Home > Archives > Additional Archives > Jim Lindelien   Jim Lindelien TimeLogic Corporation Crystal Bay, NV 92093 jiml@timelogic.com http://www.timelogic.com   Abstract: Server farm speed that fits on your desktop? Reconfigurable Computing yields Substantial Performance and Price-Performance Improvements for Biosequence Analysis A conventional server augmented with accelerator cards employing Field Programmable Gate Array (FPGA) technology yields substantial gains in absolute speed and price-performance for large-scale biosequence analysis requiring Heuristic or Dynamic Programming algorithms. Popular examples of these algorithms include BLAST, Hidden Markov Models, Profilesearch, Smith-Waterman, and Framesearch. Rapid on-chip reconfigurability of FPGA device technology (so called "soft hardware") allows each analysis to run on a parallel array of ideal algorithm-specific processors and data path topology. The processors themselves and the topology interconnecting them is synthesized in real-time just prior to the start of each task, and persist only for the duration of each analysis. Software running on the host server's CPUs controls overall job flow, FPGA chip logical redefinition, and pipelines pre- and post-process CPU loads during accelerated bulk query-vs-database combinatorics running on the FPGAs. Data storage and transport bottlenecks commonly encountered in academic bioinformatics software are avoided by design, permitting very fast accelerated speed on a single small server, without costly RAM caching of entire large genetic databases. Wall clock relative speed gains of two to three orders of magnitude per server are realized, allowing one such server to replace or reclaim computing capacity equal to a large scale farm.
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