Skip to content

Puhti and Mahti computing services have been decommissioned. Puhti and Mahti login nodes and storage services will remain available until 15 October 2026, but are no longer covered by service contracts. Please clean up and migrate your data to Roihu ASAP. See Roihu data migration guide for instructions.

MrBayes

MrBayes is a program for Bayesian inference on phylogenies.

License

Free to use and open source under GNU GPLv3.

Available

  • Roihu-CPU: 3.2.7a, via the bio-apps module.

Usage

MrBayes is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the MrBayes module:

module load bio-apps/v202603
module load mrbayes/3.2.7a

MrBayes is started with the mb command. The same MPI-enabled binary runs serially when started directly:

mb

and in parallel when launched with srun in a batch job. When using the parallel version, you should note that MrBayes assigns one chain to one core, so for optimal performance you should use as many cores as the total number of chains in your job. If, for example, you have specified nchains=4, nruns=2 you should use 4 * 2 = 8 cores.

Batch jobs

Running MrBayes analysis might take considerable amount of CPU time and memory. It is, therefore, recommended running it through the batch job system on Roihu. Shorter test runs can be run in interactive mode using sinteractive. The serial version is recommended for interactive use.

To run a batch job you need to:

  1. Write a MrBayes command file (here mb_com.nex) or include a MrBayes command block in your .nex file. For details, see Chapter 5.5.1 of the MrBayes manual.
  2. Write a batch job script (here mb_batch)
  3. Make sure you have all your input files (here primates.nex)
  4. Submit your job into the queue

MrBayes command file should include the commands you would type in MrBayes in interactive mode. This example runs the analysis mentioned in Chapter 2 of the MrBayes 3.2 manual.

begin mrbayes;
    set autoclose=yes nowarn=yes;
    execute primates.nex;
    lset nst=6 rates=invgamma;
    mcmc nchains=4 nruns=2 ngen=20000 samplefreq=100 printfreq=100 diagnfreq=1000;
    sump;
    sumt;
end;

Below is an example batch job script for Roihu using 8 cores. We are using 8 cores since our example uses nchains=4, nruns=2, so 4 * 2 = 8.

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --job-name=my_mrbjob
#SBATCH --error=my_mrbjob_err%j
#SBATCH --output=my_mrbjob_out%j
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --ntasks=8
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4000

module load bio-apps/v202603
module load mrbayes/3.2.7a

srun mb mb_com.nex >log.txt

To submit the job:

sbatch mb_batch

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information