High-Performance Computing

568 Pages·1999·50.294 MB·English

by  R. J. Allan, M. F. Guest, A. D. Simpson, D. S. Henty, D. A. Nicole (auth.), R. J. Allan, M. F. Guest, A. D. Simpson, D. S. Henty, D. A. Nicole (eds.)

High-Performance Computing
High-Performance Computing
Edited by
R. J. Allan
and
M. F. Guest
HPCICentre
CLRCDaresburyLaboratory
Daresbury, England
A. D. Simpson
and
D. S. Henty
EPCC
UniversityofEdinburgh
Edinburgh, ScoUand
and
D. A. Nicole
HPCICentre
UniversityofSouthampton
Southampton, England
KLUWER ACADEMIC I PLENUM PUBLISHERS
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ProceedingsofttleHigh-Performal'lCBComputingInitiallve(HPCI)Conference.
heldJanuary12-14.1998,inManchester,England
ISBN0-306-46034-3
C 1999KluwerAcademicIPlenumPublishers,NewYork
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PREFACE
Over the past decade high performance computinghas demonstrated the ability
to model and predict accurately a wide range of physical properties and phenomena.
Many of these have had an important impact in contributing to wealth creation and
improving the quality oflife through the developmentofnew products and processes
with greater efficacy, efficiencyor reduced harmfulside effects, and in contributingto
our ability to understand and describe the world around us.
Followingasurveyofthe U.K.'s urgent needfor asupercomputingfacilityfor aca
demic research (see next chapter), a 256-processor T3D system from Cray Research
Inc. went into operation at the UniversityofEdinburgh in the summerof1994. The
High Performance Computing Initiative, HPCI, was established in November 1994 to
support and ensure theefficientand effectiveexploitationoftheT3D (andfuture gen
erations ofHPC systems) by a number ofconsortiaworking in the "frontier" areas of
computational research. The Cray T3D, now comprising 512 processors and total of
32 CB memory, represented a very significant increase in computing power, allowing
simulationsto moveforward on a numberoffronts.
The three-fold aims of the HPCI may be summarised as follows; (1) to seek and
maintainaworldclasspositionincomputationalscienceandengineering,(2) tosupport
and promote exploitation of HPC in industry, commerce and business, and (3) to
support education and training in HPC and its application.
A number of research grant awards have been made under the auspices of the
HPCI, toboth(i)establishanumberofConsortiaofresearchgroups, withprovisionof
post-doctoral research associates (to theso-called "directlysupported" consortia), plus
travel and computer time (to both "directly" and "indirectly supported" consortia),
and (ii) establish three HPCI centres to support new application developmentand to
interact with education, training and technology transfer programmes.
TheHPCI Centreat CLRC Daresbury Laboratory, with assistancefrom the Cen
tres at the Universities of Edinburgh and Southampton, organised the first National
HPCI Conference designed to overview the success of this service and to provide a
forum for identifying someof the key scientificrequirements likely to be encountered
during the comingthree years.
Theevent took place at the Manchester Conference Centre Renold's complexon
the UMIST campus from 12-14th January 1998. Organisation of the conference had
taken a considerableeffort and it was therefore pleasing to have nearly 140 registered
attendees including representatives of most of the companies active in HPC who, to
gether with NERC and EPSRC, provided generous sponsorship enabling the event to
take place.
v
There were8plenary talks, including those from:
Dr. Richard Blake (CLRC), "Background to the U.K. High-Performance Computing
Initiative";
Dr. David Dixon (PNNL, Richland, USA), "Computational Environmental Molecular
Science: Relevance to DOE Cleanup Problems";
Dr. Alfred Geiger (HLRS, Stuttgart), "Supercomputing and Applications in German
Research and Industry";
Prof. Alan O'Neilland Dr. Lois Steenman-Clark (UniversityofReading), "Modelling
ClimateVariabilityon High-PerformanceComputersand DataHandlingStrategiesfor
EnvironmentalModels";
Richard M. Russell (Tera Computer Company, USA), "Early Experience with Tera
MTA";
Stuart Ward (EPSRC), "Progress with the HPC'97 Procurement";
Prof. David Crighton FRS (UniversityofCambridge), "The UniversityofCambridge
High PerformanceComputingFacility";
Prof. DavidWalker(UniversityofCardiff), "SoftwareStandardsfor High Performance
Computing".
