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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.

Available modules

Packages with modules

Module NeSI Cluster
RAxML/8.2.10-gimkl-2017a pan
RAxML/7.3.0-goolf-1.5.14-hybrid-sse3 pan
RAxML/8.2.2-foss-2015a pan
RAxML/8.2.2-intel-2015a pan

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 Pan 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-per-cpu   2G
#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-SSE3 -T $SLURM_CPUS_PER_TASK -m GTRCAT -s aln.fasta -n tree.out

Documentation

raxmlHPC-SSE3 -help and the RAxML manual.

Parallel Versions

Each of our RAxML environment modules contains multiple RAxML executables:

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

These all implement the RAxML algorithm, but one is serial, one multithreaded, one MPI, and one MPI+threads.
MPI is only useful for bootstrapped trees.

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

  • raxmlHPC-SSE3 with 1 task of 1 CPU.
  • raxmlHPC-PTHREADS-SSE3 with 1 task which has multiple CPUs.
  • raxmlHPC-MPI-SSE3 with multiple tasks of 1 CPU each.
  • raxmlHPC-HYBRID-SSE3 with multiple tasks, each of which has 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.

"SSE3" is the name for a set of Intel SIMD (Single Instruction Multiple Data) instructions.
On the nodes which support the newer AVX SIMD instructions there are also -AVX versions of RAxML (e.g., raxmlHPC-HYBRID-AVX) which can be 10-30% faster, so for example:

#!/bin/bash -e
#SBATCH --time          01:00:00
#SBATCH --cpus-per-task 4
#SBATCH --mem-per-cpu   2G
#SBATCH -C avx
srun raxmlHPC-PTHREADS-AVX -T $SLURM_CPUS_PER_TASK -m GTRCAT -s aln.fasta -n tree.out

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