High Performance Computing in Science and Engineering: Second International Conference, HPCSE 2015, Soláň, Czech Republic, May 25-28, 2015, Revised Selected Papers PDF
Preview High Performance Computing in Science and Engineering: Second International Conference, HPCSE 2015, Soláň, Czech Republic, May 25-28, 2015, Revised Selected Papers
Tomáš Kozubek · Radim Blaheta Jakub Šístek · Miroslav Rozložník Martin Cermák (Eds.) 1 1 6 9 High Performance Computing S C in Science and Engineering N L Second International Conference, HPCSE 2015 Soláň, Czech Republic, May 25–28, 2015 Revised Selected Papers 123 Lecture Notes in Computer Science 9611 Commenced Publication in 1973 Founding and Former Series Editors: Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen Editorial Board David Hutchison Lancaster University, Lancaster, UK Takeo Kanade Carnegie Mellon University, Pittsburgh, PA, USA Josef Kittler University of Surrey, Guildford, UK Jon M. Kleinberg Cornell University, Ithaca, NY, USA Friedemann Mattern ETH Zurich, Zürich, Switzerland John C. Mitchell Stanford University, Stanford, CA, USA Moni Naor Weizmann Institute of Science, Rehovot, Israel C. Pandu Rangan Indian Institute of Technology, Madras, India Bernhard Steffen TU Dortmund University, Dortmund, Germany Demetri Terzopoulos University of California, Los Angeles, CA, USA Doug Tygar University of California, Berkeley, CA, USA Gerhard Weikum Max Planck Institute for Informatics, Saarbrücken, Germany More information about this series at http://www.springer.com/series/7407 áš Tom Kozubek Radim Blaheta (cid:129) Ší ž í Jakub stek Miroslav Rozlo n k (cid:129) Č á Martin erm k (Eds.) High Performance Computing in Science and Engineering Second International Conference, HPCSE 2015 áň – Sol , Czech Republic, May 25 28, 2015 Revised Selected Papers 123 Editors TomášKozubek Miroslav Rozložník VSB- Technical University of Ostrava Institute of Computer Science of the CAS Ostrava Prague Czech Republic Czech Republic Radim Blaheta Martin Čermák Institute of Geonics of theCAS VSB- Technical University of Ostrava Ostrava Ostrava Czech Republic Czech Republic JakubŠístek Institute of Mathematics of the CAS Prague Czech Republic ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notesin Computer Science ISBN 978-3-319-40360-1 ISBN978-3-319-40361-8 (eBook) DOI 10.1007/978-3-319-40361-8 LibraryofCongressControlNumber:2016940813 LNCSSublibrary:SL1–TheoreticalComputerScienceandGeneralIssues ©SpringerInternationalPublishingSwitzerland2016 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodologynow knownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookare believedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissionsthatmayhavebeenmade. Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerInternationalPublishingAGSwitzerland Preface This volume comprises the proceedings of the Second International Conference on High Performance Computing in Science and Engineering, HPCSE 2015, which was held at the Hotel Soláň in the heart of the Beskydy Mountains, Czech Republic, from 25th – 28th May, 2015. The biennial conference was organized by IT4Innovations National Supercomputing Center at the VSB-Technical University of Ostrava and its goal was to bring together specialists inapplied mathematics, numerical methods, and parallelcomputingtoshareexperienceandinitiatenewresearchcollaborations.Weare pleased that our invitation was accepted by distinguished experts from leading inter- national research institutions. The conference has become an international forum for exchanging ideas among researchers involved in scientific and parallel computing, including theory and appli- cations as well as applied and computational mathematics. The focus of HPCSE 2015 was on models, algorithms, and software tools that facilitate efficient and convenient utilization of modern parallel and distributed computing architectures, as well as on large-scale applications. The Scientific Committee of HPCSE 2015 comprised Radim Blaheta, Zdeněk Dostál, Tomáš Kozubek, Miroslav Tůma, Jakub Šístek, Zdeněk Strakoš, and Vít Vondrák. The plenary talks were presented by: (cid:129) Owe Axelsson from the Institute of Geonics of the CAS (Czech Republic) (cid:129) Cevdet Aykanat from Bilkent University, Ankara (Turkey) (cid:129) Marc Baboulin from Inria, Paris (France) (cid:129) Santiago Badia from CIMNE, Barcelona (Spain) (cid:129) Jed Brown from the Argonne National Laboratory, Illinois (USA) (cid:129) Fehmi Cirak from the University of Cambridge (UK) (cid:129) Jacek Gondzio from the University of Edinburgh (UK) (cid:129) Akhtar A. Khan from Rochester Institute of Technology, Rochester (USA) (cid:129) Johannes Kraus from the University of Essen (Germany) (cid:129) Jaroslav Kruis from the Czech Technical University in Prague (Czech Republic) (cid:129) Julien Langou from the University of Colorado, Denver (USA) (cid:129) Jan Mandel from the University of Colorado, Denver (USA) (cid:129) Dan Negrut from the University of