wasade/cluster_jobs.py

## cluster_jobs.py
#!/bin/env python
#cluster_jobs.py
"""
Simple helper script to make pbs jobs and submit to the cluster

Will only work if run on bmf or hemisphere

Can run from command line or import into python code.

Author: Micah Hamady
Status: Prototype
"""

from os import makedirs, removedirs
from commands import getoutput
from string import strip
from time import sleep
from random import choice

__author__ = "Micah Hamady"
__copyright__ = "Copyright 2012, PyCogent"
__credits__ = ["Micah Hamady", "Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.5.3-dev"
__maintainer__ = "Daniel McDonald"
__email__ = "mcdonadt@colorado.edu"
__status__ = "Development"

# module constants

# qsub template
QSUB_TEXT = """# Walltime Limit: hh:nn:ss
#PBS -l walltime=%s

# Node Specification: Two CPUs on one node
#PBS -l ncpus=%d -l nodes=%d%s -l pvmem=%s

# Mail: options are (a) aborted, (b) begins execution, (e) ends execution
# use -M <email> for additional recipients
# Queue: Defaults to friendlyq
#PBS -q %s

# supress email notification
#PBS -m n

# Job Name:
#PBS -N %s

#PBS -k %s

# discard output
%s

######################################################################

# Executable commands go here. Make sure that mpirun -np and -npn match the
# number of processors you requested from PBS! If you are using ppn and want
# npn=2, then you can leave -np and -npn off and PBS will add it for you. If
# you want npn=1, then you have to request all of the processors on all of the
# nodes, and then force it to use less using -npn.

echo ------------------------------------------------------
echo PBS: qsub is running on $PBS_O_HOST
echo PBS: originating queue is $PBS_O_QUEUE
echo PBS: executing queue is $PBS_QUEUE
echo PBS: working directory is $PBS_O_WORKDIR
echo PBS: execution mode is $PBS_ENVIRONMENT
echo PBS: job identifier is $PBS_JOBID
echo PBS: job name is $PBS_JOBNAME
echo PBS: node file is $PBS_NODEFILE
echo PBS: current home directory is $PBS_O_HOME
echo PBS: PATH = $PBS_O_PATH
echo ------------------------------------------------------
cd $PBS_O_WORKDIR
%s
"""

# qsub command
QSUB_CMD = "qsub %s"

#QSUB_CMD = "/usr/pbs/bin/qsub %s"

# command line usage string
USAGE_STR = """Usage: cluster_jobs.py <-m|-ms|-clean|-kill> [<name of commands file> <jobs prefix>]

Options:

  -m        just make jobs. this will create a "jobs" directory in the current
              directory and write out the pbs job files there.
  -ms       make and submit jobs.
  -clean    clean up temp and output files (std and stderrror) from previous
              run(s).
  -cleansave clean up temp and output files (std and stderrror) from previous
              run(s) and move to saved directory

  -kill     kill all of queued or running jobs for current user.

The following are required if -m or -ms specified (2nd and 3rd arguments):

  <name of commands file>   name of file with one command per line.
  <jobs_prefix>             prefix of jobs, 10 chars. e.g. micah_blat
"""


class ClusterJobs:
    """
    Wrapper to queue managament system.

    Creates and/or sumbits jobs to cluster.
    """
    # bmf typical settings
    def __init__(self, commands_list, jobs_prefix, jobs_dir="jobs",
             ppn=1, nnodes=1, ncpus=1, num_jobs=50, wall_time="999:00:00",
             queue_name="memroute", job_range=None,
             use_mpirun = False, qstat_prefix = "compy", delay_secs=5.0,
             verbose=True, keep_output="oe", discard_output=False,
             memory='4gb'):

    # hemisphere typical settings
    #def __init__(self, commands_list, jobs_prefix, jobs_dir="jobs",
    #             ppn=1, nnodes=1, ncpus=1, num_jobs=48, wall_time="144:00:00",
    #             queue_name="friendlyq", job_range=(16,32),
    #             use_mpirun = False, qstat_prefix = "hemispher",
    # delay_secs=1.0, verbose=False, keep_output="oe", discard_output=False):
        """
        Initialize jobs

        commands_list: list of commands to run on cluster

            **PLEASE NOTE** path to executable must be fully qualified.
            e.g. to run a python script, the job must look something like
            /usr/local/bin/python2.4 my_script.py 'script params'

