ecearth3/sources/tm5mp/bin/submit_tm5_tools.py

#
# TM5 run tools
#

# ***


def Command_Line( rcf, exe, args, in_debugger ) :

    """
    Return command line that runs executable.
    
    ARGUMENTS
        rcf
                Rcfile with settings.
        exe
                Name of executable.
        args
                Arguments to be passed to executable.
        in_debugger
                Set to 'True' if the job should be run in a debugger.

    RETURN VALUES
        cmndline
                Command line to be executed.
    """

    # external
    import socket
    import logging
    
    # mpi run ?
    if rcf.get('par.mpi','bool') :
         
        # number of mpi tasks:
        ntask = rcf.get('par.ntask','int')
 
        # get command line:
        cmnd_exec = rcf.get('mpirun.command')
        cmnd_args = rcf.get('mpirun.args'   )
 
        # write command file ?
        cmdfile = rcf.get('mpirun.cmdfile',default='')
        if len(cmdfile) > 0 :
            # write command line for each task:
            f = open(cmdfile,'w')
            for i in range(ntask) : f.write( '%s %s\n' % (exe,args) )
            f.close()
        else :
            # otherwise, add the executable and its arguments:
            cmnd_args = '%s %s %s' % (cmnd_args,exe,args)
        #endif

        # write host file ? PLS: This is done too early, and should be done
        # inside the *_run.jb script : that will let you specify nodes
        # scattered on different hosts (eg, linux cluster), and also different
        # from the current host (which probably is a login node)!! See
        # WriteJob below for cases of Loadleveler and Slurm.
        # 
        # Leave it here for other cases not handled in WriteJob yet.
        hostfile = rcf.get('mpirun.hostfile',default='')
        if len(hostfile) > 0 :
            # get hostname:
            hname = socket.gethostname()
            # write hostname for each task:
            f = open(hostfile,'w')
            for i in range(ntask) : f.write( '%s\n' % hname )
            f.close()
            
    else :
        
        # standard run:
        cmnd_exec = exe
        cmnd_args = args
            
    # run in debugger ?
    if in_debugger :

        # debugger type:
        debugger = rcf.get( 'debugger' )
        # get debugger command:
        debugger_call = rcf.get( 'debugger.command' )
        # large differences ...
        if debugger == 'totalview' :
            # syntaxis: totalview <executable> [-a <arguments>]
            # pass executable:
            cmndline = '%s %s' % (debugger_call,cmnd_exec)
            # add arguments ?
            if len(cmnd_args) > 0 :
                cmndline = '%s -a %s' % (cmndline,cmnd_args)
            #endif
        elif debugger == 'idb' :
            # syntaxis: idb [-args <executable> <arguments>]
            # fill executable and arguments:
            cmndline = '%s -args %s %s' % (debugger_call,cmnd_exec,cmnd_args)
        else :
            logging.error('unsupported debugger : %s' % debugger )
            raise Exception
        #endif
        
    else :
    
        # standard line:
        cmndline = '%s %s' % (cmnd_exec,cmnd_args)
    
    # ok
    return cmndline
    
# ***

def WriteAndSubmitNewJob( rcfile, bindir ) :

    """
    Write first or next rcfile and job files(s) in the job chain;
    if chain is not finished yet, submit a new job.
    
    The argument could be the name of an rcfile or an rcfile object itself,
    since the submit script might have changed some values given
    the provided command line arguments.
    
    The following function is used:
    
      submit_tm5_setup_rcfile.WriteRcfile         # writes the new rcfile
    
    This is placed in a seperate file since users might need to
    change these routines for their specific projects.
    """
    
    # external:
    import sys
    import logging
    import rc
    
    # import setup module:
    import submit_tm5_setup_rcfile
    
    # name provided ?
    if type(rcfile) == str :
        # load:
        rcf = rc.RcFile( rcfile )
    else :
        # just copy ..
        rcf = rcfile
    #endif

    # write next rfile, return name:
    try :
        rcfile_next = submit_tm5_setup_rcfile.WriteRcfile( rcf ) 
    except :
        logging.error( sys.exc_info()[1] )
        logging.error( 'exception from WriteRcfile' )
        raise Exception
    
    # finished ?
    if rcfile_next == None :
        logging.info( '  end of job chain !' )
    else :
        # write job file(s) for this period and return the (first) name;
        # last command in a file should submit the next job if necessary:
        logging.info( '  write jobfile for %s ...' % rcfile_next )
        try :
            jobfile_next = WriteJob( rcfile_next, bindir )
        except :
            logging.error( sys.exc_info()[1] )
            logging.error( 'exception from WriteJob' )
            raise Exception

        logging.info( '  submit next job : %s' % jobfile_next )
        try :
            jobid = SubmitJob( jobfile_next, rcfile_next )
        except :
            logging.error( sys.exc_info()[1] )
            logging.error( 'exception from SubmitJob' )
            raise Exception
    
    return

# ***

def WriteJob( rcfile, bindir ) :

    """
    jobfile = WriteJob(rcfile)
    Write job file given the settings in rcfile.
    The name of the jobfile is based on the name of the rcfile.
    The last command in the job should submit the next job,
    and the script is therefore written in python.
    """
    
