High Performance Computing on an IBM Cell Processor

1. High Performance Computing on an IBM Cell Processor Introduction Design Method & Results Problem Statement Design Method Parts / Vendor List Biological researchers are faced with ever increasing computational time due to the exponentially growing data needed to be processed. Currently commodity computing hardware is unable to provide adequate performance. • Two possible ways to parallelize DNAPenny will be explored: • Parallelize entire algorithm • Parallelize performance-critical section • of algorithm • PlayStation 3 was provided by the department • All software used is open source Proposed Concept Sketch / System Description Test Plan The team believes that the Cell Broadband Engine (Cell/B.E.) found in the PlayStation 3 (PS3) will offer superior performance to commodity computing hardware at an affordable price. The team will port an application from the BioPerf suite to the Cell/B.E. running on Linux. BioPerf is a benchmark suite of representative bioinformatics applications for use with high-performance computing. Created script to ensure ported application produces the same output as the original application with a wide variety of input files. Engineering Specification • Input/Output: • Text of DNA sequence / Parsimonious tree • Hardware: • PlayStation 3, Cell/B.E. • Software: • Fedora Linux, DNAPenny 3.6 • User Interface: • Command line Test Procedure / Results • Execute script and verify output has not changed with the original output by using the diff utility. • The output did not change. Project and Design Requirements Benchmarking Methods Design Objective User Interface Prototype Created script to time the execution of significant revisions of the ported application and the original application. An additional script calculates the average run time and automatically generates graphs of the results. A few examples of the generated graphs are shown below. To parallelize and port a BioPerf application to the PlayStation 3 so that it takes full advantage of the performance of the Cell/B.E. Biologists and bioinformaticists will use the ported application the same way they would use the original, using the command line. DNAPenny was ported to the Cell/B.E. taking advantage of the parallel nature of the hardware. Another parallelized version of DNAPenny was created that runs on a standard desktop PC. Assumptions Functional Requirements • User has access to a PlayStation 3 running Linux • User knows how to use original application • Ported application shall run on the Cell/B.E. • Ported application shall return the same results as the original application. • The running time of the ported application shall be recorded for comparison to the original application. Operating Environment • Dry • Temperature controlled (less than 70° F) Nonfunctional Requirements • Algorithm must be parallelizable • Data must be able to be stored in the limited memory of the PlayStation 3 • Must run faster than the original Deliverables • Application ported to Cell/B.E. • Benchmarks to document performance improvement System Block Diagram Literature Survey The system block diagram below shows an overview of the project. The same input data is fed to two versions of the applications – the original code and the ported version – and identical output data is produced at a faster rate. • V. Sachdeva, M. Kistler, E. Speight and T.-H. K. Tzeng, Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications, March 2007. • R. Desaraju, A Parallel Implementation Of A Parsimony-Based Method For Phylogenetic Inference, May 2005 Risks • Proposed implementation may not be faster • Other teams may complete the same work before the team does Resources & Work Breakdown Work Breakdown Structure Financial Resources Other resources • Open source software packages (gcc, gdb, gprof, vim, gnuplot, ssh, bash, lxr, svn, viewvc, diff, cscope) • BioPerf suite (CLUSTALW, DNAPenny, and many others) • Sample input data from NCBI GenBank Closing Summary The team has successfully ported DNAPenny to the Cell/B.E. The ported version of DNAPenny produces the same output for the same input faster than the original application running on a typical desktop PC. With the ported application, bioinformaticists will have a cheap and efficient way to analyze DNA sequences. Total Hours = 564.5 Team May08-24: Faculty Adviser: Team Website: Zhao Zhang http://seniord.ece.iastate.edu/may0824 Bryan Venteicher Shannon McCormick Kyle Byerly Matt Rohlf