killmyjobs

#!/bin/bash

running_only=false

print_usage () {
  cat << EOM
Usage: $0 [-n nodelist] [-g] [-e JOBID [-e JOBID ... ]] 
    Kills all your jobs! By default, also kills those you have queued up too.
    To only kill your running jobs, use the -g flag.
    Jobs that are not to be killed can be indicated using the -e flag.

Arguments:
    -n    (optional) specify nodes, either comma separated list, or summarised.
          Mirrors slurm command -n usage in sinfo, and -w usage for squeue." 
    -g    (optional) will only kill running jobs, not jobs in the queue 
    -e    (optional) a job to exclude, can specify multiple times

EOM
}

while getopts 'n:ge:' flag; do
  case "${flag}" in
    n) nodes="${OPTARG}" ;;
    g) running_only=true ;;
    e) exclude+=("$OPTARG") ;;
    *) print_usage
       exit 1 ;;
  esac
done

if [ "$running_only" = true ]; then
    if [ -z ${nodes+x} ]; then
        nodes=`sinfo --format="%N" --noheader`
    fi
    echo "not killing jobs in queue"
    jobids="$(squeue -u `whoami` --nodelist=${nodes} -o "%i" --noheader | LC_ALL=C sort)"
else
    echo "killing jobs in queue as well as running jobs"
    jobids="$(squeue -r -u `whoami` -o "%i" --noheader | LC_ALL=C sort)"
fi
if [[ -n ${exclude+1} ]]; then
    echo "excluding ${exclude[@]}"
    excl=`printf '%s\n' "${exclude[@]}" | LC_ALL=C sort`
    jobids=`comm -13 <(echo "$excl") <(echo "$jobids") | tr '\n' ' '`
fi
if [ "${jobids}" = "" ]; then
    echo "well I would...but you've got no jobs to kill m8"
else
    echo "killing $jobids"
    parallel 'scancel {}' ::: ${jobids} 
fi