Automatically create and submit Torque job script with specified commands to qsub.

qwrap.py

#!/usr/bin/env python

"""
Automatically create and submit Torque job script with specified commands to qsub.
"""

import argparse
import os
import pwd 
import tempfile

parser = argparse.ArgumentParser()
parser.add_argument('-l', nargs=1, default='nodes=1:gpus=4:ppn=4', help='qsub resources')
parser.add_argument('-n', nargs=1, default=None,
                    help='string to use as job basename (default is username-[unique suffix])')
parser.add_argument('-c', required=True, nargs=argparse.REMAINDER, help='commands to submit')
args = parser.parse_args()

if type(args.l) is list:
    args.l = args.l[0]

username = pwd.getpwuid(os.getuid()).pw_name

if args.n is None:
    fd, name = tempfile.mkstemp(dir=os.path.expanduser('~'), prefix=username+'-')
else:
    name = args.n[0]

with open(name, 'w') as f:
    f.write('#!/bin/sh\n')
    f.write('#PBS -l '+args.l+'\n')
    f.write('cd '+os.getcwd()+'\n')
    f.write(' '.join(args.c)+'\n')

os.system('/usr/bin/qsub %s' % name)
os.remove(name)