In addition a further invited speaker, Ken Turner, entertained us after the Con
ference Dinner, with adescriptionofthe Manchester "Baby" computerrebuild project
whichisnearingcompletion. Thiswasespeciallyfittingfornotonlyis1998the50than
niversaryofthis, theworld'sfirst stored-programcomputer(known as theSmall-Scale
Experimental Machine, SSEM), but the replica machine is shortly to be exhibited in
the Manchester MuseumofScienceand Industry wherethe dinner took place.
The ambitious programme also had space for 40 speakers presenting submitted
talks in parallelsessions and afurther postersessionwith some15contributedpapers.
ThuswewereabletocovertheworkofalltheHPCI-supportedconsortiaplusanumber
ofother related U.K. projects.
This book contains most ofthe papers presented at the conference. Itisintended
to act as a record of the scientific achievements of three years usage of the HPCI
supported Cray T3D at EPCC and to indicate a subset of the anticipated scientific
requirementsover the comingthreeyears.
In addition to the scientific material presented as talks or posters, a number of
computervendorsexhibited products at the Conference. Theseincluded:
Silicon GraphicsjCray Research, http://www.cray.com;
Hitachi Europe Ltd., http://www.hitachi-eu.com;
Fujitsu SystemsEurope, http://www.fujitsu.com;
NEC, http://www.nec.com;
IBM UK, http://www.uk.ibm.com;
Quadrics Supercomputers World Ltd., http://www.quadrics.com;
TERA Computer Company, http://www.tera.com;
Digital Equipment Company, http://www.europe.digital.com;
Progress Computers, http://www.progress.co.uk, and
The ManchesterMarkI Rebuild Project, http://www.computer50.org;
Finally, we thank the many sponsors of the HPCI Conference, without whom
the event could not have taken place. These include, EPSRC; NERC; CLRC; Silicon
GraphicsjCray Research; Hitachi Europe Ltd.; Fujitsu Systems Europe; NEC; IBM
UK; Digital Equipment Company; NAG Ltd. and Quadrics Supercomputers World.
R.J.Allan,M.F.Guest,
A. D.Simpson,D.S.Henty,andD.A.Nicole
March1998
vi
Lefttoright:DavidEmerson(CLRC),AmeetDave(SGlfCrayLimited),RobertAllan(CLRC).
andStephenBooth(EPCC).
HPCI 1998DelegatesattheMuseumofScienceandIndustry.Manchester.
vii
CONTENTS
THE U.K.HIGH-PERFORMANCECOMPUTINGINITIATIVE
Introduction ............................................................ 3
R.1.Allan,M. F.Guest,A. D. Simpson,D. S.Henty,andD.A.Nicole
ScienceSupportfromtheEPCCHPCICentre. ................................ 11
AlanD. SimpsonandDavidS.Henty
TheCLRCHPCICentreatDaresburyLaboratory 21
R.1.Allan,I.1.Bush,K.Kleese,A. G.Sunderland,andM.F.Guest
SouthamptonHigh PerformanceComputingCentre ..... ....................... 33
DenisNicole,Kenji Takeda,IvanWolton,andSimonCox
OPTIMISATION,ALGORITHMSANDSOFTWARE
PerformanceOptimisationontheCrayT3E 45
StephenBooth
FromFLOPStoUDAPS: Algorithms,Benchmarking,andTuning 53
NickMacLaren
IsPredictiveTracingtoolateforHPCUsers? , 57
