Software for Exascale Computing - SPPEXA 2016-2019

624 Pages·2020·20.783 MB·English

by  Hans-Joachim Bungartz, Severin Reiz, Benjamin Uekermann, Philipp Neumann, Wolfgang E. Nagel

136
Hans-Joachim Bungartz · Severin Reiz
Benjamin Uekermann · Philipp Neumann
Wolfgang E. Nagel Editors
Software for
Exascale Computing
SPPEXA
Editorial Board
T. J.Barth
2016 – 2019
M.Griebel
D.E.Keyes
R.M.Nieminen
D.Roose
T.Schlick
Lecture Notes
136
in Computational Science
and Engineering
Editors:
TimothyJ.Barth
MichaelGriebel
DavidE.Keyes
RistoM.Nieminen
DirkRoose
TamarSchlick
Moreinformationaboutthisseriesathttp://www.springer.com/series/3527
Hans-Joachim Bungartz • Severin Reiz (cid:129)
Benjamin Uekermann (cid:129) Philipp Neumann (cid:129)
Wolfgang E. Nagel
Editors
Software for Exascale
Computing - SPPEXA
2016-2019
Editors
Hans-JoachimBungartz SeverinReiz
TechnischeUniversita¨tMu¨nchen TechnischeUniversita¨tMu¨nchen
Garching,Germany Garching,Germany
BenjaminUekermann PhilippNeumann
DepartmentofMechanicalEngineering Helmut-Schmidt-Universita¨tHamburg
EindhovenUniversityofTechnology Hamburg,Germany
Eindhoven,TheNetherlands
WolfgangE.Nagel
TechnischeUniversita¨tDresden
Dresden,Germany
ISSN1439-7358 ISSN2197-7100 (electronic)
LectureNotesinComputationalScienceandEngineering
ISBN978-3-030-47955-8 ISBN978-3-030-47956-5 (eBook)
https://doi.org/10.1007/978-3-030-47956-5
MathematicsSubjectClassification:82-08
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Preface
This volume summarizes the research done and results obtained in the second
funding phase of the Priority Program 1648 “Software for Exascale Computing”
(SPPEXA) of the German Research Foundation (DFG). In that respect, it both
provides an overview of SPPEXA’s achievements and represents a continuation
of Vol. 113 in Springer’s series “Lecture Notes in Computational Science and
Engineering”,thecorrespondingreportofSPPEXA’sfirstfundingphase.
ForsomegeneralremarksontheuniquenessofSPPEXA—asthefirststrategic,
i.e. board-initiated Priority Program of DFG; as the first tri-national Priority
ProgramwithsynchronizedcollaborativeresearchinGermany,France,andJapan;
as a multi-disciplinary endeavor involving informatics and mathematics, but also
variousfieldsfromengineering,thesciences,andthelifesciences;andasthefirst
holistic approach to research on High-Performance Computing (HPC) software
at the level of fundamental research—we refer to the overview contribution of
Bungartz et al. (see chapter “Software for Exascale Computing: Some Remarks
on the Priority ProgramSPPEXA”) in this volume.There,also some statistics are
provided.
The spirit of the international collaboration, whether in a bi-lateral (German–
Japanese) or in a tri-lateral (French–Japanese–German)setting, can be found and
felt in several of the reports of 16 out of 17 SPPEXA consortia. This structured
and institutionalized collaboration was not easy to establish, and we are grateful
forthesharedenthusiasm,commitment,andsupportofthethreeinvolvedfunding
agencies: the German Research Foundation (DFG), the Agence Nationale de la
Recherche (ANR), and the Japan Science and Technology Agency (JST). The
synergies emerging from bringing together the expertise of groups from three
countries did not only boost the respective project work itself, it also prepared
the groundforongoingpartnershipsas well asfor a topicalextensiontowardsthe
interplayofHPCandArtificialIntelligence—afieldthatbothbenefitstremendously
fromHPCand,atthesametime,fostersHPCwithnewconcepts.
