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UMBC High Performance Computing Facility
Please note that this page is under construction. We are documenting the 240-node cluster maya that will be available after Summer 2014. Currently, the 84-node cluster tara still operates independently, until it becomes part of maya at the end of Summer 2014. Please see the 2013 Resources Pages under the Resources tab for tara information.
How to run MrBayes on tara

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.