The design, implementation, and evaluation of mpiBLAST

Conference · Wed Jan 01 04:00:00 EST 2003

OSTI ID:976625

Darling, A E ^[1]; Carey, L ^[2]; Feng, W C ^[3]

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1. Aaron E.
2. Lucas
3. Wu-Chun

mpiBLAST is an open-source parallelization of BLAST that achieves superlinear speed-up by segmenting a BLAST database and then having each node in a computational cluster search a unique portion of the database. Database segmentation permits each node to search a smaller portion of the database, eliminating disk I/O and vastly improving BLAST performance. Because database segmentation does not create heavy communication demands, BLAST users can take advantage of low-cost and efficient Linux cluster architectures such as the bladed Beowulf. In addition to presenting the software architecture of mpiBLAST we present a detailed performance analysis of mpiBLAST to demonstrate its scalability.

• Research Organization: Los Alamos National Laboratory
• Sponsoring Organization: DOE
• OSTI ID: 976625
• Report Number(s): LA-UR-03-2862
• Country of Publication: United States
• Language: English

Related Subjects

99 GENERAL AND MISCELLANEOUS
COMMUNICATIONS
COMPUTER ARCHITECTURE
COMPUTERS
DESIGN
EVALUATION
IMPLEMENTATION
PARALLEL PROCESSING
PERFORMANCE