GPU Computing Gems: Emerald Edition

889 Pages·2011·20.17 MB·English

by  Wen-mei W. Hwu

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GPU Computing Gems
Emerald Edition
ELS Dunn 01-fm-i-iv-9780123849885 — 2011/1/8 — 12:46 — page ii — #2
Morgan Kaufmann’s Applications of GPU Computing Series
Computing is quickly becoming the third pillar of scientific research, due in large part to the perfor-
mance gains achieved through graphics processing units (GPUs), which have become ubiquitous in
handhelds, laptops, desktops, and supercomputer clusters. Morgan Kaufmann’sApplications of GPU
Computing series offers training, examples, and inspiration for researchers, engineers, students, and
supercomputingprofessionalswhowanttoleveragethepowerofGPUsincorporatedintotheirsimu-
lations or experiments. Each high-quality, peer-reviewed book is written by leading experts uniquely
qualifiedtoprovideparallelcomputinginsightsandguidance.
Each GPU Computing Gems volume offers a snapshot of the state of parallel computing across a
carefullyselectedsubsetofindustrydomains,givingyouawindowintothelead-edgeresearchoccur-
ring across the breadth of science, and the opportunity to observe others’ algorithm work that might
applytoyourownprojects.Findoutmoreathttp://mkp.com/gpu-computing-gems.
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ELS Dunn 01-fm-i-iv-9780123849885 — 2011/1/8 — 12:46 — page iii — #3
GPU Computing Gems
Emerald Edition
Wen-mei W. Hwu
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ELS Dunn 01-fm-i-iv-9780123849885 — 2011/1/8 — 12:46 — page iv — #4
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GPUcomputinggems/editor,Wen-meiW.Hwu.
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Includesbibliographicalreferences.
ISBN978-0-12-384988-5
1.Graphicsprocessingunits–Programming.2.Imagingsystems.3.Computergraphics.4.Image
processing–Digitaltechniques.I.Hwu,Wen-mei.
T385.G68752011
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2010047487
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Contents
Editors,Reviewers,andAuthors ....................................................................... xi
Introduction.............................................................................................. xix
Wen-meiW.Hwu
SECTION 1 SCIENTIFIC SIMULATION
RobertM.Farber
CHAPTER 1 GPU-AcceleratedComputationandInteractiveDisplayofMolecular
Orbitals.......................................................................... 5
JohnE.Stone,DavidJ.Hardy,JanSaam,KirbyL.Vandivort,KlausSchulten
CHAPTER 2 Large-ScaleChemicalInformaticsonGPUs..................................... 19
ImranS.Haque,VijayS.Pande
CHAPTER 3 DynamicalQuadratureGrids:ApplicationsinDensityFunctional
Calculations..................................................................... 35
NathanLuehr,IvanUfimtsev,ToddMartinez
CHAPTER 4 FastMolecularElectrostaticsAlgorithmsonGPUs.............................. 43
DavidJ.Hardy,JohnE.Stone,KirbyL.Vandivort,DavidGohara,ChristopherRodrigues,
KlausSchulten
CHAPTER 5 QuantumChemistry:PropagationofElectronicStructureonaGPU............. 59
JacekJakowski,StephanIrle,KeijiMorokuma
CHAPTER 6 AnEfficientCUDAImplementationoftheTree-BasedBarnesHutn-Body
Algorithm........................................................................ 75
MartinBurtscher,KeshavPingali
CHAPTER 7 LeveragingtheUntappedComputationPowerofGPUs:FastSpectral
SynthesisUsingTextureInterpolation........................................... 93
RichardTownsend,KarthikeyanSankaralingam,MatthewD.Sinclair
