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Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs

Published:06 February 2014Publication History
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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.

References

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  4. T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. J Mol Biol, 147 (1): 195--197, 1981.Google ScholarGoogle ScholarCross RefCross Ref

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            • Published in

              cover image ACM SIGPLAN Notices
              ACM SIGPLAN Notices  Volume 49, Issue 8
              PPoPP '14
              August 2014
              390 pages
              ISSN:0362-1340
              EISSN:1558-1160
              DOI:10.1145/2692916
              Issue’s Table of Contents
              • cover image ACM Conferences
                PPoPP '14: Proceedings of the 19th ACM SIGPLAN symposium on Principles and practice of parallel programming
                February 2014
                412 pages
                ISBN:9781450326568
                DOI:10.1145/2555243

              Copyright © 2014 Owner/Author

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              Association for Computing Machinery

              New York, NY, United States

              Publication History

              • Published: 6 February 2014

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