Parallel design pattern for computational biology and scientific computing applications
Weiguo Liu, Bertil Schmidt · 2003
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 semiautomatically generate parallel programs. In this paper we present a new parallel programs called the "block-cyclic based wavefront" to parallelize typical biology and scientific computing. We show how this technique leads to significant runtime savings on PC clusters.