Python Settings.get_long_queue_name方法代码示例

# 需要导入模块: from settings import Settings [as 别名]
# 或者: from settings.Settings import get_long_queue_name [as 别名]
def run_on_cluster(cmd, job_name, cluster_output_dir, cluster_scripts_dir=None,
                   queue_type=None, cmd_name="qsub", settings=None):
    print "Submitting job: %s" %(job_name)
    queue_name = None

    # Load command name from settings file
    if settings != None:
        load_settings(settings)
        cmd_name = Settings.get_cluster_command()

    if queue_type == "long":
        queue_name = Settings.get_long_queue_name()
    elif queue_type == "short":
        queue_name = Settings.get_short_queue_name()
    else:
        print "Warning: Unknown queue type: %s" %(queue_type)
        queue_name = queue_type
    

    if queue_type == None:
        print "  - queue: unspecified"
    else:
        print "  - queue: %s, using queue name %s" %(queue_type,
                                                     queue_name)

    #print "  - cmd: %s" %(cmd)
    if cluster_scripts_dir == None:
	cluster_scripts_dir = os.path.join(cluster_output_dir, 'cluster_scripts')
	if not os.path.isdir(cluster_scripts_dir):
	    os.mkdir(cluster_scripts_dir)
    scripts_output_dir = os.path.join(cluster_output_dir, 'scripts_output')
    if not os.path.isdir(scripts_output_dir):
	os.mkdir(scripts_output_dir)
    scripts_output_dir = os.path.abspath(scripts_output_dir)
    #qsub_call = 'qsub -V -q \"%s\" -o \"%s\" -e \"%s\"' %(queue_type, scripts_output_dir, scripts_output_dir)
    qsub_call = '%s -o \"%s\" -e \"%s\"' %(cmd_name, scripts_output_dir,
                                           scripts_output_dir)

    # Add queue type if given one
    if queue_name != None:
        qsub_call += ' -q \"%s\"' %(queue_name)
        
    script_name = valid_qsub_name(os.path.join(cluster_scripts_dir,
                                               '%s_time_%s.sh' %(job_name,
                                                                 time.strftime("%m-%d-%y_%H:%M:%S"))))
    make_bash_script(script_name, cmd)
    qsub_cmd = qsub_call + ' \"%s\"' %(script_name)
    os.system(qsub_cmd)

# 需要导入模块: from settings import Settings [as 别名]
# 或者: from settings.Settings import get_long_queue_name [as 别名]
def run_on_cluster(
    cmd, job_name, cluster_output_dir, cluster_scripts_dir=None, queue_type=None, cmd_name="qsub", settings_fname=None
):
    print "Submitting job: %s" % (job_name)
    queue_name = None

    # Load command name from settings file
    if settings_fname != None:
        load_settings(settings_fname)
        cmd_name = Settings.get_cluster_command()

    if queue_type == "long":
        queue_name = Settings.get_long_queue_name()
    elif queue_type == "short":
        queue_name = Settings.get_short_queue_name()
    else:
        print "Warning: Unknown queue type: %s" % (queue_type)
        queue_name = queue_type

    if queue_type is None:
        print "  - queue type: unspecified"
    else:
        print "  - queue type: %s" % (queue_type)
    if queue_name is None:
        print " - queue name unspecified"
    else:
        print " - queue name: %s" % (queue_name)

    misc_utils.make_dir(cluster_output_dir)
    if cluster_scripts_dir == None:
        cluster_scripts_dir = os.path.join(cluster_output_dir, "cluster_scripts")
        misc_utils.make_dir(cluster_scripts_dir)
    scripts_output_dir = os.path.join(cluster_output_dir, "scripts_output")
    misc_utils.make_dir(scripts_output_dir)
    scripts_output_dir = os.path.abspath(scripts_output_dir)
    cluster_call = '%s -o "%s" -e "%s"' % (cmd_name, scripts_output_dir, scripts_output_dir)
    # Add queue type if given one
    if queue_name != None:
        cluster_call += ' -q "%s"' % (queue_name)

    script_name = valid_cluster_name(
        os.path.join(cluster_scripts_dir, "%s_time_%s.sh" % (job_name, time.strftime("%m-%d-%y_%H:%M:%S")))
    )
    make_bash_script(script_name, cmd)
    cluster_cmd = cluster_call + ' "%s"' % (script_name)
    job_id = launch_job(cluster_cmd, cmd_name)
    return job_id

