Performance Analysis of AccelrysPerformance Analysis of AccelrysEnterprise Platform 9.0 on IBMEnterprise Platform 9.0 on I...
© 2013 IBM CorporationContent• Performance of AEP 9.0– NGS collection: Bowtie, Bowtie2, BWA• Effect of File System on Perf...
© 2013 IBM CorporationPerformance of AEP 9.0
© 2013 IBM CorporationSystem Configuration
© 2013 IBM CorporationTest Case Description• Mapping Module:– Bowtie, Bowtie2 and BWA Mapper in the NGS Collection• Experi...
© 2013 IBM CorporationBowtie Mapping Protocol
© 2013 IBM CorporationPerformance of Bowtie Protocol3031609265213135 1251879753360501001502002503003508 16 32 64Number of ...
© 2013 IBM CorporationScalability Analysis of Bowtie ProtocolBowtie benchmark comparative performance1879753361.001.933.53...
© 2013 IBM CorporationBowtie 2 Mapping Protocol
© 2013 IBM CorporationPerformance of Bowtie2 protocol38518911982301196 18925412969480501001502002503003504004508 16 32 64N...
© 2013 IBM CorporationBowtie2 benchmark comparative performance25412969481.001.973.685.290501001502002503008.0 16.0 32.0 6...
© 2013 IBM CorporationBWA Mapping Protocol
© 2013 IBM CorporationPerformance of BWA protocol305162937417910075 750501001502002503003508 16 32 64Number of NodesElapse...
© 2013 IBM CorporationScalability Analysis of BWA ProtocolBWA benchmark comparative performance17910075 751.001.792.39 2.3...
© 2013 IBM CorporationSummary of performance of NGS collectionElapsed time for mapping 30x coverage of human genomeon 2.6 ...
© 2013 IBM CorporationEffect of File System on Performance
© 2013 IBM CorporationFile System Description4 x DCS3700 (240 x 2TB, SAS, 7.2K RPM)/vol/xcae1DDN SFA12k (280 x 3TB, SAS, 7...
© 2013 IBM CorporationEnergy Minimization Test CasesEnergy Minimization Protocol with SD FilesEnergy Minimization Protocol...
© 2013 IBM CorporationEnergy Minimization Benchmarks228227No SD file629356Write SD file/vol/xcae1/gpfsTest Case* Benchmark...
© 2013 IBM CorporationBowtie2 Benchmarks437119Bowtie2/vol/xcae1/gpfsTest Caseon 2.6 GHz iDataPlex with GPFS and NFSElapsed...
© 2013 IBM CorporationFile Cache Library Improves I/O PerformanceWithout cache library With cache libraryWithout cache lib...
© 2013 IBM CorporationBest Practice
© 2013 IBM CorporationIBM Reference Architecture for AEP
© 2013 IBM Corporation• Refined / matured for past 13 years• Over 100,000 GPFS licenses worldwide• In academic, commercial...
© 2013 IBM CorporationQ & A
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(ATS6-GS04) Performance Analysis of Accelrys Enterprise Platform 9.0 on IBM’s Scalable IT solution

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IBM recently completed a benchmarking study of several key modules of the Accelrys Enterprise Platform (AEP) 9.0, using IBM’s iDataPlex and General Parallel File System (GPFS). The results show that the performance of IO intensive workloads, such as Next Generation Sequencing (NGS), can be improved significantly by using GPFS. NGS workloads can also benefit from better load balancing implemented on AEP 9.0. Best practices for scalable IT solutions will also be discussed.

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(ATS6-GS04) Performance Analysis of Accelrys Enterprise Platform 9.0 on IBM’s Scalable IT solution

