Difference between revisions of "MrBayes"

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__NOEDITSECTION__
 
__NOEDITSECTION__
 
[[Category:Software]][[Category:Phylogenetics]]
 
[[Category:Software]][[Category:Phylogenetics]]
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<!-- ########  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:app|mrbayes}}
 
|{{#vardefine:url|http://mrbayes.sourceforge.net/}}
 
|{{#vardefine:url|http://mrbayes.sourceforge.net/}}
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<!--Compiler and MPI settings - OPTIONAL -->
 
−
|{{#vardefine:intel|11.1}} <!-- E.g. "11.1" -->
 
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|{{#vardefine:mpi|openmpi/1.4.3}} <!-- E.g. "openmpi/1.3.4" -->
 
−
<!--Choose sections to enable - OPTIONAL-->
 
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
−
|{{#vardefine:pbs|1}} <!--Enable PBS script wiki page link-->
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|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
 
|{{#vardefine:policy|}} <!--Enable policy section -->
 
|{{#vardefine:policy|}} <!--Enable policy section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
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{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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{{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.
 
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-->
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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.
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{{App_Location|app={{#var:app}}|{{#var:ver}}}}
 
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<!--Versions-->
 
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==Available versions==
 
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* 3.1.2
 
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* 3.2.1
 
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<!-- -->
 
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==Running the application using modules==
 
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Multiple versions of MrBayes are installed in /apps/mrbayes/, and can be used through loading different sets of module files.
 
  
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For information about the MrBayes module options, run the module spider command:
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<!--Modules-->
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$module spider mrbayes/3.2.1
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==Required Modules==
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or
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[[Modules|modules documentation]]
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$module spider mrbayes/3.1.2
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===Serial===
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*{{#var:app}}
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'''MrBayes 3.2.1 versions are compiled with Intel 11.1, while MrBayes 3.1.2 versions are compiled with Intel 10.1.''' In either case, you will need to load the Intel module first.
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===Parallel (OpenMP)===
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*intel
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*{{#var:app}}
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For the serial (single core) version load MrBayes:
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===Parallel (OpenMPI)===
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$module load intel/11.1 mrbayes
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*intel
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*openmpi
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The recommended MPI version is the OpenMPI 1.4.3 compiled version. To use this load:
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*{{#var:app}}
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$module load intel/11.1 openmpi/1.4.3 mrbayes
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==System Variables==
−
 
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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For MrBayes 3.1.2, we also have an MPI version compiled with MVAPICH/0.9.9
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<!--Additional-->
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$module load intel/10.1 mvapich/0.9.9 mrbayes
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{{#if: {{#var: exe}}|==Additional Information==
−
 
 
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{{#if: {{#var: exe}}|==How To Run==
 
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
{{#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==|}}
−
 
 
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).
 
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}}
 
{{#fileAnchor: mrbayes.MPI.pbs}}
 
Download raw source of the [{{#fileLink: mrbayes.MPI.pbs}} mrbayes.MPI.pbs]
 
Download raw source of the [{{#fileLink: mrbayes.MPI.pbs}} mrbayes.MPI.pbs]
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# Use modules to configure your environment for mrbayes
 
# Use modules to configure your environment for mrbayes
 
#
 
#
−
module load intel/11.1
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module load intel
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module load openmpi/1.4.3
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module load openmpi
 
module load mrbayes
 
module load mrbayes
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#
 
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# This section tests for an infiniband interconnect and
 
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# sets things up for best performance either way.
 
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#
 
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IbEnabled=`/usr/local/sbin/IbEnabled`
 
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if [ $IbEnabled -gt 0 ]; then
 
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  echo "Running on IB-enabled node set"
 
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  MPIRUN="mpiexec --mca btl self,sm,openib"
 
−
else
 
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  echo "Running on GigE-enabled node set"
 
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  MPIRUN="mpiexec --mca btl ^udapl,openib --mca btl_tcp_if_include eth0"
 
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fi
 
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echo This job has allocated $NPROCS nodes
 
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echo $MPIRUN mb my_nexus.nex
 
 
#
 
#
 
# Run MrBayes using the command line from documentation.
 
# Run MrBayes using the command line from documentation.
 
#
 
#
−
$MPIRUN mb my_nexus.nex
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mpiexec mb my_nexus.nex
 
</source>
 
</source>
  
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#PBS -l walltime=01:00:00
 
#PBS -l walltime=01:00:00
 
#
 
#
−
 
+
# Change to the directory from which the job was submitted
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#Change to the directory where the job was launched from
+
#
 
cd $PBS_O_WORKDIR
 
cd $PBS_O_WORKDIR
−
 
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#
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#Use modules to load the environment for MrBayes
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# Use modules to configure your environment for mrbayes
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module load intel/11.1
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#
 
module load mrbayes
 
module load mrbayes
−
 
+
#
 +
# launch the executable
 +
#
 
mb my_nexus.nex
 
mb my_nexus.nex
−
 
 
</source>
 
</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)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Revision as of 21:23, 6 December 2019

Description

mrbayes 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.

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).



Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=MrBayes&oldid=19488"