TurboBLAST(r): A Parallel Implementation of BLAST Built on the TurboHub
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
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IPDPS '03 Proceedings of the 17th International Symposium on Parallel and Distributed Processing
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Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Massively parallel genomic sequence search on the Blue Gene/P architecture
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The Basic Local Alignment Search BLAST is one of the most widely used bioinformatics programs for searching all available sequence databases for similarities between a protein or DNA query and predefined sequences, using sequence alignment technique. Recently, many attempts have been made to make the algorithm practical to run against the publicly available genome databases. This paper presents our experience in mapping and evaluating both the serial and parallel BLAST algorithms onto a large Infiniband-based High Performance Cluster. The evaluation is performed using two commonly used parallel compilers, Intel and Portland's PGI. The paper also presents the evaluation methodology along with the experimental results to illustrate the scalability of the BLAST algorithm on our state-of-the-art HPC system. Our results show that BLAST runtime scalability can be achieved with up to 87% efficiency when considering the right combination of the MPI suite, the parallel compiler, the cluster interconnect and the CPU technology.