subqchem

#!/bin/bash

dir=$(pwd)
PGM_NAME="subqchem submit script"
PGM_VERSION="1.1"
BINARY_LOCATION=""

### SET DEFAULT VARIABLES

ncores_default=2
nnodes_default=1
jobtime_default=480
#memory=2

jobhold=""
holdid=""
debug=""
queue=""
user=$USER
copyall="no"

function usage {
  cat <<-EOF
$PGM_NAME $PGM_VERSION
Usage: $PGM_NAME [-j JOB_ID] [-t TIME]  [-m SIZE] [-N NAME] [-p CPUS] [-n NODES] [-a COPY BACK ALL FILES] INPUT_FILE
EOF

  exit 2

}

function printExit {
  case $1 in
  [iI]) echo INFO: "$2" ;;
  [wW]) echo WARNING: "$2" ;;
  [eE])
    echo ERROR: "$2"
    exit 1
    ;;
  *) echo "$1" ;;
  esac
}

function testFile {
  if [ ! -r "$1" -o ! -f "$1" ]; then
    if [ "$2" = "return" ]; then
      returncode="1"
    else
      printExit E "Inputfile \"$1\" was not found."
    fi
  else
    returncode="0"
  fi

  return "$returncode"
}

### PROCESS OPTIONS

while getopts adhj:m:N:p:n:q:t: options; do
  case $options in
  N)
    jobnamefix=$OPTARG
    ;;
  p)
    ncores=$OPTARG
    ;;
  n)
    nnodes=$OPTARG
    ;;
  a)
    copyall="yes"
    ;;
  m)
    memory=$OPTARG
    ;;
  j)
    holdid=$OPTARG
    jobhold=1
    echo "Not yet implemented."
    exit 1
    ;;
  q)
    queue=$OPTARG
    ;;
  d)
    debug=1
    ;;
  h)
    usage
    exit 0
    ;;
  t)
    jobtime=$OPTARG
    ;;
  \?)
    echo "Invalid option: -$OPTARG"
    exit 1
    ;;
  \:)
    echo "Option -$OPTARG requires an argument."
    exit 1
    ;;
  *)
    usage
    exit 1
    ;;
  esac
done

shift $((OPTIND - 1))

### CHECK FOR INPUT ARGUMENTS

if [ -z "$1" ]; then
  echo "No filename specified."
  exit 1
else
  myname=$1
fi

### CREATE DEFAULT JOBNAME

jobname_default="$(echo $dir | sed "s/\/data\/$USER\//d/" | sed "s/\/home\/$USER\//h/ ; s/\//./g").$myname"

### PROCESS VARIABLES

if [ -z "$jobnamefix" ]; then
  jobnamefix=$jobname_default
fi
if [ -z "$ncores" ]; then
  ncores=$ncores_default
fi
if [ -z "$nnodes" ]; then
  nnodes=$nnodes_default
fi
if [ -z "$memory" ]; then
  memory=8
fi
if [ -z "$jobtime" ]; then
  jobtime=$jobtime_default
fi

### CONSTRUCT OUTPUT FILENAME

if [ -z "$1" ]; then
  usage
  printExit E "No filename specified."
else
  myname=$1
fi

#
# Assemble the names for the input, output and error file.
#

inputsuffix=(.com .in .gjf .mol .umol)
outputsuffix=(.log .out .log)
choices=${#inputsuffix[*]}
found=""

if [ "${myname##*.}" != "$myname" ]; then
  for ((suffix = 0; suffix < choices; suffix++)); do
    if [ ".${myname##*.}" = "${inputsuffix[$suffix]}" ]; then
      testFile "$myname"
      found="1"
      jobname=${myname%${inputsuffix[$suffix]}}
      if [ "${jobname:0:1}" = "/" ]; then
        infile=$jobname${inputsuffix[$suffix]}
        outfile=$jobname${outputsuffix[$suffix]}
        scriptfile=$jobname.sh
      else
        infile=$PWD/$jobname${inputsuffix[$suffix]}
        outfile=$PWD/$jobname${outputsuffix[$suffix]}
        scriptfile=$PWD/$jobname.sh
      fi
      break
    fi
  done
fi

if [ -z "$found" ]; then
  jobname="$myname"
  for ((suffix = 0; suffix < choices; suffix++)); do
    if testFile "$jobname${inputsuffix[$suffix]}" "return"; then
      if [ -n "$found" ]; then
        printExit E "The name \"$myname\" is ambiguous, because more than one file with the possible suffixes [ ${inputsuffix[*]} ] exist."
      else
        found="1"
        if [ "${jobname:0:1}" = "/" ]; then
          infile=$jobname${inputsuffix[$suffix]}
          outfile=$jobname${outputsuffix[$suffix]}
          scriptfile=$jobname.sh
        else
          infile=$PWD/$jobname${inputsuffix[$suffix]}
          outfile=$PWD/$jobname${outputsuffix[$suffix]}
          scriptfile=$PWD/$jobname.sh
        fi
      fi
    fi
  done
  if [ -z "$found" ]; then
    if testFile "$myname" "return"; then
      printExit E "Your file \"$myname\" was found, but you have to append a suffix { ${inputsuffix[*]} } for clearness."
    else
      printExit E "No file \"$myname\" ending in [ ${inputsuffix[*]} ] was found."
    fi
  fi
fi

