Sustained Simulation Performance 2017 : Proceedings of the Joint Workshop on Sustained Simulation Performance, University of Stuttgart (HLRS) and Tohoku University, 2017 PDF
Preview Sustained Simulation Performance 2017 : Proceedings of the Joint Workshop on Sustained Simulation Performance, University of Stuttgart (HLRS) and Tohoku University, 2017
Michael M. Resch · Wolfgang Bez Erich Focht · Michael Gienger Hiroaki Kobayashi Editors SSuussttaaiinneedd SSiimmuullaattiioonn PPeeeeerrrrrfffffooooorrrrrmmmmmaaaaannnnnccccceeeee 2017 123 Sustained Simulation Performance 2017 Michael M. Resch • Wolfgang Bez (cid:129) Erich Focht (cid:129) Michael Gienger (cid:129) Hiroaki Kobayashi Editors Sustained Simulation Performance 2017 Proceedings of the Joint Workshop on Sustained Simulation Performance, University of Stuttgart (HLRS) and Tohoku University, 2017 123 Editors MichaelM.Resch WolfgangBez HighPerformanceComputing NECHighPerformanceComputing Center(HLRS) EuropeGmbH UniversityofStuttgart DuRsseldorf,Germany Stuttgart,Germany ErichFocht MichaelGienger NECHighPerformanceComputing HighPerformanceComputing EuropeGmbH Center(HLRS) Stuttgart,Germany UniversityofStuttgart Stuttgart,Germany HiroakiKobayashi CyberscienceCenter TohokuUniversity Sendai,Japan FigureonFrontCover:Streamlineandslicevisualisationofthevelocityfieldatpeaksystoleinanaortic arcwithaneurysm.Thevortexstructuresintheascendingaorticarcaswellastheaneurysmarevisualised bythegrey-coloured,transparentisosurface.ThedataprovidedbyFraunhoferMEVISarerecordedby phasecontrastmagnetresonanceimagingandserveasthecalibration andtestdataforthetwopaper contributionsofUweKüster,AndreasRuoppandRalfSchneider. ISBN978-3-319-66895-6 ISBN978-3-319-66896-3 (eBook) DOI10.1007/978-3-319-66896-3 LibraryofCongressControlNumber:2017955381 Mathematics Subject Classification (2010): 65-XX, 65Exx, 65Fxx, 65Kxx, 68-XX, 68Mxx, 68Uxx, 68Wxx,70-XX,70Fxx,70Gxx,76-XX,76Fxx,76Mxx,92-XX,92Cxx ©SpringerInternationalPublishingAG2017 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof thematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbook arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsor theeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforany errorsoromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictional claimsinpublishedmapsandinstitutionalaffiliations. Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerInternationalPublishingAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface ThefieldofHighPerformanceComputingiscurrentlyundergoingamajorparadigm shift.Firstly,large-scalesupercomputingsystemswithmassivelyimprovednumber crunching capabilities are now available to computational scientists all over the world.Atthesametime,ourknowledgeofhowtomostefficientlyexploitmodern processorsandperformanceachievementsisgrowingbyleapsandbounds. However, many domains of computational science have reached a saturation point with regard to their problem size: many scientists no longer wish to solve largerproblems.Instead,theyaimtosolvesmallerproblemsinashorteramountof time,so asto quicklygainknowledgeandrecognisepotentialissuesearlyon.Yet the currentarchitecturesare much better suited to addressing large problemsthan theyareforthemorerelevantsmallerproblemsizes. This particular series of workshops focuses on Sustained Simulation Perfor- mance,i.e.HighPerformanceComputingforstate-of-the-artapplicationusecases, rather than on peak performance, which is the scope of artificial problem sizes. The series of workshops was first established in 2004 under the name Teraflop Workshop and was renamed Workshop for Sustained Simulation Performance in 2012.Ingeneral,thescopeoftheworkshopserieshasexpandedfromoptimisation for vector computers only to future challenges, productivity, and exploitation of currentandfutureHighPerformanceComputingsystems. This book presents the combined outcomes of the 24th and 25th workshops in the series. The 24th workshop was held at the High Performance Computing Center, Stuttgart, Germany, in December 2016. The subsequent 25th workshop was held in March 2017 at the Cyberscience Center, Tohoku University, Japan. The topics studied by the contributed papers include developing novel system management concepts (Part I), leveraging innovative mathematical methods and approaches (Part II), applying optimisation as well as vectorisation techniques (PartIII),implementingComputationalFluidDynamicsapplications(PartIV),and finally,exploitingHighPerformanceDataAnalytics(PartV). v vi Preface We would like to thank all the contributors and organisers of this book and the Sustained Simulation Performance project. We especially thank Prof. Hiroaki Kobayashi for the close collaboration over the past years and look forward to intensifyingourcooperationinthefuture. Stuttgart,Germany MichaelM.Resch July2017 MichaelGienger Contents PartI SystemManagement TheoryandPracticeofEfficientSupercomputerManagement ............ 