High-performance scientific computing : algorithms and applications

361 Pages·2012·7.581 MB·English

by  Michael W. Berry, Kyle A. Gallivan, Efstratios Gallopoulos, Ananth Grama, Bernard Philippe, Yousef Saad, Faisal Saied (eds.)

High-Performance Scientific Computing

Michael W. Berry (cid:2) Kyle A. Gallivan (cid:2)
Efstratios Gallopoulos (cid:2) Ananth Grama (cid:2)
Bernard Philippe (cid:2) Yousef Saad (cid:2) Faisal Saied
Editors
High-Performance
Scientific
Computing
Algorithms and Applications
Editors
MichaelW.Berry BernardPhilippe
Dept.ElectricalEng.&ComputerScience IRISA
UniversityofTennessee INRIARennes-BretagneAtlantique
Knoxville,TN,USA Rennes,France
KyleA.Gallivan YousefSaad
DepartmentofMathematics Dept.ofComputerScience&Engineering
FloridaStateUniversity UniversityofMinnesota
Tallahassee,FL,USA Minneapolis,MN,USA
EfstratiosGallopoulos
FaisalSaied
Dept.ComputerEngineering&Informatics
DepartmentofComputerScience
UniversityofPatras
PurdueUniversity
Patras,Greece
WestLafayette,IN,USA
AnanthGrama
DepartmentofComputerScience
PurdueUniversity
WestLafayette,IN,USA
ISBN978-1-4471-2436-8 e-ISBN978-1-4471-2437-5
DOI10.1007/978-1-4471-2437-5
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Preface
ThiscollectionisatributetotheintellectualleadershipandlegacyofProf.Ahmed
H.Sameh.HissignificantcontributionstothefieldofParallelComputing,overhis
longanddistinguishedcareer,havehadaprofoundinfluenceonhighperformance
computingalgorithms,applications,andsystems.Hisdefiningcontributionstothe
fieldofComputationalScienceandEngineering,anditsassociatededucationalpro-
gram, resulted in a generation of highly trained researchers and practitioners. His
high moral character and fortitude serve as exemplars for many in the community
andbeyond.
Prof. Sameh did his graduate studies in Civil Engineering at the University of
Illinois at Urbana-Champaign (UIUC). Upon completion of his Ph.D. in 1966, he
wasrecruitedbyDanielL.Slotnick,ProfessorandDirectoroftheIlliacIVproject,
to develop various numerical algorithms. Prof. Sameh joined the Department of
ComputerScienceasaResearchAssistantProfessor,subsequentlybecomingaPro-
fessor,andalongwithProfs.DuncanLawrie,DanielGajskiandEdwardDavidson
served as the Associate Director of the Center for Supercomputing Research and
Development(CSRD).CSRDwasestablishedin1984undertheleadershipofProf.
DavidJ.KucktobuildtheUniversityofIllinoisCedarmultiprocessor.Prof.Sameh
directedtheCSRDAlgorithmsandApplicationsGroup.Hisvisionary,yetpractical
outlook, in which algorithms were never isolated either from real applications or
fromarchitectureandsoftware,resultedinseminalcontributions.By1995CSRD’s
main mission had been accomplished, and Prof. Sameh moved to the University
of Minnesota as Head of the Computer Science Department and William Norris
Chair for Large-Scale Computing. After a brief interlude, back at UIUC, to lead
CSRD,duringwhichhewasveryactiveinplanningtheestablishmentofComputa-
tionalScienceandEngineeringasadisciplineandanassociatedgraduateprogram
at UIUC, he returned to Minnesota, where he remained until 1997. He moved to
Purdue University as the Head and Samuel D. Conte Professor of Computer Sci-
ence. Prof. Sameh, who is a Fellow of SIAM, ACM and IEEE, was honored with
theIEEE1999HarryH.GoodeMemorialAward“Forseminalandinfluentialwork
inparallelnumericalalgorithms”.
ItwasatPurduethatover50researchersandacademicprogenyofProf.Sameh
gatheredinOctober2010tocelebratehis70thbirthday.TheoccasionwastheCon-
v
vi Preface
ferenceonHighPerformanceScientificComputing:Architectures,Algorithms,and
Applicationsheldinhishonor.TheattendeesrecalledProf.Sameh’smanyacademic
achievements,including,notonlyhisresearchbutalsohiseffortsindefiningthein-
terdisciplinary field of Computational Science and Engineering and his leadership
andfoundingEditor-in-ChiefroleintheIEEECS&EMagazineaswellasthemany
doctoralcandidatesthathehasgraduated:AtUIUC,JonathanLermit(1971),John
Larson(1978),JohnWisniewski(1981),JosephGrcar(1981),EmmanuelKamgnia
(1983),ChandrikaKamath(1986),MarkSchaefer(1987),Hsin-ChuChen(1988),
RandallBramley(1988),Gung-ChungYang(1990),MichaelBerry(1990),FelixG.
Lou (1992), Bart Semeraro (1992) and Vivek Sarin (1997); Ananth Grama (1996)
attheUniversityofMinnesota;andZhanyeTong(1999),MattKnepley(2000),Ab-
delkader Baggag (2003), Murat Manguoglu (2009) and Carl Christian Kjelgaard
Mikkelsen(2009)atPurdue.
ThisvolumeconsistsofasurveyofProf.Sameh’scontributionstothedevelop-
ment high performance computingand sixteen editoriallyreviewed papers written
tocommemoratetheoccasionofhis70thbirthday.
Knoxville,USA MichaelW.Berry
Tallahassee,USA KyleA.Gallivan
Patras,Greece StratisGallopoulos
WestLafayette,USA AnanthGrama
Rennes,France BernardPhilippe
Minneapolis,USA YousefSaad
WestLafayette,USA FaisalSaied
Acknowledgements
We are especially grateful to Profs. Zhiyuan Li, Alex Pothen, and Bob Skeel for
many arrangements that made the conference possible. We are also grateful to
Dr.EricCox,whoundertooktheheavyloadofmakingmanyofthelocalarrange-
mentsandDr.GeorgeKolliasandMs.Eugenia-MariaKontopouloufortheirhelpin
compilingthisvolume.Finally,wethankSpringerandespeciallyMr.SimonRees
for patiently working with us on this project and Donatas Akmanavicˇius of VTeX
BookProductionforgreateditingworkincompilingthevolume.
vii

