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Implementing parallel hmm-pfam on the EARTH multithreaded architecture

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4 Author(s)
Weirong Zhu ; Dept. of Electr. & Comput. Eng., Delaware Univ., Newark, DE, USA ; Yanwei Niu ; Jizhu Lu ; Gao, G.R.

Hmmpfam is a widely used computation-intensive bioinformatics software for sequence classification. This poster describes a new parallel implementation of hmmpfam on EARTH, which is an event-driven fine-grain multithreaded programming execution model. The comparison results of the original PVM implementation and our implementation shows notable improvements on absolute speedup and scalability. On a cluster of 128 dual-CPU nodes, the execution time of a representative testbench is reduced from 15.9 hours to 4.3 minutes.

Published in:

Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE

Date of Conference:

11-14 Aug. 2003