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Author de O. Sandes, Edans F. ♦ Miranda, Guillermo ♦ Martorell, Xavier ♦ Ayguade, Eduard ♦ Melo, Alba C.M.A.
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Computer programming, programs & data
Subject Keyword Smith-waterman ♦ Gpu ♦ Biological sequence comparison
Abstract This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) algorithm for megabase DNA sequences in heterogeneous multi-GPU platforms. In our strategy, the computation of a single huge SW matrix is spread over multiple GPUs, which communicate border elements to the neighbour, using a circular buffer mechanism that hides the communication overhead. We compared 4 pairs of human-chimpanzee homologous chromosomes using 2 different GPU environments, obtaining a performance of up to 140.36 GCUPS (Billion of cells processed per second) with 3 heterogeneous GPUS.
Description Affiliation: University of Brasilia, Brasilia, Brazil (de O. Sandes, Edans F.; Melo, Alba C.M.A.) || Barcelona Supercomputing Center, Barcelona, Spain (Miranda, Guillermo; Martorell, Xavier; Ayguade, Eduard)
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 1983-05-01
Publisher Place New York
Journal ACM SIGPLAN Notices (SIGP)
Volume Number 49
Issue Number 8
Page Count 2
Starting Page 383
Ending Page 384


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Source: ACM Digital Library