The design, implementation, and evaluation of mpiBLAST
Aaron E. Darling, Lucas B. Carey, Wu-chun Feng · OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) · 2003
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.