subqchem_old

#!/bin/bash

dir=`pwd`
PGM_NAME="subqchem submit script"
PGM_VERSION="1.1"
BINARY_LOCATION=""

### SET DEFAULT VARIABLES

ncores_default=8
nnodes_default=1
jobtime_default=72
#memory=2


jobhold=""
holdid=""
debug=""
queue=""

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 "$memory" ]; then
   memory=2
fi
if [ -z "$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 [ "$jobtime" -le 2  ]; then
        queue="test"
    elif [ "$jobtime" -gt 2 ] && [ "$jobtime" -le 72 ]; then
        queue="short"
    elif [ "$jobtime" -gt 72 ]; then
        queue="long"
    fi
fi


## GET MAIL

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

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

cp $infile submitfile

memset=`grep --ignore-case %maxcore submitfile`
coreset=`grep --ignore-case %pal submitfile`

memoryMB=$((${memory}*1000))

mv submitfile $infile

### CREATE OPTION STRING FOR QSUB

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

fi

inname=$(basename $infile)
outname=$(basename $outfile)
scriptname=$(basename $scriptfile)
savedir=$(echo $outname | sed "s/.out/_files/")

### ADJUST TIME AND CHANGE INTO DAYS, HOURS

days=$(bc <<< "$jobtime/24")
hours=$(bc <<< "$jobtime-($days*24)")

### CREATE INPUT SCRIPT FOR QSUB
test -e $scriptfile && mv $scriptfile $scriptfile-OLD

cat <<EOT >> $scriptfile
#!/bin/bash

#SBATCH --job-name=$jobnamefix
#SBATCH -t $days-$hours:00
#SBATCH -n $ncores
#SBATCH -N $nnodes
#SBATCH --mem-per-cpu=${memory}G
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL
#SBATCH -o /home/${USER}/err/qchem-%j
#SBATCH --mail-user=$mail
#SBATCH -p $queue

echo "This job was submitted from the computer:"
echo "\$SLURM_SUBMIT_HOST"
echo "and the directory:"
echo "\$SLURM_SUBMIT_DIR"
echo ""
echo "It is running on the compute node:"
echo "\$SLURM_CLUSTER_NAME"
echo ""
echo "The local scratch directory (located on the compute node) is:"
echo "\$SCRATCH"
echo ""

export QC=/home/mewes/SOFTWARE/QC54_TRUNK
export QCAUX=/home/mewes/SOFTWARE/QC_AUX
export QCSCRATCH=\$SCRATCH
export QCPLATFORM=LINUX_Ix86
export QCTHREADS=$ncores
export OMP_NUM_THREADS=$ncores

# Go into Scratch
cd \$SCRATCH
cp $infile $dir/*.mol .

# Backup old out file is existing 
[ -e $outfile ] && cp $outfile ${outfile}_OLD

# Execute the program
if [ "$copyall" = "yes" ] ; then
\$QC/bin/qchem -save -np $nnodes $inname $outfile $outname.plots
else
\$QC/bin/qchem -np $nnodes $inname $outfile
fi

EOT

if [ $copyall ]; then
    cat <<EOT >> $scriptfile

#Copy plots back from Scratch 
cp -r \$SCRATCH/$outname.plots/plots \$SLURM_SUBMIT_DIR/$savedir

EOT
fi



if [ -z $debug ]; then
   sbatch $optionstring $scriptfile
   #rm $scriptfile

   cat <<EOT

Job has been submitted.
Name: $inname, #CPU: $ncores, #Nodes: $nnodes, mem: ${memory}GB.
EOT

else
   cat <<EOT

Job has been created. Submit file will be saved. 
Name: $inname, #CPU: $ncores, #Nodes: $nnodes, mem: ${memory}GB.
Submit with sbatch $scriptname!
EOT
fi 

exit 0