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A cluster-based solution for high performance hmmpfam using EARTH execution model

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5 Author(s)
W. Zhu ; Dept. of Electr. & Comput. Eng., Delaware Univ., Newark, DE, USA ; Y. Niu ; J. Lu ; C. Shen
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Hmmpfam is a widely used computation-intensive bioinformatics software for sequence classification. The contribution of this paper is the first largely scalable and robust cluster-based solution of parallel hmmpfam based on EARTH (Efficient Architecture for Running Threads), which is an event-driven fine-grain multi-threaded programming execution model. Compared with the original PVM implementation, our implementation shows notable improvements on absolute speed-up and better scalability. Experiments on two advanced supercomputing clusters at Argonne National Laboratory (ANL) achieve an absolute speedup of 222.8 on 128 dual-CPU nodes for a representative data set, which means that the total execution time is reduced from 15.9 hours (serial program) to only 4.3 minutes.

Published in:

Cluster Computing, 2003. Proceedings. 2003 IEEE International Conference on

Date of Conference:

1-4 Dec. 2003