From HPC
Jump to: navigation , search

Application Details

  • 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.
  • Versions: 3.2.6
  • Module names: mrbayes/gcc/3.2.6
  • License: Available to all; GNU General Public License version 2.0 (GPLv2)

Usage Examples


Executable Description
mb Single core and/or interactive
mb-mpi OpenMPI parallel version. Needs to be run with mpirun and following flags mpirun -mca pml cm -mca mtl psm2 mb-mpi


[username@c170 ~]$ mb

                            MrBayes v3.2.6 x64

                      (Bayesian Analysis of Phylogeny)

              Distributed under the GNU General Public License

               Type "help" or "help <command>" for information
                     on the commands that are available.

                   Type "about" for authorship and general
                       information about the program.

MrBayes >

Batch Submission

A better approach is to submit a MrBayes task as a parallel batch submission to run across multiple nodes, an example of which is:

#SBATCH -J MrBTest          # Job name, you can change it to whatever you want
#SBATCH -N 4                # Number of nodes to run across
#SBATCH -n 100              # Number of cores to run across
#SBATCH -o %N-%j.log        # Standard output will be written here
#SBATCH -e %N-%j.err        # Standard error will be written here
#SBATCH -p compute          # Slurm partition, where you want the job to be queued

module add openmpi/gcc/1.10.5 mrbayes/gcc/3.2.6

mpirun -mca pml cm -mca mtl psm2 mb-mpi input_nex_file.nex

The options for mpirun are required to make use of the Omni-Path interconnect.

This submission script can be found at /path/to/sample/script

[username@login01 ~]$ sbatch MRBayes.job
Submitted batch job 289555

Further Information