quick_q

#!/bin/sh

############################################################
#  Program: quick_q
#  Author : Ryan Layer
############################################################


## BEGIN SCRIPT
usage()
{
    cat << EOF

usage: $0 OPTIONS

version: 0.3

OPTIONS can be:
  -h           Show this message
  -m  mem      Memory (default 1gb)
  -t  threads  Threads per device (default 1)
  -d  devices  Devices (default 1)
  -T  walltime Max run time [[HH:]MM:]SS (default 168:00:00)
  -n  name     Name (default quick_q)
  -c  cmd      Command
  -q  queue    Queue name
  -p  priority Job priority (int [-1024,1023], default: 0)
  -o  output   Path for stdout of job (default jobname.ojobid)
  -e  error    Path for stderr of job (default jobname.ejobid)
  -W  attr     Additional attributes
  -M  mail     Mail results (Upon end or abort)
  -u  email address
               Email address to send results to
  -z  other    Other qsub parameters that are passed
                 directly into qsub
EOF
}

# Show usage when there are no arguments.
if test -z "$1"
then
    usage
    exit
fi

MEM="1gb"
NAME="quick_q"
THREADS=1
DEVICE=1
WALLTIME="168:00:00"
CMD=1
QUEUE=
PRIORITY=0
OUTPUT=
ERROR=
OTHER=
MAIL=false
EMAIL=

# Check options passed in.
while getopts "h m:t:n:c:d:T:q:p:o:e:W:u:z: M" OPTION
do
    case $OPTION in
        h)
            usage
            exit 1
            ;;
        m)
            MEM=$OPTARG
            ;;
        t)
            THREADS=$OPTARG
            ;;
        d)
            DEVICE=$OPTARG
            ;;
	T)
	    WALLTIME=$OPTARG
	    ;;
        n)
            NAME=$OPTARG
            ;;
        c)
            CMD=$OPTARG
            ;;
        q)
            QUEUE=$OPTARG
            ;;
	p)
	    PRIORITY=$OPTARG
	    ;;
	o)
	    OUTPUT=$OPTARG
	    ;;
	e)
	    ERROR=$OPTARG
	    ;;
	M)
	    MAIL=true
	    ;;
	u)
	    EMAIL=$OPTARG
	    ;;
	W)
	    ATTR=$OPTARG
	    ;;
	z)
	    OTHER=$OPTARG
	    ;;
        ?)
            usage
            exit
            ;;
    esac
done

#QSUB="/usr/pbs/bin/qsub"
QSUB=/usr/local/bin/qsub

# for pbs_version = PBSPro_11.2.0.113417
#QSUB_CMD="$QSUB -l select=$DEVICE:mem=$MEM:ncpus=$THREADS -m bae -N $NAME -M rl6sf@virginia.edu"
# for version: 3.0.3
QSUB_CMD="$QSUB -l nodes=$DEVICE:ppn=$THREADS,mem=$MEM,walltime=$WALLTIME -N $NAME -p $PRIORITY"

if $MAIL
then
    QSUB_CMD+=" -m ae"
else
    QSUB_CMD+=" -m n"
fi

if [ ! -z "$EMAIL" ]
then
    QSUB_CMD+=" -M $EMAIL"
fi

if [ ! -z "$QUEUE" ]
then
    QSUB_CMD+=" -q $QUEUE"
fi

if [ ! -z "$OUTPUT" ]
then
    QSUB_CMD+=" -o $OUTPUT"
fi

if [ ! -z "$ERROR" ]
then
    QSUB_CMD+=" -e $ERROR"
fi

if [ ! -z "$ATTR" ]
then
    QSUB_CMD+=" -W $ATTR"
fi

if [ ! -z "$OTHER" ]
then
    QSUB_CMD+=" $OTHER"
fi

#echo $QSUB_CMD

JID=`echo "cd \\$PBS_O_WORKDIR; $CMD" | $QSUB_CMD`
echo $JID
DATE=`date +%Y%m%d_%T`
echo $DATE > $JID.log
echo $JID >> $JID.log
echo $CMD >> $JID.log