CHAPTER 8 BlackHoleSimulationswithCUDA.............................................. 103
FrankHerrmann,JohnSilberholz,ManuelTiglio
CHAPTER 9 TreecodeandFastMultipoleMethodforN-BodySimulationwithCUDA........ 113
RioYokota,LorenaA.Barba
v
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vi Contents
CHAPTER 10 Wavelet-BasedDensityFunctionalTheoryCalculationonMassively
ParallelHybridArchitectures ................................................... 133
LuigiGenovese,MatthieuOspici,BriceVideau,ThierryDeutsch,Jean-Franc¸oisMe´haut
SECTION 2 LIFE SCIENCES
BertilSchmidt
CHAPTER 11 AccurateScanningofSequenceDatabaseswiththeSmith-Waterman
Algorithm........................................................................ 155
ŁukaszLigowski,WitoldR.Rudnicki,YongchaoLiu,BertilSchmidt
CHAPTER 12 MassiveParallelComputingtoAccelerateGenome-Matching.................. 173
BenWeiss,MikeBailey
CHAPTER 13 GPU-SupercomputerAccelerationofPatternMatching......................... 185
AliKhajeh-Saeed,J.BlairPerot
CHAPTER 14 GPUAcceleratedRNAFoldingAlgorithm........................................ 199
GuillaumeRizk,DominiqueLavenier,SanjayRajopadhye
CHAPTER 15 TemporalDataMiningforNeuroscience........................................ 211
Wu-chunFeng,YongCao,DebprakashPatnaik,NarenRamakrishnan
SECTION 3 STATISTICAL MODELING
MikeGiles
CHAPTER 16 ParallelizationTechniquesforRandomNumberGenerators .................... 231
ThomasBradley,JacquesduToit,RobertTong,MikeGiles,PaulWoodhams
CHAPTER 17 MonteCarloPhotonTransportontheGPU ...................................... 247
La´szlo´ Szirmay-Kalos,Bala´zsTo´th,Mila´nMagdics
CHAPTER 18 High-PerformanceIteratedFunctionSystems................................... 263
ChristophSchied,JohannesHanika,HolgerDammertz,HendrikP.A.Lensch
SECTION 4 EMERGING DATA-INTENSIVE APPLICATIONS
VolodymyrKindratenko
CHAPTER 19 Large-ScaleMachineLearning.................................................. 277
JerodJ.Weinman,AugustusLidaka,ShitanshuAggarwal
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Contents vii
CHAPTER 20 MulticlassSupportVectorMachine............................................. 293
SergioHerrero-Lopez
CHAPTER 21 Template-DrivenAgent-BasedModelingandSimulationwithCUDA............ 313
PaulRichmond,DanielaRomano
CHAPTER 22 GPU-AcceleratedAntColonyOptimization ...................................... 325
RobinM.Weiss
SECTION 5 ELECTRONIC DESIGN AUTOMATION
SunilP.Khatri
CHAPTER 23 High-PerformanceGate-LevelSimulationwithGP-GPUs........................ 343
DebapriyaChatterjee,AndrewDeOrio,ValeriaBertacco
CHAPTER 24 GPU-BasedParallelComputingforFastCircuitOptimization ................... 365
YifangLiu,JiangHu
SECTION 6 RAY TRACING AND RENDERING
AustinRobison
CHAPTER 25 LatticeBoltzmannLightingModels.............................................. 381
RobertGeist,JamesWestall
CHAPTER 26 PathRegenerationforRandomWalks........................................... 401
JanNova´k,VlastimilHavran,CarstenDachsbacher
CHAPTER 27 FromSparseMocaptoHighlyDetailedFacialAnimation....................... 413
BerndBickel,ManuelLang
CHAPTER 28 AProgrammableGraphicsPipelineinCUDAforOrder-Independent
Transparency.................................................................... 427
MengchengHuang,FangLiu,XuehuiLiu,EnhuaWu
SECTION 7 COMPUTER VISION
JamesFung
CHAPTER 29 FastGraphCutsforComputerVision............................................ 439
P.J.Narayanan,VibhavVineet,TimoStich
CHAPTER 30 VisualSaliencyModelonMulti-GPU............................................ 451
AnisRahman,DominiqueHouzet,DenisPellerin