            **ALSO NOTE** If your python (et al) script takes parameters from
            the command line, and you are checking the number of parameters
            you should be aware that mpirun will add parameters after the
            parameters you have passed.
            (e.g. if len(argv) != 4: <do something>, you will need to modify
            your code)

        jobs_prefix: job prefix. must be <= 10 characters. no spaces. first
            character must be a-Z. this is what you will see in the job queue,
            and will be the prifix of all of the standard out and standard
            error output. required.

        jobs_dir: path to directory to store generated jobs. default = "jobs"

        ppn: number of processors per node to use, default = 1

        nnodes: number of nodes per job, default = 1

        ncpus: number of cpus total to use

        num_jobs: number of jobs to make, default = 16

        wall_time: maximum time the job is allowed to run. friendlyq limit is
            72 hours. if debugging a program that might hang (e.g. an mpi
            program that blocks) it is a good idea to set this value very low,
            e.g. 5 minutes. format is HH:MM:SS. default = 12 hours

        queue_name: name of queue to submit jobs to. default = friendlyq

        job_range: only create/submit jobs in this range. tuple (start, stop)
            half open. e.g. includes first index, excludes last)

        use_mpirun: will run jobs using mpi run. this will send your command
            through mpirun shell script. both mpi and non-mpi programs will
            run fine when this is True. default = True

        qstat_prefix: prefix of the qstat host. e.g. execute qstat and you
            will see something like 7737.bmf or 204544.hemispher
            the qstat_prefix would be the text after the number, so

            on bmf, the qstat_prefix is "bmf"
            on hemisphere the qstat_prefix is currently "hemispher"

        delay_secs: time delay between submitting jobs - helps to avoid
            pbs crashes

        keep_output: keep standard error, standard out, both, or neither
            o=std out, e=std err, oe=both, n=neither

        verbose: when True, will print out progress, otherwise will be silent

        discard_output: when True, output will write to temp file. Using
            when running as apache user (word dir env vars stripped) and
            -k n is ignored. If not used, there is a delay when job
            finishes running but output cannot be delivered.

        memory: memory to request
        """
        if not commands_list:
            raise ValueError, "You must specify a list of commands."

        if not jobs_prefix or len(jobs_prefix) > 10:
            raise ValueError, "Jobs prefix must be a 1-10 characters long."

        if not jobs_prefix[0].isalpha():
            raise ValueError, "First letter of prefix must be a-Z."

        if ppn < 1 or ppn > 2:
            print "WARNING! Possible invalid ppn value. %d" % ppn

        if nnodes < 1 or nnodes > 8:
            print "WARNING! Possible invalid number of nodes. %d" % nnodes

        if num_jobs < 1:
            raise ValueError, "You must specify > 1 jobs to create."

        if ncpus < 1:
            raise ValueError, "You must specify > 1 cpus to use"


        if num_jobs > 256:
            print "WARNING! Large number of jobs specified! %d" % num_jobs

        # make sure that absolute path to executable is specified
        #if len(filter(lambda x: x.startswith("/"), commands_list)) != \
        #    len(commands_list):
        #    raise ValueError, "One or more commands not fully qualified."

        # try to make directory for jobs
        try:
            makedirs(jobs_dir)
        except OSError:
            # if directory already exists, ignore
            pass

        if keep_output not in ["e", "o", "oe", "eo", "n"]:
            raise ValueError, "Invalid keep_output option."

        # make sure jobs dir has training slash
        if not jobs_dir.endswith("/"):
            jobs_dir += "/"

        self.JobsDir = jobs_dir

        # store values
        self.CommandList = commands_list
        self.JobsPrefix = jobs_prefix
        self.ProcsPerNode = ppn
        self.NumNodes = nnodes
        self.NumCpus = ncpus
        self.NumJobs = num_jobs
        self.WallTime = wall_time
        self.QueueName = queue_name
        self.JobRange = job_range
        self.UseMPIRun = use_mpirun
        self.JobFilenames = []
        self.QstatPrefix = qstat_prefix
        self.DelaySecs = delay_secs
        self.Verbose = verbose
        self.KeepOutput = keep_output
        self.DiscardOutput = discard_output
        self.Memory = memory

    def makeJobs(self):
        """
        Write out jobs
        """

        out = []
        out.append("Trying to make %d jobs." %  self.NumJobs)
        out.append("Writing jobs to: %s" %  self.JobsDir)
        out.append("Delay between jobs: %.2f" % self.DelaySecs)

        ct = 0
        job_lists = {}

        # for each command, add to growing list of jobs
        for cmd in map(strip, self.CommandList):
            cur_job = ct % self.NumJobs

