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start interactive job on HPC Helix
#!/bin/bash
# Wrapper to run interactive job on helix hpc.
# @sbamin | helix
# usage
show_help() {
cat << EOF
Start interactive job on Helix: Only one job is allowed at a time.
-h display this help and exit
-j job name (default: j<random id>_username)
-w work directory (default: present work directory)
-q job queue (default: interactive)
-t walltime in HH:MM:SS (default: 01:00:00, max: 08:00:00)
-m memory in gb (default: 8, max: 64)
-n number of nodes (default: 1, max: 1)
-c cpu cores per node (default: 2, max: 12)
-o email notifications (default: a)
-e extra options to MSUB (default: none)
-d dry run (default: NO, type YES for printing command string but skip requesting interactive queue)
Usage: ${0##*/} -c <number of cores> -m <memory in gb> -t <walltime in hh:mm:ss>
Example: ${0##*/} -c 2 -m 16 -t 02:00:00
Quote variable names containig spaces and special characters.
Bare execution with ${0##*/} will request default interactive job with
1 hr walltime, 2 cores and 8gb memory
${0##*/} -h for help
Add -d YES for dry run, i.e., print qsub interactive command
EOF
}
while getopts "j:w:q:t:m:n:c:o:e:d:h" opt; do
case "$opt" in
h) show_help;exit 0;;
j) JOBNAME=$OPTARG;;
w) CWD=$OPTARG;;
q) QUEUE=$OPTARG;;
t) WALLTIME=$OPTARG;;
m) MEMORY=$OPTARG;;
n) NODES=$OPTARG;;
c) CPU=$OPTARG;;
o) EMAILOPTS=$OPTARG;;
e) EXTRA_OPTS=$OPTARG;;
d) DRYRUN=$OPTARG;;
'?')show_help >&2 exit 1 ;;
esac
done
DJOBID=$(printf "j%s_%s" "$RANDOM" "$(whoami)")
JOBNAME=${JOBNAME:-$DJOBID}
CWD=${CWD:-$(pwd)}
QUEUE=${QUEUE:-"interactive"}
WALLTIME=${WALLTIME:-"01:00:00"}
MEMORY=${MEMORY:-"8gb"}
NODES=${NODES:-"1"}
CPU=${CPU:-"2"}
EMAILOPTS=${EMAILOPTS:-"a"}
EXTRA_OPTS=${EXTRA_OPTS:-""}
DRYRUN=${DRYRUN:-"NO"}
INTCMD=$(printf "qsub -I -V -r y -S /bin/bash -m %s -q %s -l nodes=1:ppn=%s,walltime=%s,mem=%s -d %s %s" "${EMAILOPTS}" "${QUEUE}" "${CPU}" "${WALLTIME}" "${MEMORY}" "${CWD}" "${EXTRA_OPTS}")
if [[ ${DRYRUN} != "YES" ]]; then
printf "\nRequesting interactive queue using following command:\n\n%s\n\n" "${INTCMD}"
sleep 2
## request interactive job
eval "${INTCMD}"
EXITSTAT=$?
TSTAMP=$(date +%d%b%y_%H%M%S%Z)
printf "\n\nInteractive job completed at %s with exit status %s\n\n" "${TSTAMP}" "${EXITSTAT}"
else
printf "\n#### DRY RUN ####\nYou can request interactive queue using following command:\n\n%s\n\n" "${INTCMD}"
fi
## END ##
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