    # external:
    import os
    import rc
    
    # load settings:
    rcf = rc.RcFile( rcfile )
    
    # basename for scripts etc is name of rcfile minus extension:
    bname,ext = os.path.splitext(rcfile)    
    
    # loadleveler supports master job with multiple steps:
    with_master_job = (rcf.get('submit.to') == 'queue') and (rcf.get('queue') == 'loadleveler')

    # which shell ?
    job_shell = '/usr/bin/env python'

    # start master job ?    
    if with_master_job :

        ntasks = rcf.get('par.ntask')

        # name of jobfile:
        jobfile = '%s.jb' % bname

        # set header:
        header = []
        header.append( '#! %s\n' % job_shell )
        header.append( '\n' )

        # init queue options:
        qopt = QueueOptions( bname, rcf, 'default' )
    
        # init job file:
        job = []
        job.append( '# external:\n' )
        job.append( 'import os\n' )
        job.append( 'import sys\n' )
        job.append( 'import socket\n')
        job.append( 'import subprocess\n' )
        job.append( 'import logging\n' )
        job.append( '\n' )
        job.append( '# setup messages:\n' )
        job.append( "logging.basicConfig( format='%(lineno)-4s:%(filename)-30s [%(levelname)-8s] %(message)s', level=logging.INFO, stream=sys.stdout )\n" )
        job.append( '\n' )
        job.append( '# prepend locations of python modules to search path:\n' )
        job.append( "sys.path.insert( 0, '%s' )\n" % bindir )
        job.append( '\n' )
        job.append( '# tools:\n' )
        job.append( 'import submit_tm5_tools\n' )
        job.append( '\n' )
        job.append( '# current loadleveler steps:\n' )
        job.append( 'step_name = os.getenv("LOADL_STEP_NAME")\n' )
        job.append( '\n' )
        
        # HOSTFILE - Moved here from Command_Line for loadleveler.
        hostfile = rcf.get('mpirun.hostfile',default='') # calling script will create hostfile

        if (len(hostfile) > 0) and rcf.get('par.mpi','bool') :
            job.append( 'f = open("%s",\'w\') \n' % hostfile )
            job.append( 'hname = socket.gethostname() \n')
            job.append( "for i in range( %s ) : \n" % ntasks )
            job.append( "\tf.write( '%s\\n' % hname)\n" )
            job.append( 'f.close() \n')
            job.append( '\n' )

    # job step names:
    steps = rcf.get('job.steps').split(' ')
    # number of steps:
    nstep = len(steps)
    
    # loop over job steps:
    for istep in range(nstep) :

        # current:
        step = steps[istep]
        # next:
        if istep < nstep-1 : step_next = steps[istep+1]

        # list with queue option lines for this step:
        qopt_step = QueueOptions( bname, rcf, step )

        # call to actual script:
        if step == 'run' :
            # get command line:
            exe  = os.path.join( os.curdir, rcf.get('job.step.%s.exe' % step) )
            args = rcfile
            indb = rcf.get('submit.debugger','bool')
            cmndline = Command_Line( rcf, exe, args, indb )
            # <script> <commandline>
            step_command = '["%s/submit_tm5_step_%s","%s"]' % (bindir,step,cmndline)
        else :
            # <script> <rcfile>
            step_command = '["%s/submit_tm5_step_%s","%s","--bindir=%s"]' % (bindir,step,rcfile,bindir)
        #endif
        
        # add queue options to destintation:
        if with_master_job :

            # add to queue options for master job:
            qopt = qopt + qopt_step

            # add lines to run the step:        
            job.append( '# which step ?\n' )
            job.append( 'if step_name == "%s" :\n' % step )
            job.append( '    \n' )
            job.append( '    # run:\n' )
            job.append( '    retcode = subprocess.call( %s )\n' % step_command )
            job.append( '    if retcode != 0 :\n' )
            job.append( '        logging.error( sys.exc_info()[1] )\n' )
            job.append( '        logging.error( \'exception from subprocess call to : %s\' )\n' % step_command )
            job.append( '        sys.exit(1)\n' )
            job.append( '    #endif\n' )
            job.append( '    \n' )
            # last step ? then add lines to submit next job:
            if istep == nstep-1 :
                job.append( '    # write and submit next job if necessary:\n' )
                job.append( '    submit_tm5_tools.WriteAndSubmitNewJob( "%s", "%s" )\n' % (rcfile,bindir) )
                job.append( '    \n' )
            #endif
            # close step:
            job.append( '#endif\n' )
            job.append( '\n' )

        else :   # no master job, but seperate files

            # name of step job to be written:
            step_job_template = bname+'_%s.jb'

            # actual name:
            step_job = step_job_template % step
            # open:
            f = open( step_job, 'w' )

            # write header:
            f.write( '#! %s\n' % job_shell )
            f.write( '\n' )

            # add queue options:
            for line in qopt_step : f.write(line)

            # add lines to call the actual script:
            f.write( '# external:\n' )
            f.write( 'import sys\n' )
            f.write( 'import os\n' )
            f.write( 'import logging\n' )
            f.write( 'import socket\n' )
            f.write( 'import subprocess\n' )
            f.write( '\n' )
            f.write( '# go to run directory:\n' )
            f.write( 'os.chdir("%s")\n' % os.getcwd() )
            f.write( '\n' )
            f.write( '# prepend locations of python modules to search path:\n' )
            f.write( "sys.path.insert( 0, '%s' )\n" % bindir )
            f.write( '\n' )
            f.write( '# tools:\n' )
            f.write( 'import rc\n' )
            f.write( 'import submit_tm5_tools\n' )
            f.write( '\n' )
            f.write( '# setup messages:\n' )
            f.write( "logging.basicConfig( format='%(lineno)-4s:%(filename)-30s [%(levelname)-8s] %(message)s', level=logging.INFO, stream=sys.stdout )\n" )
            f.write( '\n' )
            f.write( '# info ...\n' )
            f.write( 'logging.info( "start" )\n' )
            f.write( '\n' )

