A cluster-based solution for high performance hmmpfam using EARTH execution model. (6th February 2006)

• Record Type: Journal Article
• Authors: Zhu, Weirong; Niu, Yanwei; Lu, Jizhu; Shen, Chuan; , Guang R. Gao
• Is Part Of: International journal of high performance computing and networking. Volume 2:Number 2/3/4(2004)
• Page Start: 66
• Page End: 76
• Publication Date: 2006-02-06
• Subjects: hmmpfam -- cluster-based solution -- EARTH -- dynamic load balancing -- robust -- sequence classification -- high performance computing; High performance computing -- Periodicals; Computer networks -- Periodicals; High performance computing; Periodicals; 004.05
• Languages: English
• ISSNs: 1740-0562

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.