            # check if new job
            if not cur_job in job_lists:
                job_lists[cur_job] = []

            # if UseMPIRun, prefix command with mpirun command
            mpirun = "mpirun -np %d " % self.NumCpus
            if not self.UseMPIRun:
                mpirun = ""

            # append command to current job
            job_lists[cur_job].append(mpirun + cmd)

            ct += 1

        # write out pbs files, cache job filenames
        for jkey, jlist in job_lists.items():
            job_out = "%s%s%d.pbs" %(self.JobsDir,
                                      self.JobsPrefix,
                                      jkey)

            self.JobFilenames.append(job_out)
            o_file = open(job_out, "w+")
            ppn_text = ""
            if self.ProcsPerNode > 1:
                ppn_text = ":ppn=%d" % self.ProcsPerNode

            discard_out = ""
            if self.DiscardOutput:
                picks = list('abcdefghigklmnopqrstuvwxyz0123456789')
                base = ''.join([choice(picks) for i in range(9)]) + ".discard"
                rerr = "e" + base
                rout = "o" + base
                discard_out = "#PBS -o /tmp/%s\n#PBS -e /tmp/%s" % (rout, rerr)

            o_file.write(QSUB_TEXT % (self.WallTime,
                                      self.NumCpus,
                                      self.NumNodes,
                                      ppn_text,
                                      self.Memory,
                                      self.QueueName,
                                      "%s%d" % (self.JobsPrefix, jkey),
                                      self.KeepOutput,
                                      discard_out,
                                      '\n'.join(jlist)))
            o_file.close()

        return '\n'.join(out)


    def submitJobs(self):
        """
        Submit all jobs.
        """
        if not self.JobFilenames:
            raise ValueError, "No job filenames available. Have you run makeJobs yet?"
        out = []
        job_ids = []
        out.append("Submitting %d jobs to %s queue!" % (len(self.JobFilenames),
                                                         self.QueueName))

        start_ix = 0
        stop_ix = len(self.JobFilenames)
        if self.JobRange:
            start_ix, stop_ix = self.JobRange

        for file_pt in zip(range(len(self.JobFilenames)), self.JobFilenames):

            ct, p_file = file_pt

            if ct < start_ix or ct >= stop_ix:
                if self.Verbose:
                    print "skipping: %d" % ct
                continue

            if self.Verbose:
                print "Submitting: ", p_file
            #raise ValueError, "Submitting: %s" % (QSUB_CMD % p_file)
            out_id = getoutput(QSUB_CMD % p_file)
            out.append(out_id)
            job_ids.append(out_id)
            sleep(self.DelaySecs)

        out.append("done.\nType 'qstat' or 'qstat -a' to check status of your jobs.")
        return '\n'.join(out), job_ids

from cogent.util.misc import parse_command_line_parameters
from optparse import make_option

script_info={}
script_info['brief_description']="""Submit jobs to a PBS/Torque cluster"""
script_info['script_description']="""This script consumes a list of command lines and partitions those commands into a specified number of jobs. Within each job, the commands are run serially."""
script_info['script_usage']=[]
script_info['required_options'] = [\
        make_option('-i','--input',help="file containing the input commands",
            type='str'),
        make_option('-p','--prefix',help="submission prefix", type='str'),
        make_option('-t','--runtype',help="what to do: make or make_submit "\
        "[default:%default]",type='choice', choices=['make','make_submit'],
        default='make')]
script_info['optional_options'] = [\
        make_option('-j','--jobs',help="make N jobs", type='int', default=20),
        make_option('-m','--mem',help="memory per job",type='str',default='2gb'),
        make_option('-q','--queue',help="submit queue",type='str',
            default='memroute'),
        make_option('-w','--walltime',help='walltime per job',type='str',
            default='120:00:00'),
        make_option('-d','--delay',help='job submission delay',type='float',
            default=0.1)]
script_info['version'] = __version__

if __name__ == "__main__":
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    cj = ClusterJobs(open(opts.input), opts.prefix, num_jobs=opts.jobs,
            queue_name=opts.queue,delay_secs=opts.delay,
            wall_time=opts.walltime,memory=opts.mem)

    if opts.runtype == 'make' or opts.runtype == 'make_submit':
        cj.makeJobs()

    if opts.runtype == 'make_submit':
        cj.submitJobs()
	#!/bin/env python
	#cluster_jobs.py
	"""
	Simple helper script to make pbs jobs and submit to the cluster

	Will only work if run on bmf or hemisphere

	Can run from command line or import into python code.

