OSWALD

Título:

OSWALD: openCL Smith–Waterman on Altera’s FPGA for large protein databases

Autor:

Rucci, Enzo

Colaboradores:

; García, Pablo S.; Botella, Guillermo; De Giusti, Armando Eduardo; Naiouf, Ricardo Marcelo; Prieto-Matias, Manuel

Temas:

ALGORITMOS

En:

International Journal Of High Performance Computing Applications, 32(3), pp. 337-350.

Resumen:

The well-known Smith–Waterman algorithm is a high-sensitivity method for local sequence alignment. Unfortunately, the Smith–Waterman algorithm has quadratic time complexity, which makes it computationally demanding for large protein databases. In this paper, we present OSWALD, a portable, fully functional and general implementation to accelerate Smith–Waterman database searches in heterogeneous platforms based on Altera’s FPGA. OSWALD exploits OpenMP multithreading and SIMD computing through SSE and AVX2 extensions on the host while taking advantage of pipeline and vectorial parallelism by way of OpenCL on the FPGAs. Performance evaluations on two different heterogeneous architectures with real amino acid datasets show that OSWALD is competitive in comparison with other top-performing Smith–Waterman implementations, attaining up to 442 GCUPS peak with the best GCUPS/watts ratio.

URL/DOI:

https://doi.org/10.1177/1094342016654215

Palabras clave:

bioinformática

Medio:

Soporte electrónico

Tipo de documento:

Artículo

Descripción física:

1 archivo (1,1 MB)

Idioma:

Inglés

Publicación:

, 2016

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