Exploring Accelerating Science Applications with FPGAs

Conference · Mon Jan 01 00:00:00 EST 2007

OSTI ID:931879

Storaasli, Olaf O ^[1]; Strenski, Dave ^[2]

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1. ORNL
2. Cray, Inc.

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.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Laboratory Directed Research and Development (LDRD) Program
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 931879
• Resource Relation: Conference: Reconfigurable Systems Summer Institute (RSSI) 2007, National Center for Supercomputer Applications (NCSA), Urbana, IL, USA, 20070717, 20070720
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
BIOLOGY
DNA
PERFORMANCE
SUPERCOMPUTERS
Field Programmable Gate Array FPGA HPC Reconfigurable Supercomputer DNA human Genome Opteron