4005-736-70 Parallel Computing II Building Parallel Programs Source Code Prof. Alan Kaminsky -- Spring Quarter 2012 Rochester Institute of Technology -- Department of Computer Science Part I. Preliminaries 4. A First Parallel Program   Part II. SMPs 5. Massively Parallel Problems 6. SMP Parallel Programming 7. Massively Parallel Problems, Part 2 8. Measuring Speedup 9. Cache Interference 10. Measuring Sizeup 11. Parallel Image Generation 12. Load Balancing 13. Reduction 14. Parallel Random Number Generation 15. Reduction, Part 2 16. Sequential Dependencies 17. Barrier Actions 18. Overlapping Part III. Clusters 19. A First Cluster Parallel Program 21. Massively Parallel Problems, Part 3 23. Load Balancing, Part 2 24. Measuring Communication Overhead 25. Broadcast 26. Reduction, Part 3 27. All-Gather 28. Scalability and Pipelining 29. Overlapping, Part 2 30. All-Reduce 31. All-to-All and Scan   Part IV. Hybrid SMP Clusters 32. Massively Parallel Problems, Part 4 33. Load Balancing, Part 3 34. Partitioning and Broadcast, Part 2 35. Parallel Data-Set Querying Part V. Applications 36. MRI Spin Relaxometry 37. Protein Sequence Querying 38. Phylogenetic Tree Construction Chapter 4. A First Parallel Program Program1Seq Program1Smp Chapter 5. Massively Parallel Problems Chapter 6. SMP Parallel Programming Chapter 7. Massively Parallel Problems, Part 2 Chapter 8. Measuring Speedup Chapter 9. Cache Interference Chapter 10. Measuring Sizeup edu.rit.smp.keysearch.Encrypt edu.rit.smp.keysearch.FindKeySeq edu.rit.smp.keysearch.FindKeySeq2 edu.rit.smp.keysearch.FindKeySmp edu.rit.smp.keysearch.FindKeySmp2 edu.rit.smp.keysearch.FindKeySmp3 edu.rit.smp.keysearch.MakeKey Chapter 11. Parallel Image Generation Chapter 12. Load Balancing edu.rit.smp.fractal.MandelbrotSetGray edu.rit.smp.fractal.MandelbrotSetSeq edu.rit.smp.fractal.MandelbrotSetSmp edu.rit.smp.fractal.MandelbrotSetSmp2 Chapter 13. Reduction Chapter 14. Parallel Random Number Generation edu.rit.smp.monte.PiSeq edu.rit.smp.monte.PiSeq3 edu.rit.smp.monte.PiSmp edu.rit.smp.monte.PiSmp2 edu.rit.smp.monte.PiSmp3 Chapter 15. Reduction, Part 2 edu.rit.smp.fractal.MSHistogramSeq edu.rit.smp.fractal.MSHistogramSmp edu.rit.smp.fractal.MSHistogramSmp2 edu.rit.smp.fractal.MSHistogramSmp3 Chapter 16. Sequential Dependencies edu.rit.smp.network.FloydPrint edu.rit.smp.network.FloydRandom edu.rit.smp.network.FloydSeq edu.rit.smp.network.FloydSmpCol edu.rit.smp.network.FloydSmpRow Chapter 17. Barrier Actions Chapter 18. Overlapping edu.rit.smp.ca.BigRational edu.rit.smp.ca.CCASeq edu.rit.smp.ca.CCASmp edu.rit.smp.ca.CCASmp2 Chapter 19. A First Cluster Parallel Program Program1Seq Program1Clu Chapter 21. Massively Parallel Problems, Part 3 edu.rit.clu.keysearch.Encrypt edu.rit.clu.keysearch.FindKeyClu edu.rit.clu.keysearch.FindKeyClu2 edu.rit.clu.keysearch.FindKeySeq edu.rit.clu.keysearch.FindKeySeq2 edu.rit.clu.keysearch.MakeKey Chapter 23. Load Balancing, Part 2 Chapter 24. Measuring Communication Overhead edu.rit.clu.fractal.MandelbrotSetClu edu.rit.clu.fractal.MandelbrotSetClu2 edu.rit.clu.fractal.MandelbrotSetClu3 edu.rit.clu.fractal.MandelbrotSetSeq edu.rit.clu.timing.TimeSendByte edu.rit.clu.timing.TimeSendDouble edu.rit.clu.timing.TimeSendInt Chapter 25. Broadcast edu.rit.clu.network.FloydClu edu.rit.clu.network.FloydPrint edu.rit.clu.network.FloydRandom edu.rit.clu.network.FloydSeq Chapter 26. Reduction, Part 3 edu.rit.clu.monte.PiClu edu.rit.clu.monte.PiSeq edu.rit.clu.fractal.MSHistogramClu edu.rit.clu.fractal.MSHistogramSeq Chapter 27. All-Gather Chapter 