quicksubmit.py

#!/usr/bin/python2.7
'''USAGE: quicksubmit.py "command -l parameter" [options]
This script submits your one line command as a job to the pbs job scheduler.
'''
import subprocess as s
import sys
import argparse

def submitjob(job_name, command, subtype = "qsub", walltime = "10:00:00", cput = "10:00:00", pm = "nodes=1:ppn=1:mem=2gb", mailto = "", afterok = "", verbose = False):
    '''USAGE: submitjob('my_job', 'echo "hello world!"')
    This function submits a job to the pbs job scheduler. You may need to alter the job_string as your pbs implementation requires.

    '''
    job_string = """#!/bin/bash
    #PBS -N {0}
    #PBS -l walltime={1}
    #PBS -l {2}
    #PBS -l cput={4}
    #PBS -j oe
    #PBS -o ./{0}.$PBS_JOBID.pbsout
    #PBS -V
    #PBS -q first
    #PBS -m abe {5}
    {aok}

    echo "ncpus-2.pbs"
    cat $PBS_NODEFILE
    qstat -f $PBS_JOBID

    cd $PBS_O_WORKDIR

    NCPUS=`wc -l $PBS_NODEFILE | awk '{{print $1}}'`

    {3}
    echo "qsub working directory absolute is"
    echo $PBS_O_WORKDIR
    exit""".format(job_name, walltime, pm, command, cput, mailto, aok="#PBS -W depend=afterok:%s" %(afterok) if afterok != "" else "")

    # Send job_string to qsub

    p = s.Popen(subtype, stdin=s.PIPE, stdout=s.PIPE, stderr=s.STDOUT)
    #p.stdin.write(job_string)
    out, err = p.communicate(job_string)

    # Print your job and the response to the screen
    if verbose:
        print job_string
        print out

    #returns job ID
    return out.split(".")[0]

#class MyParser(argparse.ArgumentParser):
#    def error(self, message):
#        sys.stderr.write('error: %s\n' % message)
#        self.print_help()
#        sys.exit(2)

parser = argparse.ArgumentParser(description='Quickly submit jobs to pbs. Submit multiple, dependent jobs at once using ;; as the separator.')
#parser = MyParser()
parser.add_argument('cmd', nargs='+')
parser.add_argument('--walltime', default="1:00:00", help='how long the job should run in wall time')
parser.add_argument('--cput', default="1:00:00", help='how long the job should run in cpu time')
parser.add_argument('--pm', default="nodes=1:ppn=1,mem=2gb", help='processors and memory limits in the form of nodes=1:ppn=1,mem=2gb')
parser.add_argument('--mailto', default="", help='email address to which job status should be sent')
parser.add_argument('--afterok', default="", help='run this job after JOBID has completed successfully')
parser.add_argument('--jobname', default="", help='name of your job')

if len(sys.argv)==1:
    parser.print_help()
    sys.exit(1)


args = parser.parse_args()

joblist = []

#print args
cmd = " ".join(args.cmd)

cmdlist = []
cmdlist = cmd.split(";;")
afterok = args.afterok
for com in cmdlist:
    print "submitting command: ", com
    joblist.append(submitjob(job_name = args.jobname if args.jobname !="" else cmd.split()[0], command = com, walltime = args.walltime, cput = args.cput, pm = args.pm, mailto = args.mailto, afterok = afterok))
    afterok=joblist[-1]

print "Job id(s) ", joblist