September 2007

Conference Paper

Exploring Accelerating Science Applications with FPGAs

By:
Storaasli, Olaf O; Strenski, Dave
Page Number:
1-8
Volume:
2007
Book Title:
Proceedings of the 2007 Reconfigurable Systems Summer Institute (on DVD)
Publication Date:
September 2007
Conference Name:
Reconfigurable Systems Summer Institute (RSSI) 2007, National Center for Supercomputer Applications (NCSA)
Conference Location:
Urbana, Illinois, United States of America
Conference Sponsor:
National Center for Supercomputer Applications (NCSA), OpenFPGA and Manchester University (UK)

Abstract

FPGA hardware and tools (VHDL, Viva, MitrionC and CHiMPS) are described. FPGA performance is evaluated on two Cray XD1 systems (Virtex-II Pro 50 and Virtex-4 LX160) for human genome (DNA and protein) sequence comparisons for a computational biology code (FASTA). Scalable FPGA speedups of 50X (Virtex-II) and 100X (Virtex-4) over a 2.2 GHz Opteron were achieved. Coding and IO issues faced for human genome data are described.