Exploiting fine-grained parallelism in the phylogenetic likelihood function with MPI, Pthreads, and OpenMP: A performance study

Abstract

Emerging multi- and many-core computer architectures pose new challenges with respect to efficient exploitation of parallelism. In addition, it is currently not clear which might be the most appropriate parallel programming paradigm to exploit such architectures, both from the efficiency as well as software engineering point of view. Beyond that, the application of high performance computing techniques and the use of supercomputers will be essential to deal with the explosive accumulation of sequence data. We address these issues via a thorough performance study by example of RAxML, which is a widely used Bioinformatics application for large-scale phylogenetic inference under the Maximum Likelihood criterion. We provide an overview over the respective parallelization strategies with MPI, Pthreads, and OpenMP and assess performance for these approaches on a large variety of parallel architectures. Results indicate that there is no universally best-suited paradigm with respect to efficiency and portability of the ML function. Therefore, we suggest that the ML function should be parallelized with MPI and Pthreads based on software engineering criteria as well as to enforce data locality. © 2008 Springer Berlin Heidelberg.