#!/bin/bash

# gordon_submit.py sources /etc/profile.d/modules.sh and sets MODULEPATH
# so we don't need to source .bashrc to get module load to work.  In fact
# source'ing .bashrc or modules.sh here would clobber MODULEPATH set in
# gordon_submit.py.  TODO: make the same change to trestle's submit.py 
and all the tool wrappers.  
# source $HOME/.bashrc

module load mrbayes
paramfile=$1
if [ -n "$CIPRES_THREADSPP" ]; then
    export OMP_NUM_THREADS=$CIPRES_THREADSPP
fi

echo "CIPRES_THREADSPP=$CIPRES_THREADSPP"
echo "CIPRES_NP=$CIPRES_NP"
echo "paramfile=$1"
echo "running:"
echo " mpirun -hostfile $PBS_NODEFILE -np $CIPRES_NP mb-hybrid < $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 

#OpenMPI 1.6.5 is not compatible with the machine files that torque creates by default anymore.
uniqueNodefile=$(mktemp /tmp/uniqNodefileXXX)
uniq -c $PBS_NODEFILE | awk '{print $2" slots="$1;}' > ${uniqueNodefile}

export OMP_NUM_THREADS=${CIPRES_THREADSPP}

mpirun --machinefile ${uniqueNodefile} -n ${CIPRES_NP} -x OMP_NUM_THREADS --bynode  mb-hybrid < $paramfile