RAxML

Description

RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. The RAxML home page is at https://github.com/stamatak/standard-RAxML.

 

Licensing requirements

RAxML is licensed under the terms of the GNU General Public License ("the GPL"), version 2 or (at your option) any later version. A copy of version 3 of the GPL as included with the RAxML software is available here.

Example scripts

Example script for the Mahuika cluster

#!/bin/bash -e

#SBATCH --job-name      RAxML_job
#SBATCH --account       nesi99999
#SBATCH --time          01:00:00
#SBATCH --ntasks        1
#SBATCH --cpus-per-task 4
#SBATCH --mem           2048MB
#SBATCH --output        RAxML_job.%j.out # Include the job ID in the names
#SBATCH --error         RAxML_job.%j.err # of the output and error files

module load RAxML/8.2.10-gimkl-2017a

srun raxmlHPC-PTHREADS-AVX -T $SLURM_CPUS_PER_TASK -m GTRCAT -s aln.fasta -n tree.out

Documentation

raxmlHPC-AVX -help and the RAxML manual.

Parallel Versions

Each of our RAxML environment modules contains multiple RAxML executables:

  • raxmlHPC-AVX
  • raxmlHPC-SSE3
  • raxmlHPC-PTHREADS-AVX
  • raxmlHPC-PTHREADS-SSE3
  • raxmlHPC-MPI-AVX
  • raxmlHPC-MPI-SSE3
  • raxmlHPC-HYBRID-AVX
  • raxmlHPC-HYBRID-SSE3

The combinations of Slurm settings and RAxML types which make sense are:

  • raxmlHPC-AVX or raxmlHPC-SSE3 with one task on only one CPU.
  • raxmlHPC-PTHREADS-AVX or raxmlHPC-PTHREADS-SSE3 with one task running on multiple CPUs.
  • raxmlHPC-MPI-AVX or raxmlHPC-MPI-SSE3 with multiple tasks, each running on one CPU.
  • raxmlHPC-HYBRID-AVX or raxmlHPC-HYBRID-SSE3 with multiple tasks, each of which runs on multiple CPUs.

MPI and HYBRID are only useful for bootstrapped trees.

For the multi-threaded cases (PTHREADS and HYBRID) you should tell RAxML how many threads to use with the RAxML option -T $SLURM_CPUS_PER_TASK.

The "AVX" executables use the AVX SIMD instructions, while the "SSE3" executables use the older and slower Intel SIMD (Single Instruction Multiple Data) instructions, which can be anywhere from 10% to 30% slower. There should be no need to use an SSE3 executable, unless you find that an AVX executable doesn't work for any reason.

Labels: mahuika tier1 biology app
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