ExaML

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Description

examl website  

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI.

This code implements the popular RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. It uses a radically new MPI parallelization approach that yields improved parallel efficiency, in particular on partitioned multi-gene or whole-genome datasets.

It is up to 4 times faster than RAxML-Light [1].

As RAxML-Light, ExaML also implements checkpointing, SSE3, AVX vectorization and memory saving techniques.

[1] A. Stamatakis, A.J. Aberer, C. Goll, S.A. Smith, S.A. Berger, F. Izquierdo-Carrasco: "RAxML-Light: A Tool for computing TeraByte Phylogenies", Bioinformatics 2012; doi: 10.1093/bioinformatics/bts309.

Required Modules

Parallel (MPI)

  • gcc/4.7.2
  • openmpi/1.6.5
  • examl

To discover how to load ExaML versions other than the latest one please run

$ module spider examl

followed by

$ module spider examl/version

for each version you'd like to load.

System Variables

  • HPC_EXAML_DIR

Additional Information

Note that at least for examl/3.0.14 we have two builds - the default build (examl/3.0.14 module) is built with NUM_BRANCHES set to the default value of 256. The examl/3.0.14-nb1 module makes available the NUM_BRANCES=1 build.




Validation

  • Validate 4/5/2018