Genrate slurm script

genslurm

#!/bin/bash
set -e

___EXCLUSIVE="#SBATCH --exclusive"
___CPUS_PER_TASK="1"

help(){
    echo "
Every option can be set from the command line or vie an env variable.
Command line takes priority.

    Most options have snesible defualts.

    -j --job-name NAME          Name of the job (env var JOB_NAME)
    -c --cores CORES            How many cores to use per node (env var CORES)
    -t --time TIME              Maximum run time of the job (env var TIME)
    -n --nodes NODES            How many nodes to use (env var NODES)
    -a --account NAME           Name of the account (env var ACCOUNT)
    -p --partition VAL          Partition value (env var PARTITION)
    -q --qos VAL                QoS value (env var QOS)

       --no-exclusive           Do not use exclusive exclusive flag
       --cpus-per-task CPUS     How many cpus to use per task

    -o --output FILE            Name of the output file (env var OUTPUT)

    -m --modules MODULES        Comma separated list of modules to load (env var MODULES)

    -h --help                   Print this message
    "
    exit 0
}


die(){
    >&2 echo "[ERROR]:" "$*"
    exit 1
}
warn() {
    >&2 echo "[WARN]:" "$*"
}

defaults() {
    ___DEFAULT_JOB_NAME="defaultJobName"
    ___DEFAULT_CORES="8"
    ___DEFAULT_TIME="00:00:20"
    ___DEFAULT_NODES="1"
    ___DEFAULT_ACCOUNT="m22oc-$USER"
    ___DEFAULT_PARTITION="standard"
    ___DEFAULT_QOS="standard"
    ___DEFAULT_OUTPUT="${JOB_NAME:-$___DEFAULT_JOB_NAME}.slurm"
}

args() {
    while [ -n "$1" ]; do
        case "$1" in
            -h|--help)
                help
                ;;
            -j|--job-name)
                JOB_NAME="$2"
                shift 2
                ;;
            -c|--cores)
                CORES="$2"
                shift 2
                ;;
            -t|--time)
                TIME="$2"
                shift 2
                ;;
            -n|--nodes)
                NODES="$2"
                shift 2
                ;;
            -a|--account)
                ACCOUNT="$2"
                shift 2
                ;;
            -p|--partition)
                PARTITION="$2"
                shift 2
                ;;
            -q|--qos)
                QOS="$2"
                shift 2
                ;;
            -m|--modules)
                MODULES="$2"
                shift 2
                ;;
            -o|--output)
                OUTPUT="$2"
                shift 2
                ;;
            --no-exclusive)
                ___EXCLUSIVE=
                shift
                ;;
            --cpus-per-task)
                ___CPUS_PER_TASK="$2"
                shift 2
                ;;
            -*)
                die "Option $1 not recognized"
                ;;
        esac
    done
}

setdefaults(){
    for var in JOB_NAME CORES TIME NODES ACCOUNT PARTITION QOS OUTPUT; do
        D="___DEFAULT_$var"
        if [ -z "${!var}" ]; then
            warn "$var not specified defaulting to \"${!D}\""
            declare -g "$var=${!D}"
        fi
    done
}



run (){
    if [ -f "$OUTPUT" ]; then
        die "file \"$OUTPUT\" already exists. Delete it and rerun the script if intentional"
    fi

    echo "#!/bin/bash

#SBATCH --job-name=$JOB_NAME
#SBATCH --time=$TIME
$___EXCLUSIVE
#SBATCH --nodes=$NODES
#SBATCH --tasks-per-node=$CORES
#SBATCH --cpus-per-task=$___CPUS_PER_TASK

#SBATCH --account=$ACCOUNT

#SBATCH --partition=$PARTITION

#SBATCH --qos=$QOS

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

cd \$SLURM_SUBMIT_DIR

" > "$OUTPUT"

for i in $(echo "$MODULES" | tr ',' '\n'); do
    echo "module load $i" >> "$OUTPUT"
done

}

args "$@"
defaults
setdefaults
run