Greece","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Paul","last_name":"Fischer","affiliation":"University of Illinois Urbana-Champaign","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Christos","last_name":"Frouzakis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Misun","last_name":"Min","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Konstantinos","last_name":"Boulouchos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Georgios","last_name":"Giannakopoulos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ananias","last_name":"Tomboulides","affiliation":"Aristotle University of Thessaloniki","country":"Greece","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Paul","last_name":"Fischer","affiliation":"University of Illinois Urbana-Champaign","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Christos","last_name":"Frouzakis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Misun","last_name":"Min","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Konstantinos","last_name":"Boulouchos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false}] } Presentation
ENG05 - OpenFPM for Scalable Particle-Mesh Simulations on Distributed-Memory Computers
, Pietro Incardona (Centre of System Biology Dresden, Germany)
+ Abstract { "session": {"id":"sess147","title":"Posters in Engineering","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Engineering"],"slots":[{"id":"post135","type":"poster","title":"ENG01 - Adaptive Particle Representation: A Novel Framework for Adaptive-Resolution Simulations","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"As progress in HPC hardware and software enables the numerical solution of increasingly complex non-linear models, adaptive-resolution and multi-resolution methods continue to gain importance. Models of this sort can only be efficiently simulated using self-adaptive discretization schemes like AMR and wavelets. However, these schemes are poorly suited for distributed-memory HPC systems, as they rely on global data tree structures and global mappings. We\u00a0therefore\u00a0present the Adaptive Particle Representation (APR), a novel and efficient method for adaptive-resolution simulation. The APR is based on local information only and is designed for scalability. It is based on a linear-time algorithm to construct an optimal resolution function for each point in the domain. It also provides point-wise error bounds for the function value and any derivative approximation. Differential operators can then be consistently evaluated on the evolving APR using discretization-corrected operators. While the APR combines ideas from wavelets and AMR, it effectively avoids\u00a0their performance issues. We benchmark this in numerical experiments and test the consistency and convergence of differential operators approximated on APR discretizations. These include the numerical solution of advection-diffusion of a Gaussian pulse, the two-dimensional unsteady Burgers equation, and adaptive three-dimensional Taylor-Green vortex simulation and\u00a0scaling experiments for testing performance.","filename":"post135s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bevan L.","last_name":"Cheeseman","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post147","type":"poster","title":"ENG02 - Assessment of Detached Eddy Simulation in Predicting Separated Flow over Airfoils at a Moderate Reynolds Number","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A highly scalable stabilized finite element flow solver is employed in the current study to simulate the flow around the NACA-4412 wing at a moderate chord Reynolds number (\u003Cem\u003ERe_c\u003C\/em\u003E = 400,000) with an angle of attack of 5 degrees. The flow under investigation involves a wide range of scales and complicated flow physics induced by the geometry, such as wall-bounded turbulence, flow separation, and turbulent wake flows. Previous DNS investigations have already revealed these complex flow patterns at similar Reynolds numbers. However, industry applications nowadays, targeting higher Reynolds number flows, still heavily depend on RANS or hybrid RANS\/LES approach in aircraft designs. The accurate prediction of separated flows is a cornerstone in successful CFD estimations. A delayed detached eddy simulation (DDES) turbulence model is utilized herein. The RANS model is primarily applied in near wall regions, while it gives way to LES in regions where flow is separated. To assess the readiness of this DDES approach, the obtained simulation results are to be compared with the DNS study conducted at KTH with the same flow configurations. The present research will better inform researchers the strengths and possible limitations of DDES in predicting complicated flow separation phenomenon.","filename":"post147s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jun","last_name":"Fang","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Kenneth","last_name":"Jansen","affiliation":"University of Colorado Boulder","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Philipp","last_name":"Schlatter","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ricardo","last_name":"Vinuesa","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Michel","last_name":"Rasquin","affiliation":"Cenaero","country":"Belgium","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}]},{"id":"post157","type":"poster","title":"ENG03 - Large Eddy Simulation of Tsunami Triggered Coastal Inundation in the Presence of Mitigation Parks","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years we have observed a paradigm shift from 2D shallow water models to models based on the 3D incompressible Navier-Stokes equations to simulate tsunami triggered inundation. The shift is due to the limitations of shallow water models for the simulation of onshore turbulent flows. The fully three-dimensional nature of turbulence and entrainment at the scales of coastal flooding requires massive parallel computing and the ability to have properly designed sub-grid scale models for large eddy simulation. In this poster, numerical mathematics, computational fluid dynamics, and tsunami physics are linked to understand the mechanisms that govern the coastal hydrodynamics as tsunami propagates inland. We look at what geometrical features of the coast line most affect the extension and propagation of flooding, in particular so when artificial, mitigation hills are installed at the shore line. Our numerical simulations rely on a massively parallel (hybrid MPI\/OpenMP) finite element solver of the incompressible 3D Navier-Stokes equations. Turbulence is modeled via dynamic Large Eddy Simulation.","filename":"post157s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jenny","last_name":"Suckale","affiliation":"Stanford University","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Yilang","last_name":"Xu","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Beatriz","last_name":"Eguzkitza","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Guillaume","last_name":"Houzeaux","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Mariano","last_name":"V\u00e1zquez","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post139","type":"poster","title":"ENG04 - A Low-Mach Simulation of Flow and Heat Transfer in a Motored Internal Combustion Engine Using the Spectral Element Method","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In this work, a proof-of-concept, wall-resolved implicit large eddy simulation (LES) campaign was performed to capture in-cylinder flow and heat transfer within an internal combustion engine (ICE). Over 20 cycles of the gas-exchange process was simulated, revealing variations in the intake jet impingement angle on the wall and piston surfaces from cycle-to-cycle. This calculation confirms a rising level of turbulent intensity during the compression stroke which is crucial to efficient engine operation. This work marks a milestone achievement in using Nek5000, a highly-scalable computational fluid dynamics (CFD) solver, to capture turbulent flow and thermal fields inside realistic engine geometries. In the context of an arbitrary Lagrangian-Eulerian (ALE) framework, several algorithms have been developed and integrated into Nek5000 in order overcome the computational challenges associated with moving boundaries (i.e. valves and pistons). In particular, this simulation makes use of a characteristic-based, time-stepping scheme to overcome Courant (CFL) conditions associated with standard, semi-implicit schemes. In addition, a grid-to-grid algorithm is employed to interpolate field variables from one mesh to another in order maintain spatial resolution requirements. The potential impact of this work is an unmatched, accurate, and highly-scalable tool for researchers to facilitate the efficient design of ICEs with short turn-around time.","filename":"post139s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Georgios","last_name":"Giannakopoulos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ananias","last_name":"Tomboulides","affiliation":"Aristotle University of Thessaloniki","country":"Greece","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Paul","last_name":"Fischer","affiliation":"University of Illinois Urbana-Champaign","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Christos","last_name":"Frouzakis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Misun","last_name":"Min","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Konstantinos","last_name":"Boulouchos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post134","type":"poster","title":"ENG05 - OpenFPM for Scalable Particle-Mesh Simulations on Distributed-Memory Computers","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scalable and efficient numerical simulations are of increasing importance in all areas of science and technology. This is fueled by a steady growth in the performance of computing hardware and increasing heterogeneous parallelism. However, efficiently implementing scalable simulation codes on heterogeneous, distributed hardware systems is the current bottleneck. This bottleneck can be relaxed by intermediate software layers that provide abstractions closer to the problem domain, allowing the computational scientist to focus on the simulation algorithm. Here, we present OpenFPM, an open and scalable framework that provides an abstraction layer for numerical simulations using particles and\/or meshes. OpenFPM provides transparent and scalable infrastructure for shared-memory and distributed-memory implementations of hybrid particle-mesh simulations of both discrete and continuous models. This infrastructure is complemented with portable implementations of frequently used numerical routines, as well as interfaces to third-party libraries. We present the architecture and design of OpenFPM, detail the underlying abstractions, and benchmark the framework in applications ranging from Smoothed Particle Hydrodynamics (SPH) to Molecular Dynamics (MD), Discrete Element Methods (DEM), high-dimensional Monte Carlo sampling (CMA-ES), and Reaction-Diffusion solvers, comparing it to the current state of the art and existing simulation software frameworks.","filename":"post134s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post167","type":"poster","title":"ENG06 - Wavelet Based Data Compression Strategies for Exascale CFD Simulations","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The steady increase of available computer resources has enabled engineers and scientists to use progressively more complex models to simulate a myriad of fluid flow problems. Yet, whereas modern high performance computers have seen a steady growth in computing power, the same trend has not been mirrored by a significant gain in data transfer rates. Current systems are capable of producing and processing high amounts of data quickly, while the overall performance is often limited by their ability to transfer and store the computed data. Considering that researchers invariably seek to study simulations with increasingly higher spatial and temporal resolution, the imminent move to exascale computing will consequently only exacerbate this problem. One of the major pitfalls of storing \u0027raw\u0027 simulation data lies in the implicit and redundant manner in which it represents the flow physics. Thus, using image compression algorithms to transform a large \u0027raw\u0027 into a compact data format could help to overcome the I\/O bottleneck. We therefore propose to adapt the wavelet-based JPEG-2000 compression standard for volumetric floating-point arrays.","filename":"post167s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"Rist","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post134","type":"poster","title":"ENG05 - OpenFPM for Scalable Particle-Mesh Simulations on Distributed-Memory Computers","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scalable and efficient numerical simulations are of increasing importance in all areas of science and technology. This is fueled by a steady growth in the performance of computing hardware and increasing heterogeneous parallelism. However, efficiently implementing scalable simulation codes on heterogeneous, distributed hardware systems is the current bottleneck. This bottleneck can be relaxed by intermediate software layers that provide abstractions closer to the problem domain, allowing the computational scientist to focus on the simulation algorithm. Here, we present OpenFPM, an open and scalable framework that provides an abstraction layer for numerical simulations using particles and\/or meshes. OpenFPM provides transparent and scalable infrastructure for shared-memory and distributed-memory implementations of hybrid particle-mesh simulations of both discrete and continuous models. This infrastructure is complemented with portable implementations of frequently used numerical routines, as well as interfaces to third-party libraries. We present the architecture and design of OpenFPM, detail the underlying abstractions, and benchmark the framework in applications ranging from Smoothed Particle Hydrodynamics (SPH) to Molecular Dynamics (MD), Discrete Element Methods (DEM), high-dimensional Monte Carlo sampling (CMA-ES), and Reaction-Diffusion solvers, comparing it to the current state of the art and existing simulation software frameworks.","filename":"post134s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"2","is_presenter":false}] } Presentation
ENG06 - Wavelet Based Data Compression Strategies for Exascale CFD Simulations
, Patrick Vogler (University of Stuttgart, Germany)
+ Abstract { "session": {"id":"sess147","title":"Posters in Engineering","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Engineering"],"slots":[{"id":"post135","type":"poster","title":"ENG01 - Adaptive Particle Representation: A Novel Framework for Adaptive-Resolution Simulations","begin_time":"19:30","end_time":"19:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"As progress in HPC hardware and software enables the numerical solution of increasingly complex non-linear models, adaptive-resolution and multi-resolution methods continue to gain importance. Models of this sort can only be efficiently simulated using self-adaptive discretization schemes like AMR and wavelets. However, these schemes are poorly suited for distributed-memory HPC systems, as they rely on global data tree structures and global mappings. We\u00a0therefore\u00a0present the Adaptive Particle Representation (APR), a novel and efficient method for adaptive-resolution simulation. The APR is based on local information only and is designed for scalability. It is based on a linear-time algorithm to construct an optimal resolution function for each point in the domain. It also provides point-wise error bounds for the function value and any derivative approximation. Differential operators can then be consistently evaluated on the evolving APR using discretization-corrected operators. While the APR combines ideas from wavelets and AMR, it effectively avoids\u00a0their performance issues. We benchmark this in numerical experiments and test the consistency and convergence of differential operators approximated on APR discretizations. These include the numerical solution of advection-diffusion of a Gaussian pulse, the two-dimensional unsteady Burgers equation, and adaptive three-dimensional Taylor-Green vortex simulation and\u00a0scaling experiments for testing performance.","filename":"post135s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Bevan L.","last_name":"Cheeseman","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Suryanarayana","last_name":"Maddu","affiliation":"Max Planck Institute for Molecular Cell Biology and Genetics","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post147","type":"poster","title":"ENG02 - Assessment of Detached Eddy Simulation in Predicting Separated Flow over Airfoils at a Moderate Reynolds Number","begin_time":"19:50","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A highly scalable stabilized finite element flow solver is employed in the current study to simulate the flow around the NACA-4412 wing at a moderate chord Reynolds number (\u003Cem\u003ERe_c\u003C\/em\u003E = 400,000) with an angle of attack of 5 degrees. The flow under investigation involves a wide range of scales and complicated flow physics induced by the geometry, such as wall-bounded turbulence, flow separation, and turbulent wake flows. Previous DNS investigations have already revealed these complex flow patterns at similar Reynolds numbers. However, industry applications nowadays, targeting higher Reynolds number flows, still heavily depend on RANS or hybrid RANS\/LES approach in aircraft designs. The accurate prediction of separated flows is a cornerstone in successful CFD estimations. A delayed detached eddy simulation (DDES) turbulence model is utilized herein. The RANS model is primarily applied in near wall regions, while it gives way to LES in regions where flow is separated. To assess the readiness of this DDES approach, the obtained simulation results are to be compared with the DNS study conducted at KTH with the same flow configurations. The present research will better inform researchers the strengths and possible limitations of DDES in predicting complicated flow separation