  1. 1. Performance Analysis of AccelrysPerformance Analysis of AccelrysEnterprise Platform 9.0 on IBMEnterprise Platform 9.0 on IBM’’ssScalable IT solutionScalable IT solutionKathy Tzeng, PhDSenior Technical Staff MemberIBMtzy@us.ibm.com
  2. 2. © 2013 IBM CorporationContent• Performance of AEP 9.0– NGS collection: Bowtie, Bowtie2, BWA• Effect of File System on Performance– NGS Collection: Bowtie2– Chemistry: Energy Minimization• Best Practice– Reference Architecture
  3. 3. © 2013 IBM CorporationPerformance of AEP 9.0
  4. 4. © 2013 IBM CorporationSystem Configuration
  5. 5. © 2013 IBM CorporationTest Case Description• Mapping Module:– Bowtie, Bowtie2 and BWA Mapper in the NGS Collection• Experiment:– SRX000600, Illumina sequencing of Human HapMap individual NA18507genomic paired-end library– 213 runs, 1.6 billion spots, 117.4 G bases– Input: ~158GB compressed (~600GB uncompressed) FASTQ files– Output: 180 GB BAM files (~600 GB tmp files)• Reference:– Full Human Genome (3GB) build 37.3
  6. 6. © 2013 IBM CorporationBowtie Mapping Protocol
  7. 7. © 2013 IBM CorporationPerformance of Bowtie Protocol3031609265213135 1251879753360501001502002503003508 16 32 64Number of NodesElapsedTime(minutes)Bowtie: 1 process/node, 32 threads/processBowtie: 4 process/node, 8 threads/processBowtie: 4 process/node, 8 threads/process w/ Splitteron 2.6 GHz iDataPlex with GPFS
  8. 8. © 2013 IBM CorporationScalability Analysis of Bowtie ProtocolBowtie benchmark comparative performance1879753361.001.933.535.190204060801001201401601802008.0 16.0 32.0 64.0Number of NodesElapsedTime(seconds)110RelativeSpeedupBow tie RuntimeBow tie SpeedupLinear Scaleon 2.6 GHz iDataPlex with GPFS
  9. 9. © 2013 IBM CorporationBowtie 2 Mapping Protocol
  10. 10. © 2013 IBM CorporationPerformance of Bowtie2 protocol38518911982301196 18925412969480501001502002503003504004508 16 32 64Number of NodesElapsedTime(minutes)Bowtie2: 1 process/node, 32 threads/processBowtie2: 4 process/node, 8 threads/processBowtie2: 4 process/node, 8 threads/process w/ Splitteron 2.6 GHz iDataPlex with GPFS
  11. 11. © 2013 IBM CorporationBowtie2 benchmark comparative performance25412969481.001.973.685.290501001502002503008.0 16.0 32.0 64.0Number of NodesElapsedTime(seconds)110RelativeSpeedupBow tie2 RuntimeBow tie2 SpeedupLinear ScaleScalability Analysis of Bowtie2 Protocolon 2.6 GHz iDataPlex with GPFS
  12. 12. © 2013 IBM CorporationBWA Mapping Protocol
  13. 13. © 2013 IBM CorporationPerformance of BWA protocol305162937417910075 750501001502002503003508 16 32 64Number of NodesElapsedTime(minutes)BWA: 4 process/node, 8 threads/process w/ SplitterBWA: 8 process/node, e threads/process w/ Splitter4on 2.6 GHz iDataPlex with GPFS
  14. 14. © 2013 IBM CorporationScalability Analysis of BWA ProtocolBWA benchmark comparative performance17910075 751.001.792.39 2.390204060801001201401601802008.0 16.0 32.0 64.0Number of NodesElapsedTime(seconds)110RelativeSpeedupBWA RuntimeBWA SpeedupLinear Scaleon 2.6 GHz iDataPlex with GPFS
  15. 15. © 2013 IBM CorporationSummary of performance of NGS collectionElapsed time for mapping 30x coverage of human genomeon 2.6 GHz iDataPlex with GPFS
  16. 16. © 2013 IBM CorporationEffect of File System on Performance
  17. 17. © 2013 IBM CorporationFile System Description4 x DCS3700 (240 x 2TB, SAS, 7.2K RPM)/vol/xcae1DDN SFA12k (280 x 3TB, SAS, 7.2K RPM)/gpfsStorage SystemFile System
  18. 18. © 2013 IBM CorporationEnergy Minimization Test CasesEnergy Minimization Protocol with SD FilesEnergy Minimization Protocol without SD Files
  19. 19. © 2013 IBM CorporationEnergy Minimization Benchmarks228227No SD file629356Write SD file/vol/xcae1/gpfsTest Case* Benchmark was run by using 32 processes on single nodeon 2.6 GHz iDataPlex with GPFS and NFSElapsed Time in seconds, lower is better
  20. 20. © 2013 IBM CorporationBowtie2 Benchmarks437119Bowtie2/vol/xcae1/gpfsTest Caseon 2.6 GHz iDataPlex with GPFS and NFSElapsed Time in Minutes, lower is better* Benchmark was run by using 32 nodes
  21. 21. © 2013 IBM CorporationFile Cache Library Improves I/O PerformanceWithout cache library With cache libraryWithout cache libraryWithout cache library With cache libraryWithout cache libraryElapsed Time = 1730 min ElapsedTime = 107 min
  22. 22. © 2013 IBM CorporationBest Practice
  23. 23. © 2013 IBM CorporationIBM Reference Architecture for AEP
  24. 24. © 2013 IBM Corporation• Refined / matured for past 13 years• Over 100,000 GPFS licenses worldwide• In academic, commercial and government• Proven scalability for thousands of nodes• Proven capability for greater than 10 PB in single file system• File system performance > 1,500 GB/sec• Amount of archival storage > 500 PB• http://www-03.ibm.com/systems/software/gpfs/IBM General Parallel File System
  25. 25. © 2013 IBM CorporationQ & A

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