Parallel implementation of DNAml program on message-passing architectures

Abstract

We present a new computing approach for the parallelization on message-passing computer architectures of the DNAml algorithm, one of the most powerful tools available for constructing phylogenetic trees from DNA sequences. An analysis of the data dependencies of the method gave little chances to develop an efficient parallel approach. However, a careful run-time analysis of the behaviour of the algorithm allowed us to propose a very efficient parallel implementation based on the combination of advanced dynamic scheduling strategies, speculative running-time execution decisions and I/O buffering. In this work, we discuss specific Parallel Virtual Machine (PVM)-based implementations for a cluster of workstations and for Distributed Memory multiprocessors, with high performance results. The code can be obtained from our public-domain sites.