As always, many people helped to make SPPEXA in general and this volume
in particular a great success. Concerning the first, our thanks go to the agencies
alreadymentionedandtheirresponsibleofficers;thentoalltheSPPEXAresearchers
v
vi Preface
in 17 consortia who made SPPEXA such a wonderful and productive research
experience; and finally to all helping hands that supported SPPEXA in terms of
organizingandhostingeventssuchasworkshops,doctoralretreats,minisymposia,
genderworkshops,annualplenarymeetings,andsoforth.Moreover,concerningthe
preparationof this volume, we are gratefulto Dr. Martin Peters and Leonie Kunz
from Springer for their support—as in previous cases, it was again a pleasure to
collaborate.Finally,wethankMircoTroue,TinaAngerer,andMichaelObersteiner
fortheirsupportinproofreadingandcompilingthisbook.
Thefirstexascalesystemsareexpectedtobeavailableinaboutoneyear.Forsure,
thereis still a lot ofwork to be doneto let cutting-edgescience applicationsfully
exploittheir potential.However,we arefullyconvincedthatSPPEXA contributed
significantlytopavethewaytowardsexascalecomputersandtheirusage.
Garching,Germany Hans-JoachimBungartz
Garching,Germany SeverinReiz
Eindhoven,Netherlands BenjaminUekermann
Hamburg,Germany PhilippNeumann
Dresden,Germany WolfgangE.Nagel
Contents
PartI SPPEXA:ThePriorityProgram
SoftwareforExascaleComputing:SomeRemarksonthePriority
ProgramSPPEXA ............................................................... 3
Hans-JoachimBungartz,WolfgangE.Nagel,PhilippNeumann,
SeverinReiz,andBenjaminUekermann
APerspectiveontheSPPEXACollaborationfromFrance ................. 19
NahidEmad
APerspectiveontheSPPEXACollaborationfromJapan .................. 23
TakayukiAoki
PartII SPPEXAProjectConsortiaReports
ADA-FS—AdvancedDataPlacementvia Adhoc File Systems
atExtremeScales ................................................................ 29
SebastianOeste,Marc-AndréVef,MehmetSoysal,WolfgangE.Nagel,
AndréBrinkmann,andAchimStreit
AIMES: Advanced Computation and I/O Methods
forEarth-SystemSimulations .................................................. 61
JulianKunkel,NabeehJumah,AnastasiiaNovikova,ThomasLudwig,
HisashiYashiro,NaoyaMaruyama,MohamedWahib,andJohnThuburn
DASH: Distributed Data Structures and ParallelAlgorithms
inaGlobalAddressSpace ...................................................... 103
KarlFürlinger,JoséGracia,AndreasKnüpfer,TobiasFuchs,
DenisHünich,PascalJungblut,RogerKowalewski,andJosephSchuchart
vii
viii Contents
ESSEX:EquippingSparseSolversForExascale............................. 143
ChristieL.Alappat,AndreasAlvermann,AchimBasermann,
HolgerFehske,YasunoriFutamura,MartinGalgon,GeorgHager,
SarahHuber,AkiraImakura,MasatoshiKawai,MoritzKreutzer,
BrunoLang,KengoNakajima,MelvenRöhrig-Zöllner,TetsuyaSakurai,
FaisalShahzad,JonasThies,andGerhardWellein
ExaDG:High-OrderDiscontinuousGalerkinfortheExa-Scale ........... 189
DanielArndt,NiklasFehn,GuidoKanschat,KatharinaKormann,
MartinKronbichler,PeterMunch,WolfgangA.Wall,andJuliusWitte
Exa-Dune—FlexiblePDESolvers,NumericalMethods
