Skip to content

RAxML Next Generation

Randomised Axelerated Maximum Likelihood (RAxML) is a phylogenetic tree inference tool which uses maximum-likelihood optimality criterion.

RAxML Next Generation (NG) is available as a module on Apocrita.

Versions

Each RAxML NG version on Apocrita contains two different versions:

  • The serial (PTHREADS) version, suitable for serial only jobs
  • The MPI version, suitable for parallel only jobs

Usage

To run the default installed serial version of RAxML NG, simply load the raxml-ng module:

$ module load raxml-ng
$ raxml-ng --help
Usage: raxml-ng [OPTIONS]

To run the default installed MPI version of RAxML NG, simply load the raxml-ng-mpi module:

$ module load raxml-ng-mpi
$ raxml-ng-mpi --help
Usage: raxml-ng [OPTIONS]

For usage documentation, run raxml-ng --help or raxml-ng-mpi --help depending on the version being used.

Example jobs

Serial job

Here is an example job running on 2 cores and 2GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load raxml-ng

raxml-ng \
  --parse \
  --msa input_file.phy \
  --model GTR+G \
  --prefix T2 \
  --threads ${NSLOTS}

Parallel job

Here is an example job running on 96 cores across 2 ddy nodes using MPI:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe parallel 96
#$ -l infiniband=ddy-i
#$ -l h_rt=240:0:0

module load raxml-ng-mpi

mpirun -np ${NSLOTS} \
  raxml-ng-mpi \
    --parse \
    --msa input_file.phy \
    --model GTR+G \
    --prefix T2

References