Smith-Waterman algorithm on heterogeneous systems: A case study

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. Fortunate...

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Detalles Bibliográficos
Autores principales: Rucci, Enzo, De Giusti, Armando Eduardo, Naiouf, Marcelo, García Sánchez, Carlos, Botella, Juan Guillermo, Prieto-Matías, Manuel
Formato: Objeto de conferencia
Lenguaje:Inglés
Publicado: 2014
Materias:
Ciencias Informáticas
Bioinformatics
Smith-Waterman
HPC
Intel Xeon Phi
Heterogeneous computing
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/82886
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-82886
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Ciencias Informáticas
Bioinformatics
Smith-Waterman
HPC
Intel Xeon Phi
Heterogeneous computing
spellingShingle Ciencias Informáticas
Bioinformatics
Smith-Waterman
HPC
Intel Xeon Phi
Heterogeneous computing
Rucci, Enzo
De Giusti, Armando Eduardo
Naiouf, Marcelo
García Sánchez, Carlos
Botella, Juan Guillermo
Prieto-Matías, Manuel
Smith-Waterman algorithm on heterogeneous systems: A case study
topic_facet Ciencias Informáticas
Bioinformatics
Smith-Waterman
HPC
Intel Xeon Phi
Heterogeneous computing
description 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 low-level optimisations.
format Objeto de conferencia
Objeto de conferencia
author Rucci, Enzo
De Giusti, Armando Eduardo
Naiouf, Marcelo
García Sánchez, Carlos
Botella, Juan Guillermo
Prieto-Matías, Manuel
author_facet Rucci, Enzo
De Giusti, Armando Eduardo
Naiouf, Marcelo
García Sánchez, Carlos
Botella, Juan Guillermo
Prieto-Matías, Manuel
author_sort Rucci, Enzo
title Smith-Waterman algorithm on heterogeneous systems: A case study
title_short Smith-Waterman algorithm on heterogeneous systems: A case study
title_full Smith-Waterman algorithm on heterogeneous systems: A case study
title_fullStr Smith-Waterman algorithm on heterogeneous systems: A case study
title_full_unstemmed Smith-Waterman algorithm on heterogeneous systems: A case study
title_sort smith-waterman algorithm on heterogeneous systems: a case study
publishDate 2014
url http://sedici.unlp.edu.ar/handle/10915/82886
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