Silicon Graphics, Inc. (SGI) (Nasdaq: SGIC) accelerated the Blast-n (Basic Local Alignment Search Tool for nucleotides) bioinformatics application by more than 900 times with their SGI Altix 4700 system. The RASC(TM) (Reconfigurable Application Specific Computing) enabled SGI Altix features Xilinx(R) Virtex-4 FPGAs.
The SGI Altix 4700 system was configured as a turn-key bioinformatics appliance with 64 Intel(R) Itanium(R) 2 processors and 35 RC100 RASC blades. The completed system fits into a single rack and runs a Mitrionics(TM) developed Blast-n engine to transparently accelerate a customer’s Blast-n applications using the RC100 RASC blades. Each RC100 is tightly integrated into SGI NUMAflex(TM) architecture and features two Xilinx Virtex-4 LX200 FPGAs and 10 banks of local scratchpad memory, providing a total of 70 FPGAs and 840 GB per second of local memory bandwidth in the benchmarked configuration.
The benchmark test ran a standard Blast-n query to match 25 nucleotide base pairs against 600,000 queries. The application required approximately 3 weeks to complete on a 68-node AMD Opteron cluster compared to less than 33 minutes for the Virtex(TM)-4 FPGA accelerated SGI RASC platform: a total speed improvement of more than 900 times.
Now in its 4th generation, Xilinx enabled RASC technology can scale performance across a broad range of data intensive algorithms such as those used in Blast-n, the world’s most widely used bioinformatics application. Additional applications appropriate for RASC acceleration include oil and gas exploration, defense and intelligence, financial analytics, medical imaging, and broadcast media encoding.