Speeding Genomic Searches over 1000X Over a Single Opteron Using Multiple FPGAs on a Cray XD1

Our CUG07 paper demonstrated the Cray Smith-Waterman FPGA design could achieve 50-100X speedup over a single Opteron. This paper extends that work to demonstrate loosely-coupled human chromosome-to-chromosome searches, run on 100's of FPGAs, can exceed 1000X speedup. We examine how this design performs on future FPGA-enabled Cray systems.