	Author: Micah Hamady
	Status: Prototype
	"""

	from os import makedirs, removedirs
	from commands import getoutput
	from string import strip
	from time import sleep
	from random import choice

	__author__ = "Micah Hamady"
	__copyright__ = "Copyright 2012, PyCogent"
	__credits__ = ["Micah Hamady", "Daniel McDonald"]
	__license__ = "GPL"
	__version__ = "1.5.3-dev"
	__maintainer__ = "Daniel McDonald"
	__email__ = "mcdonadt@colorado.edu"
	__status__ = "Development"

	# module constants

	# qsub template
	QSUB_TEXT = """# Walltime Limit: hh:nn:ss
	#PBS -l walltime=%s

	# Node Specification: Two CPUs on one node
	#PBS -l ncpus=%d -l nodes=%d%s -l pvmem=%s

	# Mail: options are (a) aborted, (b) begins execution, (e) ends execution
	# use -M <email> for additional recipients
	# Queue: Defaults to friendlyq
	#PBS -q %s

	# supress email notification
	#PBS -m n

	# Job Name:
	#PBS -N %s

	#PBS -k %s

	# discard output
	%s

	######################################################################

	# Executable commands go here. Make sure that mpirun -np and -npn match the
	# number of processors you requested from PBS! If you are using ppn and want
	# npn=2, then you can leave -np and -npn off and PBS will add it for you. If
	# you want npn=1, then you have to request all of the processors on all of the
	# nodes, and then force it to use less using -npn.

	echo ------------------------------------------------------
	echo PBS: qsub is running on $PBS_O_HOST
	echo PBS: originating queue is $PBS_O_QUEUE
	echo PBS: executing queue is $PBS_QUEUE
	echo PBS: working directory is $PBS_O_WORKDIR
	echo PBS: execution mode is $PBS_ENVIRONMENT
	echo PBS: job identifier is $PBS_JOBID
	echo PBS: job name is $PBS_JOBNAME
	echo PBS: node file is $PBS_NODEFILE
	echo PBS: current home directory is $PBS_O_HOME
	echo PBS: PATH = $PBS_O_PATH
	echo ------------------------------------------------------
	cd $PBS_O_WORKDIR
	%s
	"""

	# qsub command
	QSUB_CMD = "qsub %s"

	#QSUB_CMD = "/usr/pbs/bin/qsub %s"

	# command line usage string
	USAGE_STR = """Usage: cluster_jobs.py <-m\|-ms\|-clean\|-kill> [<name of commands file> <jobs prefix>]

	Options:

	-m just make jobs. this will create a "jobs" directory in the current
	directory and write out the pbs job files there.
	-ms make and submit jobs.
	-clean clean up temp and output files (std and stderrror) from previous
	run(s).
	-cleansave clean up temp and output files (std and stderrror) from previous
	run(s) and move to saved directory

	-kill kill all of queued or running jobs for current user.

	The following are required if -m or -ms specified (2nd and 3rd arguments):

	<name of commands file> name of file with one command per line.
	<jobs_prefix> prefix of jobs, 10 chars. e.g. micah_blat
	"""


	class ClusterJobs:
	"""
	Wrapper to queue managament system.

	Creates and/or sumbits jobs to cluster.
	"""
	# bmf typical settings
	def __init__(self, commands_list, jobs_prefix, jobs_dir="jobs",
	ppn=1, nnodes=1, ncpus=1, num_jobs=50, wall_time="999:00:00",
	queue_name="memroute", job_range=None,
	use_mpirun = False, qstat_prefix = "compy", delay_secs=5.0,
	verbose=True, keep_output="oe", discard_output=False,
	memory='4gb'):

	# hemisphere typical settings
	#def __init__(self, commands_list, jobs_prefix, jobs_dir="jobs",
	# ppn=1, nnodes=1, ncpus=1, num_jobs=48, wall_time="144:00:00",
	# queue_name="friendlyq", job_range=(16,32),
	# use_mpirun = False, qstat_prefix = "hemispher",
	# delay_secs=1.0, verbose=False, keep_output="oe", discard_output=False):
	"""
	Initialize jobs

	commands_list: list of commands to run on cluster

	PLEASE NOTE path to executable must be fully qualified.
	e.g. to run a python script, the job must look something like
	/usr/local/bin/python2.4 my_script.py 'script params'