Wisconsin-Madison, Madison (USA) (cid:129) Ulrich Rüde from the University of Erlangen (Germany) (cid:129) Valeria Simoncini from the University of Bologna (Italy) (cid:129) Wim Vanroose from the University of Antwerp (Belgium) (cid:129) Barbara Wohlmuth from the Technical University of Munich (Germany) (cid:129) Roman Wyrzykowski from Czestochowa University of Technology (Poland) (cid:129) Walter Zulehner from Johannes Kepler University, Linz (Austria) VI Preface The conference was supportedby IT4InnovationsNational Supercomputing Center and the project OP EC “New Creative Teams in Priorities of Scientific Research” no. CZ.1.07/2.3.00/30.0055. This project was funded by structural funds of the European Union and the State Budget of the Czech Republic. It is our pleasure to acknowledge this support. HPCSE 2015 was a fruitful event that presented interesting lectures, featuring new ideas as well as the beauty of applied mathematics, numerical linear algebra, opti- mization methods, and high performance computing; the conference facilitated the formation of new or the strengthening of the existing collaborations and friendships. Thismeetingattractedmorethan100participantsfrom11countries.Allparticipants were invited to submit an original paper to this book of proceedings. We thank for all the contributors and the reviewers of the papers for their work. We hope that readers willfindthisvolumeuseful,andwewouldliketocordiallyinvitethemtoparticipateat thenextconference,HPCSE2017,whichisplannedtobeheldinthesameplacefrom 22nd – 25th May, 2017. The proceedings have been edited by Tomáš Kozubek, Radim Blaheta, Jakub Šístek, Miroslav Rozložník, and Martin Čermák. May 2016 Tomáš Kozubek Organization Program Committee Radim Blaheta Institute of Geonics of the CAS, Czech Republic Zdeněk Dostál IT4Innovations, VŠB - Technical University of Ostrava, Czech Republic Tomáš Kozubek IT4Innovations, VŠB - Technical University of Ostrava, Czech Republic Zdeněk Strakoš Charles University in Prague, Czech Republic Jakub Šístek Institute of Mathematics of the CAS, Czech Republic Miroslav Tůma Charles University in Prague, Czech Republic Vít Vondrák IT4Innovations, VŠB - Technical University of Ostrava, Czech Republic Contents Large Scale Lattice Boltzmann Simulation for the Coupling of Free and Porous Media Flow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Ehsan Fattahi,Christian Waluga, Barbara Wohlmuth, andUlrich Rüde Chrono: An Open Source Multi-physics Dynamics Engine . . . . . . . . . . . . . 19 Alessandro Tasora, Radu Serban, Hammad Mazhar, Arman Pazouki, Daniel Melanz, Jonathan Fleischmann, Michael Taylor, Hiroyuki Sugiyama, and Dan Negrut Parallel Computing in Multi-scale Analysis of Coupled Heat and Moisture Transport in Masonry Structures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 Jaroslav Kruis, Tomáš Krejčí, and Michal Šejnoha An Equation Error Approach for the Identification of Elastic Parameters in Beams and Plates with H Regularization. . . . . . . . . . . . . . . . . . . . . . . . 60 1 P. Caya, B. Jadamba, A.A. Khan, F. Raciti, and B. Winkler A Comparison of Preconditioning Methods for Saddle Point Problems with an Application to Porous Media Flow Problems. . . . . . . . . . . . . . . . . . 68 Owe Axelsson, Radim Blaheta, and Martin Hasal Efficient Implementation of Total FETI Solver for Graphic Processing Units Using Schur Complement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 Lubomír Říha, Tomáš Brzobohatý, Alexandros Markopoulos, Tomáš Kozubek, Ondřej Meca, Olaf Schenk, and Wim Vanroose Solving Contact Mechanics Problems with PERMON . . . . . . . . . . . . . . . . . 101 Vaclav Hapla, David Horak, Lukas Pospisil, Martin Cermak, Alena Vasatova, and Radim Sojka Many Core Acceleration of the Boundary Element Method . . . . . . . . . . . . . 116 Michal Merta, Jan Zapletal, and Jiri Jaros Parallel Implementation of Collaborative Filtering Technique for Denoising of CT Images. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 Petr Strakos, Milan Jaros, Tomas Karasek, and Tomas Kozubek On Modeling of Bodies with Holes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141 Jan Franců Analysis of Model Error for a Continuum-Fracture Model of Porous Media Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 Jan Březina and Jan Stebel X Contents Probabilistic Time-Dependent Travel Time Computation Using Monte Carlo Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 Radek Tomis, Lukáš Rapant, Jan Martinovič, Kateřina Slaninová, and Ivo Vondrák Model of the Belousov-Zhabotinsky Reaction. . . . . . . . . . . . . . . . . . . . . . . 171 Dalibor Štys, Tomáš Náhlík, Anna Zhyrova, Renata Rychtáriková, Štěpán Papáček, and Petr Císař Parameter Identification Problem Based on FRAP Images: From Data Processing to Optimal Design of Photobleaching Experiments . . . . . . . . . . . 186 Ctirad Matonoha and Štěpán Papáček Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
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