Created
May 2, 2013 11:39
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Submitting jobs via qsub in Python
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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') |
Author
astrofrog
commented
May 2, 2013
Remove this line for serial runs:
#$ -pe make {slots}
I have a script file bh1.py. I am going to run it with qsub. how can I run my file with your qsub.py code?
I have a bh1.py script. i am going to use your code to submit my job. how can I do it. I have basic knowledge about PSB and cluster performance.
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