fitjob_sub

#!/bin/bash

PGM_NAME="fitjob_sub"

dir=$(pwd)
default_ncores=4
default_nnodes=1
default_queue="single"
default_jobtime=10
default_memory=8

function usage {
echo "Usage: $PGM_NAME [t TIME]  [-m SIZE] [-N NAME] [-p CPUS] [-n NODES] INPUT_FILE"
exit 2
}


### PROCESS OPTIONS
while getopts dh:m:N:p:n:q:t: options; do
    case $options in
        N)
            jobnamefix=$OPTARG
            ;;
        p)
            ncores=$OPTARG
            ;;
        n)
            nnodes=$OPTARG
            ;;
        m)
            memory=$OPTARG
            ;;
        q)
            queue=$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))"



### FILE NAME
if [ -z "$1" ]; then
    echo "No filename specified."
    usage
    exit 1
else
    infile=$(echo $(basename $1) | sed "s/res_//" | sed "s/.sh//")   
fi

### CHECK FILE
if [[ ! -f "$1" ]]; then
    echo "The res file '$1' was not found."
    exit 1
fi

if [[ ! -x $(realpath "$1") ]]; then
    echo "The res file '$1' must be executable."
    exit 1
fi



### PROCESS VARIABLES
if [ -z "$jobnamefix" ]; then
    jobnamefix=fitd4_${infile}
fi
if [ -z "$ncores" ]; then
    ncores=$default_ncores
fi
if [ -z "$nnodes" ]; then
    nnodes=$default_nnodes
fi
if [ -z "$memory" ]; then
    memory=$default_memory
fi
if [ -z "$jobtime" ]; then
    jobtime=$default_jobtime
fi
if [ -z "$queue" ]; then
    queue=$default_queue
fi


### CREATING SCRIPTFILE
scriptfile="$PWD/fitjob_$infile"

if [ -e "$scriptfile" ]; then
    echo "$scriptfile already exists! Aborting..."
    exit 1
fi

cat <<-EOT >>$scriptfile 
#!/bin/bash
# PBS Job
#PBS -V
#PBS -k n
#PBS -N $jobnamefix
#PBS -q $queue
#PBS -l nodes=1:ppn=$ncores
#PBS -l walltime=$jobtime:0:0
#PBS -l mem=${memory}G
#PBS -o pbs_${infile}.log
#PBS -e pbs_${infile}.err

# go to working directory first
cd \$PBS_O_WORKDIR

# dirs
D4=\$HOME/projects/d4-param/FIT
TMP_DIR=/tmp1/\$USER
DIR1=\$PWD


export PARNODES=\$(wc -l \$PBS_NODEFILE | gawk '{print \$1}')
export TM_PAR_FORK=1
export PATH=\$D4:\$PATH
export HOSTS_FILE=\$PBS_NODEFILE
export LC_NUMERIC=en_US.UTF-8

cat \$HOSTS_FILE >hosts_file
mkdir -p \$TMP_DIR/\$PBS_JOBID

#check file system access
if [ ! -d \$TMP_DIR/\$PBS_JOBID ]; then
  echo "Unable to create \$TMP_DIR/\$PBS_JOBID on \$HOSTNAME. Must stop."
  exit
fi

#check current location
if [ "\$PWD" == "\$HOME" ]; then
  echo "Cowardly refusing to copy the whole home directory"
  exit
fi

#copy everything to node (will NOT copy directories for safety reasons. Add an 'r' only if absolutely sure what you are doing)
#bwlimit limits bandwidth to 5000 kbytes/sec
rsync -q --bwlimit=5000 \$DIR1/set.tar.xz \$TMP_DIR/\$PBS_JOBID/
cd \$TMP_DIR/\$PBS_JOBID

#####################################################################################
#Gettimings
start=\$(date +%s)

#####################################################################################
#jobs start here (if you have no idea what this script does, only edit this part...)
module load dftd4/2.5.1
tar xf \$DIR1/set.tar.xz
mfit2 1.00000000 0.40000000 5.00000000 -n ${infile}_d4_eeq_atm -p 'run_atm.sh $infile 1.0'
#end of job      (....and stop editing here.)

#####################################################################################
#Print timings to file
end=\$(date +%s)
secs=\$(expr \$end - \$start)
printf '%dh:%dm:%02ds\n' \$((\$secs / 3600)) \$((\$secs % 3600 / 60)) \$((\$secs % 60)) >RUNTIME

#####################################################################################
#copy everything back that is smaller than 5 gbytes

rsync -q --bwlimit=5000 --max-size=5G \$TMP_DIR/\$PBS_JOBID/* \$DIR1/

cd \$DIR1
rm -r \$TMP_DIR/\$PBS_JOBID
EOT


### SUBMITTING
if [ -z $debug ]; then
    echo "Submitting job with settings:"
    echo "Name: $infile, CPUs: $ncores, Nodes: $nnodes, mem: ${memory}GB."
    qsub $scriptfile

else
    echo "Submit file created but not submitted."
    echo "Name: $infile, CPUs: $ncores, Nodes: $nnodes, mem: ${memory}GB."
    echo "Submit with qsub $(basename $scriptfile)!"
fi

exit 0