phenomenon.","filename":"post147s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jun","last_name":"Fang","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":false},{"type":"Author","first_name":"Kenneth","last_name":"Jansen","affiliation":"University of Colorado Boulder","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Philipp","last_name":"Schlatter","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ricardo","last_name":"Vinuesa","affiliation":"KTH Royal Institute of Technology","country":"Sweden","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Michel","last_name":"Rasquin","affiliation":"Cenaero","country":"Belgium","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Ramesh","last_name":"Balakrishnan","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":true}]},{"id":"post157","type":"poster","title":"ENG03 - Large Eddy Simulation of Tsunami Triggered Coastal Inundation in the Presence of Mitigation Parks","begin_time":"20:10","end_time":"20:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In recent years we have observed a paradigm shift from 2D shallow water models to models based on the 3D incompressible Navier-Stokes equations to simulate tsunami triggered inundation. The shift is due to the limitations of shallow water models for the simulation of onshore turbulent flows. The fully three-dimensional nature of turbulence and entrainment at the scales of coastal flooding requires massive parallel computing and the ability to have properly designed sub-grid scale models for large eddy simulation. In this poster, numerical mathematics, computational fluid dynamics, and tsunami physics are linked to understand the mechanisms that govern the coastal hydrodynamics as tsunami propagates inland. We look at what geometrical features of the coast line most affect the extension and propagation of flooding, in particular so when artificial, mitigation hills are installed at the shore line. Our numerical simulations rely on a massively parallel (hybrid MPI\/OpenMP) finite element solver of the incompressible 3D Navier-Stokes equations. Turbulence is modeled via dynamic Large Eddy Simulation.","filename":"post157s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Jenny","last_name":"Suckale","affiliation":"Stanford University","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Yilang","last_name":"Xu","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Beatriz","last_name":"Eguzkitza","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Guillaume","last_name":"Houzeaux","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Mariano","last_name":"V\u00e1zquez","affiliation":"Barcelona Supercomputing Center","country":"Spain","bio":"","order":"6","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simone","last_name":"Marras","affiliation":"New Jersey Institute of Technology","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post139","type":"poster","title":"ENG04 - A Low-Mach Simulation of Flow and Heat Transfer in a Motored Internal Combustion Engine Using the Spectral Element Method","begin_time":"20:30","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"In this work, a proof-of-concept, wall-resolved implicit large eddy simulation (LES) campaign was performed to capture in-cylinder flow and heat transfer within an internal combustion engine (ICE). Over 20 cycles of the gas-exchange process was simulated, revealing variations in the intake jet impingement angle on the wall and piston surfaces from cycle-to-cycle. This calculation confirms a rising level of turbulent intensity during the compression stroke which is crucial to efficient engine operation. This work marks a milestone achievement in using Nek5000, a highly-scalable computational fluid dynamics (CFD) solver, to capture turbulent flow and thermal fields inside realistic engine geometries. In the context of an arbitrary Lagrangian-Eulerian (ALE) framework, several algorithms have been developed and integrated into Nek5000 in order overcome the computational challenges associated with moving boundaries (i.e. valves and pistons). In particular, this simulation makes use of a characteristic-based, time-stepping scheme to overcome Courant (CFL) conditions associated with standard, semi-implicit schemes. In addition, a grid-to-grid algorithm is employed to interpolate field variables from one mesh to another in order maintain spatial resolution requirements. The potential impact of this work is an unmatched, accurate, and highly-scalable tool for researchers to facilitate the efficient design of ICEs with short turn-around time.","filename":"post139s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Georgios","last_name":"Giannakopoulos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ananias","last_name":"Tomboulides","affiliation":"Aristotle University of Thessaloniki","country":"Greece","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Paul","last_name":"Fischer","affiliation":"University of Illinois Urbana-Champaign","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Christos","last_name":"Frouzakis","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Misun","last_name":"Min","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Konstantinos","last_name":"Boulouchos","affiliation":"ETH Zurich","country":"Switzerland","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Saumil","last_name":"Patel","affiliation":"Argonne National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post134","type":"poster","title":"ENG05 - OpenFPM for Scalable Particle-Mesh Simulations on Distributed-Memory Computers","begin_time":"20:50","end_time":"21:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Scalable and efficient numerical simulations are of increasing importance in all areas of science and technology. This is fueled by a steady growth in the performance of computing hardware and increasing heterogeneous parallelism. However, efficiently implementing scalable simulation codes on heterogeneous, distributed hardware systems is the current bottleneck. This bottleneck can be relaxed by intermediate software layers that provide abstractions closer to the problem domain, allowing the computational scientist to focus on the simulation algorithm. Here, we present OpenFPM, an open and scalable framework that provides an abstraction layer for numerical simulations using particles and\/or meshes. OpenFPM provides transparent and scalable infrastructure for shared-memory and distributed-memory implementations of hybrid particle-mesh simulations of both discrete and continuous models. This infrastructure is complemented with portable implementations of frequently used numerical routines, as well as interfaces to third-party libraries. We present the architecture and design of OpenFPM, detail the underlying abstractions, and benchmark the framework in applications ranging from Smoothed Particle Hydrodynamics (SPH) to Molecular Dynamics (MD), Discrete Element Methods (DEM), high-dimensional Monte Carlo sampling (CMA-ES), and Reaction-Diffusion solvers, comparing it to the current state of the art and existing simulation software frameworks.","filename":"post134s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ivo","last_name":"Sbalzarini","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Pietro","last_name":"Incardona","affiliation":"Centre of System Biology Dresden","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post167","type":"poster","title":"ENG06 - Wavelet Based Data Compression Strategies for Exascale CFD Simulations","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The steady increase of available computer resources has enabled engineers and scientists to use progressively more complex models to simulate a myriad of fluid flow problems. Yet, whereas modern high performance computers have seen a steady growth in computing power, the same trend has not been mirrored by a significant gain in data transfer rates. Current systems are capable of producing and processing high amounts of data quickly, while the overall performance is often limited by their ability to transfer and store the computed data. Considering that researchers invariably seek to study simulations with increasingly higher spatial and temporal resolution, the imminent move to exascale computing will consequently only exacerbate this problem. One of the major pitfalls of storing \u0027raw\u0027 simulation data lies in the implicit and redundant manner in which it represents the flow physics. Thus, using image compression algorithms to transform a large \u0027raw\u0027 into a compact data format could help to overcome the I\/O bottleneck. We therefore propose to adapt the wavelet-based JPEG-2000 compression standard for volumetric floating-point arrays.","filename":"post167s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"Rist","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post167","type":"poster","title":"ENG06 - Wavelet Based Data Compression Strategies for Exascale CFD Simulations","begin_time":"21:10","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The steady increase of available computer resources has enabled engineers and scientists to use progressively more complex models to simulate a myriad of fluid flow problems. Yet, whereas modern high performance computers have seen a steady growth in computing power, the same trend has not been mirrored by a significant gain in data transfer rates. Current systems are capable of producing and processing high amounts of data quickly, while the overall performance is often limited by their ability to transfer and store the computed data. Considering that researchers invariably seek to study simulations with increasingly higher spatial and temporal resolution, the imminent move to exascale computing will consequently only exacerbate this problem. One of the major pitfalls of storing \u0027raw\u0027 simulation data lies in the implicit and redundant manner in which it represents the flow physics. Thus, using image compression algorithms to transform a large \u0027raw\u0027 into a compact data format could help to overcome the I\/O bottleneck. We therefore propose to adapt the wavelet-based JPEG-2000 compression standard for volumetric floating-point arrays.","filename":"post167s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"Rist","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Patrick","last_name":"Vogler","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ulrich","last_name":"Rist","affiliation":"University of Stuttgart","country":"Germany","bio":"","order":"2","is_presenter":false}] } Presentation
LIF01 - AI-GWAPA: Explainable-AI and Genome Wide Association Phytobiome Analysis
, Piet Jones (University of Tennessee, United States of America)
+ Abstract { "session": {"id":"sess148","title":"Posters in Life Sciences","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Life Sciences"],"slots":[{"id":"post179","type":"poster","title":"LIF01 - AI-GWAPA: Explainable-AI and Genome Wide Association Phytobiome Analysis","begin_time":"19:30","end_time":"19:47","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The phytobiome consists of the plant, organismal communities and their environment. The interactions between these have significant effects on observable measurable traits that have potential economic and sustainability implications. A better systems-level understanding of these interactions will enhance our capacity to design higher yield and sustainable plants. We apply a collection of machine learning and deep learning methods to elucidate the interaction between viral, microbial and the plant host systems. Metatranscriptome samples from leaf, xylem and root along with approximately 10 million SNPs called across a population of 1000 \u003Cem\u003EP. trichocarpa\u003C\/em\u003E trees, allows us to associate host genetic variants to phytobiome constituents. Factorization machines are used, in a deep learning framework, to take higher-order interactions into account producing a set of high-confidence measurements of taxa abundance, which serve as phenotypes in a Genome Wide Association Analysis. In addition, putative host driven mutualistic\/pathogenic interactions between taxa are estimated. These provide candidate proteins for a capsule network deep learning model to predict putative protein-protein interactions, taking into account the protein\u2019s quantum chemical properties. Capsule networks provide an explainable AI approach to uncover features driving important interactions. This machine\/deep learning framework provides a methodology to better understand complex biological systems.","filename":"post179s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Stephan","last_name":"Irle","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ka Hung","last_name":"Lee","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Udaya","last_name":"Kalluri","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Wellington","last_name":"Muchero","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Jay","last_name":"Chen","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Gerald","last_name":"Tuskan","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"9","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post169","type":"poster","title":"LIF02 - The Bromodomain-Peptide (Un)Binding Network","begin_time":"19:47","end_time":"20:04","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Atomistic simulations are a valuable tool for understanding the structural details involved in biological processes. However, extracting kinetic information such as (un)binding rates for complex molecular systems remains a challenge as it requires both the efficient sampling of rare events and scalable analysis tools to cope with large amounts of data. Progress index-guided sampling (PIGS) is an unsupervised and scalable algorithm capable of enhancing the conformational diversification in a focused search space by simply rewarding spontaneous fluctuations. Here we use PIGS to study the binding mode and dissociation of a tripeptide from four different bromodomains, which are protein modules involved in epigenetics. By focusing the sampling enhancement on the two distinct loops forming the peptide binding pocket we are able to observe several unbinding events. Clustering of conformations and subsequent Markov state model analysis elucidate states, kinetics, and pathways involved in the unbinding process and help to shed light on structural aspects of epigenetic regulation. Both the PIGS protocol and the analysis tools rely on scalable libraries implemented in the software CAMPARI, which can also be interfaced with other propagation codes to fully exploit the tools available on different HPC infrastructures.","bio":"","contributors":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post177","type":"poster","title":"LIF03 - Explainable Machine Learning for Systems Biology: Tensor Iterative Random Forests","begin_time":"20:04","end_time":"20:21","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A novel algorithm, Tensor iterative Random Forest (TiRF), is able to effectively build forests that can be mined for interactions within a multidimensional X matrix, a multidimensional Y matrix, and interactions between multiple dimensions in X and Y, all at the same time. TiRF uses dimension reduction techniques (such as Lasso or a nested call to iRF) on Y for the given subsets of X, thus ensuring that the new subset of Y dimensions is highly connected to the X being split upon. The dimension-reduced Y matrix can then be used in measuring node purity, ensuring that noise is reduced and that the given features in X are measured for the ability to split the appropriate dimensions in Y. The resulting trees and forest now contain paths in X, and each node also has an associated set of Y. This means that random intersection trees can be used to find sets of interacting Xs from the forest and sets of interacting Ys conditional on those sets of X. As the data sets are growing exponentially, petascale deployments of TiRFs are being targeted in order to perform systems-wide analyses of biological or other complex systems that can be represented as matrices.","filename":"post177s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ashley","last_name":"Cliff","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ben","last_name":"Brown","affiliation":"Lawrence Berkeley National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post124","type":"poster","title":"LIF04 - iReceptor: A Platform for Exploring and Analyzing Antibody\/B-cell and T-cell Receptor Repertoire Data across Federated Repositories","begin_time":"20:21","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Individuals produce an immense repertoire of antibody\/B-cell and T-cell receptor sequences in order to recognize and destroy a diverse array of pathogens. For example, it has been estimated that the number of possible human B-cell sequences is greater than 10^13, and each person produces 10^8 - 10^9 B-cells during an immune response, many of which are unique. In 2009 NGS approaches were used to characterize the Adaptive Immune Receptor Repertoire (AIRR) in exquisite detail. These AIRR-Seq data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune disease, and in developing novel therapeutics against cancer. The iReceptor system (ireceptor.org) is a platform to integrate and analyze these immense data sets by combining: 1) an international network of AIRR-Seq data repositories; 2) the ability to federate AIRR-Seq data across these distributed repositories; 3) the ability to apply advanced analytical tools using large advanced research computing (ARC) resources; and 4) a scientific gateway that hides the complexity of performing research queries and advanced analyses across these federated data. iReceptor enables these capabilities by building on the standards work being carried our by the AIRR Community (airr-community.org). iReceptor manages the staging of data and control of ARC analysis jobs through the use of the AGAVE science-as-a-service platform (agaveapi.co).","filename":"post124s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Felix","last_name":"Breden","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true}]},{"id":"post122","type":"poster","title":"LIF05 - Modeling Biological Networks with Exponential Random Graph Models","begin_time":"20:38","end_time":"20:55","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Much research in biological networks concerns \u0022motifs\u0022, small