Contents
1 ParallelNumericalComputingfromIlliacIVtoExascale—The
ContributionsofAhmedH.Sameh . . . . . . . . . . . . . . . . . . . 1
Kyle A. Gallivan, Efstratios Gallopoulos, Ananth Grama,
Bernard Philippe, Eric Polizzi, Yousef Saad, Faisal Saied, and
Danny Sorensen
2 ComputationalCapacity-BasedCodesignofComputerSystems . . . 45
DavidJ.Kuck
3 MeasuringComputerPerformance . . . . . . . . . . . . . . . . . . . 75
WilliamJalby,DavidC.Wong,DavidJ.Kuck,Jean-ThomasAcquaviva,
andJean-ChristopheBeyler
4 ACompilationFrameworkfortheAutomaticRestructuring
ofPointer-LinkedDataStructures . . . . . . . . . . . . . . . . . . . 97
HarmenL.A.vanderSpek,C.W.MattiasHolm,andHarryA.G.Wijshoff
5 DenseLinearAlgebraonAcceleratedMulticoreHardware . . . . . 123
JackDongarra,JakubKurzak,PiotrLuszczek,andStanimireTomov
6 TheExplicitSpikeAlgorithm:IterativeSolutionoftheReduced
System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
CarlChristianKjelgaardMikkelsen
7 The Spike Factorization as Domain Decomposition Method;
EquivalentandVariantApproaches . . . . . . . . . . . . . . . . . . 157
VictorEijkhoutandRobertvandeGeijn
8 ParallelSolutionofSparseLinearSystems . . . . . . . . . . . . . . . 171
MuratManguoglu
9 ParallelBlock-JacobiSVDMethods . . . . . . . . . . . . . . . . . . 185
MartinBecˇka,GabrielOkša,andMariánVajteršic
ix