MrBayes

Description

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

Required Modules

modules documentation

Serial

mrbayes

Parallel (OpenMP)

intel
mrbayes

Parallel (OpenMPI)

intel
openmpi
mrbayes

System Variables

HPC_{{#uppercase:mrbayes}}_DIR - installation directory

PBS Script Examples

For MPI jobs: Remember that the total number of cores cannot be greater than the total number of chains MrBayes is using. For example, if you have 2 runs, each with 4 chains, the maximum number of cores to request is 2*4=8 cores. As long as the number of cores is under 12, it is best to keep nodes=1 (nodes = physical machines) as that will keep all communication within a single node. If you need more than 12 cores, you will probably want to add :infiniband to the request. (e.g. nodes=4:ppn=8:infiniband).

{{#fileAnchor: mrbayes.MPI.pbs}} Download raw source of the [{{#fileLink: mrbayes.MPI.pbs}} mrbayes.MPI.pbs]

#!/bin/bash
#
#PBS -N mrbayes
#PBS -M <your e-mail>
#PBS -m abe
#PBS -o mb.$PBS_JOBID.out
#PBS -e mb.$PBS_JOBID.err
#PBS -l nodes=1:ppn=8
#PBS -l pmem=500mb
#PBS -l walltime=01:00:00
#
# Change to the directory from which the job was submitted
#
cd $PBS_O_WORKDIR
#
# Use modules to configure your environment for mrbayes
#
module load intel/2012
module load openmpi/1.6
module load mrbayes
#
# This section tests for an infiniband interconnect and
# sets things up for best performance either way.
#
IbEnabled=`/usr/local/sbin/IbEnabled`
if [ $IbEnabled -gt 0 ]; then
  echo "Running on IB-enabled node set"
  MPIRUN="mpiexec --mca btl self,sm,openib"
else
  echo "Running on GigE-enabled node set"
  MPIRUN="mpiexec --mca btl ^udapl,openib --mca btl_tcp_if_include eth0"
fi

echo This job has allocated $NPROCS nodes
echo $MPIRUN mb my_nexus.nex
#
# Run MrBayes using the command line from documentation.
#
$MPIRUN mb my_nexus.nex

Script for serial (single core) MrBayes job: {{#fileAnchor: mrbayes.serial.pbs}} Download raw source of the [{{#fileLink: mrbayes.serial.pbs}} mrbayes.serial.pbs]

#!/bin/bash
#
#PBS -N mrbayes
#PBS -M <your e-mail>
#PBS -m abe
#PBS -o mb.$PBS_JOBID.out
#PBS -e mb.$PBS_JOBID.err
#PBS -l nodes=1:ppn=1
#PBS -l pmem=500mb
#PBS -l walltime=01:00:00
#
# Change to the directory from which the job was submitted
#
cd $PBS_O_WORKDIR
#
# Use modules to configure your environment for mrbayes
#
module load mrbayes
#
# launch the executable
#
mb my_nexus.nex