subgraphs which occur more frequently than by chance, which are considered the building blocks of complex networks. Exponential random graph models (ERGMs), a well-established class of statistical models for network data which are widely used in social network analysis, represent a principled statistical method of determining whether a motif is over (or under) represented in a network. Although the use of ERGMs for analyzing biological networks was introduced into the bioinformatics literature ten years ago, the use of ERGMs in biological network analysis has been very limited since then due to problems with applying existing methods to such networks, their size being typically far larger than those social networks to which ERGMs are usually applied. Here we use high performance computing to apply our recently developed new techniques (snowball sampling, improved fixed density ERGM sampling, scalable Equilibrium Expectation algorithm) for ERGM estimation to several biological networks (protein-protein interaction networks, gene regulatory networks, and a neural network), ranging in size from a few hundred to over five thousand nodes.","filename":"post122s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Maksym","last_name":"Byshkin","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Antonietta","last_name":"Mira","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Garry","last_name":"Robins","affiliation":"The University of Melbourne","country":"Australia","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Alessandro","last_name":"Lomi","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true}]},{"id":"post178","type":"poster","title":"LIF06 - Parallel Kraken for Meta-Omic Microbiome and Phytobiome Classification","begin_time":"20:55","end_time":"21:12","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Meta-omic taxa classification allows for the identification of a wide range of micro- and macro-organisms that influence disease, physiological states, and ecological states in both host systems and environmental samples. Traditional classification methods often either use markers or subsample genomes to limit search space (and, as such, lose discriminatory power) for identifying large numbers of taxa. However, accurately identifying taxa in meta-omics datasets requires methods that simultaneously identify taxa across all kingdoms of life, utilize whole genome sequences, and are highly parallel. One drawback to utilizing whole genome sequences without subsampling or combining similar sequences is that databases of all known sequences become impractical to store in RAM. To overcome this limitation, we have developed a highly parallel version of Kraken that can run multiple sequences through multiple databases in parallel and resolve each read assignment to identify taxa in transcriptomic, proteomic, and genomic data. Additionally, we have created databases from all known whole genome sequences in NCBI totaling 115k+ genomes and 700k+ viral genomes from JGI. Parallel Kraken has been used to classify thousands of samples and billions of reads in parallel and is part of a pipeline for understanding relationships between host and microbiome\/phytobiome.","filename":"post178s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ian","last_name":"Hodge","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post170","type":"poster","title":"LIF07 - SAPPHIRE Basin Recognition: An Unsupervised Algorithm to Identify and Project Metastable and Transition States in High-Dimensional Time Series Data","begin_time":"21:12","end_time":"21:29","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The identification of states and pathways in high-dimensional data sets is a daunting task in that the number of states increases exponentially with dimensionality. While simple projection techniques are prone to introduce overlaps and shortcuts, our ability to process information does mandate that the dynamics be reduced to a small number of essential patterns. Here we present a new approach called SAPPHIRE (states and pathways projected at high resolution) Basin Recognition (SBR) and show the automatic detection of metastable and transition states for different applications ranging from molecular dynamics simulations to temporal series of complex systems taken from other scientific domains. The method is based on a reordering of the trajectory according to a short spanning tree, such that the resulting new sequence amounts to a walk along the state space basin by basin. The temporal series is used to highlight recurrence and to provide a kinetic distance. By using the kinetic distance and the original time series, SBR performs an automatic identification of the basins. By comparing with other clustering techniques, we demonstrate the suitability of the method to capture the salient slow modes of the system while maintaining a manageable number of states.","filename":"post170s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post179","type":"poster","title":"LIF01 - AI-GWAPA: Explainable-AI and Genome Wide Association Phytobiome Analysis","begin_time":"19:30","end_time":"19:47","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The phytobiome consists of the plant, organismal communities and their environment. The interactions between these have significant effects on observable measurable traits that have potential economic and sustainability implications. A better systems-level understanding of these interactions will enhance our capacity to design higher yield and sustainable plants. We apply a collection of machine learning and deep learning methods to elucidate the interaction between viral, microbial and the plant host systems. Metatranscriptome samples from leaf, xylem and root along with approximately 10 million SNPs called across a population of 1000 \u003Cem\u003EP. trichocarpa\u003C\/em\u003E trees, allows us to associate host genetic variants to phytobiome constituents. Factorization machines are used, in a deep learning framework, to take higher-order interactions into account producing a set of high-confidence measurements of taxa abundance, which serve as phenotypes in a Genome Wide Association Analysis. In addition, putative host driven mutualistic\/pathogenic interactions between taxa are estimated. These provide candidate proteins for a capsule network deep learning model to predict putative protein-protein interactions, taking into account the protein\u2019s quantum chemical properties. Capsule networks provide an explainable AI approach to uncover features driving important interactions. This machine\/deep learning framework provides a methodology to better understand complex biological systems.","filename":"post179s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Stephan","last_name":"Irle","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ka Hung","last_name":"Lee","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Udaya","last_name":"Kalluri","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Wellington","last_name":"Muchero","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Jay","last_name":"Chen","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Gerald","last_name":"Tuskan","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"9","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Stephan","last_name":"Irle","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ka Hung","last_name":"Lee","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Udaya","last_name":"Kalluri","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Wellington","last_name":"Muchero","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Jay","last_name":"Chen","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Gerald","last_name":"Tuskan","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"9","is_presenter":false}] } Presentation
LIF03 - Explainable Machine Learning for Systems Biology: Tensor Iterative Random Forests
, Jonathon Romero (University of Tennessee, United States of America)
+ Abstract { "session": {"id":"sess148","title":"Posters in Life Sciences","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Life Sciences"],"slots":[{"id":"post179","type":"poster","title":"LIF01 - AI-GWAPA: Explainable-AI and Genome Wide Association Phytobiome Analysis","begin_time":"19:30","end_time":"19:47","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The phytobiome consists of the plant, organismal communities and their environment. The interactions between these have significant effects on observable measurable traits that have potential economic and sustainability implications. A better systems-level understanding of these interactions will enhance our capacity to design higher yield and sustainable plants. We apply a collection of machine learning and deep learning methods to elucidate the interaction between viral, microbial and the plant host systems. Metatranscriptome samples from leaf, xylem and root along with approximately 10 million SNPs called across a population of 1000 \u003Cem\u003EP. trichocarpa\u003C\/em\u003E trees, allows us to associate host genetic variants to phytobiome constituents. Factorization machines are used, in a deep learning framework, to take higher-order interactions into account producing a set of high-confidence measurements of taxa abundance, which serve as phenotypes in a Genome Wide Association Analysis. In addition, putative host driven mutualistic\/pathogenic interactions between taxa are estimated. These provide candidate proteins for a capsule network deep learning model to predict putative protein-protein interactions, taking into account the protein\u2019s quantum chemical properties. Capsule networks provide an explainable AI approach to uncover features driving important interactions. This machine\/deep learning framework provides a methodology to better understand complex biological systems.","filename":"post179s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Stephan","last_name":"Irle","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ka Hung","last_name":"Lee","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Udaya","last_name":"Kalluri","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Wellington","last_name":"Muchero","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Jay","last_name":"Chen","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Gerald","last_name":"Tuskan","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"9","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post169","type":"poster","title":"LIF02 - The Bromodomain-Peptide (Un)Binding Network","begin_time":"19:47","end_time":"20:04","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Atomistic simulations are a valuable tool for understanding the structural details involved in biological processes. However, extracting kinetic information such as (un)binding rates for complex molecular systems remains a challenge as it requires both the efficient sampling of rare events and scalable analysis tools to cope with large amounts of data. Progress index-guided sampling (PIGS) is an unsupervised and scalable algorithm capable of enhancing the conformational diversification in a focused search space by simply rewarding spontaneous fluctuations. Here we use PIGS to study the binding mode and dissociation of a tripeptide from four different bromodomains, which are protein modules involved in epigenetics. By focusing the sampling enhancement on the two distinct loops forming the peptide binding pocket we are able to observe several unbinding events. Clustering of conformations and subsequent Markov state model analysis elucidate states, kinetics, and pathways involved in the unbinding process and help to shed light on structural aspects of epigenetic regulation. Both the PIGS protocol and the analysis tools rely on scalable libraries implemented in the software CAMPARI, which can also be interfaced with other propagation codes to fully exploit the tools available on different HPC infrastructures.","bio":"","contributors":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post177","type":"poster","title":"LIF03 - Explainable Machine Learning for Systems Biology: Tensor Iterative Random Forests","begin_time":"20:04","end_time":"20:21","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A novel algorithm, Tensor iterative Random Forest (TiRF), is able to effectively build forests that can be mined for interactions within a multidimensional X matrix, a multidimensional Y matrix, and interactions between multiple dimensions in X and Y, all at the same time. TiRF uses dimension reduction techniques (such as Lasso or a nested call to iRF) on Y for the given subsets of X, thus ensuring that the new subset of Y dimensions is highly connected to the X being split upon. The dimension-reduced Y matrix can then be used in measuring node purity, ensuring that noise is reduced and that the given features in X are measured for the ability to split the appropriate dimensions in Y. The resulting trees and forest now contain paths in X, and each node also has an associated set of Y. This means that random intersection trees can be used to find sets of interacting Xs from the forest and sets of interacting Ys conditional on those sets of X. As the data sets are growing exponentially, petascale deployments of TiRFs are being targeted in order to perform systems-wide analyses of biological or other complex systems that can be represented as matrices.","filename":"post177s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ashley","last_name":"Cliff","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ben","last_name":"Brown","affiliation":"Lawrence Berkeley National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post124","type":"poster","title":"LIF04 - iReceptor: A Platform for Exploring and Analyzing Antibody\/B-cell and T-cell Receptor Repertoire Data across Federated Repositories","begin_time":"20:21","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Individuals produce an immense repertoire of antibody\/B-cell and T-cell receptor sequences in order to recognize and destroy a diverse array of pathogens. For example, it has been estimated that the number of possible human B-cell sequences is greater than 10^13, and each person produces 10^8 - 10^9 B-cells during an immune response, many of which are unique. In 2009 NGS approaches were used to characterize the Adaptive Immune Receptor Repertoire (AIRR) in exquisite detail. These AIRR-Seq data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune disease, and in developing novel therapeutics against cancer. The iReceptor system (ireceptor.org) is a platform to integrate and analyze these immense data sets by combining: 1) an international network of AIRR-Seq data repositories; 2) the ability to federate AIRR-Seq data across these distributed repositories; 3) the ability to apply advanced analytical tools using large advanced research computing (ARC) resources; and 4) a scientific gateway that hides the complexity of performing research queries and advanced analyses across these federated data. iReceptor enables these capabilities by building on the standards work being carried our by the AIRR Community (airr-community.org). iReceptor manages the staging of data and control of ARC analysis jobs through the use of the AGAVE science-as-a-service platform (agaveapi.co).","filename":"post124s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Felix","last_name":"Breden","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true}]},{"id":"post122","type":"poster","title":"LIF05 - Modeling Biological Networks with Exponential Random Graph Models","begin_time":"20:38","end_time":"20:55","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Much research in biological networks concerns \u0022motifs\u0022, small subgraphs which occur more frequently than by chance, which are considered the building blocks of complex networks. Exponential random graph models (ERGMs), a well-established class of statistical models for network data which are widely used in social network analysis, represent a principled statistical method of determining whether a motif is over (or under) represented in a network. Although the use of ERGMs for analyzing biological networks was introduced into the bioinformatics literature ten years ago, the use of ERGMs in biological network analysis has been very limited since then due to problems with applying existing methods to such networks, their size being typically far larger than those social networks to which ERGMs are usually applied. Here we use high performance computing to apply our recently developed new techniques (snowball sampling, improved fixed density ERGM sampling, scalable Equilibrium Expectation algorithm) for ERGM estimation to several biological networks (protein-protein interaction networks, gene regulatory networks, and a neural network), ranging in size from a few hundred to over five thousand nodes.","filename":"post122s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Maksym","last_name":"Byshkin","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Antonietta","last_name":"Mira","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Garry","last_name":"Robins","affiliation":"The University of Melbourne","country":"Australia","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Alessandro","last_name":"Lomi","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true}]},{"id":"post178","type":"poster","title":"LIF06 - Parallel Kraken for Meta-Omic Microbiome and Phytobiome Classification","begin_time":"20:55","end_time":"21:12","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Meta-omic taxa classification allows for the identification of a wide range of micro- and macro-organisms that influence disease, physiological states, and ecological states in both host systems and environmental samples. Traditional classification methods often either use markers or subsample genomes to limit search space (and, as such, lose discriminatory power) for identifying large numbers of taxa. However, accurately identifying taxa in meta-omics datasets requires methods that simultaneously identify taxa across all kingdoms of life, utilize whole genome sequences, and are highly parallel. One drawback to utilizing whole genome sequences without subsampling or combining similar sequences is that databases of all known sequences become impractical to store in RAM. To