safe_qsub_run.py

def safe_qsub_run(cmd, jobname, script_header=_script_header, nodes=1, params="", stdout=None, stderr=None, shell=False):
    """Run a command via qsub in blocking mode so that the command waits to exit.
       Requires a header string and a job name.
    """
    
    scriptfile = tempfile.NamedTemporaryFile()
    scriptfile.write("%(header)s\n%(command)s\n" % dict(header=script_header, command=cmd))
    scriptfile.file.flush()
    
    qsub_cmd = "qsub -N %(jobname)s -l nodes=%(nodes)s -W block=true %(params)s" % dict(jobname=jobname,
                                                                                        nodes=nodes,
 											                                                                  params=params)
    
    if stdout:
        qsub_cmd += " -o %s" % stdout
    
    if stderr:
        qsub_cmd += " -e %s" % stderr

    qsub_cmd = "%(cmd)s %(script)s" % dict(cmd=qsub_cmd, script=scriptfile.name)

    proc = subprocess.Popen(shlex.split(qsub_cmd), shell=False,
                            stdin=subprocess.PIPE,
                            stderr=subprocess.STDOUT, stdout=subprocess.PIPE)

    proc.stdin.close()
    jobid = os.waitpid(proc.pid, 0)
    
    # # Another way of doing it without setting stdin=subprocess.PIPE; same results
    # stdouts, stderrs = proc.communicate()
    # jobid = stdouts.rstrip()

    scriptfile.close()

    return jobid#, stderrs