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RAxML Next Generation

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

RAxML Next Generation is available as a container on Apocrita.

Versions

The serial (PTHREADS) and MPI versions of RAxML Next Generation have been installed on Apocrita inside separate containers.

Usage

To run the default installed PTHREADS or MPI version of RAxML Next Generation, simply load the raxml-ng module:

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

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

For usage documentation, run raxml-ng --help or raxml-ng-mpi --help.

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 openmpi/3.1.2-gcc

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

References