overcome this limitation, we have developed a highly parallel version of Kraken that can run multiple sequences through multiple databases in parallel and resolve each read assignment to identify taxa in transcriptomic, proteomic, and genomic data. Additionally, we have created databases from all known whole genome sequences in NCBI totaling 115k+ genomes and 700k+ viral genomes from JGI. Parallel Kraken has been used to classify thousands of samples and billions of reads in parallel and is part of a pipeline for understanding relationships between host and microbiome\/phytobiome.","filename":"post178s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ian","last_name":"Hodge","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post170","type":"poster","title":"LIF07 - SAPPHIRE Basin Recognition: An Unsupervised Algorithm to Identify and Project Metastable and Transition States in High-Dimensional Time Series Data","begin_time":"21:12","end_time":"21:29","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The identification of states and pathways in high-dimensional data sets is a daunting task in that the number of states increases exponentially with dimensionality. While simple projection techniques are prone to introduce overlaps and shortcuts, our ability to process information does mandate that the dynamics be reduced to a small number of essential patterns. Here we present a new approach called SAPPHIRE (states and pathways projected at high resolution) Basin Recognition (SBR) and show the automatic detection of metastable and transition states for different applications ranging from molecular dynamics simulations to temporal series of complex systems taken from other scientific domains. The method is based on a reordering of the trajectory according to a short spanning tree, such that the resulting new sequence amounts to a walk along the state space basin by basin. The temporal series is used to highlight recurrence and to provide a kinetic distance. By using the kinetic distance and the original time series, SBR performs an automatic identification of the basins. By comparing with other clustering techniques, we demonstrate the suitability of the method to capture the salient slow modes of the system while maintaining a manageable number of states.","filename":"post170s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post177","type":"poster","title":"LIF03 - Explainable Machine Learning for Systems Biology: Tensor Iterative Random Forests","begin_time":"20:04","end_time":"20:21","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A novel algorithm, Tensor iterative Random Forest (TiRF), is able to effectively build forests that can be mined for interactions within a multidimensional X matrix, a multidimensional Y matrix, and interactions between multiple dimensions in X and Y, all at the same time. TiRF uses dimension reduction techniques (such as Lasso or a nested call to iRF) on Y for the given subsets of X, thus ensuring that the new subset of Y dimensions is highly connected to the X being split upon. The dimension-reduced Y matrix can then be used in measuring node purity, ensuring that noise is reduced and that the given features in X are measured for the ability to split the appropriate dimensions in Y. The resulting trees and forest now contain paths in X, and each node also has an associated set of Y. This means that random intersection trees can be used to find sets of interacting Xs from the forest and sets of interacting Ys conditional on those sets of X. As the data sets are growing exponentially, petascale deployments of TiRFs are being targeted in order to perform systems-wide analyses of biological or other complex systems that can be represented as matrices.","filename":"post177s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ashley","last_name":"Cliff","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ben","last_name":"Brown","affiliation":"Lawrence Berkeley National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ashley","last_name":"Cliff","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ben","last_name":"Brown","affiliation":"Lawrence Berkeley National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}] } Presentation
LIF04 - iReceptor: A Platform for Exploring and Analyzing Antibody/B-cell and T-cell Receptor Repertoire Data across Federated Repositories
, Brian Corrie (Simon Fraser University, Canada)
+ Abstract { "session": {"id":"sess148","title":"Posters in Life Sciences","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Life Sciences"],"slots":[{"id":"post179","type":"poster","title":"LIF01 - AI-GWAPA: Explainable-AI and Genome Wide Association Phytobiome Analysis","begin_time":"19:30","end_time":"19:47","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The phytobiome consists of the plant, organismal communities and their environment. The interactions between these have significant effects on observable measurable traits that have potential economic and sustainability implications. A better systems-level understanding of these interactions will enhance our capacity to design higher yield and sustainable plants. We apply a collection of machine learning and deep learning methods to elucidate the interaction between viral, microbial and the plant host systems. Metatranscriptome samples from leaf, xylem and root along with approximately 10 million SNPs called across a population of 1000 \u003Cem\u003EP. trichocarpa\u003C\/em\u003E trees, allows us to associate host genetic variants to phytobiome constituents. Factorization machines are used, in a deep learning framework, to take higher-order interactions into account producing a set of high-confidence measurements of taxa abundance, which serve as phenotypes in a Genome Wide Association Analysis. In addition, putative host driven mutualistic\/pathogenic interactions between taxa are estimated. These provide candidate proteins for a capsule network deep learning model to predict putative protein-protein interactions, taking into account the protein\u2019s quantum chemical properties. Capsule networks provide an explainable AI approach to uncover features driving important interactions. This machine\/deep learning framework provides a methodology to better understand complex biological systems.","filename":"post179s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Stephan","last_name":"Irle","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ka Hung","last_name":"Lee","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Udaya","last_name":"Kalluri","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Wellington","last_name":"Muchero","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Jay","last_name":"Chen","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Gerald","last_name":"Tuskan","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"9","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post169","type":"poster","title":"LIF02 - The Bromodomain-Peptide (Un)Binding Network","begin_time":"19:47","end_time":"20:04","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Atomistic simulations are a valuable tool for understanding the structural details involved in biological processes. However, extracting kinetic information such as (un)binding rates for complex molecular systems remains a challenge as it requires both the efficient sampling of rare events and scalable analysis tools to cope with large amounts of data. Progress index-guided sampling (PIGS) is an unsupervised and scalable algorithm capable of enhancing the conformational diversification in a focused search space by simply rewarding spontaneous fluctuations. Here we use PIGS to study the binding mode and dissociation of a tripeptide from four different bromodomains, which are protein modules involved in epigenetics. By focusing the sampling enhancement on the two distinct loops forming the peptide binding pocket we are able to observe several unbinding events. Clustering of conformations and subsequent Markov state model analysis elucidate states, kinetics, and pathways involved in the unbinding process and help to shed light on structural aspects of epigenetic regulation. Both the PIGS protocol and the analysis tools rely on scalable libraries implemented in the software CAMPARI, which can also be interfaced with other propagation codes to fully exploit the tools available on different HPC infrastructures.","bio":"","contributors":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post177","type":"poster","title":"LIF03 - Explainable Machine Learning for Systems Biology: Tensor Iterative Random Forests","begin_time":"20:04","end_time":"20:21","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A novel algorithm, Tensor iterative Random Forest (TiRF), is able to effectively build forests that can be mined for interactions within a multidimensional X matrix, a multidimensional Y matrix, and interactions between multiple dimensions in X and Y, all at the same time. TiRF uses dimension reduction techniques (such as Lasso or a nested call to iRF) on Y for the given subsets of X, thus ensuring that the new subset of Y dimensions is highly connected to the X being split upon. The dimension-reduced Y matrix can then be used in measuring node purity, ensuring that noise is reduced and that the given features in X are measured for the ability to split the appropriate dimensions in Y. The resulting trees and forest now contain paths in X, and each node also has an associated set of Y. This means that random intersection trees can be used to find sets of interacting Xs from the forest and sets of interacting Ys conditional on those sets of X. As the data sets are growing exponentially, petascale deployments of TiRFs are being targeted in order to perform systems-wide analyses of biological or other complex systems that can be represented as matrices.","filename":"post177s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ashley","last_name":"Cliff","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ben","last_name":"Brown","affiliation":"Lawrence Berkeley National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post124","type":"poster","title":"LIF04 - iReceptor: A Platform for Exploring and Analyzing Antibody\/B-cell and T-cell Receptor Repertoire Data across Federated Repositories","begin_time":"20:21","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Individuals produce an immense repertoire of antibody\/B-cell and T-cell receptor sequences in order to recognize and destroy a diverse array of pathogens. For example, it has been estimated that the number of possible human B-cell sequences is greater than 10^13, and each person produces 10^8 - 10^9 B-cells during an immune response, many of which are unique. In 2009 NGS approaches were used to characterize the Adaptive Immune Receptor Repertoire (AIRR) in exquisite detail. These AIRR-Seq data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune disease, and in developing novel therapeutics against cancer. The iReceptor system (ireceptor.org) is a platform to integrate and analyze these immense data sets by combining: 1) an international network of AIRR-Seq data repositories; 2) the ability to federate AIRR-Seq data across these distributed repositories; 3) the ability to apply advanced analytical tools using large advanced research computing (ARC) resources; and 4) a scientific gateway that hides the complexity of performing research queries and advanced analyses across these federated data. iReceptor enables these capabilities by building on the standards work being carried our by the AIRR Community (airr-community.org). iReceptor manages the staging of data and control of ARC analysis jobs through the use of the AGAVE science-as-a-service platform (agaveapi.co).","filename":"post124s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Felix","last_name":"Breden","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true}]},{"id":"post122","type":"poster","title":"LIF05 - Modeling Biological Networks with Exponential Random Graph Models","begin_time":"20:38","end_time":"20:55","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Much research in biological networks concerns \u0022motifs\u0022, small subgraphs which occur more frequently than by chance, which are considered the building blocks of complex networks. Exponential random graph models (ERGMs), a well-established class of statistical models for network data which are widely used in social network analysis, represent a principled statistical method of determining whether a motif is over (or under) represented in a network. Although the use of ERGMs for analyzing biological networks was introduced into the bioinformatics literature ten years ago, the use of ERGMs in biological network analysis has been very limited since then due to problems with applying existing methods to such networks, their size being typically far larger than those social networks to which ERGMs are usually applied. Here we use high performance computing to apply our recently developed new techniques (snowball sampling, improved fixed density ERGM sampling, scalable Equilibrium Expectation algorithm) for ERGM estimation to several biological networks (protein-protein interaction networks, gene regulatory networks, and a neural network), ranging in size from a few hundred to over five thousand nodes.","filename":"post122s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Maksym","last_name":"Byshkin","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Antonietta","last_name":"Mira","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Garry","last_name":"Robins","affiliation":"The University of Melbourne","country":"Australia","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Alessandro","last_name":"Lomi","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true}]},{"id":"post178","type":"poster","title":"LIF06 - Parallel Kraken for Meta-Omic Microbiome and Phytobiome Classification","begin_time":"20:55","end_time":"21:12","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Meta-omic taxa classification allows for the identification of a wide range of micro- and macro-organisms that influence disease, physiological states, and ecological states in both host systems and environmental samples. Traditional classification methods often either use markers or subsample genomes to limit search space (and, as such, lose discriminatory power) for identifying large numbers of taxa. However, accurately identifying taxa in meta-omics datasets requires methods that simultaneously identify taxa across all kingdoms of life, utilize whole genome sequences, and are highly parallel. One drawback to utilizing whole genome sequences without subsampling or combining similar sequences is that databases of all known sequences become impractical to store in RAM. To overcome this limitation, we have developed a highly parallel version of Kraken that can run multiple sequences through multiple databases in parallel and resolve each read assignment to identify taxa in transcriptomic, proteomic, and genomic data. Additionally, we have created databases from all known whole genome sequences in NCBI totaling 115k+ genomes and 700k+ viral genomes from JGI. Parallel Kraken has been used to classify thousands of samples and billions of reads in parallel and is part of a pipeline for understanding relationships between host and microbiome\/phytobiome.","filename":"post178s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ian","last_name":"Hodge","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post170","type":"poster","title":"LIF07 - SAPPHIRE Basin Recognition: An Unsupervised Algorithm to Identify and Project Metastable and Transition States in High-Dimensional Time Series Data","begin_time":"21:12","end_time":"21:29","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The identification of states and pathways in high-dimensional data sets is a daunting task in that the number of states increases exponentially with dimensionality. While simple projection techniques are prone to introduce overlaps and shortcuts, our ability to process information does mandate that the dynamics be reduced to a small number of essential patterns. Here we present a new approach called SAPPHIRE (states and pathways projected at high resolution) Basin Recognition (SBR) and show the automatic detection of metastable and transition states for different applications ranging from molecular dynamics simulations to temporal series of complex systems taken from other scientific domains. The method is based on a reordering of the trajectory according to a short spanning tree, such that the resulting new sequence amounts to a walk along the state space basin by basin. The temporal series is used to highlight recurrence and to provide a kinetic distance. By using the kinetic distance and the original time series, SBR performs an automatic identification of the basins. By comparing with other clustering techniques, we demonstrate the suitability of the method to capture the salient slow modes of the system while maintaining a manageable number of states.","filename":"post170s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post124","type":"poster","title":"LIF04 - iReceptor: A Platform for Exploring and Analyzing Antibody\/B-cell and T-cell Receptor Repertoire Data across Federated Repositories","begin_time":"20:21","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Individuals produce an immense repertoire of antibody\/B-cell and T-cell receptor sequences in order to recognize and destroy a diverse array of pathogens. For example, it has been estimated that the number of possible human B-cell sequences is greater than 10^13, and each person produces 10^8 - 10^9 B-cells during an immune response, many of which are unique. In 2009 NGS approaches were used to characterize the Adaptive Immune Receptor Repertoire (AIRR) in exquisite detail. These AIRR-Seq data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune disease, and in developing novel therapeutics against cancer. The iReceptor system (ireceptor.org) is a platform to integrate and analyze these immense data sets by combining: 1) an international network of AIRR-Seq data repositories; 2) the ability to federate AIRR-Seq data across these distributed repositories; 3) the ability to apply advanced analytical tools using large advanced research computing (ARC) resources; and 4) a scientific gateway that hides the complexity of performing research queries and advanced analyses across these federated data. iReceptor enables these capabilities by building on the standards work being carried our by the AIRR Community (airr-community.org). iReceptor manages the staging of data and control of ARC analysis jobs through the use of the AGAVE science-as-a-service platform (agaveapi.co).","filename":"post124s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Felix","last_name":"Breden","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Felix","last_name":"Breden","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"2","is_presenter":false}] } Presentation
