|mpiMrBayes: an OpenMPI implementation of MrBayes|
MrBayes has been compiled for parallel processing on HPC using GNU OpenMPI. It distributes your chains across multiple nodes for faster execution.
Using openMPI MrBayes on HPC
The OpenMPI implementation of MrBayes uses all of the same conventions and commands as the serial versiion. The command is mb_p Be sure to specifiy at least as many total chains as the number of CPUs that you specify in your MOAB script. Therefore, with MrBayes' default MCMC settings of two runs, each running four chains, the optimal number of CPUs would be eight. Here's a sample MOAB script for mpiMrBayes:
#!/bin/bash #MOAB -l nodes=8 #MOAB -j oe #MOAB -m abe #MOAB -N MRBAYES-OPENMPI source /usr/local/profile.d/openmpi-gnu.sh cd $PBS_O_WORKDIR mpirun /opt/Bio/mpimrbayes/mb_p subset.nex
Be sure that your NEXUS file contains a complete MrBayes command block through the MCMC step. It is not necessary to generate a log file within your NEXUS commands - the MOAB log file will contain a complete log of the run.