Introduction

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. To run the MrBayes software interactively on the front-end node of tara, use the command

[araim1@tara-fe1 ~]$ mb

We will now demonstrate running MrBayes on the compute nodes. This was adpated from MbWiki. First, make sure to update your switcher settings as follows

[araim1@tara-fe1 ~]$ switcher mpi = gcc-mvapich2-1.4rc2
[araim1@tara-fe1 ~]$ switcher_reload

This is necessary to match the compiler and MPI implementation originally used to configure MrBayes. Next create a .nex file as follows, with your contents instead of the placeholders.

#NEXUS

BEGIN DATA;
    ... Insert data here ...
END;

begin mrbayes;
    ... Insert MrBayes block contents here
END;

Download: ../code/mrbayes-example/my.nex

Now create a small script with commands to execute the .nex file

set autoclose=yes nowarn=yes
execute my.nex
quit

Download: ../code/mrbayes-example/batch.txt

The last step is to create a usual SLURM batch script. This script will run the MrBayes program on the compute nodes; the program will be run in parallel if multiple processes are requested. MyBayes will then run batch.txt, which will in turn execute our .nex file.

#!/bin/bash
#SBATCH --job-name=mrbayes
#SBATCH --output=slurm.out
#SBATCH --error=slurm.err
#SBATCH --partition=batch
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8

srun mb batch.txt

Download: ../code/mrbayes-example/run.slurm

Make sure you have read the how to run tutorial before attempting to use the batch system.