LIF05 - Modeling Biological Networks with Exponential Random Graph Models
, Alex Stivala (Swinburne University of Technology, Australia)
+ Abstract { "session": {"id":"sess148","title":"Posters in Life Sciences","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Life Sciences"],"slots":[{"id":"post179","type":"poster","title":"LIF01 - AI-GWAPA: Explainable-AI and Genome Wide Association Phytobiome Analysis","begin_time":"19:30","end_time":"19:47","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The phytobiome consists of the plant, organismal communities and their environment. The interactions between these have significant effects on observable measurable traits that have potential economic and sustainability implications. A better systems-level understanding of these interactions will enhance our capacity to design higher yield and sustainable plants. We apply a collection of machine learning and deep learning methods to elucidate the interaction between viral, microbial and the plant host systems. Metatranscriptome samples from leaf, xylem and root along with approximately 10 million SNPs called across a population of 1000 \u003Cem\u003EP. trichocarpa\u003C\/em\u003E trees, allows us to associate host genetic variants to phytobiome constituents. Factorization machines are used, in a deep learning framework, to take higher-order interactions into account producing a set of high-confidence measurements of taxa abundance, which serve as phenotypes in a Genome Wide Association Analysis. In addition, putative host driven mutualistic\/pathogenic interactions between taxa are estimated. These provide candidate proteins for a capsule network deep learning model to predict putative protein-protein interactions, taking into account the protein\u2019s quantum chemical properties. Capsule networks provide an explainable AI approach to uncover features driving important interactions. This machine\/deep learning framework provides a methodology to better understand complex biological systems.","filename":"post179s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Stephan","last_name":"Irle","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ka Hung","last_name":"Lee","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Udaya","last_name":"Kalluri","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Wellington","last_name":"Muchero","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Jay","last_name":"Chen","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Gerald","last_name":"Tuskan","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"9","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post169","type":"poster","title":"LIF02 - The Bromodomain-Peptide (Un)Binding Network","begin_time":"19:47","end_time":"20:04","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Atomistic simulations are a valuable tool for understanding the structural details involved in biological processes. However, extracting kinetic information such as (un)binding rates for complex molecular systems remains a challenge as it requires both the efficient sampling of rare events and scalable analysis tools to cope with large amounts of data. Progress index-guided sampling (PIGS) is an unsupervised and scalable algorithm capable of enhancing the conformational diversification in a focused search space by simply rewarding spontaneous fluctuations. Here we use PIGS to study the binding mode and dissociation of a tripeptide from four different bromodomains, which are protein modules involved in epigenetics. By focusing the sampling enhancement on the two distinct loops forming the peptide binding pocket we are able to observe several unbinding events. Clustering of conformations and subsequent Markov state model analysis elucidate states, kinetics, and pathways involved in the unbinding process and help to shed light on structural aspects of epigenetic regulation. Both the PIGS protocol and the analysis tools rely on scalable libraries implemented in the software CAMPARI, which can also be interfaced with other propagation codes to fully exploit the tools available on different HPC infrastructures.","bio":"","contributors":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post177","type":"poster","title":"LIF03 - Explainable Machine Learning for Systems Biology: Tensor Iterative Random Forests","begin_time":"20:04","end_time":"20:21","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A novel algorithm, Tensor iterative Random Forest (TiRF), is able to effectively build forests that can be mined for interactions within a multidimensional X matrix, a multidimensional Y matrix, and interactions between multiple dimensions in X and Y, all at the same time. TiRF uses dimension reduction techniques (such as Lasso or a nested call to iRF) on Y for the given subsets of X, thus ensuring that the new subset of Y dimensions is highly connected to the X being split upon. The dimension-reduced Y matrix can then be used in measuring node purity, ensuring that noise is reduced and that the given features in X are measured for the ability to split the appropriate dimensions in Y. The resulting trees and forest now contain paths in X, and each node also has an associated set of Y. This means that random intersection trees can be used to find sets of interacting Xs from the forest and sets of interacting Ys conditional on those sets of X. As the data sets are growing exponentially, petascale deployments of TiRFs are being targeted in order to perform systems-wide analyses of biological or other complex systems that can be represented as matrices.","filename":"post177s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ashley","last_name":"Cliff","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ben","last_name":"Brown","affiliation":"Lawrence Berkeley National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post124","type":"poster","title":"LIF04 - iReceptor: A Platform for Exploring and Analyzing Antibody\/B-cell and T-cell Receptor Repertoire Data across Federated Repositories","begin_time":"20:21","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Individuals produce an immense repertoire of antibody\/B-cell and T-cell receptor sequences in order to recognize and destroy a diverse array of pathogens. For example, it has been estimated that the number of possible human B-cell sequences is greater than 10^13, and each person produces 10^8 - 10^9 B-cells during an immune response, many of which are unique. In 2009 NGS approaches were used to characterize the Adaptive Immune Receptor Repertoire (AIRR) in exquisite detail. These AIRR-Seq data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune disease, and in developing novel therapeutics against cancer. The iReceptor system (ireceptor.org) is a platform to integrate and analyze these immense data sets by combining: 1) an international network of AIRR-Seq data repositories; 2) the ability to federate AIRR-Seq data across these distributed repositories; 3) the ability to apply advanced analytical tools using large advanced research computing (ARC) resources; and 4) a scientific gateway that hides the complexity of performing research queries and advanced analyses across these federated data. iReceptor enables these capabilities by building on the standards work being carried our by the AIRR Community (airr-community.org). iReceptor manages the staging of data and control of ARC analysis jobs through the use of the AGAVE science-as-a-service platform (agaveapi.co).","filename":"post124s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Felix","last_name":"Breden","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true}]},{"id":"post122","type":"poster","title":"LIF05 - Modeling Biological Networks with Exponential Random Graph Models","begin_time":"20:38","end_time":"20:55","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Much research in biological networks concerns \u0022motifs\u0022, small subgraphs which occur more frequently than by chance, which are considered the building blocks of complex networks. Exponential random graph models (ERGMs), a well-established class of statistical models for network data which are widely used in social network analysis, represent a principled statistical method of determining whether a motif is over (or under) represented in a network. Although the use of ERGMs for analyzing biological networks was introduced into the bioinformatics literature ten years ago, the use of ERGMs in biological network analysis has been very limited since then due to problems with applying existing methods to such networks, their size being typically far larger than those social networks to which ERGMs are usually applied. Here we use high performance computing to apply our recently developed new techniques (snowball sampling, improved fixed density ERGM sampling, scalable Equilibrium Expectation algorithm) for ERGM estimation to several biological networks (protein-protein interaction networks, gene regulatory networks, and a neural network), ranging in size from a few hundred to over five thousand nodes.","filename":"post122s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Maksym","last_name":"Byshkin","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Antonietta","last_name":"Mira","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Garry","last_name":"Robins","affiliation":"The University of Melbourne","country":"Australia","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Alessandro","last_name":"Lomi","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true}]},{"id":"post178","type":"poster","title":"LIF06 - Parallel Kraken for Meta-Omic Microbiome and Phytobiome Classification","begin_time":"20:55","end_time":"21:12","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Meta-omic taxa classification allows for the identification of a wide range of micro- and macro-organisms that influence disease, physiological states, and ecological states in both host systems and environmental samples. Traditional classification methods often either use markers or subsample genomes to limit search space (and, as such, lose discriminatory power) for identifying large numbers of taxa. However, accurately identifying taxa in meta-omics datasets requires methods that simultaneously identify taxa across all kingdoms of life, utilize whole genome sequences, and are highly parallel. One drawback to utilizing whole genome sequences without subsampling or combining similar sequences is that databases of all known sequences become impractical to store in RAM. To overcome this limitation, we have developed a highly parallel version of Kraken that can run multiple sequences through multiple databases in parallel and resolve each read assignment to identify taxa in transcriptomic, proteomic, and genomic data. Additionally, we have created databases from all known whole genome sequences in NCBI totaling 115k+ genomes and 700k+ viral genomes from JGI. Parallel Kraken has been used to classify thousands of samples and billions of reads in parallel and is part of a pipeline for understanding relationships between host and microbiome\/phytobiome.","filename":"post178s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ian","last_name":"Hodge","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post170","type":"poster","title":"LIF07 - SAPPHIRE Basin Recognition: An Unsupervised Algorithm to Identify and Project Metastable and Transition States in High-Dimensional Time Series Data","begin_time":"21:12","end_time":"21:29","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The identification of states and pathways in high-dimensional data sets is a daunting task in that the number of states increases exponentially with dimensionality. While simple projection techniques are prone to introduce overlaps and shortcuts, our ability to process information does mandate that the dynamics be reduced to a small number of essential patterns. Here we present a new approach called SAPPHIRE (states and pathways projected at high resolution) Basin Recognition (SBR) and show the automatic detection of metastable and transition states for different applications ranging from molecular dynamics simulations to temporal series of complex systems taken from other scientific domains. The method is based on a reordering of the trajectory according to a short spanning tree, such that the resulting new sequence amounts to a walk along the state space basin by basin. The temporal series is used to highlight recurrence and to provide a kinetic distance. By using the kinetic distance and the original time series, SBR performs an automatic identification of the basins. By comparing with other clustering techniques, we demonstrate the suitability of the method to capture the salient slow modes of the system while maintaining a manageable number of states.","filename":"post170s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post122","type":"poster","title":"LIF05 - Modeling Biological Networks with Exponential Random Graph Models","begin_time":"20:38","end_time":"20:55","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Much research in biological networks concerns \u0022motifs\u0022, small subgraphs which occur more frequently than by chance, which are considered the building blocks of complex networks. Exponential random graph models (ERGMs), a well-established class of statistical models for network data which are widely used in social network analysis, represent a principled statistical method of determining whether a motif is over (or under) represented in a network. Although the use of ERGMs for analyzing biological networks was introduced into the bioinformatics literature ten years ago, the use of ERGMs in biological network analysis has been very limited since then due to problems with applying existing methods to such networks, their size being typically far larger than those social networks to which ERGMs are usually applied. Here we use high performance computing to apply our recently developed new techniques (snowball sampling, improved fixed density ERGM sampling, scalable Equilibrium Expectation algorithm) for ERGM estimation to several biological networks (protein-protein interaction networks, gene regulatory networks, and a neural network), ranging in size from a few hundred to over five thousand nodes.","filename":"post122s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Maksym","last_name":"Byshkin","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Antonietta","last_name":"Mira","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Garry","last_name":"Robins","affiliation":"The University of Melbourne","country":"Australia","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Alessandro","last_name":"Lomi","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Maksym","last_name":"Byshkin","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Antonietta","last_name":"Mira","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Garry","last_name":"Robins","affiliation":"The University of Melbourne","country":"Australia","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Alessandro","last_name":"Lomi","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}] } Presentation
LIF06 - Parallel Kraken for Meta-Omic Microbiome and Phytobiome Classification
, Benjamin Garcia (Oak Ridge National Laboratory, United States of America)
