High-Performance Computing Infrastructure for South East Europe's Research Communities: Results of the HP-SEE User Forum 2012 PDF
Preview High-Performance Computing Infrastructure for South East Europe's Research Communities: Results of the HP-SEE User Forum 2012
Modeling and Optimization in Science and Technologies Mihnea Dulea · Aneta Karaivanova Anastasis Oulas · Ioannis Liabotis Danica Stojiljkovic · Ognjen Prnjat Editors High-Performance Computing Infrastructure for South East Europe’s Research Communities Results of the HP-SEE User Forum 2012 Modeling and Optimization in Science and Technologies Volume 2 SeriesEditors SrikantaPatnaik(Editor-in-Chief) SOAUniversity,Orissa,India IshwarK.Sethi OaklandUniversity,Rochester,USA XiaolongLi IndianaStateUniversity,TerreHaute,USA EditorialBoard LiCheng, KayChenTan, DepartmentofMechanicalEngineering, DepartmentofElectricaland TheHongKongPolytechnicUniversity, ComputerEngineering, HongKong NationalUniversityofSingapore, Singapore Jeng-HaurHorng, DepartmentofPowerMechnical Yeon-MoYang, Engineering, DepartmentofElectronicEngineering, NationalFormosaUniversity, KumohNationalInstituteofTechnology, Yulin, Gumi,SouthKorea Taiwan LiangchiZhang, PedroU.Lima, SchoolofMechanicalandManufacturing InstituteforSystemsandRobotics, Engineering, Lisbon, TheUniversityofNewSouthWales, Portugal Australia Mun-KewLeong, BaojiangZhong, InstituteofSystemsScience, SchoolofComputerScienceand NationalUniversityofSingapore Technology,SoochowUniversity, Suzhou,China MuhammadNur, FacultyofSciencesandMathematics, AhmedZobaa, DiponegoroUnersity, SchoolofEngineeringandDesign, Semarang, BrunelUniversity,Uxbridge, Indonesia Middlesex,UK Forfurthervolumes: http://www.springer.com/series/10577 · Mihnea Dulea Aneta Karaivanova · Anastasis Oulas Ioannis Liabotis · Danica Stojiljkovic Ognjen Prnjat Editors High-Performance Computing Infrastructure for South East Europe’s Research Communities Results of the HP-SEE User Forum 2012 ABC Editors MihneaDulea IoannisLiabotis HoriaHulubeiNationalInstitute GRNETS.A. forPhysicsandNuclearEngineering GreekResearchandTechnologyNetwork Magurele Athens Romania Greece AnetaKaraivanova DanicaStojiljkovic InstituteofInformationandCommunication InstituteofPhysicsBelgrade Technologies,BulgarianAcademy UniversityofBelgrade(IPB-UOB) ofSciences(IICT-BAS) Belgrade Sofia Serbia Bulgaria AnastasisOulas OgnjenPrnjat InstituteofMarineBiology,Biotechnology GRNETS.A. andAquacultures,HellenicCentrefor GreekResearchandTechnologyNetwork MarineResearch(IMBBC-HCMR) Athens Heraklion,Crete Greece Greece ISSN2196-7326 ISSN2196-7334 (electronic) ISBN978-3-319-01519-4 ISBN978-3-319-01520-0 (eBook) DOI10.1007/978-3-319-01520-0 SpringerChamHeidelbergNewYorkDordrechtLondon LibraryofCongressControlNumber:2013944765 (cid:2)c SpringerInternationalPublishingSwitzerland2014 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe materialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broad- casting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorage andretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodologynowknown orhereafterdeveloped.Exemptedfromthislegalreservationarebriefexcerptsinconnectionwithreviews orscholarly analysis ormaterial suppliedspecifically forthepurposeofbeingentered andexecuted ona computersystem,forexclusive usebythepurchaser ofthework.Duplication ofthis publication orparts thereofispermittedonlyundertheprovisionsoftheCopyrightLawofthePublisher’slocation,initscur- rentversion,andpermissionforusemustalways beobtained fromSpringer. Permissionsforusemaybe obtainedthroughRightsLinkattheCopyrightClearanceCenter.Violationsareliabletoprosecutionunder therespectiveCopyrightLaw. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Whiletheadviceandinformationinthisbookarebelievedtobetrueandaccurateatthedateofpublication, neither the authors northe editors nor the publisher can accept any legal responsibility for any errors or omissionsthatmaybemade.Thepublishermakesnowarranty,expressorimplied,withrespecttothematerial containedherein. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface High-PerformanceComputing(HPC) is one of the key enablersof scientific research and of the developmentof InformationSociety in Europe.Enabling large-scaleinno- vative research to be conducted through collaboration of distributed teams of scien- tists across the EuropeanResearchArea pavesthe way towardsa long-termvision of a sustainable, transparent, ubiquitous electronic infrastructure open to a wide range of scientific user communities.EuropeanCommission sees “strategic nature of High- PerformanceComputingasacrucialassetfortheEU’sinnovationcapacity,andcallson MemberStates,industryandthescientificcommunities,incooperationwiththeCom- mission, to step up joint efforts to ensure European leadership in the supply and use ofHPCsystemsandservicesby2020.”Pan-EuropeanPRACEinfrastructuresupports this strategy and currently provides the core of High-PerformanceComputing power for Europeanresearch. In this context, the inclusion of less-developedregionsof Eu- rope, which suffer from the digital divide and brain-drain in all fields and especially high-technology,into the wider EuropeanResearch Area is an aim closely aligned to this vision. HP-SEE project,co-fundedby FrameworkProgramme7 of the European Commission, is currently advancing the computing infrastructures in South-East Eu- rope(SEE),activatingnewusercommunitiesandenablingcollaborativeresearchacross anumberoffields,andthuscontributestoclosingtheexistingtechnologicalandscien- tificgap,andfollowingthewiderEuropeanHPCstrategy. TheHP-SEEUserForumtookplaceinBelgradeonOctober17-19,2012,atpremises ofNationalLibraryofSerbiaandhostedbytheInstitutesofPhysicsBelgrade:thissci- entificconferencegathered65participantsfrom16countriesintheregionandbeyond, withmainfocusonthefieldsofComputationalPhysics,ComputationalChemistry,Life Sciences, Scientific Computing and HPC Systems and Network Operations. Confer- enceprogrammecomprisedofseveninvitedlectures,bothfromrelatede-Infrastructure projects and HP-SEE scientific community, 26 contributed oral presentations and a poster session featuring11 poster presentations.Thisedition of papersfrom the User Forumiscomprisedof20peer-reviewedpapers:7fromComputationalPhysicsappli- cations in HPC, 5 from Computational Chemistry, 3 from Life Sciences, and 5 from ScientificcomputingandHPCoperations.TheprojectaswellasthewiderSEEcom- munityhasbenefitedgreatlyfromtheexchangeofexperiencesofleadingscientistsin VI Preface the regionin their use of High-PerformanceComputingtechnologyto empower their research. InmyroleofHP-SEEprojectmanager,Iwouldliketothanktheauthors,reviewers, editors,programmeandorganizationcommitteesandguestspeakersfortheircontribu- tionstothisevent. April2013 Dr.OgnjenPrnjat HP-SEEProjectManager Conference Topics – ComputationalPhysics – ComputationalChemistry – LifeSciences – ScientificComputing – HPCSystemsandNetworkOperation KeynoteSpeakers RegionaleInfrastructureDevelopmentforSouthEastEuropesResearchCommunities IoannisLiabotis,GRNET,Greece InternationalHPC-Buildingbiggerpyramide RichardKenway,NeSC,UK LinkSCEEM2:DevelopmentofanHPCecoSystemintheEasternMediterranean JensWiegand,CaSToRC,Cyprus TheimpactofGISELAScienceGateway(GSG)onthesupportedLatinAmericaVRC’s JesusCruzGuzman,UNAM,Mexico NumericalStudyofUltracoldQuantumGases:FormationofFaradayPatterns, GeometricResonances,andFragmentation AntunBalaž,IPB,Serbia MonteCarlomethodsforElectronTransport:ScalabilityStudyusingHP-SEE infrastructure AnetaKaraivanova,IICT-BAS,Bulgaria UseofHighPerformanceComputingin(Bio)Chemistry IvanJuranic´,FCUB,Serbia Organization OrganizationCommittee DanicaStojiljkovic´ IPB,Serbia AleksandarBelic´ IPB,Serbia AntunBalaž IPB,Serbia DušanVudragovic´ IPB,Serbia VladimirSlavnic´ IPB,Serbia IoannisLiabotis GRNET,Greece OgnjenPrnjat GRNET,Greece DimitraKotsokali GRNET,Greece NikolaGrkic´ IPB,Serbia MilicaCvetkovic´ IPB,Serbia ProgrammeCommitteeChairs MihneaDulea IFIN-HH,Romania AnetaKaraivanova IICT-BAS,Bulgaria PanayiotaPoirazi GRNET,Greece OgnjenPrnjat GRNET,Greece ProgrammeCommitteeMembers AleksandarBelic´ IPB,Serbia AlexandruNicolin IFIN-HH,Romania AnastasMishev UKIM,Macedonia AntunBalaž IPB,Serbia EmanouilAtanassov IICT-BAS,Bulgaria HrachyaAstsatryan IIAPNASRA,Armenia IoannisLiabotis GRNET,Greece KlausKlingmueller CASTORC,Cyprus ManthosG.Papadopoulos IOPC,Greece MiklosKozlovszky SZTAKI,Hungary VIII Organization NekiFrasheri PUoT,Albania