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viii Contents
CHAPTER 31 Real-TimeStereoonGPGPUUsingProgressiveMultiresolutionAdaptive
Windows ........................................................................ 473
YongZhao,GabrielTaubin
CHAPTER 32 Real-TimeSpeed-Limit-SignRecognitiononanEmbeddedSystem
UsingaGPU..................................................................... 497
PinarMuyan-O¨zc¸elik,VladimirGlavtchev,JeffreyM.Ota,JohnD.Owens
CHAPTER 33 HaarClassifiersforObjectDetectionwithCUDA................................ 517
AntonObukhov
SECTION 8 VIDEO AND IMAGE PROCESSING
TimoStich
CHAPTER 34 ExperiencesonImageandVideoProcessingwithCUDAandOpenCL .......... 547
AlptekinTemizel,TugbaHalici,BerkerLogoglu,TugbaTaskayaTemizel,
FatihOmruuzun,ErsinKaraman
CHAPTER 35 ConnectedComponentLabelinginCUDA ....................................... 569
OndrˇejSˇt´ava,BedrˇichBenesˇ
CHAPTER 36 ImageDe-Mosaicing ............................................................ 583
JoeStam,JamesFung
SECTION 9 SIGNAL AND AUDIO PROCESSING
JohnRoberts
CHAPTER 37 EfficientAutomaticSpeechRecognitionontheGPU............................ 601
JikeChong,EkaterinaGonina,KurtKeutzer
CHAPTER 38 ParallelLDPCDecoding......................................................... 619
GabrielFalcao,VitorSilva,LeonelSousa
CHAPTER 39 Large-ScaleFastFourierTransform............................................. 629
YifengChen,XiangCui,HongMei
SECTION 10 MEDICAL IMAGING
LawrenceTarbox
CHAPTER 40 GPUAccelerationofIterativeDigitalBreastTomosynthesis .................... 647
DanaSchaa,BenjaminBrown,ByunghyunJang,PerhaadMistry,RodrigoDominguez,
DavidKaeli,RichardMoore,DanielB.Kopans
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Contents ix
CHAPTER 41 ParallelizationofKatsevichCTImageReconstructionAlgorithm
onGenericMulti-CoreProcessorsandGPGPU.................................. 659
AbderrahimBenquassmi,EricFontaine,Hsien-HsinS.Lee
CHAPTER 42 3-DTomographicImageReconstructionfromRandomlyOrderedLines
withCUDA....................................................................... 679
GuillemPratx,Jing-YuCui,SvenPrevrhal,CraigS.Levin
CHAPTER 43 UsingGPUstoLearnEffectiveParameterSettingsforGPU-Accelerated
IterativeCTReconstructionAlgorithms ......................................... 693
WeiXu,KlausMueller
CHAPTER 44 UsingGPUstoAccelerateAdvancedMRIReconstructionwithField
InhomogeneityCompensation................................................... 709
YueZhuo,Xiao-LongWu,JustinP.Haldar,ThibaultMarin,Wen-meiW.Hwu,
Zhi-PeiLiang,BradleyP.Sutton
CHAPTER 45 (cid:96)1Minimizationin(cid:96)1-SPIRiTCompressedSensingMRIReconstruction....... 723
MarkMurphy,MikiLustig
CHAPTER 46 MedicalImageProcessingUsingGPU-AcceleratedITKImageFilters.......... 737
Won-KiJeong,HanspeterPfister,MassimilianoFatica
CHAPTER 47 DeformableVolumetricRegistrationUsingB-Splines........................... 751
JamesShackelford,NagarajanKandasamy,GregorySharp
CHAPTER 48 MultiscaleUnbiasedDiffeomorphicAtlasConstructiononMulti-GPUs......... 771
LinhHa,JensKru¨ger,SarangJoshi,Cla´udioT.Silva
CHAPTER 49 GPU-AcceleratedBrainConnectivityReconstructionand
VisualizationinLarge-ScaleElectronMicrographs............................. 793
Won-KiJeong,HanspeterPfister,JohannaBeyer,MarkusHadwiger
CHAPTER 50 FastSimulationofRadiographicImagesUsingaMonteCarloX-Ray
TransportAlgorithmImplementedinCUDA...................................... 813
AndreuBadal,AldoBadano
Index.............................................................................................. 831