-
-
Save arunreddy/9d7e3c3c3ee4d8a1582e5f01a2c312d7 to your computer and use it in GitHub Desktop.
Submitting jobs via qsub in Python
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
import os | |
import random | |
import string | |
import tempfile | |
import subprocess | |
def random_id(length=8): | |
return ''.join(random.sample(string.ascii_letters + string.digits, length)) | |
TEMPLATE_SERIAL = """ | |
##################################### | |
#$ -S /bin/bash | |
#$ -cwd | |
#$ -N {name} | |
#$ -e {errfile} | |
#$ -o {logfile} | |
#$ -pe make {slots} | |
##################################### | |
echo "------------------------------------------------------------------------" | |
echo "Job started on" `date` | |
echo "------------------------------------------------------------------------" | |
{script} | |
echo "------------------------------------------------------------------------" | |
echo "Job ended on" `date` | |
echo "------------------------------------------------------------------------" | |
""" | |
def submit_python_code(code, name="job", logfile="output.$JOB_ID", errfile="error.$JOB_ID", cleanup=True, prefix="", slots=1): | |
base = prefix + "submit_{0}".format(random_id()) | |
open(base + '.py', 'wb').write(code) | |
script = "python " + base + ".py" | |
open(base + '.qsub', 'wb').write(TEMPLATE_SERIAL.format(script=script, name=name, logfile=logfile, errfile=errfile, slots=slots)) | |
try: | |
subprocess.call('qsub < ' + base + '.qsub', shell=True) | |
finally: | |
if cleanup: | |
os.remove(base + '.qsub') |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment