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High performance bioinformatics

Group May 09-06 Bryan McCoy Kinit Patel Tyson Williams. High performance bioinformatics. Problem/Need Statement. Current ways to solve Bioinformatics problems are either slow or very expensive.

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High performance bioinformatics

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  1. Group May 09-06 Bryan McCoy Kinit Patel Tyson Williams High performance bioinformatics

  2. Problem/Need Statement • Current ways to solve Bioinformatics problems are either slow or very expensive. • There is a need for a way to reduce cost and still deliver high performance in a computer system that can solve Bioinformatics problems.

  3. What is Bioinformatics? • Genetic sequencing. • Massive amounts of data. • Simple operations but many of them. • Perfect for distributed computing.

  4. Proposed Solution • Use a cluster of PS3s with their embedded Cell processors.

  5. Cell Broadband Engine • Has 1 central PowerPC based PPE. • Has 8 surrounding SPEs. • The 8 SPEs are connected via the element interconnect bus.

  6. Cell Broadband Engine

  7. Functional requirements • FR1. Ported applications shall run on the Cell B.E. • FR2. The results returned shall be the same as the original program. • FR3. The applications shall return their runtime. • FR4. The applications shall execute in parallel on multiple Cell B.E.s.

  8. Non-Functional Requirements • NF1. The Cells shall all run on the Linux OS. • NF2. The resulting runtimes of the ported applications shall be faster than on the original applications. • NF3. The ported application shall be coded in the C language.

  9. Operating Environment • Use Fedora 9 OS as it is currently supported by the Cell SDK 3.1. • Uses the command line for user interface. • Use the IBM XLC compiler and/or the current GCC compiler.

  10. Market Survey • Results of the survey point to a huge speed up of computationally intensive programs. • Dr. GauravKhanna at the University of Massachusetts Dartmouth used cluster of 8 PS3s to replace a supercomputer. • Universitat Pompeu Fabra, in Barcelona, deployed in 2007 a BOINC system called PS3GRID for collaborative biological computing.

  11. Deliverables • The Source Code. • Compiled Executable. • Runtime Comparisons. • Project Final Report. • Project Poster. • Project Final Presentation.

  12. Work Breakdown Structure

  13. Costs • Time • Approximately 555 man hours total. Freely donated. Total cost $0. • Equipment • 3 PS3s • Crossbar router Provided for us by client. Total cost $0.

  14. Resource Requirements • 3 PlayStation 3s. • High performance network switch. • Books on distributed computing on Cell. • Time.

  15. Work Schedule • Gant chart

  16. Risk Assessment • Slow network speed. • Software support. • Limited RAM. • Hardware Failure. • Lower quality entertainment hardware. • Limited prior experience. • Software development schedule.

  17. Design • Further divide the application into multiple threads for SPE execution on multiple PS3s, alter the functional logic, and vectorize the code where possible.

  18. Software Decomposition Diagram

  19. System Requirements • SR1. The system shall allow the user to input multiple DNA sequences in FASTA format through a file interface. • SR2. The system shall output all of the most parsimonious trees implied by the input data to the screen. • SR3. The system shall share computational work among the PPE and SPEs available to each client/server process. • SR4. The front-end shall share computational work with available back-end processes. • SR5. The front-end shall be able to connect to at least 2 back-end processes via a high performance router.

  20. System Analysis • The key is data flow. • Broken into 3 stages. • DNA sequences distributed to the PPEs down to the SPEs • Each SPE searches every possible parsimony tree for the best possible score using a branch and bound heuristic. • Finally the results are aggregated back to the main PPE and the results output.

  21. Specifications • Input • DNA sequence files in FASTA format. • Output • Runtime of the application. • The most parsimonious phylogenetic tree. • The parsimony score of the phylogenetic tree.

  22. Specifications • User Interface • No changes to the user interface. • Uses a command line interface.

  23. Specifications • Hardware • 3 PlayStation 3s • High performance Cross-Bar network switch.

  24. Specifications • Software • Fedora 9 with Linux 2.6.25 kernel for the Power PC • IBM Cell SDK 3.1 • IBM XLC 9.0 and GCC 4.3 compilers. • DNAPenny 3.6. • Bioperf Suite

  25. Specifications • Testing • Compare benchmarked runtimes over several iterations and inputs to get averages. • Compare these runtimes with previous group’s runtimes on single Cell processor. • Compare these runtimes with previous group’s runtimes on a high performance server. • Quad-core Intel Xeon 3.0GHz, 6GB RAM.

  26. Acknowledgements • May08-24 group • Kyle Byerly • Shannon McCormick • Matt Rohlf • Bryan Venteicher • Bioperf developers • David A. Bader, Georgia Tech • Yue Li, Univ. of Florida • Tao Li, Univ. of Florida • Vipin Sachdeva, IBM Austin

  27. Questions?

  28. Previous Results and Projected Results

  29. Summary • Cost: $0. Equipment provided. • Time: 555 approximate man hours. Freely Donated. • Results: 4x the performance of a similarly priced system.

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