            # module command if needed
            module_cmd = rcf.get('module.cmd',default='')
            if (module_cmd != '') and (step == 'run'):
                f.write( 'mod_cmd="%s".split()\n' % module_cmd )
                f.write( 'retcode = subprocess.call( mod_cmd )\n' )
                f.write( 'if retcode != 0:\n' )
                f.write( '    logging.error( sys.exc_info()[1] )\n' )
                f.write( '    logging.error( \'exception from subprocess call to : %s\' )\n' % module_cmd )
                f.write( '    sys.exit(1)\n' )
                f.write( '\n' )
                    
            # openMP
            if ( (rcf.get('queue') == 'slurm') or (rcf.get('queue') == 'pbs')) and \
                   rcf.get('par.openmp','bool') and (step == 'run'):
                nthread = rcf.get( 'par.nthread', 'int' )
                f.write( "os.putenv( \'OMP_NUM_THREADS\', '%s')\n" % nthread )

            # HOSTFILE - Moved here (and adapted) from Command_Line for case of
            # "SLURM with a host file" (case of NEURON@KNMI, and not CARTESIUS@SARA).
            # Needed only if MPI, step run.
            hostfile = rcf.get('mpirun.hostfile',default='')

            if (len(hostfile) > 0)  and (rcf.get('queue') == 'slurm') and rcf.get('par.mpi','bool') and (step == 'run'):
                f.write( 'f = open("%s",\'w\') \n' % hostfile)

                # PREVIOUS:
                #f.write( 'hname = socket.gethostname() \n')
                #f.write( 'for i in range(ntask) : f.write( '%s' % hname ) \n')

                # NOW: for SLURM on NEURON, need nodelist and number of
                # tasks-per-node effectively allocated.
                
                # --Idee #1 
                # -- Use "output environment variables" to gather effective values:
                # 
                #f.write( 'for node in os.getenv('SLURM_NODELIST'):                                         \n')
                #f.write( '    for i in range(os.getenv('SLURM_NTASKS_PER_NODE'): f.write( '%s\n' % node )  \n')
                #
                # -- BUT that would not work in all imaginable cases... so we
                # -- should use SLURM_TASKS_PER_NODE instead, but its format, for eg:
                # --        2(x3),1,5,2(x5)
                # -- is a bit annoying to process. Then idee #2... good old unix command line:
                
                # --Idee #2 - Use srun | sort | awk to get ordered list
                hcommand = '[ "srun -l /bin/hostname | sort -n | awk \'{print $2}\' > %s"]' % hostfile
                f.write( 'retcode = subprocess.call( %s, shell=True )\n' % hcommand )
                f.write( 'if retcode != 0:\n' )
                f.write( '    logging.error( sys.exc_info()[1] )\n' )
                f.write( '    logging.error( \'exception from creating host file\' )\n'  )
                f.write( '    sys.exit(1)\n' )
                                     
                f.write( 'f.close() \n')
                f.write( '\n' )
                
            f.write( '# call user script:\n' )
            f.write( 'retcode = subprocess.call( %s )\n' % step_command )
            f.write( 'if retcode != 0:\n' )
            f.write( '    logging.error( sys.exc_info()[1] )\n' )
            f.write( '    logging.error( \'exception from subprocess call to : %s\' )\n' % step_command )
            f.write( '    sys.exit(1)\n' )
            f.write( '#endif\n' )
            f.write( '\n' )

            # add submission of next step?
            if istep < nstep-1 :
                # job script of next step:
                step_job_next = step_job_template % step_next
                # add submission command:
                f.write( '# submit next step:\n' )
                f.write( 'try :\n' )
                f.write( '    submit_tm5_tools.SubmitJob( "%s", "%s" )\n' % (step_job_next,rcfile)  )
                f.write( 'except:\n' )
                f.write( '    logging.error( sys.exc_info()[1] )\n' )
                f.write( '    logging.error( \'exception from SubmitJob( "%s", "%s" )\' )\n' % (step_job_next,rcfile) )
                f.write( '    sys.exit(1)\n' )
                f.write( '#endtry\n' )
                f.write( '\n' )
            else :
                # last step; might be necessary to submit a new job:
                f.write( '# write and submit next job if necessary:\n' )
                f.write( 'submit_tm5_tools.WriteAndSubmitNewJob( "%s", "%s" )\n' % (rcfile,bindir) )
                f.write( '\n' )
            
            f.write( '# info ...\n' )
            f.write( 'logging.info( "end" )\n' )
            f.write( '\n' )

            f.close()

            # make it executable and readible for all, writable for user only:
            #                   u+r    u+w    u+x    g+r    g-w    g+x    o+r    o-w    o+x
            os.chmod( step_job, 2**8 + 2**7 + 2**6 + 2**5 + 0    + 2**3 + 2**2 + 0    + 2**0 )
            
