MrBayes

Overview

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

Version 3.2.6 and 3.2.5 are installed on the CSF.

Restrictions on use

There are no restrictions on access on the CSF – the software is made available under the GNU GPL v3 license. If you use this software in your research please cite it. Run the command citations in the software for further details.

Set up procedure

To access the software you must first load the modulefile:

# Parallel (MPI) versions for multi-node (large MPI jobs - using fast InfiniBand network)
apps/gcc/mrbayes/3.2.6-mpi-ib
apps/gcc/mrbayes/3.2.6-beagle-mpi-ib

# Parallel (MPI) versions for single-node (small MPI jobs)
apps/gcc/mrbayes/3.2.6-mpi
apps/gcc/mrbayes/3.2.6-beagle

# Serial (1 core) version
apps/gcc/mrbayes/3.2.6

# Parallel (MPI) only
module load apps/gcc/mrbayes/3.2.5

The beagle versions of the modulefiles load a version of MrBayes that has been compiled against the Beagle library. You run this version in the same way as all other versions but may see some speed-up depending on the features you used in MrBayes. Please consult the MrBayes manual for more information.

Running the application

Please do not run MrBayes on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

mb myinput.nex

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Small Single-node Parallel batch job submission

This assume you have loaded one of the -mpi modulefiles. The number of cores should be no more than 24. Note that the parallel version of the MrBayes executable is named

pmb

An example jobscript is:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings
#$ -pe smp.pe 16    # Single node parallel (up to 24 cores can be used)

# $NSLOTS is automatically set to the number of cores requested above
mpirun -n $NSLOTS pmb myinput.nex
                   #
                   #
                   # Note that the executable is now 'pmb' not 'mb'

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Large Multi-node Parallel batch job submission

This assume you have loaded one of the -mpi-ib modulefiles. The number of cores must be a multiple of 24. Note that the parallel version of the MrBayes executable is named

pmb

An example jobscript is:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd               # Job will run from the current directory
#$ -V                 # Job will inherit current environment settings
#$ -pe orte-24-ib 48  # Multi node parallel job (number of cores must be a multiple of 24).

# $NSLOTS is automatically set to the number of cores requested above
mpirun -n $NSLOTS pmb myinput.nex
                   #
                   #
                   # Note that the executable is now 'pmb' not 'mb'

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Interactive use for Development

MrBayes provides an interactive command-line which can be used for testing and developing your scripts. Please do not run MrBayes on the login node. Instead you should request an interactive session on a compute node as follows:

qrsh -l inter -l short
  # Wait for an interactive session to start. If no resources
  # are free you will be asked to try again later.

# Now on the backend compute-node load the modulefile
module load apps/gcc/mrbayes/version

# Start the interactive shell
mb

# When you have finished with your interactive session, return to login node;
exit

Example Scripts

After loading one of the modulefiles, example scripts are available in the directory:

$MRBAYES_HOME/examples/

Further info

• MrBayes website

Updates

None.