High Performance Computing on an IBM Cell Processor Team May08-24: Kyle Byerly Matt Rohlf Bryan Venteicher Shannon McCormick Faculty Adviser: Team Website: Zhao Zhang Introduction Problem Statement 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. User Interface Biologists and bioinformaticists will use the ported application the same way they would use the original, using the command line. Assumptions User has access to a PlayStation 3 running Linux User knows how to use original application Operating Environment Dry Temperature controlled (less than 70° F) Deliverables Application ported to Cell/B.E. Benchmarks to document performance improvement Project and Design Requirements Design Objective 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. Functional Requirements 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 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 Design Method & Results Design Method Two possible ways to parallelize DNAPenny will be explored: Parallelize entire algorithm Parallelize performance-critical section of algorithm Test Plan Created script to ensure ported application produces the same output as the original application with a wide variety of input files. Resources & Work Breakdown Work Breakdown StructureFinancial 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 Itemw/ laborw/o labor PlayStation 3 (donated)$0 Estimated Labor $10.00/hr) $5645$0 Totals$5645$0 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. 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. 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. Proposed Concept Sketch / System Description System Block Diagram 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. Total Hours = Benchmarking Methods 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. Literature Survey V. Sachdeva, M. Kistler, E. Speight and T.- H. K. Tzeng, Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications, March 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 Prototype 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. Parts / Vendor List PlayStation 3 was provided by the department All software used is open source 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.