RAxML-OMP: an efficient program for phylogenetic inference on SMPs

Authors:
Alexandros Stamatakis;Michael Ott;Thomas Ludwig
Affiliations:
Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece;Department of Computer Science, Technical University of Munich, Garching b. München, Germany;Department of Computer Science, Ruprecht-Karls University, Heidelberg, Germany
Venue:
PaCT'05 Proceedings of the 8th international conference on Parallel Computing Technologies
Year:
2005

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Abstract

Inference of phylogenetic trees comprising hundreds or even thousands of organisms based on the Maximum Likelihood (ML) method is computationally extremely intensive. In order to accelerate computations we implemented RAxML-OMP, an efficient OpenMP-parallelization for Symmetric Multi-Processing machines (SMPs) based on the sequential program RAxML-V (Randomized Axelerated Maximum Likelihood). RAxML-V is a program for inference of evolutionary trees based upon the ML method and incorporates several advanced search algorithms like fast hill-climbing and simulated annealing. We assess performance of RAxML-OMP on the widely used Intel Xeon, Intel Itanium, and AMD Opteron architectures. RAxML-OMP scales particularly well on the AMD Opteron architecture and achieves even super-linear speedups for large datasets (with a length ≥ 5.000 base pairs) due to improved cache-efficiency and data locality. RAxML-OMP is freely available as open source code.