28. Scalability and Pipelining Chapter 29. Overlapping, Part 2 edu.rit.clu.antimatter.AntiprotonClu edu.rit.clu.antimatter.AntiprotonClu2 edu.rit.clu.antimatter.AntiprotonClu3 edu.rit.clu.antimatter.AntiprotonFile edu.rit.clu.antimatter.AntiprotonPlot edu.rit.clu.antimatter.AntiprotonSeq Chapter 30. All-Reduce edu.rit.clu.heat.HotSpotClu edu.rit.clu.heat.HotSpotGray edu.rit.clu.heat.HotSpotSeq Chapter 31. All-to-All and Scan edu.rit.clu.monte.AesTestClu edu.rit.clu.monte.AesTestSeq Chapter 32. Massively Parallel Problems, Part 4 edu.rit.hyb.keysearch.Encrypt edu.rit.hyb.keysearch.FindKeyHyb edu.rit.hyb.keysearch.FindKeySeq edu.rit.hyb.keysearch.MakeKey Chapter 33. Load Balancing, Part 3 edu.rit.hyb.fractal.MandelbrotSetHyb edu.rit.hyb.fractal.MandelbrotSetHyb2 edu.rit.hyb.fractal.MandelbrotSetSeq Chapter 34. Partitioning and Broadcast, Part 2 edu.rit.hyb.network.FloydHyb edu.rit.hyb.network.FloydPrint edu.rit.hyb.network.FloydRandom edu.rit.hyb.network.FloydSeq Chapter 35. Parallel Data-Set Querying edu.rit.hyb.prime.Prime32File edu.rit.hyb.prime.Prime32List edu.rit.hyb.prime.PrimeCountFunctionHyb edu.rit.hyb.prime.PrimeCountFunctionSeq edu.rit.hyb.prime.Sieve   101   103       107   109       113                           127       131           137   139                   149 Chapter 36. MRI Spin Relaxometry edu.rit.mri.CreateSignalDataSet edu.rit.mri.PixelAnalysis edu.rit.mri.PixelChunk edu.rit.mri.PixelSchedule edu.rit.mri.PixelSignal edu.rit.mri.PixelTissues edu.rit.mri.PlotPixel edu.rit.mri.R1Distribution edu.rit.mri.R1Histogram edu.rit.mri.R1Image edu.rit.mri.SignalDataSetReader edu.rit.mri.SignalDataSetWriter edu.rit.mri.SpinRelaxometryClu edu.rit.mri.SpinRelaxometrySeq edu.rit.mri.SpinSignalDifference edu.rit.mri.SpinSignalImage edu.rit.mri.SpinSignal edu.rit.mri.TissuesDataSetReader edu.rit.mri.TissuesDataSetWriter Chapter 37. Protein Sequence Querying edu.rit.compbio.seq.AlignmentPrinter edu.rit.compbio.seq.Alignment edu.rit.compbio.seq.AlignmentStats edu.rit.compbio.seq.Blosum62 edu.rit.compbio.seq.DefaultAlignmentStats edu.rit.compbio.seq.FindProteinHyb2 edu.rit.compbio.seq.FindProteinHyb edu.rit.compbio.seq.FindProteinSeq edu.rit.compbio.seq.ProteinDatabase edu.rit.compbio.seq.ProteinLocalAlignmentSeq edu.rit.compbio.seq.ProteinLocalAlignment edu.rit.compbio.seq.ProteinLocalAlignmentSmp edu.rit.compbio.seq.ProteinSequence edu.rit.compbio.seq.Sequence Chapter 38. Phylogenetic Tree Construction edu.rit.compbio.phyl.Distance edu.rit.compbio.phyl.DnaSequenceList edu.rit.compbio.phyl.DnaSequence edu.rit.compbio.phyl.DnaSequenceTree edu.rit.compbio.phyl.DrawTree edu.rit.compbio.phyl.FitchParsimony edu.rit.compbio.phyl.HammingDistance edu.rit.compbio.phyl.JukesCantorDistance edu.rit.compbio.phyl.LeastSquaresBranchLengths edu.rit.compbio.phyl.MaximumParsimonyBnbHyb edu.rit.compbio.phyl.MaximumParsimonyBnbSeq edu.rit.compbio.phyl.MaximumParsimonyBnbSmp edu.rit.compbio.phyl.MaximumParsimonyExhSeq edu.rit.compbio.phyl.MaximumParsimonyResults edu.rit.compbio.phyl.PhylogenyParsBnbHyb edu.rit.compbio.phyl.PhylogenyParsBnbSeq edu.rit.compbio.phyl.PhylogenyParsBnbSmp edu.rit.compbio.phyl.PhylogenyParsExhSeq edu.rit.compbio.phyl.Results edu.rit.compbio.phyl.TreeDrawing edu.rit.compbio.phyl.Upgma Parallel Computing II • 4005-736-70 • Spring Quarter 2012 Course Page Alan Kaminsky • Department of Computer Science • Rochester Institute of Technology • 4486 + 2220 = 6706 Home Page Copyright © 2012 Alan Kaminsky. All rights reserved. Last updated 06-Mar-2012. Please send comments to ark­@­cs.rit.edu.