DarrenJ. Kerbyson,EfstathiosPapaefstathiou,JohnS.Harper,StewardC. Perry,
andG.R.Nudd
SolvingDenseSymmetricEigenproblemsontheCrayT3D...................... 69
K.Murphy,M.Clint,andR. H.Perrott
PARASOL: AnIntegratedProgrammingEnvironmentforParallelSparseMatrix
Solvers........................................ 79
PatrickAmestoy,lainS.Duff,JeanYvesL'Excellent,andPetrPlechac
ComputationalModellingofMulti-PhysicsProcessesonHighPerformanceParallel
ComputerSystems 91
M.Cross,K. McManus,S.P.Johnson,C. S. lerotheou,C.Walshaw,C.Bailey,
andK. A.Pericleous
ix
PortingIndustrialCodestoMPPSystemsusingHPF ........................... 103
L.M. Delves
DecompositionIndependenceinParallelPrograms 113
S. Booth
SoftwarePortabilityandMaintenance ... .................................... 119
KenjiTakeda,IvanWolton,andDenisNicole
ADesignEnvironmentforStructuredMappingofSignalProcessingApplications
onParallelProcessors ................................................ 127
MoeRazaz
MATERIALSCHEMISTRYANDSIMULATION
NewVistasforFirst-PrinciplesSimulation 137
G. Ackland,D.Bird,P. Bristowe,M.Finnis,M.1.Gillan,N. M. Harrison,
V.Heine, P. A. Madden,M.C. Payne,andA. P. Sutton
OntheQuasi-ParticleSpectraofYBa Cup7 147
2
W M.Temmerrnan,M.L.Gyorffy,Z. Szotek,O.K.Andersen,andO.Jepsen
AbInitioStudiesofHydrogenMoleculesinSilicon 155
B.Hourahine,R.Jones,S.Oberg,R.C. Newman, P. R. Briddon,andE. Roduner
QuantumMonteCarloSimulationsofRealSolids 165
W M.C. Foulkes,M.Nekovee,R.L.Gaudoin,M.L. Stedman,R.1.Needs,
R. Q. Hood,G. Rajagopal,M. D.Towler, P. R. C.Kent,Y. Lee,W-K. Leung,
A. R. Porter,andS.1. Breuer
AbInitioInvestigationsoftheDynamicalpropertiesofIce 175
I. Morrison, S. Jenkins,J. C.Li,andD.K. Ross
PhaseSeparationofTwoImmiscibleLiquids 185
S.I.Jury,P. Bladon,S. Krishna,andM.E.Cates
ComputerSimulationofLiquidCrystalsontheT3D/TJE 193
MarkR.Wilson,MichaelP.Allen,MaureenP.Neal,ChristopherM.Care,and
DouglasJ. Cleaver
AFirstPrinciplesStudyofSubstitutionalGoldinGeremanium 203
1.Coomer,A.Resende,P. R. Briddon,S.Oberg,andR. Jones
ApplicationsofSelf-InteFactionCorrectiontoLocalizedStatesinSolids 207
Z.Szotek,W M.Temmerrnan,A.Svane,H.Winter,S.V. Beiden,G.A. Gehring,
S.L.Dudarev,andA. P. Sutton
COMPUTATIONALCHEMISTRY
ComputationalChemistryintheEnvironmentalMolecularSciencesLaboratory ..... 215
DavidA. Dixon,ThornDunning,Jr.,Michel Dupuis,DavidFeller,
DeborahGracio, RobertJ. Harrison, DonaldR.Jones,RickyA. Kendall,
JeffereyA.Nichols, KarenSchuchardt,andTjerekStraatsma
x
MacromolecularModellingontheCrayDD 229
MatthewD.Cooper,JuliaM.Goodfellow,IanH.Hillier,
ChristopherA. Reynolds,W. GrahamRichards,MichaelA.Robb,
PaulSherwood,andIanH. Williams
AccurateConfigurationInteractionComputationsofPotentialEnergySurfaces
usingMassivelyParallelComputers..................................... 237
AbigailJ. DobbynandPeterKnowles
MolecularPropertiesfromFirstPrinciples 249
C.J. Adam,S.J. Clark,G.J. Ackland,and1.Crain
