bubba

#!/bin/bash

# primitive bsub convenience wrapper, see below.

set -euo pipefail

thequeue=long
themem=5000
thetag="bubba"
usegroup=""
nproc=1
logdir=logs
TEST=

while getopts :q:n:m:g:l:t:hT opt
do
    case "$opt" in
    q)
      thequeue=$OPTARG
      ;;
    l)
      logdir=$OPTARG
      ;;
    g)
      usegroup="-g /$OPTARG"
      ;;
    m)
      themem=$OPTARG
      ;;
    n)
      nproc=$OPTARG
      ;;
    t)
      thetag=$OPTARG
      ;;
    T)
      TEST=echo
      ;;
    h)
      cat <<EOU
Usage: bubba [options] thecommand [with] [optional] [arguments]
  ● Primitive bsub wrapper.
  ● Options can change things like queues, memory, and log file names/destination.
  ● Use -T to just print the bsub command.
  ● The command thecommand is checked for existence.
-q queue (default $thequeue)
-m memory (default $themem)
-n nproc (default $nproc)
-g group (default none)
-t thetag (default $thetag)
-l logdir (default $logdir, use "." for current directory)
-T        test: show the bsub command, do not run it
EOU
      exit
      ;;
    :) echo "Flag $OPTARG needs argument"
        exit 1;;
    ?) echo "Flag $OPTARG unknown"              # Yes that's right, $OPTARG. bash bish bosh.
        exit 1;;
   esac
done

# The OPTIND lines below ensure that the opt-parsed arguments are removed from $@
# (the name of the array where command line arguments are stored in a bash script).
# The remaining trailing arguments are the only ones left; we pass those on to bsub, below.

OPTIND=$(($OPTIND-1))
shift $OPTIND


(( $# == 0 )) &&          echo "No command to run" && false

! command -v "$1" > /dev/null &&      echo "Command $1 not found" && false

[[ $thetag =~ " " ]] &&   echo "No space please: [$thetag]" && false

[[ ! -d $logdir ]] &&     echo "Not a directory: $logdir" && false

$TEST bsub -n$nproc -R'span[hosts=1]' \
    -e "$logdir/eee.$thetag.%J.txt" \
    -o "$logdir/ooo.$thetag.%J.txt" \
    -q $thequeue $usegroup \
    -R"'select[mem>$themem] rusage[mem=$themem]'" -M$themem \
    "$@"