+ Abstract { "session": {"id":"sess148","title":"Posters in Life Sciences","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Life Sciences"],"slots":[{"id":"post179","type":"poster","title":"LIF01 - AI-GWAPA: Explainable-AI and Genome Wide Association Phytobiome Analysis","begin_time":"19:30","end_time":"19:47","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The phytobiome consists of the plant, organismal communities and their environment. The interactions between these have significant effects on observable measurable traits that have potential economic and sustainability implications. A better systems-level understanding of these interactions will enhance our capacity to design higher yield and sustainable plants. We apply a collection of machine learning and deep learning methods to elucidate the interaction between viral, microbial and the plant host systems. Metatranscriptome samples from leaf, xylem and root along with approximately 10 million SNPs called across a population of 1000 \u003Cem\u003EP. trichocarpa\u003C\/em\u003E trees, allows us to associate host genetic variants to phytobiome constituents. Factorization machines are used, in a deep learning framework, to take higher-order interactions into account producing a set of high-confidence measurements of taxa abundance, which serve as phenotypes in a Genome Wide Association Analysis. In addition, putative host driven mutualistic\/pathogenic interactions between taxa are estimated. These provide candidate proteins for a capsule network deep learning model to predict putative protein-protein interactions, taking into account the protein\u2019s quantum chemical properties. Capsule networks provide an explainable AI approach to uncover features driving important interactions. This machine\/deep learning framework provides a methodology to better understand complex biological systems.","filename":"post179s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Stephan","last_name":"Irle","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ka Hung","last_name":"Lee","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Udaya","last_name":"Kalluri","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Wellington","last_name":"Muchero","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Jay","last_name":"Chen","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Gerald","last_name":"Tuskan","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"9","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post169","type":"poster","title":"LIF02 - The Bromodomain-Peptide (Un)Binding Network","begin_time":"19:47","end_time":"20:04","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Atomistic simulations are a valuable tool for understanding the structural details involved in biological processes. However, extracting kinetic information such as (un)binding rates for complex molecular systems remains a challenge as it requires both the efficient sampling of rare events and scalable analysis tools to cope with large amounts of data. Progress index-guided sampling (PIGS) is an unsupervised and scalable algorithm capable of enhancing the conformational diversification in a focused search space by simply rewarding spontaneous fluctuations. Here we use PIGS to study the binding mode and dissociation of a tripeptide from four different bromodomains, which are protein modules involved in epigenetics. By focusing the sampling enhancement on the two distinct loops forming the peptide binding pocket we are able to observe several unbinding events. Clustering of conformations and subsequent Markov state model analysis elucidate states, kinetics, and pathways involved in the unbinding process and help to shed light on structural aspects of epigenetic regulation. Both the PIGS protocol and the analysis tools rely on scalable libraries implemented in the software CAMPARI, which can also be interfaced with other propagation codes to fully exploit the tools available on different HPC infrastructures.","bio":"","contributors":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post177","type":"poster","title":"LIF03 - Explainable Machine Learning for Systems Biology: Tensor Iterative Random Forests","begin_time":"20:04","end_time":"20:21","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A novel algorithm, Tensor iterative Random Forest (TiRF), is able to effectively build forests that can be mined for interactions within a multidimensional X matrix, a multidimensional Y matrix, and interactions between multiple dimensions in X and Y, all at the same time. TiRF uses dimension reduction techniques (such as Lasso or a nested call to iRF) on Y for the given subsets of X, thus ensuring that the new subset of Y dimensions is highly connected to the X being split upon. The dimension-reduced Y matrix can then be used in measuring node purity, ensuring that noise is reduced and that the given features in X are measured for the ability to split the appropriate dimensions in Y. The resulting trees and forest now contain paths in X, and each node also has an associated set of Y. This means that random intersection trees can be used to find sets of interacting Xs from the forest and sets of interacting Ys conditional on those sets of X. As the data sets are growing exponentially, petascale deployments of TiRFs are being targeted in order to perform systems-wide analyses of biological or other complex systems that can be represented as matrices.","filename":"post177s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ashley","last_name":"Cliff","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ben","last_name":"Brown","affiliation":"Lawrence Berkeley National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post124","type":"poster","title":"LIF04 - iReceptor: A Platform for Exploring and Analyzing Antibody\/B-cell and T-cell Receptor Repertoire Data across Federated Repositories","begin_time":"20:21","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Individuals produce an immense repertoire of antibody\/B-cell and T-cell receptor sequences in order to recognize and destroy a diverse array of pathogens. For example, it has been estimated that the number of possible human B-cell sequences is greater than 10^13, and each person produces 10^8 - 10^9 B-cells during an immune response, many of which are unique. In 2009 NGS approaches were used to characterize the Adaptive Immune Receptor Repertoire (AIRR) in exquisite detail. These AIRR-Seq data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune disease, and in developing novel therapeutics against cancer. The iReceptor system (ireceptor.org) is a platform to integrate and analyze these immense data sets by combining: 1) an international network of AIRR-Seq data repositories; 2) the ability to federate AIRR-Seq data across these distributed repositories; 3) the ability to apply advanced analytical tools using large advanced research computing (ARC) resources; and 4) a scientific gateway that hides the complexity of performing research queries and advanced analyses across these federated data. iReceptor enables these capabilities by building on the standards work being carried our by the AIRR Community (airr-community.org). iReceptor manages the staging of data and control of ARC analysis jobs through the use of the AGAVE science-as-a-service platform (agaveapi.co).","filename":"post124s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Felix","last_name":"Breden","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true}]},{"id":"post122","type":"poster","title":"LIF05 - Modeling Biological Networks with Exponential Random Graph Models","begin_time":"20:38","end_time":"20:55","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Much research in biological networks concerns \u0022motifs\u0022, small subgraphs which occur more frequently than by chance, which are considered the building blocks of complex networks. Exponential random graph models (ERGMs), a well-established class of statistical models for network data which are widely used in social network analysis, represent a principled statistical method of determining whether a motif is over (or under) represented in a network. Although the use of ERGMs for analyzing biological networks was introduced into the bioinformatics literature ten years ago, the use of ERGMs in biological network analysis has been very limited since then due to problems with applying existing methods to such networks, their size being typically far larger than those social networks to which ERGMs are usually applied. Here we use high performance computing to apply our recently developed new techniques (snowball sampling, improved fixed density ERGM sampling, scalable Equilibrium Expectation algorithm) for ERGM estimation to several biological networks (protein-protein interaction networks, gene regulatory networks, and a neural network), ranging in size from a few hundred to over five thousand nodes.","filename":"post122s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Maksym","last_name":"Byshkin","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Antonietta","last_name":"Mira","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Garry","last_name":"Robins","affiliation":"The University of Melbourne","country":"Australia","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Alessandro","last_name":"Lomi","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true}]},{"id":"post178","type":"poster","title":"LIF06 - Parallel Kraken for Meta-Omic Microbiome and Phytobiome Classification","begin_time":"20:55","end_time":"21:12","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Meta-omic taxa classification allows for the identification of a wide range of micro- and macro-organisms that influence disease, physiological states, and ecological states in both host systems and environmental samples. Traditional classification methods often either use markers or subsample genomes to limit search space (and, as such, lose discriminatory power) for identifying large numbers of taxa. However, accurately identifying taxa in meta-omics datasets requires methods that simultaneously identify taxa across all kingdoms of life, utilize whole genome sequences, and are highly parallel. One drawback to utilizing whole genome sequences without subsampling or combining similar sequences is that databases of all known sequences become impractical to store in RAM. To overcome this limitation, we have developed a highly parallel version of Kraken that can run multiple sequences through multiple databases in parallel and resolve each read assignment to identify taxa in transcriptomic, proteomic, and genomic data. Additionally, we have created databases from all known whole genome sequences in NCBI totaling 115k+ genomes and 700k+ viral genomes from JGI. Parallel Kraken has been used to classify thousands of samples and billions of reads in parallel and is part of a pipeline for understanding relationships between host and microbiome\/phytobiome.","filename":"post178s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ian","last_name":"Hodge","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post170","type":"poster","title":"LIF07 - SAPPHIRE Basin Recognition: An Unsupervised Algorithm to Identify and Project Metastable and Transition States in High-Dimensional Time Series Data","begin_time":"21:12","end_time":"21:29","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The identification of states and pathways in high-dimensional data sets is a daunting task in that the number of states increases exponentially with dimensionality. While simple projection techniques are prone to introduce overlaps and shortcuts, our ability to process information does mandate that the dynamics be reduced to a small number of essential patterns. Here we present a new approach called SAPPHIRE (states and pathways projected at high resolution) Basin Recognition (SBR) and show the automatic detection of metastable and transition states for different applications ranging from molecular dynamics simulations to temporal series of complex systems taken from other scientific domains. The method is based on a reordering of the trajectory according to a short spanning tree, such that the resulting new sequence amounts to a walk along the state space basin by basin. The temporal series is used to highlight recurrence and to provide a kinetic distance. By using the kinetic distance and the original time series, SBR performs an automatic identification of the basins. By comparing with other clustering techniques, we demonstrate the suitability of the method to capture the salient slow modes of the system while maintaining a manageable number of states.","filename":"post170s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post178","type":"poster","title":"LIF06 - Parallel Kraken for Meta-Omic Microbiome and Phytobiome Classification","begin_time":"20:55","end_time":"21:12","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Meta-omic taxa classification allows for the identification of a wide range of micro- and macro-organisms that influence disease, physiological states, and ecological states in both host systems and environmental samples. Traditional classification methods often either use markers or subsample genomes to limit search space (and, as such, lose discriminatory power) for identifying large numbers of taxa. However, accurately identifying taxa in meta-omics datasets requires methods that simultaneously identify taxa across all kingdoms of life, utilize whole genome sequences, and are highly parallel. One drawback to utilizing whole genome sequences without subsampling or combining similar sequences is that databases of all known sequences become impractical to store in RAM. To overcome this limitation, we have developed a highly parallel version of Kraken that can run multiple sequences through multiple databases in parallel and resolve each read assignment to identify taxa in transcriptomic, proteomic, and genomic data. Additionally, we have created databases from all known whole genome sequences in NCBI totaling 115k+ genomes and 700k+ viral genomes from JGI. Parallel Kraken has been used to classify thousands of samples and billions of reads in parallel and is part of a pipeline for understanding relationships between host and microbiome\/phytobiome.","filename":"post178s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ian","last_name":"Hodge","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ian","last_name":"Hodge","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}] } Presentation
LIF07 - SAPPHIRE Basin Recognition: An Unsupervised Algorithm to Identify and Project Metastable and Transition States in High-Dimensional Time Series Data
, Francesco Cocina (University of Zurich, Switzerland)
+ Abstract { "session": {"id":"sess148","title":"Posters in Life Sciences","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Life Sciences"],"slots":[{"id":"post179","type":"poster","title":"LIF01 - AI-GWAPA: Explainable-AI and Genome Wide Association Phytobiome Analysis","begin_time":"19:30","end_time":"19:47","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The phytobiome consists of the plant, organismal communities and their environment. The interactions between these have significant effects on observable measurable traits that have potential economic and sustainability implications. A better systems-level understanding of these interactions will enhance our capacity to design higher yield and sustainable plants. We apply a collection of machine learning and deep learning methods to elucidate the interaction between viral, microbial and the plant host systems. Metatranscriptome samples from leaf, xylem and root along with approximately 10 million SNPs called across a population of 1000 \u003Cem\u003EP. trichocarpa\u003C\/em\u003E trees, allows us to associate host genetic variants to phytobiome constituents. Factorization machines are used, in a deep learning framework, to take higher-order interactions into account producing a set of high-confidence measurements of taxa abundance, which serve as phenotypes in a Genome Wide Association Analysis. In addition, putative host driven mutualistic\/pathogenic interactions between taxa are estimated. These provide candidate proteins for a capsule network deep learning model to predict putative protein-protein interactions, taking into account the protein\u2019s quantum chemical properties. Capsule networks provide an explainable AI approach to uncover features driving important interactions. This machine\/deep learning framework provides a methodology to better understand complex biological systems.","filename":"post179s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Stephan","last_name":"Irle","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ka Hung","last_name":"Lee","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Udaya","last_name":"Kalluri","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Wellington","last_name":"Muchero","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Jay","last_name":"Chen","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Gerald","last_name":"Tuskan","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"9","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post169","type":"poster","title":"LIF02 - The Bromodomain-Peptide (Un)Binding Network","begin_time":"19:47","end_time":"20:04","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Atomistic simulations are a valuable tool for understanding the structural details involved in biological processes. However, extracting kinetic information such as (un)binding rates for complex molecular systems remains a challenge as it requires both the efficient sampling of rare events and scalable analysis tools to cope with large amounts of data. Progress index-guided sampling (PIGS) is an unsupervised and scalable algorithm capable of enhancing the conformational diversification in a focused search space by simply rewarding spontaneous fluctuations. Here we use PIGS to study the binding mode and dissociation of a tripeptide from four different bromodomains, which are protein modules involved in epigenetics. By focusing the sampling enhancement on the two distinct loops forming the peptide binding pocket we are able to observe several unbinding events. Clustering of conformations and subsequent Markov state model analysis elucidate states, kinetics, and pathways involved in the unbinding process and help to shed light on structural aspects of epigenetic regulation. Both the PIGS protocol and the analysis tools rely on scalable libraries implemented in the software CAMPARI, which can also be interfaced with other propagation codes to fully exploit the tools available on different HPC infrastructures.","bio":"","contributors":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Cassiano","last_name":"Langini","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]},{"id":"post177","type":"poster","title":"LIF03 - Explainable Machine Learning for Systems Biology: Tensor Iterative Random Forests","begin_time":"20:04","end_time":"20:21","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"A novel algorithm, Tensor iterative Random Forest (TiRF), is able to effectively build forests that can be mined for interactions within a multidimensional X matrix, a multidimensional Y matrix, and interactions between multiple dimensions in X and Y, all at the same time. TiRF uses dimension reduction techniques (such as Lasso or a nested call to iRF) on Y for the given subsets of X, thus ensuring that the new subset of Y dimensions is highly connected to the X being split upon. The dimension-reduced Y matrix can then be used in measuring node purity, ensuring that noise is reduced and that the given features in X are measured for the ability to split the appropriate dimensions in Y. The resulting trees and forest now contain paths in X, and each node also has an associated set of Y. This means that random intersection trees can be used to find sets of interacting Xs from the forest and sets of interacting Ys conditional on those sets of X. As the data sets are growing exponentially, petascale deployments of TiRFs are being targeted in order to perform systems-wide analyses of biological or other complex systems that can be represented as matrices.","filename":"post177s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Ashley","last_name":"Cliff","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Ben","last_name":"Brown","affiliation":"Lawrence Berkeley National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Jonathon","last_name":"Romero","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post124","type":"poster","title":"LIF04 - iReceptor: A Platform for Exploring and Analyzing Antibody\/B-cell and