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SUPERCOMPUTING IN SCIENCE AND ENGINEERING IT4Innovations National Supercomputing Center Czech Republic 2017 nova_verze.indd 1 03.04.2017 15:16:08 VŠB – Technical University of Ostrava Supercomputing in Science and Engineering Editors: Karina Pešatová, Barbora Poláková, John Cawley Ostrava, 2017 Published by VŠB – Technical University of Ostrava Design and typesetting: Milan Smetana, Emílie Smetanová Page count: 224 Edition: 1st Printed by: Knowlimits, s.r.o. Copies: 300 Not for sale © IT4Innovations National Supercomputing Center This work is subject to copyright. All rights reserved. Reproduction or publication of this material, even partial, is allowed only with the editors’ permission. ISBN 978-80-248-4037-6 2 nova_verze.indd 2 03.04.2017 15:16:08 SUPERCOMPUTING IN SCIENCE AND ENGINEERING IT4Innovations National Supercomputing Center Czech Republic 2017 Editors: Karina Pešatová, Barbora Poláková, John Cawley Reviewers: Martin Palkovič, Branislav Jansík, Vít Vondrák, Tomáš Kozubek, Jan Martinovič, René Kalus, Tomáš Brzobohatý This publication was supported by The Ministry of Education, Youth and Sports from the Large Infrastructures for Research, Experimental Development and Innovations project „IT4Innovations National Supercomputing Center – LM2015070“ 3 nova_verze.indd 3 03.04.2017 23:20:09 Table of contents Director’s introduction 9 Martin Palkovič The infrastructure of IT4Innovations 10 01 ASTROPHYSICS Computational Planetology: Timing of Water Plume Eruptions on Enceladus Explained 16 by Interior Viscosity Structure Marie Běhounková Star Formation in Gaseous Layers 19 František Dinnbier Accretion and Jet Launching in Young Stellar Objects 22 Ivana Orlitová Origin of the Second Stellar Generation in Globular Clusters 24 Richard Wünsch 02 COMPUTATIONAL SCIENCES Verification of MPI Applications Defined in Kaira 30 Marek Běhálek Benchmarking of the CFD Codes on Salomon Cluster 33 Tomáš Brzobohatý Stochastic Estimation of the Diagonal of the Inverse (SEDI) 36 Greg Hernandez Permon Toolbox Development 40 David Horák Tsunami Simulation with Parallel Adaptive Mesh Refinement on the Xeon Phi Nodes of Salomon 43 Michael Bader Parallelisation of the Pragtic Software for an Automated Fatigue Damage Calculation 46 David Horák Convolutional Neural Networks for Image Restoration 49 Michal Hradiš Rendering in Blender Cycles Using MPI and Intel® Xeon Phi™ 52 Milan Jaroš Evaluation of Parallel I/O Strategies for Distributed Sparse Matrices 56 Daniel Langr Parallel Boundary Element Method for Sound-hard Scattering 59 Michal Merta Development of a Parallel Algorithm for Fuzzy Association Rules Mining 62 Viktor Pavliska Task Programming and Asynchronous Communication for Irregular Computations 65 Eric Petit Sparse Block Matrix Linear Algebra (SBMLA) 68 Lukáš Polok ESPRESO – Accelerated Solver Library for Intel Xeon Phi Systems 70 Lubomír Říha, Tomáš Brzobohatý Computational Methods for Solving Stochastic Equilibrium Models 73 Olaf Schenk, Simon Scheidegger MATSOL – Development, Testing and Support Libraries 77 Oldřich Vlach BEM4I – Vectorised Boundary Element Library for Many-core Systems 80 Michal Merta 4 nova_verze.indd 4 03.04.2017 23:20:09 03 EARTH AND ENVIRONMENTAL SCIENCES HPC Framework for Rainfall-Runoff Uncertainty Modelling 86 Štěpán Kuchař Urban Canopy Climate Forcing on a Regional Scale Modelled by the RegCM and WRF Models 90 Peter Huszár Parallelization of Flood Model Calibration 93 Štěpán Kuchař Hydrological Model Remote Execution and HPC as a Service 97 Jan Martinovič, Štěpán Kuchař, Václav Svatoň, Vít Vondrák Large-scale Geosimulations Using GEM and Trilinos 100 Jiří Starý Adjoint Tomography of Surface Waves: Choice of Regularisation Based on Synthetic Tests 104 Ľubica Valentová Parallel Modeling of Ocean Flows and their Magnetic Signatures 108 Jakub Velímský 04 ENGINEERING AND COMPUTATIONAL FLUID DYNAMICS Axially and Radially Cooled Brake Disc with Cover 114 Marek Gebauer Solving Non-Linear Structural Dynamics Problems on a Supercomputer 117 Tomáš Karásek HPC for Modelling Strongly Nonlinear Processes in Mechanics, Parts I.