The design, implementation, and evaluation of mpiBLAST

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Description

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.

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14 p.

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Darling, A. E. (Aaron E.); Carey, L. (Lucas) & Feng, W. C. (Wu-Chun) January 1, 2003.

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Description

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.

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14 p.

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  • "Submitted to: ClusterWorld Conference&Expo 2003"

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  • Report No.: LA-UR-03-2862
  • Grant Number: none
  • Office of Scientific & Technical Information Report Number: 976625
  • Archival Resource Key: ark:/67531/metadc927913

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Office of Scientific & Technical Information Technical Reports

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  • January 1, 2003

Added to The UNT Digital Library

  • Nov. 13, 2016, 7:26 p.m.

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  • Dec. 9, 2016, 11:04 p.m.

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Darling, A. E. (Aaron E.); Carey, L. (Lucas) & Feng, W. C. (Wu-Chun). The design, implementation, and evaluation of mpiBLAST, article, January 1, 2003; United States. (digital.library.unt.edu/ark:/67531/metadc927913/: accessed September 21, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.