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Fifth IEEE International Conference on Cluster Computing (CLUSTER'03)
Parallel Design Pattern for Computational Biology and Scientific Computing Applications
Hong Kong
December 01-December 04
ISBN: 0-7695-2066-9
Weiguo Liu, Nanyang Technological University
Bertil Schmidt, Nanyang Technological University
Dynamic programming is an important algorithm design technique in computational biology and scientific computing. Typical applications using this technique are very compute-intensive and suffer from long runtimes on sequential architectures. Parallel program design patterns provide a new tool to semi-automatically generate parallel programs. In this paper we present a new parallel pattern called the "block-cyclic based wavefront" to parallelize typical dynamic programming algorithms in computational biology and scientific computing. We show how this technique leads to significant run-time savings on PC clusters.
Citation:
Weiguo Liu, Bertil Schmidt, "Parallel Design Pattern for Computational Biology and Scientific Computing Applications," cluster, pp.456, Fifth IEEE International Conference on Cluster Computing (CLUSTER'03), 2003
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