            # fill return value:
            if istep == 0 : jobfile = step_job


    # write master job:
    if with_master_job :
        # combine:
        job = header + qopt + job
        # write:
        f = open(jobfile,'w')
        f.writelines(job)
        f.close()
        # make it executable and readible for all, writable for user only:
        #                  u+r    u+w    u+x    g+r    g-w    g+x    o+r    o-w    o+x
        os.chmod( jobfile, 2**8 + 2**7 + 2**6 + 2**5 + 0    + 2**3 + 2**2 + 0    + 2**0 )
     
    return jobfile

# ***

def WriteAndSubmitBuildJob( rcf, command ):
    """
    Write bash script that run 'command' after being submitted to the
    queue. Written to compile TM5 in the queue.
    """
    import os

    orig_val = rcf.get('submit.to')
    dummy = rcf.replace('submit.to','queue')
    
    source_dir = os.getcwd()            #  assume that it is called from
                                        #  source directory
    jobfile = os.path.join(source_dir,'build.jb')

    f = open( jobfile, 'w' )
    f.write( '#! /bin/bash\n' )
    f.write( '\n' )
    
    qopt = QueueOptions( 'buildTM', rcf, 'build' )
    for line in qopt : f.write(line)

    f.write( "cd %s \n" % source_dir )
    f.write( '%s' % ' '.join(command) )
    f.write( '\n' )
    f.close()

    id=SubmitJob( jobfile, rcf )

    dummy = rcf.replace('submit.to', orig_val)

    return

# ***

def QueueOptions( bname, rcf, step ) :
    
    """
    Return list with queue option lines.
    """

    # modules:
    import logging

    # submit to queue ?
    if rcf.get('submit.to') == 'queue' :
    
        # queue type:
        queue = rcf.get('queue')

        # different options and commands:
        if queue == 'loadleveler' :
            qopt = QueueOptions_LoadLeveler( bname, rcf, step )
        elif queue == 'bsub' :
            qopt = QueueOptions_BSub( bname, rcf, step )
        elif queue == 'qsub' :
            qopt = QueueOptions_QSub( bname, rcf, step )
        elif queue == 'pbs' :
            qopt = QueueOptions_PBS( bname, rcf, 'all' )     # init result with the "all" step
            qopt = qopt + QueueOptions_PBS( bname, rcf, step )
        elif queue == 'slurm' :
            qopt = QueueOptions_Slurm( bname, rcf, step )
        else :
            # not supported ...
            logging.error( 'unsupported queue : %s' % queue )
            raise Exception

    else:    
        qopt = []
        
    return qopt
    
# ***

def SubmitJob( job_script, rcfile ) :

    """
    Submit jobscript.  Where to submit to (foreground,background, queue) is
    read from rcfile settings.  Returns jobid if submitting to queue (for now
    dummy for all cases except PBS).
    """
    
    import sys
    import logging
    import rc

    jobid='not-a-real-jobid-yet'        # default
    
    # settings
    if type(rcfile) == str :
        rcf = rc.RcFile( rcfile )
    else :
        rcf = rcfile
    
    # where to ?
    submit_to = rcf.get('submit.to')
    # info ...
    logging.info( 'submit %s to %s ...' % (job_script,submit_to) )

    # call specific submit routines:
    if submit_to == 'foreground' :

        # call run script, catch errors:
        try :
            Run_Job_In_Foreground( job_script )
        except :
            logging.error( sys.exc_info()[1] )
            logging.error( 'from Run_Job_In_Foreground for %s' % job_script )
            raise Exception
        
    elif submit_to == 'background' :
    
        # call run script, catch errors:
        try :
            Submit_Job_To_Background( job_script, rcf )
        except :
            logging.error( 'from Submit_Job_To_Background for %s' % job_script )
            raise Exception

    elif submit_to == 'queue' :
    
        # queue type:
        queue = rcf.get('queue')

        # different options and commands:
        if queue == 'loadleveler' :
            Submit_Job_To_LoadLeveler( job_script, rcf )
        elif queue == 'bsub' :
            Submit_Job_To_BSub( job_script, rcf )
        elif queue == 'qsub' :
            Submit_Job_To_QSub( job_script, rcf )
        elif queue == 'pbs' :
            jobid = Submit_Job_To_PBS( job_script, rcf )
        elif queue == 'slurm' :
            Submit_Job_To_Slurm( job_script, rcf )
        else :
            # not supported ...
            logging.error( 'unsupported queue : %s' % queue )
            raise Exception
    else :
    
        # not supported ...
        logging.error( 'unsupported run environment : %s' % submit_to )
        sys.exit(1)
        
    return jobid
    


# ======================================================================
# ===
# === foreground
# ===
# ======================================================================


def Run_Job_In_Foreground( job_script ) :

    """
    Run job script in foreground.
    """
    
    # external:
    import sys
    import os
    import logging
    import subprocess

    # setup command line, e.g. './myscript.jb' :
    command = os.path.join(os.curdir,job_script)

    # execute:
    retcode = subprocess.call( command )
    if retcode != 0 :
        logging.error( sys.exc_info()[1] )
        logging.error( 'from subprocess call to : %s' % command )
        raise Exception
    
    return

# ======================================================================
# ===
# === background
# ===
# ======================================================================

def  Submit_Job_To_Background( job_script, rcf ) :

