MrBayes

MrBayes has been installed on the cluster. We currently have two different versions installed:

/apps/mrbayes/bin/mb-mpi   <- Parallel Version
/apps/mrbayes/bin/mb       <- Single processor version

Website

MrBayes Home Website

Sample PBS Script (MPI)

#!/bin/sh
#PBS -N mbtest
#PBS -m bea
#PBS -M <EMAIL ADDRESS>
#PBS -o pbsJobLog
#PBS -e pbsJobErr
#PBS -l nodes=4:ppn=1:infiniband
#PBS -l pmem=2400mb
#PBS -l walltime=5:00:00
#
# This job's working directory
echo Working directory is $PBS_O_WORKDIR
cd $PBS_O_WORKDIR

echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
echo This jobs runs on the following processors:
echo `cat $PBS_NODEFILE`
# Define number of processors
NPROCS=`wc -l < $PBS_NODEFILE`

IbEnabled=`/usr/local/sbin/IbEnabled`
if [ $IbEnabled -gt 0 ]; then
  echo "Running on IB-enabled node set"
  MPIRUN="mpirun --mca btl openib"
else
  echo "Running on GigE-enabled node set"
  MPIRUN="mpirun --mca btl ^udapl,openib --mca btl_tcp_if_include eth0"
fi
echo MPIRUN = $MPIRUN

echo This job has allocated $NPROCS nodes
echo $MPIRUN -np $NPROCS /apps/mrbayes/bin/mb-mpi indel_all_mb.dat \> log.txt
$MPIRUN -np $NPROCS /apps/mrbayes/mb-mpi indel_all_mb.dat > log.txt

To change this to a serial only run, remove the $MPIRUN portion at the end and use /apps/mrbayes/mb for the executable instead.