QsubPyBsc

#!/usr/bin/env python
"""This is a script to isolate each qsub implementation from
the user. It needs to be modified for each cluster:

std_file is a template pbs file
The command line options and replace are machine dependent
"""
import os, string
import sys
import optparse

#check command line

def main():

    std_file="""
#!/bin/bash
# @ job_name         = XXXjobIDXXX
# @ initialdir       = XXXiniDIRXXX
# @ output           = OUTPUT/XXXjobIDXXX_%j.out
# @ error            = OUTPUT/XXXjobIDXXX_%j.err
# @ total_tasks      = XXXtasksXXX
# @ cpus_per_task    = XXXppnXXX
# @ wall_clock_limit = XXXhoursXXX:00:00

# Environment
export OBJECT_MODE=64
export MP_RSH=ssh

mkdir -p OUTPUT
python XXXscriptXXX

    """.strip()#note strip removes first newline

    #check command line

    ####Crunchy####
    parser = optparse.OptionParser("usage: %prog [options] protocols_file.py")
    parser.add_option("-t", "--time", dest="wallClockTime",
                      default="72", type="int",
                      help="Maximum execution time in wallclock hours (default=24)")
    parser.add_option("-i", "--id", dest="jobID", default='-1',
                      type="string", help="Job ID (default=-1)")

    #options are the options ;-)
    #arg the values that do not requiere '-flags', that is, the python script
    (options, args) = parser.parse_args()
    if len(args) < 1:
        parser.print_help()
        return

    wallClockTime = options.wallClockTime
    jobID         = options.jobID

    inFileName       = args[1]

    #get NumberOfMpiProcesses and NumberOfThreads from protocol script itself

    pyFile = open(inFileName,"r")
    doParallel = False
    numberOfThreads = 1
    numberOfNodes = 1
    while 1:
        line = (pyFile.readline()).replace('\n','')
        if (line.find("WorkingDir") == 0):
            myline=line.split("=")
            workingDir=myline[1].replace('/','_')
        elif (line.find("NumberOfThreads") == 0):
            myline=line.split("=")
            numberOfThreads = int(myline[1])
        elif (line.find("DoParallel=True") == 0):
            doParallel = True
        elif (line.find("NumberOfMpiProcesses") == 0):
            myline=line.split("=")
            numberOfNodes = int(myline[1])
        elif (line.find("end-of-header") > 0):
            break

    if (not doParallel):
        numberOfNodes = 1

    if (jobID == '-1'):
        jobID=workingDir.replace("'","")
        jobID=jobID.replace('"','')

    numberOfTasks = numberOfNodes * numberOfThreads

    iniDIR = str(os.getcwd())

    #Replace old words with new ones
    outFileName=inFileName.replace(".py",".job");
    o = open(outFileName,"w")
    std_file = std_file.replace("XXXjobIDXXX",jobID)
    std_file = std_file.replace("XXXiniDIRXXX",iniDIR)
    std_file = std_file.replace("XXXtasksXXX",str(numberOfTasks))
    std_file = std_file.replace("XXXppnXXX",str(numberOfThreads))
    std_file = std_file.replace("XXXhoursXXX",str(wallClockTime))
    std_file = std_file.replace("XXXscriptXXX",inFileName)

    #create command and add it (as a comment) to the job file
    command = "mnsubmit "
    command += outFileName
    o.write(std_file)
    o.close()

    # Give the user some feedback
    print "---------------------------------------"
    print "qsub.py made job with:"
    print "# @ job_name         = " + jobID
    print "# @ initialdir       = " + iniDIR
    print "# @ output           = OUTPUT/" + jobID + "_%j.out"
    print "# @ error            = OUTPUT/" + jobID + "_%j.err"
    print "# @ total_tasks      = " + str(numberOfTasks)
    print "# @ cpus_per_task    = " + str(numberOfThreads)
    print "# @ wall_clock_limit = " + str(wallClockTime) + ":00:00"
    print " "
    print "and submitted this script using command:"
    print command
    print "---------------------------------------"

    # Really submit the job to the queue
    os.system(command)



if __name__ == '__main__':
    main()