    """
    Submit job to background.
    """
    
    # external:
    import sys
    import os
    import logging
    import subprocess

    # basename for scripts etc is name of rcfile minus extension:
    bname,ext = os.path.splitext(job_script)    
    
    # output files:    
    job_stdout = bname+'.out'
    job_stderr = bname+'.err'
    job_info   = bname+'.info'

    # setup command line, e.g. './myscript.jb' :
    command = os.path.join(os.curdir,job_script)

    # re-direct standard output:
    command  = command+' > %s' % job_stdout
    # write error messages to seperate file:
    #command  = command+' 2> %s' % job_stderr
    command  = command+' 2>&1'
    
    # run in background, return process id:
    logging.info( 'run shell command : "%s" ...' % command )
    p = subprocess.Popen( command, shell=True )

    # info ...
    infotext = []
    infotext.append( '\n' )
    infotext.append( 'Summary:\n' )
    infotext.append( '\n' )
    infotext.append( '  job script      : %s\n' % job_script )
    infotext.append( '  standard output : %s\n' % job_stdout )
    infotext.append( '  standard error  : %s\n' % job_stderr )
    infotext.append( '\n' )
    infotext.append( 'Process snapshot:\n')
    infotext.append( '\n')
    p2 = subprocess.Popen( '/bin/ps -f -p %i' % p.pid, shell=True, 
                             stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
    for line in p2.stdout.readlines() : infotext.append( line )
    infotext.append( '\n')
    infotext.append( 'To manage this process:\n' )
    infotext.append( '\n' )
    infotext.append( '  # show process snapshot:\n' )
    infotext.append( '  ps -f -p %i\n' % p.pid )
    infotext.append( '  \n' )
    infotext.append( '  # kill process:\n' )
    infotext.append( '  kill %i\n' % p.pid )
    infotext.append( '  \n' )
    infotext.append( '  # follow standard output:\n' )
    infotext.append( '  tail -f %s\n' % job_stdout )
    infotext.append( '\n' )

    # write to log:
    for line in infotext : logging.info( line.strip() )

    # write to file:
    f = open( job_info, 'w' )
    f.writelines(infotext)
    f.close()
        
    return

# ======================================================================
# ===
# === LoadLeveler queue
# ===
# ======================================================================

def QueueOptions_LoadLeveler( bname, rcf, step ) :

    """
    Return list with queue options.
    """

    # external:
    import math
    
    # init result:
    qopt = []

    # which step ?
    if step == 'default' :
    
        # list with options:
        opts = rcf.get( 'queue.ll.options.%s' % step ).split()
        # default options:
        for opt in opts :
            # get value:
            val = rcf.get( 'queue.ll.option.%s.%s' % (step,opt) )
            # write:
            qopt.append( '#@ %-20s = %s\n' % (opt,val) )
        #endfor
        # layout ...
        qopt.append( '\n' )

    else :
    
        # list with options:
        opts = rcf.get( 'queue.ll.options.%s' % step ).split()
        # default options:
        for opt in opts :
            # get value:
            val = rcf.get( 'queue.ll.option.%s.%s' % (step,opt) )
            # to be set ?
            if val == '<auto>' :
                # differs per option ...
                if opt == 'output' :
                    val = '%s_%s.out' % (bname,step)
                elif opt == 'error' :
                    val = '%s_%s.err' % (bname,step)
                elif opt == 'tasks_per_node' :
                    t_mpi = rcf.get( 'par.ntask', 'int' )
                    t_omp = rcf.get( 'par.nthread', 'int' )
                    val = str(t_omp*t_mpi)
                #endif
            #endif
            # no, empty, or normal value ?
            if val == '<none>' :
                # skip this keyword:
                continue
            elif val == '' :
                # just the keyword:
                qopt.append( '#@ %s\n' % opt )
            else :
                # keyword and value:
                qopt.append( '#@ %-20s = %s\n' % (opt,val) )
            #endif
        #endfor
        # layout ...
        qopt.append( '\n' )
                
    return qopt

# ***

def Submit_Job_To_LoadLeveler( job_script, rcf ) :

    """
    Submit job to LoadLeveler queue.
    """
    
    # external:
    import sys
    import os
    import logging
    import subprocess

    # basename for scripts etc is name of rcfile minus extension:
    bname,ext = os.path.splitext(job_script)    
    
    # output files:    
    job_info   = bname+'.info'

    # options passed directly to submission command:
    qopts = rcf.get( 'queue.ll.submit.options' )
    # add options passed to submit script:
    qopts = qopts+' '+rcf.get('submit.options')

    # info ...
    logging.info( '    launch ...' )

    # setup command line:
    command = 'llsubmit '+qopts
    # last argument is script:
    command = command+' '+job_script

    # info ...
    logging.info( '      command: %s' % command )
    
    # init submission info file:
    infotext = []
    infotext.append(  '\n' )

    # call submit command, trap errors:
    try:
        # submit; redirect errors to standard output:
        p = subprocess.Popen( command.split(), stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
    except :
        logging.error( sys.exc_info()[1] )
        logging.error( 'from subprocess.Popen( %s )' % command.split() )
        raise Exception
    #endtry
    # extract:
    outlines = p.stdout.readlines()
    # add to help info message:
    infotext = infotext + outlines
    # extract job id from last line:
    #   llsubmit: The job "c1a0303.4290133" with 3 job steps has been submitted.
    firstwords = 'llsubmit: The job'
    lastline = outlines[-1]
    if lastline.startswith(firstwords) :
        job_id = lastline.lstrip(firstwords).split()[0].replace('"','')
    else :
        job_id = '<job-id>'
    #endif
    
