Difference between revisions of "MrBayes"

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{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
{{#if: {{#var: pbs}}|==PBS Script Examples==
+
{{#if: {{#var: pbs}}|==PBS Script Examples==|}}
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} 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.
 +
 
 +
{{#fileAnchor: mrbayes.MPI.pbs}}
 +
Download raw source of the [{{#fileLink: mrbayes.MPI.pbs}} mrbayes.MPI.pbs]
 +
<source lang=bash>
 +
#!/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 where the job was launched from
 +
cd $PBS_O_WORKDIR
 +
 
 +
#Use modules to load the environment for MrBayes
 +
module load intel/10.1
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module load openmpi/1.2.7
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module load mrbayes
 +
 
 +
# Define number of processors
 +
NPROCS=`wc -l < $PBS_NODEFILE`
 +
 
 +
IbEnabled=`/usr/local/sbin/IbEnabled`
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if [ $IbEnabled -gt 0 ]; then
 +
  echo "Running on IB-enabled node set"
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  MPIRUN="mpirun --mca btl openib"
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else
 +
  echo "Running on GigE-enabled node set"
 +
  MPIRUN="mpirun --mca btl ^udapl,openib --mca btl_tcp_if_include eth0"
 +
fi
 +
 
 +
echo This job has allocated $NPROCS nodes
 +
echo $MPIRUN -np $NPROCS mb my_nexus.nex
 +
 
 +
#Run MrBayes using the beast command line from documentation.
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$MPIRUN -np $NPROCS mb my_nexus.nex
 +
 
 +
</source>
 
{{#if: {{#var: policy}}|==Usage policy==
 
{{#if: {{#var: policy}}|==Usage policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}

Revision as of 14:23, 17 May 2012

Description

{{{name}}} website  
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.

Template:App Location

Available versions

  • 3.1.2

Running the application using modules

Multiple versions of MrBayes are installed in /apps/mrbayes/3.1.2/, and can be used through loading different sets of module files.

For information about the MrBayes module options, run the module spider command:

$module spider mrbayes/3.1.2

All versions are compiled with Intel 10.1, so load this first in all cases.

For the serial (single core) version load MrBayes:

$module load intel/10.1 mrbayes

The recommended MPI version is the OpenMPI 1.2.7 compiled version. To use this load:

$module load intel/10.1 openmpi/1.2.7 mrbayes

We also have an MPI version compiled with MVAPICH/0.9.9

$module load intel/10.1 mvapich/0.9.9 mrbayes


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.

{{#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 where the job was launched from
cd $PBS_O_WORKDIR

#Use modules to load the environment for MrBayes
module load intel/10.1
module load openmpi/1.2.7
module load mrbayes

# Define number of processors
NPROCS=`wc -l < $PBS_NODEFILE`

IbEnabled=`/usr/local/sbin/IbEnabled`
if [ $IbEnabled -gt 0 ]; then
  echo "Running on IB-enabled node set"
  MPIRUN="mpirun --mca btl openib"
else
  echo "Running on GigE-enabled node set"
  MPIRUN="mpirun --mca btl ^udapl,openib --mca btl_tcp_if_include eth0"
fi

echo This job has allocated $NPROCS nodes
echo $MPIRUN -np $NPROCS mb my_nexus.nex

#Run MrBayes using the beast command line from documentation.
$MPIRUN -np $NPROCS mb my_nexus.nex