ExaBayes

ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.

manual

Standalone version:

module load openmpi-apps/1.6.4/exabayes/1.4.2 gcc/4.9.1
yggdrasil -f aln.phy -m DNA -n myRun -s $RANDOM

MPI

If you want a working example to start from just run:

wget http://www.hpc.uidaho.edu/examples/exabayes-mpi.tar.bz2
tar -xf exabayes-mpi.tar.bz2
cd exabayes-mpi
qsub exabayes-mpi.pbs

(you will need to be logged into fortytwo)

Here’s what the PBS script looks like:

exabayes-mpi.pbs

#!/bin/sh
#PBS -l nodes=5:ppn=1
#PBS -q short
#PBS -N exabayes-mpi-tester

source /usr/modules/init/bash
module load openmpi-apps/1.6.4/exabayes/1.4.2 gcc/4.9.1

cd $PBS_O_WORKDIR

mpirun --mca btl openib,self,sm exabayes -f aln.phy -q aln.part -n exabayes-mpi-test -s 9999 -c config.nex -R 5