Difference between revisions of "MrBayes"

Revision as of 21:23, 6 December 2019

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.

In addition to the official MrBayes distribution, a modified version that uses the Gamma-Dirichlet and Inverse Gamma-Dirichlet priors for branch lengths (Rannala et al. in press; Zhang et al. 2012). This also includes the two exponential priors on internal and external branch lengths described by Yang & Rannala (2005) and Yang (2007). Please see Ziheng Yang's site for more information and citations. The modified version is only installed for openmpi and is called mb_Dirichlet. To run this version, simply replace mb with mb_Dirichlet in the examples below.

Required Modules

modules documentation

Serial

mrbayes

Parallel (OpenMP)

intel
mrbayes

Parallel (OpenMPI)

intel
openmpi
mrbayes

System Variables

HPC_MRBAYES_DIR - installation directory

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).

@@ Line 2: / Line 2: @@
 __NOEDITSECTION__
 [[Category:Software]][[Category:Phylogenetics]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--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:pbs|}} <!--Enable PBS script wiki page link-->
 |{{#vardefine:policy|}} <!--Enable policy section -->
 |{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
@@ Line 31: / Line 16: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 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.
-<!--Location-->
+In addition to the official MrBayes distribution, a modified version that uses the Gamma-Dirichlet and Inverse Gamma-Dirichlet priors for branch lengths (Rannala et al. in press; Zhang et al. 2012). This also includes the two exponential priors on internal and external branch lengths described by Yang & Rannala (2005) and Yang (2007). Please see [http://abacus.gene.ucl.ac.uk/software.html Ziheng Yang's site] for more information and citations. The modified version is only installed for openmpi and is called mb_Dirichlet. To run this version, simply replace mb with mb_Dirichlet in the examples below.
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
-<!--Versions-->
-==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:
+<!--Modules-->
- $module load intel/10.1 openmpi/1.2.7 mrbayes
+==Required Modules==
+[[Modules|modules documentation]]
-We also have an MPI version compiled with MVAPICH/0.9.9
+===Serial===
- $module load intel/10.1 mvapich/0.9.9 mrbayes
+*{{#var:app}}
+===Parallel (OpenMP)===
-{{#if: {{#var: exe}}|==How To Run==
+*intel
+*{{#var:app}}
+===Parallel (OpenMPI)===
+*intel
+*openmpi
+*{{#var:app}}
+==System Variables==
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
+<!--Additional-->
+{{#if: {{#var: exe}}|==Additional Information==
 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==|}}
 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]
@@ Line 80: / Line 59: @@
 #PBS -l walltime=01:00:00
 #
+# Change to the directory from which the job was submitted
-#Change to the directory where the job was launched from
+#
 cd $PBS_O_WORKDIR
+#
-#Use modules to load the environment for MrBayes
+# Use modules to configure your environment for mrbayes
-module load intel/10.1
+#
-module load openmpi/1.2.7
+module load intel
+module load openmpi
 module load mrbayes
+#
+# Run MrBayes using the command line from documentation.
+#
+mpiexec mb my_nexus.nex
+</source>
-# 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 $NPROCS mb my_nexus.nex
-#Run MrBayes using the command line from documentation.
-$MPIRUN -np $NPROCS mb my_nexus.nex
+'''Script for serial (single core) MrBayes job:'''
+{{#fileAnchor: mrbayes.serial.pbs}}
+Download raw source of the [{{#fileLink: mrbayes.serial.pbs}} mrbayes.serial.pbs]
+<source lang=bash>
+#!/bin/bash
+#
+#PBS -N mrbayes
+#PBS -M <your e-mail>
+#PBS -m abe
+#PBS -o mb.$PBS_JOBID.out
+#PBS -e mb.$PBS_JOBID.err
+#PBS -l nodes=1:ppn=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
 </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)|}}
 {{#if: {{#var: testing}}|==Performance==