Smith-Waterman protein search with OpenCL on an FPGA

Título:

Smith-Waterman protein search with OpenCL on an FPGA

Autor:

Rucci, Enzo

Colaboradores:

; De Giusti, Armando Eduardo; Naiouf, Ricardo Marcelo; García, Carlos Diego; Botella, Guillermo; Prieto-Matias, Manuel

Temas:

ALGORITMOS

En:

IEEE International Conference on Trust, Security and Privacy in Computing and Communications (14ta : 2015 : Helsinki, Finlandia)

Resumen:

The well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. Unfortunately, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many scenarios. Previous research has shown that massively parallel architectures such as GPUs and FPGAs are able to mitigate the computational problems and achieve impressive speedups. In this paper we explore SW acceleration on an FPGA with OpenCL. We efficiently exploit data and thread-level parallelism on an Altera Stratix V FPGA, obtaining up to 39 GCUPS with less than 25 watt of power consumption.

URL/DOI:

http://dx.doi.org/10.1109/Trustcom.2015.634

Palabras clave:

Smith-Waterman

Medio:

Soporte electrónico

Tipo de documento:

Artículo

Descripción física:

1 archivo (361,0 kB)

Idioma:

Inglés

Publicación:

, 2015

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