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
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