Smith-Waterman algorithm on heterogeneous systems

Título:

Smith-Waterman algorithm on heterogeneous systems : a case study

Autor:

Rucci, Enzo

Colaboradores:

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

Temas:

ALGORITMOS

En:

IEEE International Conference on Cluster Computing (2014 : Madrid, España)

Resumen:

The well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. However, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many applications. Some heuristics are possible but at the expense of losing sensitivity. Fortunately, previous research have shown that new computing platforms such as GPUs and FPGAs are able to accelerate SW and achieve impressive speedups. In this paper we have explored SW acceleration on a heterogeneous platform equipped with an Intel Xeon Phi coprocessor. Our evaluation, using the well-known Swiss-Prot database as a benchmark, has shown that a hybrid CPU-Phi heterogeneous system is able to achieve competitive performance (62.6 GCUPS), even with moderate lowlevel optimisations.

URL/DOI:

http://dx.doi.org/10.1109/CLUSTER.2014.6968784

Palabras clave:

Smith-Waterman bioinformática

Medio:

Soporte electrónico

Tipo de documento:

Artículo

Descripción física:

1 archivo (302,6 kB)

Idioma:

Inglés

Publicación:

, 2014

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