A Generic Parallel Pattern-Based System for Bioinformatics

Abstract. Parallel program design patterns provide users a new way to get parallel programs without much effort. However, it is always a serious limitation for most existing parallel pattern-based systems that there is no generic description for the structure and behavior of a pattern at application level. This limitation has so far greatly hindered the practical use of these systems. In this paper, we present a new parallel pattern-based system for bioinformatics. The underlying programming techniques are based on generic programming, a programhnique suited for the generic representation of abstract concepts. This allows the new system to be built in a generic way at application level. We show how this system efficiently addresses the shortcomings of existing systems and leads to significant runtime savings for some popular applications in bioinformatics on PC clusters.

• Type: Conference
• Year: 2004
• Where: EUROPAR
• Authors: Weiguo Liu, Bertil Schmidt
• Keywords: EUROPAR 2004, Parallel Pattern-based Systems, Parallel Program Design, Parallel Programs