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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
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.