Performance evaluation of MPI-HMMER on the OBIGrid

Yasuyo Kofune; Takahiro Koita; Akira Fukuda

Performance evaluation of MPI-HMMER on the OBIGrid

Yasuyo Kofune, Takahiro Koita, Akira Fukuda

Advanced Software Engineering

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

Abstract

HMMER is a very useful genomic application program and widely used. Reducing the execution time of HMMER is important for analyzing genomic information within a practical time period. However, HMMER can currently be executed only on a small PC cluster with PVM and cannot be executed on the Grid, which can provide far more processing power. In this paper, MPI-HMMER, which can be executed on the Grid, is implemented, and MPI-HMMER is evaluated using PCs on OBIGrid (Open Bioinformatics Grid). This is an experimental Grid for bioinformatics being developed by Japan Committees. The modified MPI-HMMER is also implemented to improve the execution time.

Original language	English
Title of host publication	Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04
Editors	H.R. Arabnia
Pages	476-480
Number of pages	5
Publication status	Published - 2004
Event	Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04 - Las Vegas, NV, United States Duration: Jun 21 2004 → Jun 24 2004

Publication series

Name	Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04
Volume	1

Other

Other	Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04
Country/Territory	United States
City	Las Vegas, NV
Period	6/21/04 → 6/24/04

All Science Journal Classification (ASJC) codes

Engineering(all)

Cite this

Kofune, Y., Koita, T., & Fukuda, A. (2004). Performance evaluation of MPI-HMMER on the OBIGrid. In H. R. Arabnia (Ed.), Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04 (pp. 476-480). (Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04; Vol. 1).

Performance evaluation of MPI-HMMER on the OBIGrid. / Kofune, Yasuyo; Koita, Takahiro; Fukuda, Akira.
Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04. ed. / H.R. Arabnia. 2004. p. 476-480 (Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04; Vol. 1).

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

Kofune, Y, Koita, T & Fukuda, A 2004, Performance evaluation of MPI-HMMER on the OBIGrid. in HR Arabnia (ed.), Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04. Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04, vol. 1, pp. 476-480, Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04, Las Vegas, NV, United States, 6/21/04.

Kofune, Yasuyo ; Koita, Takahiro ; Fukuda, Akira. / Performance evaluation of MPI-HMMER on the OBIGrid. Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04. editor / H.R. Arabnia. 2004. pp. 476-480 (Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, PDPTA'04).

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Performance evaluation of MPI-HMMER on the OBIGrid

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