### SET QUEUE TO DEFAULT IF $QUEUE IS EMPTY

if [ -z "$queue" ]; then

  if [ "$jobtime" -le 2 ]; then
    queue="batch"
  elif [ "$jobtime" -gt 2 ] && [ "$jobtime" -le 72 ]; then
    queue="batch"
  elif [ "$jobtime" -gt 72 ]; then
    queue="batch"
  fi
fi

## GET MAIL

#mail=`cat /home/${USER}/.forward`

### set %mem and %nproc according to qsub

echo "Trying to figure out ncores and memory from infile..."
if grep --ignore-case threads $infile; then
  coreset=$(grep -m 1 --ignore-case threads $infile | awk '{print $2}')
  ncores=$coreset
  echo "Found threads and setting ncores accordingly"
else
  echo "Threads not found, using ncores=$ncores from command-line/default"
fi

echo ""

if grep --ignore-case mem_total $infile; then
  memset=$(grep -m 1 --ignore-case mem_total $infile | awk '{print $2}')
  memory=$(echo "$memset/1000+2" | bc)
  echo "Found mem_total and setting memory accordingly."
else
  echo "mem_total not found, using memory=$memory from command-line/default"
fi
echo ""
### CREATE OPTION STRING FOR QSUB

if [ -z "$jobhold" ]; then
  optionstring=""
else
  optionstring="-W depend=afterok:$holdid"
fi

inname=$(basename $infile)
outname=$(basename $outfile)
pbs_logfile=$(echo $inname | sed "s/.in/.pbslog/")
pbs_errorfile=$(echo $inname | sed "s/.in/.pbserr/")
#echo pbs_outname $pbs_outname pbs_errorname $pbs_errorname
scriptname=$(basename $scriptfile)
savedir=$(echo $outname | sed "s/.out/_files/")

#somehow this takes the last 19 characters of the jobname
jobident=$(echo $jobnamefix | sed 's/.*\(...................\)/\1/')

### CREATE INPUT SCRIPT FOR QSUB
test -e $scriptfile && mv $scriptfile ${scriptfile}_OLD

cat <<EOT >>$scriptfile
#!/bin/bash
# PBS Job
#PBS -V
#PBS -N $jobident
#PBS -m ae
#PBS -q $queue
#PBS -l nodes=1:ppn=$ncores
#PBS -l walltime=$jobtime:0:0
#PBS -l mem=${memory}G
#PBS -o $pbs_logfile
#PBS -e $pbs_errorfile
echo "Job is running on the compute node:"
echo "\$PBS_NODEFILE"
echo ""
echo "The local scratch directory (located on the compute node) is:"
echo "/tmp1/$user/"
echo ""

module load q-chem/gcc+mkl/5.4.2
#export QCAUX=/home/mewes/SOFTWARE/QC_AUX
#export QCSCRATCH=/tmp1/$user/
#export QCPLATFORM=LINUX_Ix86

cd 
# Backup old out files if existing 
[ -e ${outfile}_OLD ] && cp $outfile ${outfile}_OLDER
[ -e $outfile ] && cp $outfile ${outfile}_OLD
cd $dir
# Execute the program
if [ "$copyall" = "yes" ] ; then
\$QC/bin/qchem -save $inname $outname $savedir
else
\$QC/bin/qchem $inname $outname
fi
EOT

if [ $copyall ]; then
  cat <<EOT >>$scriptfile
#Copy plots back from Scratch 
cp -r /tmp1/$user/$savedir/plots . 
EOT
fi

if [ -z $debug ]; then
  cat <<EOT
Submitting job with settings:
Name: $jobident, #CPU: $ncores, #Nodes: $nnodes, mem: ${memory}GB, cpy-all? ${copyall}.
EOT
  qsub $optionstring $scriptfile

else
  cat <<EOT
Submit file created but not submitted. 
Name: $inname, #CPU: $ncores, #Nodes: $nnodes, mem: ${memory}GB, cpy-all? ${copyall}.
Submit with qsub $scriptname!
EOT
fi

exit 0