#!/bin/bash

#we want to use the default modules on Gordon.
source /etc/profile.d/modules.sh

module load mrbayes
paramfile=$1

THEBINARY=mb

#remove offensive "set autoclose=no" from input files.
sed -i~ '/begin\s\s*mrbayes/I,/^\s*end\s*;/I { /autoclose\s*$/I { N }; /autoclose\s*=\s*$/I { N }; s/autoclose\s*=\s*no/autoclose=yes/gI };' infile.nex
rm infile.nex~


echo "CIPRES_THREADSPP=$CIPRES_THREADSPP"
echo "CIPRES_NP=$CIPRES_NP"
echo "paramfile=$1"
echo "running:"
echo " mpirun -hostfile $PBS_NODEFILE -np $CIPRES_NP ${THEBINARY} < $paramfile"

# Don't allow files greater than 1 gig (specified in 1024 byte blocks)
# ulimit -f 1048576
# Don't allow files greater than 8 gig (specified in 1024 byte blocks)
ulimit -f 8388608 


mpirun -hostfile $PBS_NODEFILE -np $CIPRES_NP ${THEBINARY} < $paramfile