Parallel CLUSTAL W for PC clusters

Authors:
James Cheetham;Frank Dehne;Sylvain Pitre;Andrew Rau-Chaplin;Peter J. Taillon
Affiliations:
Institute of Biochemistry, Carleton University, Ottawa ON Canada;School of Computer Science, Carleton University,Ottawa, ON Canada;School of Computer Science, Carleton University, Ottawa, ON Canada;Faculty of Computer Science, Dalhousie University, Halifax, NS Canada;School of Computer Science, Carleton University, Ottawa, ON Canada
Venue:
ICCSA'03 Proceedings of the 2003 international conference on Computational science and its applications: PartII
Year:
2003

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Abstract

This paper presents a parallel version of CLUSTAL W, called pCLUSTAL. In contrast to the commercial SGI parallel Clustal, which requires an expensive shared memory SGI multiprocessor, pCLUSTAL can be run on a range of distributed and shared memory parallel machines, from high-end parallel multiprocessors (e.g. Sunfire 6800, IBM SP2, etc.) to PC clusters, to simple networks of workstations. We have implemented pCLUSTAL using C and the MPI communication library, and tested it on a PC cluster. Our experimental evaluation shows that our pCLUSTAL code achieves similar or better speedup on a distributed memory PC clusters than the commercial SGI parallel Clustal on a shared memory SGI multiprocessor.