submit

#!/bin/bash

OUTPUT_LOCATION=~/output
SCHEDULER_QUEUE=${OUTPUT_LOCATION}/scheduler_queue
#SCHEDULER_QUEUE="/tmp/scheduler_queue"

JOB_LIST=${OUTPUT_LOCATION}/job_list
touch ${JOB_LIST}

# get a lock so only one command will be submitted at a time
exec 200>>$JOB_LIST
flock 200

# create a script to run the command
JOB_ID=$(wc -l $JOB_LIST | awk '{print $1}')

SCRIPT_FILE=${OUTPUT_LOCATION}/${JOB_ID}"_script.sh" 

echo "#!/bin/bash" > ${SCRIPT_FILE}
# start the command, and make sure we set the current working directory
echo "env --chdir=`pwd` \\" >> ${SCRIPT_FILE}
# preserve all enviornment variables
env | awk 'BEGIN { FS="="; OFS="=" } {print $1,"\x27"$2"\x27" " \\"}' >> ${SCRIPT_FILE}

echo "$@" " \\" >> ${SCRIPT_FILE}
# redirect input from /dev/null (the application should not take input)
# output redirected to a single file.  To split std and err, modify this line
echo "</dev/null &>"${OUTPUT_LOCATION}/${JOB_ID}"_out" >> ${SCRIPT_FILE}

# after the job has finished, write the return value to a "finished" file, so we know it is done running.
echo 'printf $? > '${OUTPUT_LOCATION}/${JOB_ID}"_finished" >> ${SCRIPT_FILE}

# make the script executable
chmod u+x ${SCRIPT_FILE}

# log in our history file that we started this job
echo "$@" >> ${JOB_LIST}

# put the job on the queue
# use timeout, so it can be placed on the job list without queueing.
# with timeout, the job script is written.  It might not be able to
# queue because the scheduler is not running, and jobs are being added to
# the job list to be queued when the scheduler starts.
timeout 5s -k 10s echo ${SCRIPT_FILE} > ${SCHEDULER_QUEUE}

echo ${JOB_ID}