	ALSO NOTE If your python (et al) script takes parameters from
	the command line, and you are checking the number of parameters
	you should be aware that mpirun will add parameters after the
	parameters you have passed.
	(e.g. if len(argv) != 4: <do something>, you will need to modify
	your code)

	jobs_prefix: job prefix. must be <= 10 characters. no spaces. first
	character must be a-Z. this is what you will see in the job queue,
	and will be the prifix of all of the standard out and standard
	error output. required.

	jobs_dir: path to directory to store generated jobs. default = "jobs"

	ppn: number of processors per node to use, default = 1

	nnodes: number of nodes per job, default = 1

	ncpus: number of cpus total to use

	num_jobs: number of jobs to make, default = 16

	wall_time: maximum time the job is allowed to run. friendlyq limit is
	72 hours. if debugging a program that might hang (e.g. an mpi
	program that blocks) it is a good idea to set this value very low,
	e.g. 5 minutes. format is HH:MM:SS. default = 12 hours

	queue_name: name of queue to submit jobs to. default = friendlyq

	job_range: only create/submit jobs in this range. tuple (start, stop)
	half open. e.g. includes first index, excludes last)

	use_mpirun: will run jobs using mpi run. this will send your command
	through mpirun shell script. both mpi and non-mpi programs will
	run fine when this is True. default = True

	qstat_prefix: prefix of the qstat host. e.g. execute qstat and you
	will see something like 7737.bmf or 204544.hemispher
	the qstat_prefix would be the text after the number, so

	on bmf, the qstat_prefix is "bmf"
	on hemisphere the qstat_prefix is currently "hemispher"

	delay_secs: time delay between submitting jobs - helps to avoid
	pbs crashes

	keep_output: keep standard error, standard out, both, or neither
	o=std out, e=std err, oe=both, n=neither

	verbose: when True, will print out progress, otherwise will be silent

	discard_output: when True, output will write to temp file. Using
	when running as apache user (word dir env vars stripped) and
	-k n is ignored. If not used, there is a delay when job
	finishes running but output cannot be delivered.

	memory: memory to request
	"""
	if not commands_list:
	raise ValueError, "You must specify a list of commands."

	if not jobs_prefix or len(jobs_prefix) > 10:
	raise ValueError, "Jobs prefix must be a 1-10 characters long."

	if not jobs_prefix[0].isalpha():
	raise ValueError, "First letter of prefix must be a-Z."

	if ppn < 1 or ppn > 2:
	print "WARNING! Possible invalid ppn value. %d" % ppn

	if nnodes < 1 or nnodes > 8:
	print "WARNING! Possible invalid number of nodes. %d" % nnodes

	if num_jobs < 1:
	raise ValueError, "You must specify > 1 jobs to create."

	if ncpus < 1:
	raise ValueError, "You must specify > 1 cpus to use"


	if num_jobs > 256:
	print "WARNING! Large number of jobs specified! %d" % num_jobs

	# make sure that absolute path to executable is specified
	#if len(filter(lambda x: x.startswith("/"), commands_list)) != \
	# len(commands_list):
	# raise ValueError, "One or more commands not fully qualified."

	# try to make directory for jobs
	try:
	makedirs(jobs_dir)
	except OSError:
	# if directory already exists, ignore
	pass

	if keep_output not in ["e", "o", "oe", "eo", "n"]:
	raise ValueError, "Invalid keep_output option."

	# make sure jobs dir has training slash
	if not jobs_dir.endswith("/"):
	jobs_dir += "/"

	self.JobsDir = jobs_dir

	# store values
	self.CommandList = commands_list
	self.JobsPrefix = jobs_prefix
	self.ProcsPerNode = ppn
	self.NumNodes = nnodes
	self.NumCpus = ncpus
	self.NumJobs = num_jobs
	self.WallTime = wall_time
	self.QueueName = queue_name
	self.JobRange = job_range
	self.UseMPIRun = use_mpirun
	self.JobFilenames = []
	self.QstatPrefix = qstat_prefix
	self.DelaySecs = delay_secs
	self.Verbose = verbose
	self.KeepOutput = keep_output
	self.DiscardOutput = discard_output
	self.Memory = memory

	def makeJobs(self):
	"""
	Write out jobs
	"""

	out = []
	out.append("Trying to make %d jobs." % self.NumJobs)
	out.append("Writing jobs to: %s" % self.JobsDir)
	out.append("Delay between jobs: %.2f" % self.DelaySecs)

	ct = 0
	job_lists = {}

	# for each command, add to growing list of jobs
	for cmd in map(strip, self.CommandList):
	cur_job = ct % self.NumJobs

	# check if new job
	if not cur_job in job_lists:
	job_lists[cur_job] = []

	# if UseMPIRun, prefix command with mpirun command
	mpirun = "mpirun -np %d " % self.NumCpus
	if not self.UseMPIRun:
	mpirun = ""