MassiveParallelism: TheHardwareforComputationalChemistry? 259
M.F.Guest, P. Sherwood,and1.A.Nichols
ATOMICPHYSICS
TheMultiphotonandElectronCollisionsConsortiumandtheHeliumCode 275
K. T.Taylor,J. S. Parker,andE. S. Smyth
Applicationof6DIME:(y,2e)onHe 285
1.Rasch,Co1mT. Whelan,S.P.Lucey,andH.R. J. Walters
ParallelisationofAtomicR-MatrixScatteringPrograms 293
A. Sunderland,P. G. Burke,V. M. Burke,andC.1.Noble
PartialWave Integrals 30I
1.RaschandColmT. Whelan
MolecularRotation-VibrationCalculationsusingMassivelyParallelComputers ..... 307
HamseY.Mussa,JonathanTennyson,C.J.Noble,andR.1.Allan
ENVIRONMENTALMODELLING
ModellingClimateVariabilityonHPC Platforms 317
LoisSteenman-ClarkandAlanO'Neill
TheU. K. OceanCirculationandAdvancedModellingProject(OCCAM) 325
BeverlyA.deCuevas,DavidJ. Webb,AndrewC.Coward,
CatherineS. Richmond,andElizabethRourke
TheSouthampton-EastAnglia(SEA)Model: AGeneralPurposeParallelOcean
CirculationModel 337
MatthewBeare
HighResolutionModellingofAirflowovertheIsleofArran 347
AlanGadian,IanStromberg,andRobertWood
DevelopmentofPortableShelfSeaModelsforMassivelyParallelMachines 359
RogerProctor,PeterLockey,andIan D.James
SatelliteAltimeterDataAssimilationintheOCCAMGlobalOceanModel 365
AlanD.Fox,KeithHaines,BeverlyA. deCuevas,andAndrewC.Coward
xi
ParallelisationandPerformanceofaStratosphericChemicalTransportModel 371
CateBridgeman
SupercomputingandApplicationsinGermanResearchandIndustry 379
AlfredGeigerandRolandRuhle
InvestigationofSequencingEffectsontheSimulationofFluid-StructureInteraction .. 385
1.K. Badcock,G. S.L.Goura,andB.E. Richards
DirectNumericalSimulationofTurbulentFlames 395
Karl W. Jenkins,W. Kendal Bushe,LaurentL. Leboucher,andL. R. StewartCant
UnderstandingTurbulenceinFluidsusingDirectSimulationData 407
M. Alam,E.Avital,T.1.Craft,S.P. Fiddes,H. P. Horton,R.1.A. Howard,
D.P.Jones,K.H.Luo,N. D.Sandham,A. M. Savill,T.G. Thomas,
P. R:'Voke,andJ.1. R. Williams
ParallelProcessingandDirectSimulationofTransientPremixedLaminarFlames
withDetailedChemicalKinetics 417
R. P.LindstedtandV. Sakthitharan
TimeDomainElectromagnetic ScatteringSimulationsonUnstructuredGrids 429
P.1.Brookes,O.Hassan,K. Morgan,R. Said,andN. P. Weatherill
Large-EddySimulationoftheVortexSheddingProcessintheNear-FieldWake
behinda SquareCylinder 437
F.diMareandW. P.Jones
Self-Adaptive,Parallel SolutionMethodsforComplexFEMProblemsinCFDand
RadiationModelling 449
XiaoXu,ChristopherC.Pain,CassianoR.E.deOliveira,AdrianP.Umpleby,
andAntonyJ. H.Goddard
HUMANSYSTEMSANDINFORMATION
HPCandHumanGeographicSocialScienceResearch 457
StanOpenshaw
ApplicationofPatternRecognitiontoConceptDiscoveryinGeography 467
IanTurton
HighPerformanceComputinginBanking 479
J.A. Keane
LegacySystems-TheFutureofHPC 487
1.A. Keane,M.F.P.O'Boyle,andR. Sakellariou
ASTROPHYSICSANDCOSMOLOGY
SimulationsofLatticeQuantumChromodynamicsontheCrayT3DandT3E 497
DavidRichards
xii