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SGI (NASDAQ:SGIC), Sunnyvale, Calif., has built the world's largest Field Programmable Gate Array (FPGA) supercomputer configuration, then ran a broadly used bioinformatics application more than 900 times faster than the same application would run on a traditional cluster.
SGI's reconfigurable supercomputer featured 70 FPGAs, more than any single system built to date. SGI's FPGA supercomputer accelerated the performance of a complex BLAST-n query by more than 900 times, completing in less than 33 minutes what took a 68-node Opteron-based cluster approximately three weeks to finish. (1) The application matched 20 nucleotide base pairs against 600,000 queries.
SGI configured the system using only off-the-shelf components, including its SGI(R) RASC(TM) (Reconfigurable Application Specific Computing) appliance for bioinformatics -- Featuring Mitrion(TM)- Accelerated BLAST-n. No hardware or software was modified for the test. (2)
Bill Mannel, SGI's director of marketing for servers, compared the SGI RASC system to earlier FPGA systems of similar...