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High Performance Computing on an IBM Cell Processor Bioinformatics

This document outlines the functional requirements and proposed design for porting bioinformatics applications to the IBM Cell/B.E. platform. Objectives include ensuring that ported applications run with identical outputs to their originals while improving performance and benchmarking running times. The specifications detail the necessity for compatibility with the Cell processor, utilization of the Synergistic Processing Elements (SPEs), and maintaining the integrity of results as per the BioPerf Suite standards. The proposed design involves profiling code to identify hotspots and opportunities for parallelization to maximize efficiency.

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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. 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

  3. Block Diagram

  4. Functional decomposition • Cannot be done at this time as we have not chosen the software we are porting.

  5. Specifications • It should be able to be compiled on the Cell/B.E. and take advantage of the SPEs when applicable • When the user runs the program it shall seem no different other than perhaps faster than running it on any other computer. • Ported applications shall return their running time for comparisons in the same format as the BioPerf Suite

  6. Proposed Design Method • Run a profiler on the code • Find hotspots • Find parallelizable hotspots • Parallelize for SPEs • Testing • Benchmark

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