	# append command to current job
	job_lists[cur_job].append(mpirun + cmd)

	ct += 1

	# write out pbs files, cache job filenames
	for jkey, jlist in job_lists.items():
	job_out = "%s%s%d.pbs" %(self.JobsDir,
	self.JobsPrefix,
	jkey)

	self.JobFilenames.append(job_out)
	o_file = open(job_out, "w+")
	ppn_text = ""
	if self.ProcsPerNode > 1:
	ppn_text = ":ppn=%d" % self.ProcsPerNode

	discard_out = ""
	if self.DiscardOutput:
	picks = list('abcdefghigklmnopqrstuvwxyz0123456789')
	base = ''.join([choice(picks) for i in range(9)]) + ".discard"
	rerr = "e" + base
	rout = "o" + base
	discard_out = "#PBS -o /tmp/%s\n#PBS -e /tmp/%s" % (rout, rerr)

	o_file.write(QSUB_TEXT % (self.WallTime,
	self.NumCpus,
	self.NumNodes,
	ppn_text,
	self.Memory,
	self.QueueName,
	"%s%d" % (self.JobsPrefix, jkey),
	self.KeepOutput,
	discard_out,
	'\n'.join(jlist)))
	o_file.close()

	return '\n'.join(out)


	def submitJobs(self):
	"""
	Submit all jobs.
	"""
	if not self.JobFilenames:
	raise ValueError, "No job filenames available. Have you run makeJobs yet?"
	out = []
	job_ids = []
	out.append("Submitting %d jobs to %s queue!" % (len(self.JobFilenames),
	self.QueueName))

	start_ix = 0
	stop_ix = len(self.JobFilenames)
	if self.JobRange:
	start_ix, stop_ix = self.JobRange

	for file_pt in zip(range(len(self.JobFilenames)), self.JobFilenames):

	ct, p_file = file_pt

	if ct < start_ix or ct >= stop_ix:
	if self.Verbose:
	print "skipping: %d" % ct
	continue

	if self.Verbose:
	print "Submitting: ", p_file
	#raise ValueError, "Submitting: %s" % (QSUB_CMD % p_file)
	out_id = getoutput(QSUB_CMD % p_file)
	out.append(out_id)
	job_ids.append(out_id)
	sleep(self.DelaySecs)

	out.append("done.\nType 'qstat' or 'qstat -a' to check status of your jobs.")
	return '\n'.join(out), job_ids

	from cogent.util.misc import parse_command_line_parameters
	from optparse import make_option

	script_info={}
	script_info['brief_description']="""Submit jobs to a PBS/Torque cluster"""
	script_info['script_description']="""This script consumes a list of command lines and partitions those commands into a specified number of jobs. Within each job, the commands are run serially."""
	script_info['script_usage']=[]
	script_info['required_options'] = [\
	make_option('-i','--input',help="file containing the input commands",
	type='str'),
	make_option('-p','--prefix',help="submission prefix", type='str'),
	make_option('-t','--runtype',help="what to do: make or make_submit "\
	"[default:%default]",type='choice', choices=['make','make_submit'],
	default='make')]
	script_info['optional_options'] = [\
	make_option('-j','--jobs',help="make N jobs", type='int', default=20),
	make_option('-m','--mem',help="memory per job",type='str',default='2gb'),
	make_option('-q','--queue',help="submit queue",type='str',
	default='memroute'),
	make_option('-w','--walltime',help='walltime per job',type='str',
	default='120:00:00'),
	make_option('-d','--delay',help='job submission delay',type='float',
	default=0.1)]
	script_info['version'] = __version__

	if __name__ == "__main__":
	option_parser, opts, args = parse_command_line_parameters(**script_info)

	cj = ClusterJobs(open(opts.input), opts.prefix, num_jobs=opts.jobs,
	queue_name=opts.queue,delay_secs=opts.delay,
	wall_time=opts.walltime,memory=opts.mem)

	if opts.runtype == 'make' or opts.runtype == 'make_submit':
	cj.makeJobs()

	if opts.runtype == 'make_submit':
	cj.submitJobs()