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dc.contributor.authorDe Sandes, Edans
dc.contributor.authorMiranda Álamo, Guillermo
dc.contributor.authorMelo, Alba
dc.contributor.authorMartorell Bofill, Xavier
dc.contributor.authorAyguadé Parra, Eduard
dc.contributor.otherUniversitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors
dc.date.accessioned2014-05-29T11:56:32Z
dc.date.created2014
dc.date.issued2014
dc.identifier.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.
dc.identifier.isbn978-1-4503-2656-8
dc.identifier.urihttp://hdl.handle.net/2117/23094
dc.description.abstractThis 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.
dc.format.extent2 p.
dc.language.isoeng
dc.publisherAssociation for Computing Machinery (ACM)
dc.rightsAttribution-NonCommercial-NoDerivs 3.0 Spain
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/es/
dc.subjectÀrees temàtiques de la UPC::Informàtica::Arquitectura de computadors::Arquitectures paral·leles
dc.subject.lcshParallel programming (Computer science)
dc.subject.otherBiological sequence comparison
dc.subject.otherGPU
dc.subject.otherSmith-Waterman
dc.titleFine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs
dc.typeConference report
dc.subject.lemacProgramació en paral·lel (Informàtica)
dc.contributor.groupUniversitat Politècnica de Catalunya. CAP - Grup de Computació d'Altes Prestacions
dc.identifier.doi10.1145/2555243.2555280
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttp://dl.acm.org/citation.cfm?id=2555280
dc.rights.accessRestricted access - publisher's policy
local.identifier.drac14149076
dc.description.versionPostprint (published version)
dc.date.lift10000-01-01
local.citation.authorDe Sandes, E.; Miranda, G.; Melo, A.; Martorell, X.; Ayguade, E.
local.citation.contributorACM SIGPLAN Symposium on Principles and Practice of Parallel Programming
local.citation.pubplaceOrlando, FL
local.citation.publicationNamePPoPP'14: proceedings of the 2014 ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming: Orlando, FL, USA: February 15-19, 2014
local.citation.startingPage383
local.citation.endingPage384


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