andApplications ................................................................. 225
PeterBastian,MircoAltenbernd,Nils-ArneDreier,ChristianEngwer,
JorritFahlke,RenéFritze,MarkusGeveler,DominikGöddeke,
OlegIliev,OlafIppisch,JanMohring,SteffenMüthing,MarioOhlberger,
DirkRibbrock,NikolayShegunov,andStefanTurek
ExaFSA:ParallelFluid-Structure-AcousticSimulation..................... 271
FlorianLindner,AminTotounferoush,MiriamMehl,
BenjaminUekermann,NedaEbrahimiPour,VerenaKrupp,SabineRoller,
ThorstenReimann,DörteC.Sternel,RyusukeEgawa,HiroyukiTakizawa,
andFrédéricSimonis
EXAHD: A Massively Parallel Fault Tolerant Sparse Grid
ApproachforHigh-DimensionalTurbulentPlasmaSimulations........... 301
RafaelLago,MichaelObersteiner,TheresaPollinger,JohannesRentrop,
Hans-JoachimBungartz,TilmanDannert,MichaelGriebel,FrankJenko,
andDirkPflüger
EXAMAG:TowardsExascaleSimulationsoftheMagneticUniverse ..... 331
VolkerSpringel,ChristianKlingenberg,RüdigerPakmor,ThomasGuillet,
andPraveenChandrashekar
EXASTEEL: TowardsaVirtualLaboratoryforthe Multiscale
SimulationofDual-PhaseSteelUsingHigh-PerformanceComputing..... 351
AxelKlawonn,MartinLanser,MatthiasUran,OliverRheinbach,
StephanKöhler,JörgSchröder,LisaScheunemann,DominikBrands,
DanielBalzani,AshutoshGandhi,GerhardWellein,MarkusWittmann,
OlafSchenk,andRadimJanalík
ExaStencils:AdvancedMultigridSolverGeneration........................ 405
ChristianLengauer,SvenApel,MatthiasBolten,ShigeruChiba,
UlrichRüde,JürgenTeich,ArminGrößlinger,FrankHannig,
HaraldKöstler,LisaClaus,AlexanderGrebhahn,StefanGroth,
StefanKronawitter,SebastianKuckuk,HannahRittich,ChristianSchmitt,
andJonasSchmitt
Contents ix
ExtraPeak:AdvancedAutomaticPerformanceModelingforHPC
Applications....................................................................... 453
AlexandruCalotoiu,MarcinCopik,TorstenHoefler,MarcusRitter,
SergeiShudler,andFelixWolf
FFMK:A Fast andFault-TolerantMicrokernel-BasedSystem
forExascaleComputing......................................................... 483
CarstenWeinhold,AdamLackorzynski,JanBierbaum,MartinKüttler,
MaksymPlaneta,HannesWeisbach,MatthiasHille,HermannHärtig,
AlexanderMargolin,DrorSharf,ElyLevy,PavelGak,AmnonBarak,
MasoudGholami,FlorianSchintke,ThorstenSchütt,
AlexanderReinefeld,MatthiasLieber,andWolfgangE.Nagel
GROMEX: A Scalable and Versatile Fast Multipole Method
forBiomolecularSimulation.................................................... 517
BartoszKohnke,ThomasR.Ullmann,AndreasBeckmann,
IvoKabadshow,DavidHaensel,LauraMorgenstern,PlamenDobrev,
GerritGroenhof,CarstenKutzner,BerkHess,HolgerDachsel,
andHelmutGrubmüller
MYX: Runtime CorrectnessAnalysisfor Multi-LevelParallel
ProgrammingParadigms........................................................ 545
JoachimProtze,MiwakoTsuji,ChristianTerboven,ThomasDufaud,
HitoshiMurai,SergePetiton,NahidEmad,MatthiasS.Müller,
andTaisukeBoku
TerraNeo—MantleConvectionBeyondaTrillionDegreesofFreedom.... 569
SimonBauer,Hans-PeterBunge,DanielDrzisga,SiavashGhelichkhan,
MarkusHuber,NilsKohl,MarcusMohr,UlrichRüde,DominikThönnes,
andBarbaraWohlmuth