Difference between revisions of "MrBayes"

Latest revision as of 12:28, 19 August 2022

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.

Environment Modules

Run module spider mrbayes to find out what environment modules are available for this application.

System Variables

HPC_MRBAYES_DIR - installation directory

Additional Information

For MPI jobs

As a rule of thumb ntasks should be set to the total number of chains (MrBayes default is 4 chains * 2 runs = 8 chains)

As long as the number of cores is under 12, it is best to use a single node ("SBATCH --nodes=1") where nodes are physical computers as that will keep all communication within a single node.

@@ Line 1: / Line 1: @@
-MrBayes has been installed on the cluster. We currently have two different versions installed:
+[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
+{|<!--CONFIGURATION: REQUIRED-->
+|{{#vardefine:app|mrbayes}}
+|{{#vardefine:url|http://nbisweden.github.io/MrBayes}}
+<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
+|{{#vardefine:conf|}}           <!--CONFIGURATION-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
+|{{#vardefine:policy|}}         <!--POLICY-->
+|{{#vardefine:testing|}}       <!--PROFILING-->
+|{{#vardefine:faq|}}             <!--FAQ-->
+|{{#vardefine:citation|}}       <!--CITATION-->
+|{{#vardefine:installation|}} <!--INSTALLATION-->
+|}
+<!--BODY-->
+<!--Description-->
+{{#if: {{#var: url}}|
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
- /apps/mrbayes/bin/mb-mpi   <- Parallel Version
+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       <- Single processor version
-==Website==
+<!--Modules-->
-[http://mrbayes.scs.fsu.edu/ MrBayes Home Website]
+==Environment Modules==
-==Sample PBS Script==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-<pre>
+==System Variables==
-#!/bin/sh
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-#PBS -N mbtest
+<!--Configuration-->
-#PBS -m bea
+{{#if: {{#var: conf}}|==Configuration==
-#PBS -M <EMAIL ADDRESS>
+See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
-#PBS -o pbsJobLog
+|}}
-#PBS -e pbsJobErr
+<!--Run-->
-#PBS -l nodes=4:ppn=1:infiniband
+{{#if: {{#var: exe}}|==Additional Information==
-#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 MPI jobs:
-echo Time is `date`
+* As a rule of thumb ntasks should be set to the total number of chains (MrBayes default is 4 chains * 2 runs = 8 chains)
-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`
+* As long as the number of cores is under 12, it is best to use a single node ("SBATCH --nodes=1") where nodes are physical computers as that will keep all communication within a single node.
-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
+|}}
-echo $MPIRUN -np $NPROCS /apps/mrbayes/bin/mb-mpi indel_all_mb.dat \> log.txt
+<!--Job Scripts-->
-$MPIRUN -np $NPROCS /apps/mrbayes/mb-mpi indel_all_mb.dat > log.txt
+{{#if: {{#var: job}}|==Job Script Examples==
-</pre>
+See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
+|}}
+<!--Policy-->
+{{#if: {{#var: policy}}|==Usage Policy==
+WRITE USAGE POLICY HERE (Licensing, usage, access).
+|}}
+<!--Performance-->
+{{#if: {{#var: testing}}|==Performance==
+WRITE_PERFORMANCE_TESTING_RESULTS_HERE
+|}}
+<!--Faq-->
+{{#if: {{#var: faq}}|==FAQ==
+*'''Q:''' **'''A:'''|}}
+<!--Citation-->
+{{#if: {{#var: citation}}|==Citation==
+If you publish research that uses {{#var:app}} you have to cite it as follows:
+WRITE_CITATION_HERE
+|}}
+<!--Installation-->
+{{#if: {{#var: installation}}|==Installation==
+See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
+<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
+__NOTOC____NOEDITSECTION__