3 VadimVoevodin TowardsASoftwareDefinedSecureDataStagingMechanism............. 15 Susumu Date, Takashi Yoshikawa, Kazunori Nozaki, Yasuhiro Watashiba, YoshiyukiKido, Masahiko Takahashi, Masaya Muraki, andShinjiShimojo PartII MathematicalMethodsandApproaches TheNumericalApproximationofKoopmanModesofaNonlinear OperatorAlongaTrajectory ................................................... 27 UweKüster,RalfSchneider,andAndreasRuopp PartIII OptimisationandVectorisation Code Modernization Tools for Assisting Users in Migrating toFutureGenerationsofSupercomputers.................................... 55 RituAroraandLarsKoesterke VectorizationofHigh-OrderDGinAtelesfortheNECSX-ACE .......... 75 HaraldKlimach,JiaxingQi,StephanWalter,andSabineRoller VectorizationofCellularAutomaton-BasedLabelingof3-DBinary Lattices............................................................................ 89 PeterZinterhof PartIV ComputationalFluidDynamics TurbulenceinaFluidStratifiedbyaHighPrandtl-NumberScalar ....... 113 ShinyaOkinoandHideshiHanazaki vii viii Contents Wavelet-BasedCompressionofVolumetricCFDDataSets................. 123 PatrickVoglerandUlrichRist ValidationofParticle-LadenLarge-EddySimulation UsingHPCSystems.............................................................. 137 KonstantinFröhlich,LennartSchneiders,MatthiasMeinke, andWolfgangSchröder CoupledSimulationwithTwoCouplingApproaches onParallelSystems .............................................................. 151 NedaEbrahimiPour,VerenaKrupp,HaraldKlimach,andSabineRoller MRI-BasedComputationalHemodynamicsinPatients..................... 165 AndreasRuoppandRalfSchneider PartV HighPerformanceDataAnalytics ADataAnalyticsPipelineforSmartHealthcareApplications.............. 181 ChonhoLee,SeiyaMurata,KoboIshigaki,andSusumuDate Part I System Management Theory and Practice of Efficient Supercomputer Management VadimVoevodin Abstract Theefficiencyof usingmodernsupercomputersystemsisverylow due to theirhighcomplexity.Itis gettingharderto controlthe state of supercomputer, but the cost of low efficiency can be very significant. In order to solve this issue, software for efficient supercomputermanagementis needed. This paper describes a set of tools being developed in Research Computing Center of Lomonosov Moscow State University (RCC MSU) that is intended to provide a holistic approachtoefficiencyanalysisfromdifferentpointsofview.Efficiencyofparticular user applications and whole supercomputer job flow, efficiency of computational resources utilization, supercomputer reliability, HPC facility management—all thesequestionsarebeingstudiedbythedescribedtools. 1 Introduction Modern supercomputing system consists of a huge amount of different software andhardwarecomponents:computenodes,network,storage,systemsoftwaretools, softwarepackages,etc.Ifwewanttoachieveefficientsupercomputermanagement, we need to think about all behavior aspects of these components.How efficiently users of supercomputer center consume computational resources, what jobs they run, what projects they form, how efficiently partitions and quotas are organized, issystemsoftwareconfiguredproperly—allofthese(andnotonlythese)questions needtobetakenintoaccount,otherwisetheefficiencyofthesupercomputerusage can be significantly decreased. This means that we need to control everything happeninginthesupercomputer. Asthesupercomputersaregettingbiggerandmorecomplex,thistaskisgetting harderandharder.Thisexplainsthefactthattheefficiencyofmostsupercomputing systems is very low. For example, the average Flops performance of one core on oldMSUsystem calledChebyshevfor3daysisjustabove3%[17].Thesituation isquitethesameonmanyothercurrentsupercomputersystems. V.Voevodin((cid:2)) ResearchComputingCenterofLomonosovMoscowStateUniversity,Moscow,Russia e-mail:[email protected] ©SpringerInternationalPublishingAG2017 3 M.M.Reschetal.(eds.),SustainedSimulationPerformance2017, DOI10.1007/978-3-319-66896-3_1
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