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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

We have installed the v0.9.0 serial (pthreads) and MPI versions of RAxML Next Generation version, in separate containers under /data/containers/raxml-ng/.

Serial version

To run the serial version of RAxML Next Generation on a single node, use the /data/containers/raxml-ng/raxml-ng container.

MPI version

To run the MPI version of RAxML Next Generation on multiple nodes, use the /data/containers/raxml-ng/raxml-ng-mpi container and also load the openmpi module, as shown below.

Usage

To run either installed version, first load the singularity and gcc/7.1.0 modules, then run the relevant version of RAxML Next Generation version, as described above.

Serial usage

$ module load singularity gcc/7.1.0
$ singularity run /data/containers/raxml-ng/raxml-ng --help

Usage: raxml-ng [OPTIONS]

For full usage documentation, run the container with the --help switch.

MPI usage

$ module load singularity gcc/7.1.0 openmpi/3.1.2-gcc
$ singularity run /data/containers/raxml-ng/raxml-ng-mpi --help

Usage: raxml-ng [OPTIONS]

For full usage documentation, run the container with the --help switch.

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 singularity/2.6.1 gcc/7.1.0

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

MPI job

Here is an example MPI job running on two sdv nodes (48 cores):

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe parallel 48
#$ -l infiniband=sdv-i
#$ -l h_rt=1:0:0

module load singularity/2.6.1 gcc/7.1.0 openmpi/3.1.2-gcc

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

References