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

Authors: Weirong Zhu, Yanwei Niu, Jizhu Lu, Chuan Shen, Guang R. Gao

Addresses: Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA. ' Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA. ' Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA. ' Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA. ' Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA

Abstract: 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 eventdriven fine-grain multi-threaded programming execution model. When 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 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 h (serial program) to only 4.3 min.

Keywords: hmmpfam; cluster-based solution; EARTH; dynamic load balancing; robust; sequence classification; high performance computing.

DOI: 10.1504/IJHPCN.2004.008893

International Journal of High Performance Computing and Networking, 2004 Vol.2 No.2/3/4, pp.66 - 76

Published online: 02 Feb 2006 *

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