Applications of heterogeneous structure of Cell Broadband Engine Architecture for biological database similarity search

Hieu Tri Nim; Chee Keong Kwoh; Adrianto Wirawan; Bertil Schmidt

Applications of heterogeneous structure of Cell Broadband Engine Architecture for biological database similarity search

Hieu Tri Nim, Chee Keong Kwoh, Adrianto Wirawan, Bertil Schmidt

Research output: Chapter in Book/Report/Conference proceeding › Conference Paper › Research

Abstract

In this paper, we present a technique to optimize the performance of database similarity search in the specific context of Cell Broadband Engine Architecture (CBEA). The technique applied was Striped Smith-Waterman algorithm for SIMD and heterogeneous task distribution in MIMD.In terms of sensitivity, the technique preserves the optimality of original Smith- Waterman algorithm. In addition, the performance recorded shows a remarkable speedup of 1.7 to 8.8 folds of this new architecture, as compared to other platforms such as Streaming SIMD Extensions 2 (SSE2) and Graphics Processing Unit (GPU).

Original language	English
Title of host publication	Proceedings of The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008)
Subtitle of host publication	May 16-18, 2008, Shanghai, China
Publisher	IEEE, Institute of Electrical and Electronics Engineers
Pages	5-8
Number of pages	4
ISBN (Print)	9781424417483
Publication status	Published - 2008
Externally published	Yes
Event	International Conference on Bioinformatics and Biomedical Engineering 2008 - Shanghai, China Duration: 16 May 2008 → 18 May 2008 Conference number: 2nd

Conference

Conference	International Conference on Bioinformatics and Biomedical Engineering 2008
Abbreviated title	(iCBBE)
Country/Territory	China
City	Shanghai
Period	16/05/08 → 18/05/08

Keywords

Sequence alignment
Smith-Waterman
cell broadband engine
SSE2
SIMD
MIMD
GPU

Access to Document

http://ieeexplore.ieee.org.ezproxy.lib.monash.edu.au/document/4534888/

Cite this

Nim, H. T., Kwoh, C. K., Wirawan, A., & Schmidt, B. (2008). Applications of heterogeneous structure of Cell Broadband Engine Architecture for biological database similarity search. In Proceedings of The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008): May 16-18, 2008, Shanghai, China (pp. 5-8). IEEE, Institute of Electrical and Electronics Engineers. http://ieeexplore.ieee.org.ezproxy.lib.monash.edu.au/document/4534888/

Nim, Hieu Tri ; Kwoh, Chee Keong ; Wirawan, Adrianto ; Schmidt, Bertil. / Applications of heterogeneous structure of Cell Broadband Engine Architecture for biological database similarity search. Proceedings of The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008): May 16-18, 2008, Shanghai, China. IEEE, Institute of Electrical and Electronics Engineers, 2008. pp. 5-8

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title = "Applications of heterogeneous structure of Cell Broadband Engine Architecture for biological database similarity search",

abstract = "In this paper, we present a technique to optimize the performance of database similarity search in the specific context of Cell Broadband Engine Architecture (CBEA). The technique applied was Striped Smith-Waterman algorithm for SIMD and heterogeneous task distribution in MIMD.In terms of sensitivity, the technique preserves the optimality of original Smith- Waterman algorithm. In addition, the performance recorded shows a remarkable speedup of 1.7 to 8.8 folds of this new architecture, as compared to other platforms such as Streaming SIMD Extensions 2 (SSE2) and Graphics Processing Unit (GPU).",

keywords = "Sequence alignment, Smith-Waterman, cell broadband engine, SSE2, SIMD, MIMD, GPU",

author = "Nim, {Hieu Tri} and Kwoh, {Chee Keong} and Adrianto Wirawan and Bertil Schmidt",

year = "2008",

language = "English",

isbn = "9781424417483",

pages = "5--8",

booktitle = "Proceedings of The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008)",

publisher = "IEEE, Institute of Electrical and Electronics Engineers",

address = "United States of America",

note = "International Conference on Bioinformatics and Biomedical Engineering 2008, (iCBBE) ; Conference date: 16-05-2008 Through 18-05-2008",

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Nim, HT, Kwoh, CK, Wirawan, A & Schmidt, B 2008, Applications of heterogeneous structure of Cell Broadband Engine Architecture for biological database similarity search. in Proceedings of The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008): May 16-18, 2008, Shanghai, China. IEEE, Institute of Electrical and Electronics Engineers, pp. 5-8, International Conference on Bioinformatics and Biomedical Engineering 2008, Shanghai, China, 16/05/08. <http://ieeexplore.ieee.org.ezproxy.lib.monash.edu.au/document/4534888/>

Applications of heterogeneous structure of Cell Broadband Engine Architecture for biological database similarity search. / Nim, Hieu Tri; Kwoh, Chee Keong; Wirawan, Adrianto; Schmidt, Bertil.

Proceedings of The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008): May 16-18, 2008, Shanghai, China. IEEE, Institute of Electrical and Electronics Engineers, 2008. p. 5-8.

Research output: Chapter in Book/Report/Conference proceeding › Conference Paper › Research

TY - GEN

T1 - Applications of heterogeneous structure of Cell Broadband Engine Architecture for biological database similarity search

AU - Nim, Hieu Tri

AU - Kwoh, Chee Keong

AU - Wirawan, Adrianto

AU - Schmidt, Bertil

N1 - Conference code: 2nd

PY - 2008

Y1 - 2008

N2 - In this paper, we present a technique to optimize the performance of database similarity search in the specific context of Cell Broadband Engine Architecture (CBEA). The technique applied was Striped Smith-Waterman algorithm for SIMD and heterogeneous task distribution in MIMD.In terms of sensitivity, the technique preserves the optimality of original Smith- Waterman algorithm. In addition, the performance recorded shows a remarkable speedup of 1.7 to 8.8 folds of this new architecture, as compared to other platforms such as Streaming SIMD Extensions 2 (SSE2) and Graphics Processing Unit (GPU).

AB - In this paper, we present a technique to optimize the performance of database similarity search in the specific context of Cell Broadband Engine Architecture (CBEA). The technique applied was Striped Smith-Waterman algorithm for SIMD and heterogeneous task distribution in MIMD.In terms of sensitivity, the technique preserves the optimality of original Smith- Waterman algorithm. In addition, the performance recorded shows a remarkable speedup of 1.7 to 8.8 folds of this new architecture, as compared to other platforms such as Streaming SIMD Extensions 2 (SSE2) and Graphics Processing Unit (GPU).

KW - Sequence alignment

KW - Smith-Waterman

KW - cell broadband engine

KW - SSE2

KW - SIMD

KW - MIMD

KW - GPU

M3 - Conference Paper

SN - 9781424417483

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EP - 8

BT - Proceedings of The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008)

PB - IEEE, Institute of Electrical and Electronics Engineers

T2 - International Conference on Bioinformatics and Biomedical Engineering 2008

Y2 - 16 May 2008 through 18 May 2008

ER -

Nim HT, Kwoh CK, Wirawan A, Schmidt B. Applications of heterogeneous structure of Cell Broadband Engine Architecture for biological database similarity search. In Proceedings of The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008): May 16-18, 2008, Shanghai, China. IEEE, Institute of Electrical and Electronics Engineers. 2008. p. 5-8