Preparing RAxML for the SPEC MPI Benchmark Suite

Michael Ott () and Alexandros Stamatakis ()
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Michael Ott: Technische Universität München, Department of Computer Science
Alexandros Stamatakis: Technische Universität München, Department of Computer Science

A chapter in High Performance Computing in Science and Engineering, Garching/Munich 2009, 2010, pp 757-768 from Springer

Abstract: Abstract Inferring phylogenetic trees from molecular sequence data is considered to be a grand challenge in Bioinformatics due to its immense computational requirements. Efficient parallel implementations of programs for phylogenetic inference and the utilization of high performance computing infrastructure are therefore of paramount importance for facilitating large-scale phylogenetic analyses. RAxML is a widely used tool for phylogenetic inference and its PThreads- and MPI-based parallelizations have already been shown to scale up to thousands of processors. The MPI version has recently been chosen to become a part of the upcoming SPEC MPI 2.0 benchmark suite.

Keywords: Branch Length; Tree Search; Likelihood Score; Benchmark Suite; Input Alignment (search for similar items in EconPapers)
Date: 2010
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DOI: 10.1007/978-3-642-13872-0_63

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