    # add help text to submission info:
    infotext.append(  '\n' )
    infotext.append(  'To manage LoadLeveler jobs:\n' )
    infotext.append(  '\n' )
    infotext.append(  '  llq [-u ${USER}]         # list [your] current jobs\n' )
    infotext.append(  '  llq %s             # list this job\n' % job_id )
    infotext.append(  '  llcancel %s        # kill this job\n' % job_id )
    infotext.append(  '\n' )

    # write to log:
    for line in infotext : logging.info( line.rstrip() )

    # write to file:
    f = open( job_info, 'w' )
    f.writelines(infotext)
    f.close()
    
    # ok
    return

#enddef
        

# ======================================================================
# ===
# === BSUB queue
# ===
# ======================================================================


def QueueOptions_BSub( bname, rcf, step ) :

    """
    Return list with queue options.
    """

    # init result:
    qopt = []

    # List of options for specified step:
    opts = rcf.get( 'queue.bsub.options.%s' % step ).split()

    # loop over options:
    for opt in opts :
        # get value:
        val = rcf.get( 'queue.bsub.option.%s.%s' % (step,opt) )

        # default options:
        if val == '<auto>' :
            if opt in ['o','oo'] :
                val = '%s_%s.out' % (bname,step)
            elif opt in ['e','eo'] :
                val = '%s_%s.err' % (bname,step)
            #endif
        #endif # <auto> value

        # define option key:
        #    queue.bsub.options.R   :  20     ->  -R 20
        #    queue.bsub.options.Rx  :  -R 20  ->  -R 20
        if val.startswith('-') :
            qopt.append( '#BSUB %s\n' % (val) )
        else :
            qopt.append( '#BSUB -%s %s\n' % (opt,val) )
        #endif
    #endfor  # opts

    # layout ...
    qopt.append( '\n' )
                
    # ok
    return qopt
    
#enddef QueueOptions_BSub


# ***


def Submit_Job_To_BSub( job_script, rcf ) :

    """
    Submit job to BSUB queue.
    """
    
    # external:
    import os
    import logging
    import subprocess

    # basename for scripts etc is name of rcfile minus extension:
    bname,ext = os.path.splitext(job_script)    
    
    # output files:    
    job_info   = bname+'.info'

    # options passed directly to submission command:
    qopts = rcf.get( 'queue.bsub.submit.options' )
    # add options passed to submit script:
    qopts = qopts+' '+rcf.get('submit.options')
    
    # info ...
    logging.info( '    launch ...' )

    # setup command line:
    command = 'bsub '+qopts
    # pass job script to std.input:
    command = command+' < '+job_script

    # info ...
    logging.info( '      command: %s' % command )

    # prepare for OS errors (file does not exist etc.)    
    try:
        # submit; redirect errors to standard output:
        p = subprocess.Popen( command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
    except OSError, err :
        logging.error( 'OSError: '+err.strerror )
        logging.error( 'from call : %s' % command )
        raise Exception
    #endtry
    # extract:
    outlines = p.stdout.readlines()
    # display:
    for line in outlines : logging.info( '      %s' % line.rstrip() )
    # standard output is:
    #   <jobname> <jobnr>
    # extract job nr:
    job_nr = outlines[0].split()[1].strip('<>')

    # info ...
    infotext = []
    infotext.append(  '\n' )
    infotext.append(  'Summary:\n' )
    infotext.append(  '\n' )
    infotext.append(  '  current dir     : %s\n' % os.getcwd() )
    infotext.append(  '  job script      : %s\n' % job_script )
    infotext.append(  '\n' )
    infotext.append(  'To manage this job:\n' )
    infotext.append(  '  \n' )
    infotext.append(  '  # kill job:\n' )
    infotext.append(  '  bkill %s\n' % job_nr )
    infotext.append(  '  \n' )
    infotext.append(  'To show all your running jobs:\n' )
    infotext.append(  '  \n' )
    infotext.append(  '  bjobs\n' )
    infotext.append(  '  \n' )

    # write to log:
    for line in infotext : logging.info( line.rstrip() )

    # write to file:
    f = open( job_info, 'w' )
    f.writelines(infotext)
    f.close()
    
    # ok
    return

#enddef
        

# ======================================================================
# ===
# === QSUB queue
# ===
# ======================================================================


def QueueOptions_QSub( bname, rcf, step ) :

    """
    Return list with queue options.
    """

    # init result:
    qopt = []

    # list with options:
    opts = rcf.get( 'queue.qsub.options' ).split()
    append_jobstep = rcf.get('queue.qsub.name.append.jobstep',default=False)

    # default options:
    for opt in opts :

        # look first for a jobstep-specific qsub option
        val = rcf.get( 'queue.qsub.option.%s.%s' % (opt,step), default='STEP_SPECIFIC_KEY_MISSING' )

