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 5: / Line 5: @@
 |{{#vardefine:app|mrbayes}}
 |{{#vardefine:url|http://mrbayes.sourceforge.net/}}
-<!--Compiler and MPI settings - OPTIONAL -->
-|{{#vardefine:intel|11.1}} <!-- E.g. "11.1" -->
-|{{#vardefine:mpi|openmpi/1.4.3}} <!-- E.g. "openmpi/1.3.4" -->
 |{{#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 23: / Line 19: @@
 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.
-<!--Modules-->
-==Execution Environment and Modules==
-Multiple versions of MrBayes are installed in /apps/mrbayes/, and can be used through loading different sets of module files.
-For information about the MrBayes module options, run the module spider command:
+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.
- $module spider mrbayes/3.2.1
- or
- $module spider mrbayes/3.1.2
-'''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.
+<!--Modules-->
+==Required Modules==
-For the serial (single core) version load MrBayes:
+[[Modules|modules documentation]]
- $module load intel/11.1 mrbayes
+===Serial===
+*{{#var:app}}
-The recommended MPI version is the OpenMPI 1.4.3 compiled version. To use this load:
+===Parallel (OpenMP)===
- $module load intel/11.1 openmpi/1.4.3 mrbayes
+*intel
+*{{#var:app}}
-For MrBayes 3.1.2, we also have an MPI version compiled with MVAPICH/0.9.9
+===Parallel (OpenMPI)===
- $module load intel/10.1 mvapich/0.9.9 mrbayes
+*intel
+*openmpi
-{{#if: {{#var: exe}}|==How To Run==
+*{{#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 71: / Line 65: @@
 # Use modules to configure your environment for mrbayes
 #
-module load intel/11.1
+module load intel
-module load openmpi/1.4.3
+module load openmpi
 module load mrbayes
-#
-# This section tests for an infiniband interconnect and
-# sets things up for best performance either way.
-#
-IbEnabled=`/usr/local/sbin/IbEnabled`
-if [ $IbEnabled -gt 0 ]; then
-  echo "Running on IB-enabled node set"
-  MPIRUN="mpiexec --mca btl self,sm,openib"
-else
-  echo "Running on GigE-enabled node set"
-  MPIRUN="mpiexec --mca btl ^udapl,openib --mca btl_tcp_if_include eth0"
-fi
-echo This job has allocated $NPROCS nodes
-echo $MPIRUN mb my_nexus.nex
 #
 # Run MrBayes using the command line from documentation.
 #
-$MPIRUN mb my_nexus.nex
+mpiexec mb my_nexus.nex
 </source>
@@ Line 118: / Line 97: @@
 # Use modules to configure your environment for mrbayes
 #
-module load intel/11.1
 module load mrbayes
 #
@@ Line 125: / Line 103: @@
 mb my_nexus.nex
 </source>
+-->
 {{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}