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.
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Digital Library
- T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. J Mol Biol, 147 (1): 195--197, 1981.Google Scholar
Cross Ref
Index Terms
Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs
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