-III. 119 Pavel Maršálek, Petr Horyl, Tomáš Karásek CFD Proxy – Strong Scaling in CFD 122 Christian Simmendinger Scalable Solvers for Subsurface Flow Simulations 125 Jakub Šístek Multilevel Domain Decomposition Solvers for Incompressible Flows 128 Jakub Šístek ACLA – Active Load Alleviation 131 Petr Vrchota 05 CHEMISTRY AND MATERIAL SCIENCES Benchmarking of New Accurate Multi-reference Coupled Cluster Methods 136 Jiří Brabec Atomic-scale Design of Opticaly Active Nanostructured Amorphous Silica 139 Antonio Cammarata, Luisa Spallino, Paolo Nicolini, Benjamin Irving Quantum Simulations of Doped Helium Nanodroplets I. Photoabsorption Spectra 141 of Charged Helium Clusters Rajko Ćosić Molecular Docking on High Performance Computing Clusters 144 Rafael Doležal The SQM/COSMO Scoring Function Reliably Describes Noncovalent Interactions 147 in Protein-ligand Complexes Pavel Hobza 5 nova_verze.indd 5 03.04.2017 23:20:09 Theoretical Study of the State-selected Reactions of Electronically Excited Oxygen Ions 150 with Methane Relevant for Titan’s Atmosphere Jan Hrušák Conformational Transitions and Membrane Binding of the Neuronal Calcium Sensor Recoverin 153 Pavel Jungwirth Modelling of Elementary Processes in Cold Rare-gas Plasmas 156 René Kalus Enzymatic Reaction Mechanisms Investigated by Car-Parrinello ab Initio Dynamics 159 Jaroslav Koča Detecting Materials in Coal-polyurethane Geocomposite CT-scans 162 Marek Pecha, Martin Čermák, David Horák Periodic DFT Studies of Zeolite Based Catalysts I. 165 Štěpán Sklenák Periodic DFT Studies of Zeolite Based Catalysts II. 168 Štěpán Sklenák Periodic DFT Studies of Zeolite Based Catalysts III. 171 Štěpán Sklenák Quantum-mechanical Simulations of Interfaces in Advanced Materials 174 Mojmír Šob Exploring the Effect of Loading Conditions on the Ideal Tensile Strength 177 Mojmír Šob Hydrophobic Impurities in Water Clusters 180 Aleš Vítek 06 LIFE SCIENCES AND BIOLOGY Estimation of Empirical Distribution Function for Testing of Modality of 3D Particle Sizes Based on 2D Observations 186 Michal Burda A non-Newtonian Model of Blood Capturing Segregation of Erythrocytes – First Step to Proper Modelling of the Blood Coagulation Process 189 Marek Čapek FEM Model of the Soft Tissues – Comparison with Ultrasound Elastography 192 Jan Grepl Convergence Testing of a K-space Pseudospectral Scheme for Transcranial Time-reversal Focusing 195 Jiří Jaroš, Bradley E. Treeby Structural Investigations of the Human Mitochondrial Lon Protease 198 Lubomír Kováčik Enhancement of the IT4IBlender Tool for Parallel Image Segmentation of Computer Tomography and Magnetic Resonance Images 202 Tomáš Karásek Modelling Beam Distortion During Focused Ultrasound Surgery in the Prostate Using k-Wave 205 Jiří Jaroš 07 PHYSICS Quantum Collisions of Electrons with Hydrogen Atoms 210 Jakub Benda, Karel Houfek TEBDOL – Parallel Simulation of Ultracold Atoms in Optical Lattices 213 Miroslav Urbánek, Pavel Soldán One-dimensional and Two-dimensional Magnetic Systems 216 Dominik Legut Comprehensive Modelling Long Time Evolution of Suddenly Ionised Rare Gas Clusters Through Multiscale Model and Full Dynamics Calculations 218 Ivan Janeček 6 nova_verze.indd 6 03.04.2017 23:20:09 7 nova_verze.indd 7 03.04.2017 23:20:09 8 nova_verze.indd 8 03.04.2017 23:20:09 DIRECTOR’S INTRODUCTION Dear readers, we proudly present to you this selection of bleeding edge scientific and engineering projects that have been made possible through the use of the large research e-infrastructure at IT4Innovations National Supercomputing Center. I strongly believe our supercomputing facility is a crucial asset, helping to improve the excellence of Czech science. The IT4Innovations National Supercomputing Center was established at the end of 2011 with the clear goal to implement and operate large research e-infrastructure in High Performance Computing (HPC) in the Czech Republic. Our first cluster, Anselm, became operational in May 2013. Anselm was the first, and for two years the only large High Performance Computing system publicly available for Czech scientists and researchers nationwide complying with the principles of open access. In September 2015 the supercomputer Salomon was inaugurated and became available. At the time of its completion it was the 14th fastest supercomputer in Europe, and rated 40th in the world, according to the TOP500 list. The computational resources of the e-infrastructure are allocated via open access competitions that are announced three times a year. IT4Innovations National Supercomputing Center is not just a computational cycle provider, we also offer high quality HPC related expertise and research, world class training and unique MSc. and Ph.D. study programmes in the HPC domain. Our membership in the pan-European infrastructure PRACE allows Czech scientists access to the largest HPC systems in Europe, should even larger scale systems than nationally available be required for particular research tasks. Our membership in ETP4HPC allows us to influence the HPC Strategic Research Agenda, the document that outlines a roadmap for the achievement of exa-scale capabilities by the European High Performance Computing ecosystem. So that we may better serve our users, we continually strive to improve all aspects of the services we offer. I hope that we maintain your goodwill towards the IT4Innovations National Supercomputing Center, and that our e-infrastructure will continue to help you make breakthroughs in your research
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