MrBayes: Difference between revisions

Revision as of 14:09, 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

See the MrBayes_PBS page for mrbayes PBS script examples.

@@ Line 1: / Line 1: @@
-MrBayes has been installed on the cluster. We currently have two different versions installed:
+__NOTOC__
+__NOEDITSECTION__
+[[Category:Software]][[Category:Phylogenetics]]
+<!-- ########  Template Configuration ######## -->
+<!--Edit definitions of the variables used in template calls
+Required variables:
+app - lowercase name of the application e.g. "amber"
+url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
+Optional variables:
+INTEL - Version of the Intel Compiler e.g. "11.1"
+MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
+-->
+{|
+<!--Main settings - REQUIRED-->
+|{{#vardefine:app|mrbayes}}
+|{{#vardefine:url|http://mrbayes.sourceforge.net/}}
+<!--Compiler and MPI settings - OPTIONAL -->
+|{{#vardefine:intel|10.1}} <!-- E.g. "11.1" -->
+|{{#vardefine:mpi|openmpi/1.2.7}} <!-- E.g. "openmpi/1.3.4" -->
+<!--Choose sections to enable - OPTIONAL-->
+|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
+|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
+|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
+|{{#vardefine:pbs|1}} <!--Enable PBS script wiki page link-->
+|{{#vardefine:policy|}} <!--Enable policy section -->
+|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
+|{{#vardefine:faq|}} <!--Enable FAQ section -->
+|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
+|}
+<!-- ########  Template Body ######## -->
+<!--Description-->
+{{#if: {{#var: url}}|
+{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+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.
- /apps/mrbayes/bin/mb-mpi   <- Parallel Version
+<!--Location-->
- /apps/mrbayes/bin/mb       <- Single processor version
+{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+<!--Versions-->
+==Available versions==
+* 3.1.2
+<!-- -->
+==Running the application using modules==
-==Website==
+Multiple versions of MrBayes are installed in /apps/mrbayes/3.1.2/, and can be used through loading different sets of module files.
-[http://mrbayes.scs.fsu.edu/ MrBayes Home Website]
-==Sample PBS Script (MPI)==
-<pre>
-#!/bin/sh
-#PBS -N mbtest
-#PBS -m bea
-#PBS -M <EMAIL ADDRESS>
-#PBS -o pbsJobLog
-#PBS -e pbsJobErr
-#PBS -l nodes=4:ppn=1:infiniband
-#PBS -l pmem=2400mb
-#PBS -l walltime=5:00:00
-#
-# This job's working directory
-echo Working directory is $PBS_O_WORKDIR
-cd $PBS_O_WORKDIR
-echo Running on host `hostname`
+For information about the MrBayes module options, run the module spider command:
-echo Time is `date`
+ $module spider mrbayes/3.1.2
-echo Directory is `pwd`
-echo This jobs runs on the following processors:
-echo `cat $PBS_NODEFILE`
-# Define number of processors
-NPROCS=`wc -l < $PBS_NODEFILE`
-IbEnabled=`/usr/local/sbin/IbEnabled`
+'''All versions are compiled with Intel 10.1, so load this first in all cases.'''
-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 MPIRUN = $MPIRUN
-echo This job has allocated $NPROCS nodes
+For the serial (single core) version load MrBayes:
-echo $MPIRUN -np $NPROCS /apps/mrbayes/bin/mb-mpi indel_all_mb.dat \> log.txt
+ $module load intel/10.1 mrbayes
-$MPIRUN -np $NPROCS /apps/mrbayes/mb-mpi indel_all_mb.dat > log.txt
-</pre>
+The recommended MPI version is the OpenMPI 1.2.7 compiled version. To use this load:
-To change this to a serial only run, remove the $MPIRUN portion at the end and use ''/apps/mrbayes/mb'' for the executable instead.
+ $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
+{{#if: {{#var: exe}}|==How To Run==
+WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
+{{#if: {{#var: conf}}|==Configuration==
+See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
+{{#if: {{#var: pbs}}|==PBS Script Examples==
+See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
+{{#if: {{#var: policy}}|==Usage policy==
+WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
+{{#if: {{#var: testing}}|==Performance==
+WRITE PERFORMANCE TESTING RESULTS HERE|}}
+{{#if: {{#var: faq}}|==FAQ==
+*'''Q:''' **'''A:'''|}}
+{{#if: {{#var: citation}}|==Citation==
+If you publish research that uses {{{app}}} you have to cite it as follows:
+WRITE CITATION HERE
+|}}