# 需要导入模块: from settings import Settings [as 别名]
# 或者: from settings.Settings import get_long_queue_name [as 别名]
def run_SGEarray_cluster(
    arg_list,
    argfile,
    cluster_output_dir,
    queue_type="long",
    cluster_scripts_dir=None,
    chunk=2500,
    settings=None,
    cmd_name="qsub",
    job_name="miso_job",
):
    """
    Run MISO jobs on cluster using SGE.

    Function contributed by Michael Lovci, UCSD.
    """
    misc_utils.make_dir(cluster_output_dir)
    # Create arguments file to pass on to job
    f = open(argfile, "w")
    nargs = len(arg_list)
    if nargs % chunk == 0:
        njobs = nargs / chunk
    else:
        njobs = 1 + (nargs / chunk)

    for args in arg_list:
        f.write(args[0] + "\n")
    f.close()

    if cluster_scripts_dir == None:
        cluster_scripts_dir = os.path.join(cluster_output_dir, "cluster_scripts")
    misc_utils.make_dir(cluster_scripts_dir)
    scripts_output_dir = os.path.join(cluster_output_dir, "scripts_output")
    misc_utils.make_dir(scripts_output_dir)
    scripts_output_dir = os.path.abspath(scripts_output_dir)
    script_error = os.path.join(scripts_output_dir, string.join([job_name, "err"], "."))
    script_out = os.path.join(scripts_output_dir, string.join([job_name, "out"], "."))
    cluster_script = os.path.join(cluster_scripts_dir, "run_miso.sh")

    if settings != None:
        load_settings(settings)
        cmd_name = Settings.get_cluster_command()

    if queue_type == "long":
        queue_name = Settings.get_long_queue_name()
    elif queue_type == "short":
        queue_name = Settings.get_short_queue_name()
    else:
        raise Exception, "Unknown queue type: %s" % (queue_type)

    if queue_type == None:
        print "  - queue: unspecified"
    else:
        print "  - queue: %s, using queue name %s" % (queue_type, queue_name)
    cs = open(cluster_script, "w")
    cs.write("#!/bin/sh" + "\n")
    cs.write("#$ -N %s\n" % (job_name))
    cs.write("#$ -S /bin/sh\n")
    cs.write("#$ -p -1023\n")
    cs.write("#$ -o %s\n" % (script_out))
    cs.write("#$ -e %s\n" % (script_error))
    cs.write("#$ -t 1-%s\n" % (njobs))

    ##execute from current working directory
    cs.write("#$ -cwd\n")

    ## import environment variables
    cs.write("#$ -V\n")
    if queue_name:
        cs.write("#$ -l %s\n" % (queue_name))
    cs.write('echo "hostname is:"\n')
    cs.write("hostname\n")
    cs.write("ARGFILE=%s\n" % argfile)
    cs.write("SEQ=/usr/bin/seq\n")
    cs.write("index=0\n")
    cs.write("lastindex=0\n")
    cs.write('let "index = $SGE_TASK_ID * %s"\n' % (chunk))
    chunk2 = chunk - 1
    cs.write('let "lastindex = $index - %s"\n' % (chunk2))
    if chunk2 > 0:
        cs.write("for i in `$SEQ $lastindex $index`\n")
    else:
        cs.write("for i in $index\n")  # if user chooses 1 for chunk size
    cs.write("do\n")
    cs.write("  line=$(cat $ARGFILE | head -n $i | tail -n 1)\n")
    cs.write("  eval $line\n")
    cs.write("done\n")
    cs.close()

    # Make script executable
    os.system('chmod +x "%s"' % (cluster_script))
    qsub_cmd = cmd_name + ' "%s"' % (cluster_script)

    os.system(qsub_cmd)