NenadVukmirovic´ IPB,Serbia PéterStefán NIIF,Hungary PetruBogatencov RENAM,Moldova RamazKvatadze GRENA,Georgia Referees N.Anastopoulos M.Ifti A.Oulas E.Atanassov D.Jakimovski Lj.Pejov A.Balaž A.Karaivanova B.Rybakin V.Baran P.Korosoglou M.Spassova A.Belic´ M.Kozlovszky P.Stefán A.Chatziioannou I.Liabotis S.Stefanov N.I.Dodoff A.Nicolin N.G.Vassilev R.Gábor K.Nikas N.Vukmirovic´ HP-SEEUserForum2012wasorganizedbytheInstituteofPhysicsBelgradeunderthe umbrella of High-PerformanceComputing Infrastructure for South East Europes Re- searchCommunities(HP-SEE),aprojectsupportedbyEuropeanCommissionthrough EUFP7underthe“ResearchInfrastructures”action(contractnumber261499). The Editorsand the HP-SEE projectwouldlike to acknowledgevaluablehelp and supportbytheNationalLibraryofSerbiawhichhostedtheconference. Contents ComputationalPhysics Simulation of Electron Transport Using HPC Infrastructure inSouth-EasternEurope ........................................... 1 EmanouilAtanassov,TodorGurov,AnetaKaraivanova Density Waves in Dipolar Bose-Einstein Condensates by Means ofSymbolicComputations.......................................... 15 AlexandruI.Nicolin,IonelRata Using ParallelComputing to Calculate Static InterquarkPotential inLQCD......................................................... 23 DafinaXhako,RudinaZeqirllari,ArtanBoriçi ModellingofDisasterSpreadingDynamics ............................ 31 IgorStankovic´,MilanŽeželj,JelenaSmiljanic´,AleksandarBelic´ DeterminationofZoneofFlowInstabilityinaGasFlowPastaSquare ParticleinaNarrowMicrochannel................................... 43 KirilShterev,StefanStefanov QuenchedHadronSpectroscopyUsingFermiQCD ..................... 51 RudinaZeqirllari,DafinaXhako,ArtanBoriçi Self-AvoidingHamiltonianWalksCountinginParallelProcessingMode ... 59 IgorŠevo,SretenLekic´,MihajloSavic´ ComputationalChemistry ConformationalAnalysisandHFabinitioGeometryOptimizationof KyotorphineandItsSulfo-AnaloguesNorsulfoarginine-Tyrosineand Tyrosine-Norsulfoarginine .......................................... 67 NicolayI.Dodoff,TatyanaA.Dzimbova,TamaraI.Pajpanova X Contents DynamicsofUninhibitedandCovalentlyInhibitedCysteineProteaseon Non-physiologicalpH .............................................. 75 BrankoJ.Drakulic´,MarijaGavrovic´-Jankulovic´ MechanismsofPolarization......................................... 83 AggelosAvramopoulos,HeribertReis,ManthosG.Papadopoulos SomeAspectsoftheComparativeStudyofSemi-empiricalCombustion ModelsonFLUENTandOpenFOAMCodes .......................... 93 SretenLekic´,MihajloSavic´,PetarGvero Developmentofa HybridStatisticalPhysics–QuantumMechanical MethodologyforComputerSimulationsofCondensedPhasesandIts ImplementationonHigh-PerformanceComputingSystems .............. 99 LjupcˇoPejov,DraganSahpaski,EmilijaKohls,AnastasMishev LifeSciences SolvatochromicEffectfortheDenaturationandMutationProcessesin DNA:ComputationalStudy......................................... 109 JumberKereselidze,MarineKvaraia,ZurabPachulia,GeorgeMikuchadze DynamicFeaturesofComplexSystems:AMolecularSimulationStudy .... 117 ArmenPoghosyan,LevonArsenyan,HrachyaAstsatryan UsingAdaptiveMeshRefinementStrategyforNumericalSolvingofGas DynamicsProblemsonMulticoreComputers .......................... 123 BorisRybakin,PeterBogatencov,GrigoreSecrieru,NicolaiIluha ScientificComputingandHPCOperations NumberTheoryAlgorithmsonGPUClusters.......................... 131 EmanouilAtanassov,DobromirGeorgiev,NikolaiManev AdvancedVulnerabilityAssessmentToolforDistributedSystems ......... 139 SandorAcs,MiklosKozlovszky,PeterKotcauer PerformanceandScalabilityEvaluationofShortFragmentSequence AlignmentApplications ............................................ 147 GergelyWindisch,MiklosKozlovszky,ÁkosBalaskó ImplementationandBenchmarkingofNewFFTLibrariesinQuantum ESPRESSO ...................................................... 155 DušanStankovic´,Petar Jovanovic´,AleksandarJovic´, VladimirSlavnic´, DušanVudragovic´,AntunBalaž AnAnalysisofFFTWandFFTEPerformance......................... 163 MilošNikolic´,AleksandarJovic´,JosipJakic´,VladimirSlavnic´,AntunBalaž AuthorIndex ........................................................ 171
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