        # if jobstep-specific option is missing, look for one without jobstep
        if val == 'STEP_SPECIFIC_KEY_MISSING':
            val = rcf.get( 'queue.qsub.option.%s' % opt)

        if (opt == 'N') and append_jobstep:
            jobstep = rcf.get('jobstep')
            val = val + '_%03d' % (int(jobstep))

        # fill option line:
        qopt.append( '#PBS -%s %s\n' % (opt,val) )
    #endfor
    # layout ...
    qopt.append( '\n' )
                
    # ok
    return qopt
    
#enddef


# ***


def Submit_Job_To_QSub( job_script, rcf ) :

    """
    Submit job to QSUB queue.
    """
    
    # external:
    import os
    import logging
    import subprocess

    # basename for scripts etc is name of rcfile minus extension:
    bname,ext = os.path.splitext(job_script)    
    
    # output files:    
    job_info   = bname+'.info'

    # options passed directly to submission command:
    qopts = rcf.get( 'queue.qsub.submit.options' )
    # add options passed to submit script:
    qopts = qopts+' '+rcf.get('submit.options')
    
    # info ...
    logging.info( '    launch ...' )

    # setup command line:
    command = 'qsub '+qopts
    # last argument is script:
    command = command+' '+job_script

    # info ...
    logging.info( '      command: %s' % command )

    # prepare for OS errors (file does not exist etc.)    
    try:
        # submit; redirect errors to standard output:
        p = subprocess.Popen( command.split(), stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
    except OSError, err :
        logging.error( 'OSError: '+err.strerror )
        logging.error( 'from call : %s' % command )
        raise Exception
    #endtry
    # extract:
    outlines = p.stdout.readlines()
    # display:
    for line in outlines : logging.info( '      %s' % line.rstrip() )
    # standard output is:
    #    jobnr
    # extract job nr:
    job_nr = outlines[0].split()[0]

    # info ...
    infotext = []
    infotext.append(  '\n' )
    infotext.append(  'Summary:\n' )
    infotext.append(  '\n' )
    infotext.append(  '  current dir     : %s\n' % os.getcwd() )
    infotext.append(  '  job script      : %s\n' % job_script )
    infotext.append(  '\n' )
    infotext.append(  'To manage this job:\n' )
    infotext.append(  '  \n' )
    infotext.append(  '  # kill job:\n' )
    infotext.append(  '  qdel %s\n' % job_nr )
    infotext.append(  '  \n' )
    infotext.append(  'To show all your running jobs:\n' )
    infotext.append(  '  \n' )
    infotext.append(  '  qstat [-u ${USER}]\n' )
    infotext.append(  '  \n' )

    # write to log:
    for line in infotext : logging.info( line.rstrip() )

    # write to file:
    f = open( job_info, 'w' )
    f.writelines(infotext)
    f.close()
    
    # ok
    return

        
# ======================================================================
# ===
# === PBS queue (PBSpro)
# ===
# === Note that there are several implementations of PBS and the "pbs queue"
# === here, although it also uses the qsub command, differs from the "qsub
# === queue" defined above. The later uses #$ directives, while the pbsPro
# === directives start with #PBS.
# ===
# ======================================================================

def QueueOptions_PBS( bname, rcf, step ) :

    """
    Return list with queue options. To call twice, first for pseudo-step
    'all'. See QueueOptions above.
    """
    import os

    qopt = []     # init result
    
    opts = rcf.get( 'queue.pbs.options.%s' % step ).split() # list with options

    # use fully qualified filename for log files
    if step != 'build':
        fqpath = rcf.get('rundir')
    else:
        fqpath = rcf.get('build.sourcedir')
    fqname = os.path.join( fqpath, bname )

    # build list of job directives
    for opt in opts :
        val = rcf.get( 'queue.pbs.option.%s.%s' % (step,opt) )

        # deal w/ multiple options with -l
        if opt == 'l':
            l_vals = val.split()
            for lval in l_vals: qopt.append( '#PBS -l %s\n' % lval )
            continue

        # options still to be set
        if val == '<auto>' :
            if opt == 'o' :
                val = '%s_%s.out' % (fqname,step)
            elif opt == 'e' :
                val = '%s_%s.err' % (fqname,step)

        # none, empty or plain normal value ?
        if val == '<none>' :
            continue                                   # skip this option
        elif val == '' :
            qopt.append( '#PBS -%s\n' % opt )             # just the keyword
        else :
            qopt.append( '#PBS -%s %s\n' % (opt,val) ) # keyword and value

    qopt.append( '\n' )

    return qopt


def Submit_Job_To_PBS( job_script, rcf ) :

    """
    Submit job to PBS queue.
    """
    import os
    import logging
    import subprocess

    # basename for scripts etc is name of rcfile minus extension:
    bname,ext = os.path.splitext(job_script)    
    
    # output files:    
    job_info   = bname+'.info'

    # Two set of options to pass directly unmodified at the submission command :
    qopts = rcf.get( 'queue.pbs.submit.options' )  # (1) from machine or queue (if separated from machine) rcfile
    qopts = qopts+' '+rcf.get('submit.options')    # (2) from expert rcfile
    
