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

Authors:
Weirong Zhu;Yanwei Niu;Jizhu Lu;Chuan Shen;Guang R. Gao
Affiliations:
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
Venue:
International Journal of High Performance Computing and Networking
Year:
2004

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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.