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Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs

Autor
De Sandes, E.; Miranda, G.; De Melo, A.; Martorell, X.; Ayguade, E.
Tipus d'activitat
Article en revista
Revista
ACM SIGPLAN notices
Data de publicació
2014-08-01
Volum
49
Número
8
Pàgina inicial
383
Pàgina final
384
DOI
https://doi.org/10.1145/2555243.2555280 Obrir en finestra nova
Projecte finançador
Computación de Altas Prestaciones VI
Repositori
http://hdl.handle.net/2117/27492 Obrir en finestra nova
URL
http://dl.acm.org/citation.cfm?id=2555280 Obrir en finestra nova
Resum
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 perf...
Citació
De Sandes, E. [et al.]. Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs. "ACM SIGPLAN notices", 01 Agost 2014, vol. 49, núm. 8, p. 383-384.
Paraules clau
Alignments, Biological Sequence Comparison, GPU, Smith-Waterman
Grup de recerca
CAP - Grup de Computació d'Altes Prestacions

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