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High Performance Computing on an IBM Cell Processor Bioinformatics

This project, guided by Dr. Zhao Zhang, explores the application of the IBM Cell Broadband Engine in bioinformatics. We aim to address the challenges posed by exponentially growing data sets within limited budgets. By porting a suite of bioinformatics applications (BioPerf) to the Cell/B.E. architecture, we ensure that they maintain accuracy while significantly increasing processing efficiency. Our work will demonstrate the feasibility and performance gains associated with using the Cell Processor for large-scale bioinformatics data processing on platforms like the PlayStation 3.

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High Performance Computing on an IBM Cell Processor Bioinformatics

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  1. Team Members Kyle Byerly Shannon McCormick Matt Rohlf Bryan Venteicher Advisor Dr. Zhao Zhang High Performance Computing on an IBM Cell ProcessorBioinformatics

  2. Cell Broadband Engine Inexpensive Uniquely suited for the data sets Problem Statement and Solution • Increased data amount to process • Exponentially growing data sets • Limited budgets

  3. Block Diagram

  4. System Description • Cell Broadband Engine • 1 PPE, up to 8 SPE • PPE is a dual core PowerPC processor • SPE is vector processor • BioPerf • Suite of bioinformatics applications used for benchmarking

  5. Operating Environment • Linux • PlayStation 3 • Room temperature • Dry

  6. User Interface • root@ps3:/#

  7. Functional Requirements • Ported applications shall run on the Cell/B.E. • Ported applications shall return the same results as the original applications • Ported applications shall return their running time for comparisons

  8. Non-functional Requirements • Performance

  9. Market Survey • 'Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications' by Sachdeva, Kistler, Speight, and Tzeng • Jinxu Ding, graduate student at ISU • Risk: A group completes all BioPerf applications before we do

  10. Deliverables • Source code to two ported BioPerf applications • Benchmarks

  11. Work Breakdown Structure

  12. Resource Requirements • PlayStation 3 • Algorithms books • Bioinformatics information

  13. Project Schedule

  14. Questions?

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