T-cell Receptor Repertoire Data across Federated Repositories","begin_time":"20:21","end_time":"20:38","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Individuals produce an immense repertoire of antibody\/B-cell and T-cell receptor sequences in order to recognize and destroy a diverse array of pathogens. For example, it has been estimated that the number of possible human B-cell sequences is greater than 10^13, and each person produces 10^8 - 10^9 B-cells during an immune response, many of which are unique. In 2009 NGS approaches were used to characterize the Adaptive Immune Receptor Repertoire (AIRR) in exquisite detail. These AIRR-Seq data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune disease, and in developing novel therapeutics against cancer. The iReceptor system (ireceptor.org) is a platform to integrate and analyze these immense data sets by combining: 1) an international network of AIRR-Seq data repositories; 2) the ability to federate AIRR-Seq data across these distributed repositories; 3) the ability to apply advanced analytical tools using large advanced research computing (ARC) resources; and 4) a scientific gateway that hides the complexity of performing research queries and advanced analyses across these federated data. iReceptor enables these capabilities by building on the standards work being carried our by the AIRR Community (airr-community.org). iReceptor manages the staging of data and control of ARC analysis jobs through the use of the AGAVE science-as-a-service platform (agaveapi.co).","filename":"post124s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Felix","last_name":"Breden","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"2","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Brian","last_name":"Corrie","affiliation":"Simon Fraser University","country":"Canada","bio":"","order":"1","is_presenter":true}]},{"id":"post122","type":"poster","title":"LIF05 - Modeling Biological Networks with Exponential Random Graph Models","begin_time":"20:38","end_time":"20:55","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Much research in biological networks concerns \u0022motifs\u0022, small subgraphs which occur more frequently than by chance, which are considered the building blocks of complex networks. Exponential random graph models (ERGMs), a well-established class of statistical models for network data which are widely used in social network analysis, represent a principled statistical method of determining whether a motif is over (or under) represented in a network. Although the use of ERGMs for analyzing biological networks was introduced into the bioinformatics literature ten years ago, the use of ERGMs in biological network analysis has been very limited since then due to problems with applying existing methods to such networks, their size being typically far larger than those social networks to which ERGMs are usually applied. Here we use high performance computing to apply our recently developed new techniques (snowball sampling, improved fixed density ERGM sampling, scalable Equilibrium Expectation algorithm) for ERGM estimation to several biological networks (protein-protein interaction networks, gene regulatory networks, and a neural network), ranging in size from a few hundred to over five thousand nodes.","filename":"post122s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Maksym","last_name":"Byshkin","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Antonietta","last_name":"Mira","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Garry","last_name":"Robins","affiliation":"The University of Melbourne","country":"Australia","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Alessandro","last_name":"Lomi","affiliation":"Universit\u00e0 della Svizzera italiana","country":"Switzerland","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Alex","last_name":"Stivala","affiliation":"Swinburne University of Technology","country":"Australia","bio":"","order":"1","is_presenter":true}]},{"id":"post178","type":"poster","title":"LIF06 - Parallel Kraken for Meta-Omic Microbiome and Phytobiome Classification","begin_time":"20:55","end_time":"21:12","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Meta-omic taxa classification allows for the identification of a wide range of micro- and macro-organisms that influence disease, physiological states, and ecological states in both host systems and environmental samples. Traditional classification methods often either use markers or subsample genomes to limit search space (and, as such, lose discriminatory power) for identifying large numbers of taxa. However, accurately identifying taxa in meta-omics datasets requires methods that simultaneously identify taxa across all kingdoms of life, utilize whole genome sequences, and are highly parallel. One drawback to utilizing whole genome sequences without subsampling or combining similar sequences is that databases of all known sequences become impractical to store in RAM. To overcome this limitation, we have developed a highly parallel version of Kraken that can run multiple sequences through multiple databases in parallel and resolve each read assignment to identify taxa in transcriptomic, proteomic, and genomic data. Additionally, we have created databases from all known whole genome sequences in NCBI totaling 115k+ genomes and 700k+ viral genomes from JGI. Parallel Kraken has been used to classify thousands of samples and billions of reads in parallel and is part of a pipeline for understanding relationships between host and microbiome\/phytobiome.","filename":"post178s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Piet","last_name":"Jones","affiliation":"University of Tennessee","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Ian","last_name":"Hodge","affiliation":"Stanford University","country":"United States of America","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Doug","last_name":"Hyatt","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Daniel","last_name":"Jacobson","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"5","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Benjamin","last_name":"Garcia","affiliation":"Oak Ridge National Laboratory","country":"United States of America","bio":"","order":"1","is_presenter":true}]},{"id":"post170","type":"poster","title":"LIF07 - SAPPHIRE Basin Recognition: An Unsupervised Algorithm to Identify and Project Metastable and Transition States in High-Dimensional Time Series Data","begin_time":"21:12","end_time":"21:29","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The identification of states and pathways in high-dimensional data sets is a daunting task in that the number of states increases exponentially with dimensionality. While simple projection techniques are prone to introduce overlaps and shortcuts, our ability to process information does mandate that the dynamics be reduced to a small number of essential patterns. Here we present a new approach called SAPPHIRE (states and pathways projected at high resolution) Basin Recognition (SBR) and show the automatic detection of metastable and transition states for different applications ranging from molecular dynamics simulations to temporal series of complex systems taken from other scientific domains. The method is based on a reordering of the trajectory according to a short spanning tree, such that the resulting new sequence amounts to a walk along the state space basin by basin. The temporal series is used to highlight recurrence and to provide a kinetic distance. By using the kinetic distance and the original time series, SBR performs an automatic identification of the basins. By comparing with other clustering techniques, we demonstrate the suitability of the method to capture the salient slow modes of the system while maintaining a manageable number of states.","filename":"post170s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post170","type":"poster","title":"LIF07 - SAPPHIRE Basin Recognition: An Unsupervised Algorithm to Identify and Project Metastable and Transition States in High-Dimensional Time Series Data","begin_time":"21:12","end_time":"21:29","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The identification of states and pathways in high-dimensional data sets is a daunting task in that the number of states increases exponentially with dimensionality. While simple projection techniques are prone to introduce overlaps and shortcuts, our ability to process information does mandate that the dynamics be reduced to a small number of essential patterns. Here we present a new approach called SAPPHIRE (states and pathways projected at high resolution) Basin Recognition (SBR) and show the automatic detection of metastable and transition states for different applications ranging from molecular dynamics simulations to temporal series of complex systems taken from other scientific domains. The method is based on a reordering of the trajectory according to a short spanning tree, such that the resulting new sequence amounts to a walk along the state space basin by basin. The temporal series is used to highlight recurrence and to provide a kinetic distance. By using the kinetic distance and the original time series, SBR performs an automatic identification of the basins. By comparing with other clustering techniques, we demonstrate the suitability of the method to capture the salient slow modes of the system while maintaining a manageable number of states.","filename":"post170s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Francesco","last_name":"Cocina","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Marco","last_name":"Bacci","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Vitalis","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Amedeo","last_name":"Caflisch","affiliation":"University of Zurich","country":"Switzerland","bio":"","order":"4","is_presenter":false}] } Presentation
PHY02 - Hydrodynamical High Performance Simulations of an Accretion Disk surrounding a Supermassive Black Hole and its Interactions
, Fabian Klein (University of Heidelberg, Germany)
+ Abstract { "session": {"id":"sess149","title":"Posters in Physics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Physics"],"slots":[{"id":"post159","type":"poster","title":"PHY01 - AFiD-GPU: A Versatile Navier-Stokes Solver for Wall-Bounded Turbulent Flows on GPU Clusters","begin_time":"19:30","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The AFiD code, an open source solver for the incompressible Navier-Stokes equations (http:\/\/www.afid.eu), has been ported to GPU clusters to tackle large-scale wall-bounded turbulent flow simulations. The GPU porting has been carried out in CUDA Fortran with the extensive use of kernel loop directives (CUF kernels) in order to have a source code as close as possible to the original CPU version; just a few routines have been manually rewritten. A new transpose scheme has been devised to improve the scaling of the Poisson solver, which is the main bottleneck of incompressible solvers. For large meshes the GPU version of the code shows good strong scaling characteristics, and the wall-clock time per step for GPU version is an order of magnitude smaller than for the CPU version of the code. Due to the increased performance and efficient use of memory, the GPU version of AFiD can perform simulations in parameter ranges that are unprecedented in thermally-driven wall-bounded turbulence. To verify the accuracy of the code, turbulent Rayleigh-B\u00e9nard convection and plane Couette flow are simulated and the results are in excellent agreement with the experimental and\u00a0computational data that have been published in literature.","bio":"","contributors":[{"type":"Author","first_name":"Xiaojue","last_name":"Zhu","affiliation":"University of Twente","country":"Netherlands","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Everett","last_name":"Phillips","affiliation":"NVIDIA Corporation","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vamsi","last_name":"Spandan","affiliation":"University of Twente","country":"Netherlands","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"John","last_name":"Donners","affiliation":"SURFsara","country":"Netherlands","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Gregory","last_name":"Ruetsch","affiliation":"NVIDIA Corporation","country":"United States of America","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Josh","last_name":"Romero","affiliation":"NVIDIA Corporation","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Rodolfo","last_name":"Ostilla-M\u00f3nico","affiliation":"University of Houston","country":"United States of America","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Yantao","last_name":"Yang","affiliation":"Peking University","country":"China","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Detlef","last_name":"Lohse","affiliation":"University of Twente","country":"Netherlands","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Roberto","last_name":"Verzicco","affiliation":"University of Rome Tor Vergata","country":"Italy","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Massimiliano","last_name":"Fatica","affiliation":"NVIDIA Corporation","country":"United States of America","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Richard","last_name":"Stevens","affiliation":"University of Twente","country":"Netherlands","bio":"","order":"12","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Xiaojue","last_name":"Zhu","affiliation":"University of Twente","country":"Netherlands","bio":"","order":"1","is_presenter":true}]},{"id":"post151","type":"poster","title":"PHY02 - Hydrodynamical High Performance Simulations of an Accretion Disk surrounding a Supermassive Black Hole and its Interactions","begin_time":"20:10","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"This computational and numerical project is aiming to improve the modelling of star-gas disk interactions in active galactic nuclei (AGN) disks. In the context of the StarD-isk project ([Just et al., 2012]) we consider an AGN system (central star cluster, supermassive black hole (SMBH) and accretion disk (AD)). The AD creates dissipative forces acting on stars in the disk, resulting in an increased mass flow to the SMBH and asymmetries in the phase space distribution due to its rotation. We employ a vertically extended Keplerian disk (alpha formulation [Shakura and Sunyaev, 1973]), allowing a fully self-consistent treatment of stellar dynamics including the dissipative force originating from star-gas ram pressure effects. [Kennedy et al., 2016] is treating the disk stationary (no bi-directional feedback, no checks of the disk\u2019s lifetime and stability). We are using an ideal monotonic gas, alpha viscosity, the disk\u0027s self-gravity and radiation transport in flux-limited diffusion limit (FLD). Additionally, force equilibrium-ensuring initial conditions are used. We employ the PLUTO Code ([Mignone et al., 2007]) with modifications and modules (self-gravity and FLD) developed by Rolf Kuiper ([Kuiper et al., 2010a]) in order to carry out the numerical simulations of the resulting Navier-Stokes equations including massively parallel runs as offered by PLUTO.","filename":"post151s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Fabian","last_name":"Klein","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Rainer","last_name":"Spurzem","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Just","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Kuiper","affiliation":"Universit\u00e4t T\u00fcbingen","country":"Germany","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Fabian","last_name":"Klein","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post132","type":"poster","title":"PHY03 - A Performance Model for Quantum ESPRESSO\u2019s PWscf","begin_time":"20:50","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Performance modelling of applications is essential to co-design of future exascale architecture. To this end, the parallel execution of PWscf (Plane-Wave Self Consistent Field), one of the most used components of the Quantum ESPRESSO open-source suite, has been carefully profiled and analyzed on modern many-core systems. The results were categorized and grouped in a set of distinct kernels that describe the execution flow of the application and can be used to reproduce the absolute execution time, as a function of the input data, on different architectures. In this poster presentation we will describe the strategy used to define the model, the outcomes that it can provide and the future perspective for this work.","filename":"post132s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Pietro","last_name":"Bonf\u00e0","affiliation":"CINECA","country":"Italy","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabio","last_name":"Affinito","affiliation":"CINECA","country":"Italy","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlo","last_name":"Cavazzoni","affiliation":"CINECA","country":"Italy","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Pietro","last_name":"Bonf\u00e0","affiliation":"CINECA","country":"Italy","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post151","type":"poster","title":"PHY02 - Hydrodynamical High Performance Simulations of an Accretion Disk surrounding a Supermassive Black Hole and its Interactions","begin_time":"20:10","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"This computational and numerical project is aiming to improve the modelling of star-gas disk interactions in active galactic nuclei (AGN) disks. In the context of the StarD-isk project ([Just et al., 2012]) we consider an AGN system (central star cluster, supermassive black hole (SMBH) and accretion disk (AD)). The AD creates dissipative forces acting on stars in the disk, resulting in an increased mass flow to the SMBH and asymmetries in the phase space distribution due to its rotation. We employ a vertically extended Keplerian disk (alpha formulation [Shakura and Sunyaev, 1973]), allowing a fully self-consistent treatment of stellar dynamics including the dissipative force originating from star-gas ram pressure effects. [Kennedy et al., 2016] is treating the disk stationary (no bi-directional feedback, no checks of the disk\u2019s lifetime and stability). We are using an ideal monotonic gas, alpha viscosity, the disk\u0027s self-gravity and radiation transport in flux-limited diffusion limit (FLD). Additionally, force equilibrium-ensuring initial conditions are used. We employ the PLUTO Code ([Mignone et al., 2007]) with modifications and modules (self-gravity and FLD) developed by Rolf Kuiper ([Kuiper et al., 2010a]) in order to carry out the numerical simulations of the resulting Navier-Stokes equations including massively parallel runs as offered by PLUTO.","filename":"post151s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Fabian","last_name":"Klein","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Rainer","last_name":"Spurzem","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Just","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Kuiper","affiliation":"Universit\u00e4t T\u00fcbingen","country":"Germany","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Fabian","last_name":"Klein","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Fabian","last_name":"Klein","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Rainer","last_name":"Spurzem","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Just","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Kuiper","affiliation":"Universit\u00e4t T\u00fcbingen","country":"Germany","bio":"","order":"4","is_presenter":false}] } Presentation
