Abstract
Four FPGA systems were evaluated: the Cray XD1 system
with 6 FPGAs at ORNL and Cray, the Cray XD1 system
with 150 FPGAs at NRL* and the 64 FPGAs on
Edinburgh�s �Maxwell�. Their hardware and software
architectures, programming tools and performance on
scientific applications are discussed. FPGA speedup (over
a 2.2 GHz Opteron) of 10X was typical for matrix equation
solution, molecular dynamics and weather/climate codes
and upto 100X for human genome DNA sequencing. Large
genome comparisons requiring 12.5 years for an Opteron
took less than 24 hours on NRL�s Cray XD1 with 150 Virtex
FPGAs for a 7,350X speedup.
pipeline so each query and database character are compared
in parallel, resulting in a table of scores.
Genome Sequencing Results:
FPGA timing results (for up to 150 FPGAs) were obtained
and compared with up to 150 Opterons for sequences of
varying size and complexity (e.g. 4GB openfpga.org human
DNA benchmark and 155M human vs. 166M mouse DNA).
1 FPGA: Bacillus_anthracis DNA compare: Genomes