Smith-Waterman algorithm on heterogeneous systems: A case study

Author

Rucci, Enzo ; De Giusti, Armando ; Naiouf, Marcelo ; Botella, Guillermo ; Garcia, Christophe ; Prieto-Matias, Manuel

Author_Institution

Inst. de Investig. en Inf. LIDI (III-LIDI), Univ. Nac. de La Plata, Buenos Aires, Argentina

fYear

2014

fDate

22-26 Sept. 2014

Firstpage

323

Lastpage

330

Abstract

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.

Keywords

bioinformatics; coprocessors; field programmable gate arrays; graphics processing units; CPU-Phi heterogeneous system; FPGA; GPU; Intel Xeon Phi coprocessor; SW algorithm; Smith-Waterman algorithm; Swiss-Prot database; bioinformatics; field programmable gate array; graphics processing unit; local alignment; Coprocessors; Databases; Heuristic algorithms; Instruction sets; Optimization; Vectors; Bioinformatics; HPC; Intel Xeon Phi; Smith-Waterman; heterogeneous computing;

fLanguage

English

Publisher

ieee

Conference_Titel

Cluster Computing (CLUSTER), 2014 IEEE International Conference on

Conference_Location

Madrid

Type

conf

DOI

10.1109/CLUSTER.2014.6968784

Filename

6968784