PHY03 - A Performance Model for Quantum ESPRESSO’s PWscf
, Pietro Bonfà (CINECA, Italy)
+ Abstract { "session": {"id":"sess149","title":"Posters in Physics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Physics"],"slots":[{"id":"post159","type":"poster","title":"PHY01 - AFiD-GPU: A Versatile Navier-Stokes Solver for Wall-Bounded Turbulent Flows on GPU Clusters","begin_time":"19:30","end_time":"20:10","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The AFiD code, an open source solver for the incompressible Navier-Stokes equations (http:\/\/www.afid.eu), has been ported to GPU clusters to tackle large-scale wall-bounded turbulent flow simulations. The GPU porting has been carried out in CUDA Fortran with the extensive use of kernel loop directives (CUF kernels) in order to have a source code as close as possible to the original CPU version; just a few routines have been manually rewritten. A new transpose scheme has been devised to improve the scaling of the Poisson solver, which is the main bottleneck of incompressible solvers. For large meshes the GPU version of the code shows good strong scaling characteristics, and the wall-clock time per step for GPU version is an order of magnitude smaller than for the CPU version of the code. Due to the increased performance and efficient use of memory, the GPU version of AFiD can perform simulations in parameter ranges that are unprecedented in thermally-driven wall-bounded turbulence. To verify the accuracy of the code, turbulent Rayleigh-B\u00e9nard convection and plane Couette flow are simulated and the results are in excellent agreement with the experimental and\u00a0computational data that have been published in literature.","bio":"","contributors":[{"type":"Author","first_name":"Xiaojue","last_name":"Zhu","affiliation":"University of Twente","country":"Netherlands","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Everett","last_name":"Phillips","affiliation":"NVIDIA Corporation","country":"United States of America","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Vamsi","last_name":"Spandan","affiliation":"University of Twente","country":"Netherlands","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"John","last_name":"Donners","affiliation":"SURFsara","country":"Netherlands","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Gregory","last_name":"Ruetsch","affiliation":"NVIDIA Corporation","country":"United States of America","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Josh","last_name":"Romero","affiliation":"NVIDIA Corporation","country":"United States of America","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Rodolfo","last_name":"Ostilla-M\u00f3nico","affiliation":"University of Houston","country":"United States of America","bio":"","order":"7","is_presenter":false},{"type":"Author","first_name":"Yantao","last_name":"Yang","affiliation":"Peking University","country":"China","bio":"","order":"8","is_presenter":false},{"type":"Author","first_name":"Detlef","last_name":"Lohse","affiliation":"University of Twente","country":"Netherlands","bio":"","order":"9","is_presenter":false},{"type":"Author","first_name":"Roberto","last_name":"Verzicco","affiliation":"University of Rome Tor Vergata","country":"Italy","bio":"","order":"10","is_presenter":false},{"type":"Author","first_name":"Massimiliano","last_name":"Fatica","affiliation":"NVIDIA Corporation","country":"United States of America","bio":"","order":"11","is_presenter":false},{"type":"Author","first_name":"Richard","last_name":"Stevens","affiliation":"University of Twente","country":"Netherlands","bio":"","order":"12","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Xiaojue","last_name":"Zhu","affiliation":"University of Twente","country":"Netherlands","bio":"","order":"1","is_presenter":true}]},{"id":"post151","type":"poster","title":"PHY02 - Hydrodynamical High Performance Simulations of an Accretion Disk surrounding a Supermassive Black Hole and its Interactions","begin_time":"20:10","end_time":"20:50","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"This computational and numerical project is aiming to improve the modelling of star-gas disk interactions in active galactic nuclei (AGN) disks. In the context of the StarD-isk project ([Just et al., 2012]) we consider an AGN system (central star cluster, supermassive black hole (SMBH) and accretion disk (AD)). The AD creates dissipative forces acting on stars in the disk, resulting in an increased mass flow to the SMBH and asymmetries in the phase space distribution due to its rotation. We employ a vertically extended Keplerian disk (alpha formulation [Shakura and Sunyaev, 1973]), allowing a fully self-consistent treatment of stellar dynamics including the dissipative force originating from star-gas ram pressure effects. [Kennedy et al., 2016] is treating the disk stationary (no bi-directional feedback, no checks of the disk\u2019s lifetime and stability). We are using an ideal monotonic gas, alpha viscosity, the disk\u0027s self-gravity and radiation transport in flux-limited diffusion limit (FLD). Additionally, force equilibrium-ensuring initial conditions are used. We employ the PLUTO Code ([Mignone et al., 2007]) with modifications and modules (self-gravity and FLD) developed by Rolf Kuiper ([Kuiper et al., 2010a]) in order to carry out the numerical simulations of the resulting Navier-Stokes equations including massively parallel runs as offered by PLUTO.","filename":"post151s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Fabian","last_name":"Klein","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Rainer","last_name":"Spurzem","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Andreas","last_name":"Just","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Rolf","last_name":"Kuiper","affiliation":"Universit\u00e4t T\u00fcbingen","country":"Germany","bio":"","order":"4","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Fabian","last_name":"Klein","affiliation":"University of Heidelberg","country":"Germany","bio":"","order":"1","is_presenter":true}]},{"id":"post132","type":"poster","title":"PHY03 - A Performance Model for Quantum ESPRESSO\u2019s PWscf","begin_time":"20:50","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Performance modelling of applications is essential to co-design of future exascale architecture. To this end, the parallel execution of PWscf (Plane-Wave Self Consistent Field), one of the most used components of the Quantum ESPRESSO open-source suite, has been carefully profiled and analyzed on modern many-core systems. The results were categorized and grouped in a set of distinct kernels that describe the execution flow of the application and can be used to reproduce the absolute execution time, as a function of the input data, on different architectures. In this poster presentation we will describe the strategy used to define the model, the outcomes that it can provide and the future perspective for this work.","filename":"post132s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Pietro","last_name":"Bonf\u00e0","affiliation":"CINECA","country":"Italy","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabio","last_name":"Affinito","affiliation":"CINECA","country":"Italy","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlo","last_name":"Cavazzoni","affiliation":"CINECA","country":"Italy","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Pietro","last_name":"Bonf\u00e0","affiliation":"CINECA","country":"Italy","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post132","type":"poster","title":"PHY03 - A Performance Model for Quantum ESPRESSO\u2019s PWscf","begin_time":"20:50","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"Performance modelling of applications is essential to co-design of future exascale architecture. To this end, the parallel execution of PWscf (Plane-Wave Self Consistent Field), one of the most used components of the Quantum ESPRESSO open-source suite, has been carefully profiled and analyzed on modern many-core systems. The results were categorized and grouped in a set of distinct kernels that describe the execution flow of the application and can be used to reproduce the absolute execution time, as a function of the input data, on different architectures. In this poster presentation we will describe the strategy used to define the model, the outcomes that it can provide and the future perspective for this work.","filename":"post132s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Pietro","last_name":"Bonf\u00e0","affiliation":"CINECA","country":"Italy","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabio","last_name":"Affinito","affiliation":"CINECA","country":"Italy","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlo","last_name":"Cavazzoni","affiliation":"CINECA","country":"Italy","bio":"","order":"3","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Pietro","last_name":"Bonf\u00e0","affiliation":"CINECA","country":"Italy","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Pietro","last_name":"Bonf\u00e0","affiliation":"CINECA","country":"Italy","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Fabio","last_name":"Affinito","affiliation":"CINECA","country":"Italy","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Carlo","last_name":"Cavazzoni","affiliation":"CINECA","country":"Italy","bio":"","order":"3","is_presenter":false}] } Presentation
SED01 - Extreme Scale Global Convection Models for Flow-Induced Topography
, Simon Bauer (Ludwig Maximilian University of Munich, Germany)
+ Abstract { "session": {"id":"sess150","title":"Posters in Solid Earth Dynamics","date":"Tuesday, July 3rd 2018","begin_time":"19:30","end_time":"21:30","room":"Foyer 2nd Floor","contributors":[],"view_type":"X","view_type_id":"evtt109","tracks":["Solid Earth Dynamics"],"slots":[{"id":"post156","type":"poster","title":"SED01 - Extreme Scale Global Convection Models for Flow-Induced Topography","begin_time":"19:30","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The asthenosphere is a mechanically weak layer in the uppermost part of the Earth\u0027s mantle, lying beneath the outermost rigid layer, i.e., the lithosphere. While there is robust evidence for the existence of such a weak layer, the thickness of the asthenosphere remains debated. In this study, we investigate the effect of several asthenosphere channel thicknesses on dynamic topography, i.e. topography caused by global mantle flow. We start from a thickness of 1000 km going down to an extremely narrow channel of 100 km with significant contrasts in the viscosity of up to three orders of magnitude. Additionally, we add lateral viscosity variations using a present day temperature field. We employ a prototype of a new mantle convection framework, based on a matrix-free finite element implementation. We demonstrate that our framework is capable to simulate such highly complex scenarios and present results with an unprecedented global resolution close to 1 km using more than 60,000 compute cores on a peta-scale system. This yields systems with \u003Cem\u003EO\u003C\/em\u003E(10^12) degrees of freedom. These results will serve us to gain insights into the current debate on the power spectrum of the observed surface dynamic topography of the Earth.","filename":"post156s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simon","last_name":"Bauer","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Hans-Peter","last_name":"Bunge","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Siavash","last_name":"Ghelichkhan","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Huber","affiliation":"TU Munich","country":"Germany","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marcus","last_name":"Mohr","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Barbara","last_name":"Wohlmuth","affiliation":"TU Munich","country":"Germany","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simon","last_name":"Bauer","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"1","is_presenter":true}]}]}, "slot": {"id":"post156","type":"poster","title":"SED01 - Extreme Scale Global Convection Models for Flow-Induced Topography","begin_time":"19:30","end_time":"21:30","has_begin_end_time":true,"has_just_one_minute":false,"is_parent":false,"abstract":"The asthenosphere is a mechanically weak layer in the uppermost part of the Earth\u0027s mantle, lying beneath the outermost rigid layer, i.e., the lithosphere. While there is robust evidence for the existence of such a weak layer, the thickness of the asthenosphere remains debated. In this study, we investigate the effect of several asthenosphere channel thicknesses on dynamic topography, i.e. topography caused by global mantle flow. We start from a thickness of 1000 km going down to an extremely narrow channel of 100 km with significant contrasts in the viscosity of up to three orders of magnitude. Additionally, we add lateral viscosity variations using a present day temperature field. We employ a prototype of a new mantle convection framework, based on a matrix-free finite element implementation. We demonstrate that our framework is capable to simulate such highly complex scenarios and present results with an unprecedented global resolution close to 1 km using more than 60,000 compute cores on a peta-scale system. This yields systems with \u003Cem\u003EO\u003C\/em\u003E(10^12) degrees of freedom. These results will serve us to gain insights into the current debate on the power spectrum of the observed surface dynamic topography of the Earth.","filename":"post156s2.pdf","bio":"","contributors":[{"type":"Author","first_name":"Simon","last_name":"Bauer","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Hans-Peter","last_name":"Bunge","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Siavash","last_name":"Ghelichkhan","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Huber","affiliation":"TU Munich","country":"Germany","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marcus","last_name":"Mohr","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Barbara","last_name":"Wohlmuth","affiliation":"TU Munich","country":"Germany","bio":"","order":"7","is_presenter":false}],"has_presenters":true,"presenters":[{"type":"Author","first_name":"Simon","last_name":"Bauer","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"1","is_presenter":true}]}, "slotContributors": [{"type":"Author","first_name":"Simon","last_name":"Bauer","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"1","is_presenter":true},{"type":"Author","first_name":"Hans-Peter","last_name":"Bunge","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"2","is_presenter":false},{"type":"Author","first_name":"Siavash","last_name":"Ghelichkhan","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"3","is_presenter":false},{"type":"Author","first_name":"Markus","last_name":"Huber","affiliation":"TU Munich","country":"Germany","bio":"","order":"4","is_presenter":false},{"type":"Author","first_name":"Marcus","last_name":"Mohr","affiliation":"Ludwig Maximilian University of Munich","country":"Germany","bio":"","order":"5","is_presenter":false},{"type":"Author","first_name":"Ulrich","last_name":"R\u00fcde","affiliation":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","country":"Germany","bio":"","order":"6","is_presenter":false},{"type":"Author","first_name":"Barbara","last_name":"Wohlmuth","affiliation":"TU Munich","country":"Germany","bio":"","order":"7","is_presenter":false}] } Presentation
Best Posters Awards
Further information on the Posters Awards is available here.
First Place
CSM20 - Practical Communication-Optimal Algorithm for Dense Matrix-Matrix Multiplication, Marko Kabic, Thibault Notargiacomo, Raffaele Solcà, Joost VandeVondele (ETH Zurich / CSCS, Switzerland)
LIF02 - The Bromodomain-Peptide (Un)Binding Network, Cassiano Langini, Marco Bacci, Andreas Vitalis, Amedeo Caflisch (University of Zurich, Switzerland)
Second Place
LIF06 - Parallel Kraken for Meta-Omic Microbiome and Phytobiome Classification, Benjamin Garcia, Doug Hyatt, Daniel Jacobson (Oak Ridge National Laboratory, USA), Piet Jones (University of Tennessee, USA), Ian Hodge (Stanford University, USA)
CSM02 - Adaptive Grid Refinement Techniques for Particulate Flow Simulations with the Lattice Boltzmann Method, Christoph Rettinger, Ulrich Rüde (Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany)
Third place
CSM09 - High Performance Topology Optimization, Ezekiel Barnett, Sameer Rawat, Sumeet Gyanchandani, Dimosthenis Pasadakis (Università della Svizzera italiana, Switzerland)
LIF07 - SAPPHIRE Basin Recognition: An Unsupervised Algorithm to Identify and Project Metastable and Transition States in High-Dimensional Time Series Data, Francesco Cocina, Marco Bacci, Andreas Vitalis, Amedeo Caflisch (University of Zurich, Switzerland)
ENG02 - Assessment of Detached Eddy Simulation in Predicting Separated Flow over Airfoils at a Moderate Reynolds Number, Ramesh Balakrishnan, Jun Fang (Argonne National Laboratory, USA), Ariane Frere, Koen Hillewaert, Michel Rasquin (CENAERO, Belgium), Kenneth Jansen (University of Colorado Boulder, USA), Philipp Schlatter, Ricardo Vinuesa (Royal Institute of Technology, Sweden)