Parallel Design Pattern for Computational Biology and Scientific Computing Applications

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.