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High Performance Computing on an IBM Cell Processor --- Bioinfomatics

High Performance Computing on an IBM Cell Processor --- Bioinfomatics. Advisor: Dr. Zhao Zhang. Kyle Byerly Shannon McCormick Matt Rohlf Bryan Venteicher. May08-24. Introduction. Problem Statement

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High Performance Computing on an IBM Cell Processor --- Bioinfomatics

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  1. High Performance Computing on an IBM Cell Processor --- Bioinfomatics Advisor: Dr. Zhao Zhang Kyle Byerly Shannon McCormick Matt Rohlf Bryan Venteicher May08-24

  2. Introduction • Problem Statement • Researchers need to tackle more complex and computational demanding problems, but are faced with limited budgets • Proposed Solution • Use the PlayStation 3 and Cell processor to achieve improved performance of BioInfomatics applications at a low cost Senior Design May08-24

  3. Bioinformatics • What is it? • Field involving the use of computers for the organization and manipulation of data related to biological structures such as DNA, RNA and proteins • Takes advantage of mathematics and science to solve computational problems involving molecular structures Senior Design May08-24

  4. Bioinformatics (cont) • Example bioinformatics application: Clustal • A multiple sequence alignment tool • Takes multiple sequences of DNA, RNA, or proteins as input • Arranges them to illustrate similarities between all sequences • Can be used to identify structural, functional, or evolutionary similarities Senior Design May08-24

  5. Literature Survey • Previous work done by Sachdeva, Vipin; Kistler, Michael; Speight, Evan; Tzeng, Tzy-Hwa Kathy. 2007. “Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications.” IBM. • Positive results – up to100x speedup Senior Design May08-24

  6. Cell Processor • Sony, Toshiba, and IBM (STI) Alliance • Work began in 2000 • February 2005 – First technical disclosures • May 2005 – First public demonstration • “Super-computer on a chip” • Multi-core processor • Home entertainment to distributed computing • Heterogeneous Processor • Power Processor Element (PPE) • Synergistic Processing Element (SPE) • Element Interconnect Bus (EIB) www.power.org/resources/devcorner/cellcorner/CellTraining_Track, L1T1H1-02 Cell Overview Senior Design May08-24

  7. Project Plan Summary • Project is broken into several steps • Basic understanding of bioinformatics • Will study selected applications algorithm in depth • Research, experimentation with Cell/B.E. programming • Understanding of parallel algorithms • Determine which applications to port • Actual porting process • Verify port correctness, document performance improvements Senior Design May08-24

  8. Project Schedule • Next Semester Plans • Finalize application selection • Port applications • Testing Senior Design May08-24

  9. System Block Diagram Senior Design May08-24

  10. Operating Environment • Linux operating system on the Sony PlayStation 3 • Dry • Temperature controlled environment Senior Design May08-24

  11. Deliverables • Source code to two ported BioPerf applications • Publishable paper if results warrant and time allows Senior Design May08-24

  12. Requirements • Functional • Ported applications shall run on Cell/B.E. • Ported applications shall produce the same output as un-ported applications • Ported applications shall return their execution time • Non-functional • Ported applications shall run faster with the SPEs than without • User interface will not be altered Senior Design May08-24

  13. Work Breakdown Structure Senior Design May08-24

  14. Resource Requirements • PlayStation 3 • Algorithms Books Senior Design May08-24

  15. Design Method • Three methods to port applications to Cell/B.E. • Depend entirely on the compiler • Keep functional logic intact, but split application apart so parts of it can run in multiple threads on the SPE’s • Break application into multiple threads for SPE execution, alter functional logic, vectorized code where possible Senior Design May08-24

  16. Specifications • Input • Two applications from the BioPerf suite • Must not be applications already ported • Limited data set sizes • Should have parallelizable blocks/functions of code • Output • Execution time will be compared • The GNU Profiler, GProf will be used to analyze modified code Senior Design May08-24

  17. Specifications (cont) • User Interface • No plans to alter existing interface • Sample $ sh use-bioperf.shYou can do the following:[R] Run BioPerf[I] Install BioPerf on  your architecture (if your architecture is not PowerPc, x86)[C] Clean outputs in /home/seniord/BioPerf.profile/Outputs[D] Display all versions of the installed codes Senior Design May08-24

  18. Specifications (cont) • Hardware • PlayStation 3 • Powerful servers to do comparisons with • Quad-core Intel Xeon 3.0GHz, 6GB RAM Senior Design May08-24

  19. Specifications (cont) • Software • Fedora 7 with Linux 2.6.23.1 kernel • IBM SDK 3.0 • IBM XLC 9.0, gcc 4.1.1 • GProf 2.17.5 • Testing • Benchmark ported applications with 0, 1, 3, and 6 SPE threads • Verify the output is correct Senior Design May08-24

  20. Conclusions & Questions • Conclusions • Project is interesting • Project is feasible • Porting process will be difficult Senior Design May08-24

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