#!/bin/sh

#$ -o parcas.stdout
#$ -N parcas

#$ -q phys.q
#$ -S /bin/bash
#$ -V
#$ -cwd
#$ -m be
#$ -j y
#$ -M myemailaddress@helsinki.fi
#$ -l h_cpu=500:00:00
#$ -notify

sdir=`pwd`

# Establish the submission work directory.
echo "Date is `date`"
echo "Submission directory is $sdir"
echo "Host is" `hostname`

# Check for file space on /tmp
space=`df | grep "/tmp" | awk '{ print $5+0.0; }'`
echo "Space on /tmp:" $space "%"
if test $space -ge 80
then
    echo "qsub script check: File space on tmp on node" `hostname` 
    echo "is dangerously low. Aborting job."
    echo "Please ask an administrator to clean up /tmp on that node"
    echo `df | grep "/tmp"`
    exit
fi


cd  $sdir

# Create the computation work directory.
if [ ! -d /tmp/$USER ]; then
   mkdir /tmp/$USER
fi
cd    /tmp/$USER

dir=${sdir/$HOME/}
dir=${dir//\//__}
mkdir $dir
cd $dir

# Copy everything from submission directory here
cp -f -r $sdir/* .

# Copy required executable here
cp $HOME/md/parcas .

echo "Running on host `hostname`"
echo "Time is `date`"
echo "Directory is `pwd`"

# Run your executable
#############################################################################

./parcas > out.parcas

#############################################################################

# Store stdout into backup file (otherwise some parts removed at end)
cp $sdir/parcas.stdout $sdir/parcas.stdout.stored

# Copy results back to submission work directory.
cp -f -r * $sdir/
cd $sdir