sjs_qsub

#!/usr/bin/python

# See file COPYING distributed with sjs for copyright and license.

import sys
import os
import getopt
import sjs

def parse_opts(argv):

    """parse options in the passed list

    the qsub command line and the options that can be declared by #$ in the 
    job script are the same, so we abstract out the parsing here
    """

    try:
        (opts, args) = getopt.getopt(argv, option_string)
    except getopt.error, data:
        if argv is sys.argv:
            sys.stderr.write('%s: %s\n' % (progname, str(data)))
        else:
            sys.stderr.write('%s: in script: %s\n' % (progname, str(data)))
        return None

    for (option, value) in opts:
        if option == '-@':
            if argv is sys.argv:
                cluster.log('qsub: ignoring "-@ %s"' % value)
            else:
                cluster.log('qsub: ignoring "-@ %s" in script' % value)
        if option == '-a':
            if argv is sys.argv:
                cluster.log('qsub: ignoring "-a %s"' % value)
            else:
                cluster.log('qsub: ignoring "-a %s" in script' % value)
        if option == '-o':
            options['stdout'] = value
        if option == '-e':
            options['stderr'] = value
        if option == '-S':
            options['shell'] = value
        if option == '-V':
            if argv is sys.argv:
                cluster.log('qsub: ignoring "-V %s"' % value)
            else:
                cluster.log('qsub: ignoring "-V %s" in script' % value)

    return args

progname = os.path.basename(sys.argv.pop(0))

option_string = 'o:e:V@:a:S:'

options = {'stdout': '$HOME/$JOB_NAME.o$JOB_ID', 
           'stderr': '$HOME/$JOB_NAME.e$JOB_ID', 
           'shell': '/bin/csh'}

try:
    cluster = sjs.Cluster()
except sjs.SJSError, data:
    sys.stderr.write('%s: %s\n' % (progname, str(data)))
    sys.exit(1)

args = parse_opts(sys.argv)
if args is None:
    sys.exit(1)

if not args:
    cluster.log('qsub reading from stdin')
    job_name = 'STDIN'
    script = sys.stdin.read()
    script_args = []
else:
    cluster.log('qsub reading from %s' % args[0])
    job_name = os.path.basename(args[0])
    script = open(args[0]).read()
    script_args = args[1:]

script_argv = []
for line in script.split('\n'):
    line = line.strip()
    if not line.startswith('#$'):
        continue
    script_argv.extend(line[2:].strip().split())
script_opts = parse_opts(script_argv)
if script_opts is None:
    sys.exit(1)
if script_opts:
    msg = '%s: in script: option %s not recognized\n' % (progname, 
                                                         script_opts[0])
    sys.stderr.write(msg)
    sys.exit(1)

job = cluster.submit(job_name, 
                     options['shell'], 
                     script, 
                     script_args, 
                     options['stdout'], 
                     options['stderr'])

print 'Your job %d ("%s") has been submitted' % (job.id, job.name)

cluster.start_runner()

sys.exit(0)

# eof