High-Performance Computing Infrastructure for South East Europe's Research Communities: Results of the HP-SEE User Forum 2012

177 Pages·2014·8.119 MB·English

by  Emanouil Atanassov, Todor Gurov (auth.), Mihnea Dulea, Aneta Karaivanova, Anastasis Oulas, Ioannis Liabotis, Danica Stojiljkovic, Ognjen Prnjat (eds.)

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
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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