MrBayes

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.

Finding available modules

[name@server ~]$ module spider mrbayes

For more on finding and selecting a version of MrBayes using module commands see Using modules

Examples

Sequential

The following job script uses only one CPU core (--cpus-per-task=1). The example uses an input file (primates.nex) distributed with MrBayes.

File : submit-mrbayes-seq.sh

#!/bin/bash
#SBATCH --account=def-someuser  # replace with your PI account
#SBATCH --cpus-per-task=1 
#SBATCH --mem-per-cpu=3G        # increase as needed
#SBATCH --time=1:00:00          # increase as needed

module load mrbayes/3.2.7
cd $SCRATCH 
cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex .

mb primates.nex

The job script can be submitted with

[name@server ~]$ sbatch submit-mrbayes-seq.sh

Parallel

MrBayes can be run on multiple cores, on multiple nodes, and on GPUs.

MPI

The following job script will use 8 CPU cores in total, on one or more nodes. Like the previous example, it uses an input file (primates.nex) distributed with MrBayes.

File : submit-mrbayes-parallel.sh

#!/bin/bash
#SBATCH --account=def-someuser  # replace with your PI account
#SBATCH --ntasks=8 				# increase as needed
#SBATCH --mem-per-cpu=3G        # increase as needed
#SBATCH --time=1:00:00          # increase as needed

module load mrbayes/3.2.7
cd $SCRATCH 
cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex .

srun mb primates.nex

The job script can be submitted with

[name@server ~]$ sbatch submit-mrbayes-parallel.sh

GPU

The following job script will use a GPU. Like the previous examples, it uses an input file (primates.nex) distributed with MrBayes.

File : submit-mrbayes-gpu.sh

#!/bin/bash
#SBATCH --account=def-someuser  # replace with your PI account
#SBATCH --cpus-per-task=1
#SBATCH --gpus=1
#SBATCH --mem-per-cpu=3G        # increase as needed
#SBATCH --time=1:00:00          # increase as needed

module load gcc cuda/12 mrbayes/3.2.7
cd $SCRATCH 
cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex .

srun mb primates.nex

The job script can be submitted with

[name@server ~]$ sbatch submit-mrbayes-gpu.sh

Checkpointing

If you need very long runs of MrBayes, we suggest you break up the work into several small jobs rather than one very long job. Long jobs have are more likely to be interrupted by hardware failure or maintenance outage. Fortunately, MrBayes has a mechanism for creating checkpoints, in which progress can be saved from one job and continued in a subsequent job.

Here is an example of how to split a calculation into two Slurm jobs which will run one after the other. Create two files, job1.nex and job2.nex, as shown below. Notice that the key difference between them is the presence of the append keyword in the second.

File : job1.nex

execute primates.nex;

mcmc ngen=10000000 nruns=2 temp=0.02 mcmcdiag=yes samplefreq=1000 
stoprule=yes stopval=0.005 relburnin=yes burninfrac=0.1 printfreq=1000 
checkfreq=1000;

File : job2.nex

execute primates.nex;

mcmc ngen=20000000 nruns=2 temp=0.02 mcmcdiag=yes samplefreq=1000
stoprule=yes stopval=0.005 relburnin=yes burninfrac=0.1 printfreq=1000
append=yes checkfreq=1000;

Then create a job script. This example is a job array, which means that one script and one sbatch command will be sufficient to launch two Slurm jobs, and therefore both parts of the calculation. See Job arrays for more about the --array parameter and the $SLURM_ARRAY_TASK_ID variable used here.

File : submit-mrbayes-cp.sh

#!/bin/bash
#SBATCH --account=def-someuser  # replace with your PI account
#SBATCH --ntasks=8 				# increase as needed
#SBATCH --mem-per-cpu=3G        # increase as needed
#SBATCH --time=1:00:00          # increase as needed
#SBATCH --array=1-2%1           # match the number of sub-jobs, only 1 at a time

module load gcc mrbayes/3.2.7
cd $SCRATCH 
cp -v $EBROOTMRBAYES/share/examples/mrbayes/primates.nex .

srun mb job${SLURM_ARRAY_TASK_ID}.nex

The example can be submitted with

[name@server ~]$ sbatch submit-mrbayes-cp.sh

Message Passing Interface