    # info ...
    logging.info( '    launch ...' )

    # setup command line:
    command = 'qsub '+qopts
    # last argument is script:
    command = command+' '+job_script

    # info ...
    logging.info( '      command: %s' % command )

    # prepare for OS errors (file does not exist etc.)    
    try:
        # submit; redirect errors to standard output:
        p = subprocess.Popen( command.split(), stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
    except OSError, err :
        logging.error( 'OSError: '+err.strerror )
        logging.error( 'from call : %s' % command )
        raise Exception

    # log output
    outlines = p.stdout.readlines()
    for line in outlines : logging.info( '      %s' % line.rstrip() )
    # standard output is:
    #    jobnr
    # extract job nr:
    job_nr = outlines[0].split()[0]

    # info ...
    infotext = []
    infotext.append(  '\n' )
    infotext.append(  'Summary:\n' )
    infotext.append(  '\n' )
    infotext.append(  '  current dir     : %s\n' % os.getcwd() )
    infotext.append(  '  job script      : %s\n' % job_script )
    infotext.append(  '\n' )
    infotext.append(  'To manage this job:\n' )
    infotext.append(  '  \n' )
    infotext.append(  '  # kill job:\n' )
    infotext.append(  '  qdel %s\n' % job_nr )
    infotext.append(  '  \n' )
    infotext.append(  'To show all your running jobs:\n' )
    infotext.append(  '  \n' )
    infotext.append(  '  qstat [-u ${USER}]\n' )
    infotext.append(  '  \n' )
    infotext.append(  'To monitor this running job (ECMWF only!):\n' )
    infotext.append(  '  \n' )
    infotext.append(  '  qcat %s\n' % job_nr )
    infotext.append(  '  \n' )

    # write to log:
    for line in infotext : logging.info( line.rstrip() )

    # write to file:
    f = open( job_info, 'w' )
    f.writelines(infotext)
    f.close()
    
    return job_nr

# ======================================================================
# ===
# === SLURM queue
# ===
# ======================================================================

def QueueOptions_Slurm( bname, rcf, step ) :

    """
    Return list with queue options directives, that will be at the top of
    script.

    Script for run step (NEURON@KNMI) should contains:

    #SBATCH -n ${par.nthread}*${ntask}
    
    export OMP_NUM_THREADS=${par.nthread}

    mpiexec.hydra -machinefile ./mpd.hosts -np ${ntask} ./$bin
    
    """
    qopt = [] # init result

    # List of options for specified step:
    opts = rcf.get( 'queue.slurm.options.%s' % step ).split()

    for opt in opts :

        # get value:
        val = rcf.get( 'queue.slurm.option.%s.%s' % (step,opt) )

        # default options:
        if val == '<auto>' :
            if opt == 'o' :
                val = '%s_%s.out' % (bname,step)
            elif opt == 'e' :
                val = '%s_%s.err' % (bname,step)

        # skip unset (empty) directives
        if opt == 'p' or 'w':
            if len(val)==0 : continue
    
        qopt.append( '#SBATCH -%s %s\n' % (opt,val) )


    # layout ...
    qopt.append( '\n' )
                
    # ok
    return qopt
    


def Submit_Job_To_Slurm( job_script, rcf ) :

    """
    Submit job to SLURM queue.
    """
    
    # external:
    import os
    import logging
    import subprocess

    # basename for scripts etc is name of rcfile minus extension:
    bname,ext = os.path.splitext(job_script)    
    
    # output files:    
    job_info   = bname+'.info'

    # Two set of options to pass directly unmodified at the submission command :
    qopts = rcf.get( 'queue.slurm.submit.options' )   # (1) from pycassso-queue-slurm.rc
    qopts = qopts+' '+rcf.get('submit.options')       # (2) from pycasso-tm5-expert.rc
    
    # info ...
    logging.info( '    launch ...' )

    # setup command line:
    command = 'sbatch '+qopts
    
    # last argument is script:
    command = command+' '+job_script

    # info ...
    logging.info( '      command: %s' % command )

    # prepare for OS errors (file does not exist etc.)    
    try:
        # submit; redirect errors to standard output:
        p = subprocess.Popen( command.split(), stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
    except OSError, err :
        logging.error( 'OSError: '+err.strerror )
        logging.error( 'from call : %s' % command )
        raise Exception
    
    # extract:
    outlines = p.stdout.readlines()

    # display:
    for line in outlines : logging.info( '      %s' % line.rstrip() )

    # standard output is:
    #    jobnr
    # extract job nr:
    job_nr = outlines[0].split()[0]

    # info ...
    infotext = []
    infotext.append(  '\n' )
    infotext.append(  'Summary:\n' )
    infotext.append(  '\n' )
    infotext.append(  '  current dir     : %s\n' % os.getcwd() )
    infotext.append(  '  job script      : %s\n' % job_script )
    infotext.append(  '\n' )
    infotext.append(  'To manage this job:\n' )
    infotext.append(  '  \n' )
    infotext.append(  '  # kill job:\n' )
    infotext.append(  '  scancel %s\n' % job_nr )
    infotext.append(  '  \n' )
    infotext.append(  'To show all your running jobs:\n' )
    infotext.append(  '  \n' )
    infotext.append(  '  squeue [-u ${USER}]\n' )
    infotext.append(  '  \n' )

    # write to log:
    for line in infotext : logging.info( line.rstrip() )

    # write to file:
    f = open( job_info, 'w' )
    f.writelines(infotext)
    f.close()
    
    return

# ======================================================================
# ===
# === end
# ===
# ======================================================================