Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs
Document typeConference report
PublisherAssociation for Computing Machinery (ACM)
Rights accessRestricted access - publisher's policy
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.
CitationDe Sandes, E. [et al.]. Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs. A: ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. "PPoPP'14: proceedings of the 2014 ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming: Orlando, FL, USA: February 15-19, 2014". Orlando, FL: Association for Computing Machinery (ACM), 2014, p. 383-384.
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