MadGraphUtils.py

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# Copyright (C) 2002-2025 CERN for the benefit of the ATLAS collaboration
 
# Pythonized version of MadGraph steering executables
#    written by Zach Marshall <zach.marshall@cern.ch>
#    updates for aMC@NLO by Josh McFayden <mcfayden@cern.ch>
#    updates to LHE handling and SUSY functionality by Emma Kuwertz <ekuwertz@cern.ch>
#  Attempts to remove path-dependence of MadGraph
 
import os,time,subprocess,glob,re
# These Import lines are temporary for backwards compatibility of clients.
from MCJobOptionUtils.JOsupport import check_reset_proc_number # noqa: F401
from MCJobOptionUtils.LHAPDFsupport import get_LHAPDF_DATA_PATH # noqa: F401
from MCJobOptionUtils.LHEsupport import remap_lhe_pdgids # noqa: F401
from MCJobOptionUtils.LHAPDFsupport import get_lhapdf_id_and_name # noqa: F401
from MCJobOptionUtils.LHAPDFsupport import get_LHAPDF_PATHS # noqa: F401
from MCJobOptionUtils.JOsupport import get_physics_short 
from AthenaCommon import Logging
from MadGraphControl.MGC import MGControl
mglog = Logging.logging.getLogger('MadGraphUtils')
my_MGC_instance = None
 
# Import that allows transparent migration for current users
from MadGraphControl.MadGraphUtilsHelpers import modify_param_card # noqa: F401
 
# Name of python executable
python='python'
# Magic name of gridpack directory
MADGRAPH_GRIDPACK_LOCATION='madevent'
# Name for the run (since we only have 1, just needs consistency)
MADGRAPH_RUN_NAME='run_01'
# For error handling
MADGRAPH_CATCH_ERRORS=True
# PDF setting (global setting)
MADGRAPH_PDFSETTING=None
MADGRAPH_COMMAND_STACK = []
 
 
import shutil
 
 
from MadGraphControl.MadGraphUtilsHelpers import error_check,get_mg5_version
from MadGraphControl.MadGraphSystematicsUtils import systematics_run_card_options,get_pdf_and_systematic_settings
from MadGraphControl.MadGraphParamHelpers import check_PMG_updates
 
def stack_subprocess(command,**kwargs):
    global MADGRAPH_COMMAND_STACK
    MADGRAPH_COMMAND_STACK += [' '.join(command)]
    return subprocess.Popen(command,**kwargs)
 
def generate_prep(process_dir):
    global MADGRAPH_COMMAND_STACK
    if not os.access('Cards_bkup',os.R_OK):
        shutil.copytree(process_dir+'/Cards','Cards_bkup')
        shutil.copyfile(process_dir+'/Source/make_opts','Cards_bkup/make_opts_bkup')
        MADGRAPH_COMMAND_STACK += ['# In case this fails, Cards_bkup should be in your original run directory']
        MADGRAPH_COMMAND_STACK += ['# And ${MGaMC_PROCESS_DIR} can be replaced with whatever process directory exists in your stand-alone test']
        MADGRAPH_COMMAND_STACK += ['cp '+os.getcwd()+'/Cards_bkup/*dat ${MGaMC_PROCESS_DIR}/Cards/']
        MADGRAPH_COMMAND_STACK += ['cp '+os.getcwd()+'/Cards_bkup/make_opts_bkup ${MGaMC_PROCESS_DIR}/Source/make_opts']
    else:
        mglog.warning('Found Cards_bkup directory existing. Suggests you are either running generation twice (a little funny) or are not using a clean directory.')
        bkup_v = 1
        while os.access('Cards_bkup_'+str(bkup_v),os.R_OK) and bkup_v<100:
            bkup_v += 1
        if bkup_v<100:
            shutil.copytree(process_dir+'/Cards','Cards_bkup_'+str(bkup_v))
            shutil.copyfile(process_dir+'/Source/make_opts','Cards_bkup_'+str(bkup_v)+'/make_opts_bkup')
            MADGRAPH_COMMAND_STACK += ['# In case this fails, Cards_bkup should be in your original run directory']
            MADGRAPH_COMMAND_STACK += ['# And ${MGaMC_PROCESS_DIR} can be replaced with whatever process directory exists in your stand-alone test']
            MADGRAPH_COMMAND_STACK += ['cp '+os.getcwd()+'/Cards_bkup_'+str(bkup_v)+'/*dat ${MGaMC_PROCESS_DIR}/Cards/']
            MADGRAPH_COMMAND_STACK += ['cp '+os.getcwd()+'/Cards_bkup_'+str(bkup_v)+'/make_opts_bkup ${MGaMC_PROCESS_DIR}/Source/make_opts']
        else:
            mglog.warning('Way too many Cards_bkup* directories found. Giving up -- standalone script may not work.')
 
 
def new_process(process='generate p p > t t~\noutput -f', plugin=None, keepJpegs=False, usePMGSettings=False):
    global my_MGC_instance
    my_MGC_instance = MGControl(process, plugin, keepJpegs, usePMGSettings)
    return my_MGC_instance.process_dir
 
def get_default_runcard(process_dir=MADGRAPH_GRIDPACK_LOCATION):
    """ Copy the default runcard from one of several locations
    to a local file with name run_card.tmp.dat"""
    output_name = 'run_card.tmp.dat'
 
    # Get the run card from the installation
    run_card=process_dir+'/Cards/run_card.dat'
    if os.access(run_card,os.R_OK):
        mglog.info('Copying default run_card.dat from '+str(run_card))
        shutil.copy(run_card,output_name)
        return output_name
    else:
        run_card=process_dir+'/Cards/run_card_default.dat'
        mglog.info('Fetching default run_card.dat from '+str(run_card))
        if os.access(run_card,os.R_OK):
            shutil.copy(run_card,output_name)
            return output_name
        else:
            raise RuntimeError('Cannot find default run_card.dat or run_card_default.dat! I was looking here: %s'%run_card)
 
 
def generate(process_dir='PROC_mssm_0', grid_pack=False, gridpack_compile=False, extlhapath=None, required_accuracy=0.01, runArgs=None, bias_module=None, requirePMGSettings=False):
    global my_MGC_instance # noqa: F824
 
    
    # Just in case
    my_MGC_instance.setup_path_protection()
    
    # Set consistent mode and number of jobs
    mode = 0
    njobs = 1
    if 'ATHENA_CORE_NUMBER' in os.environ and int(os.environ['ATHENA_CORE_NUMBER'])>0:
        njobs = int(os.environ['ATHENA_CORE_NUMBER'])
        mglog.info('Lucky you - you are running on a full node queue.  Will re-configure for '+str(njobs)+' jobs.')
        mode = 2
 
    cluster_type = get_cluster_type()
    if cluster_type is not None:
        mode = 1
 
    if is_gen_from_gridpack():
        mglog.info('Running event generation from gridpack (using smarter mode from generate() function)')
        generate_from_gridpack(runArgs=runArgs,extlhapath=extlhapath,gridpack_compile=gridpack_compile,requirePMGSettings=requirePMGSettings)
        return
    else:
        mglog.info('Did not identify an input gridpack.')
        if grid_pack:
            mglog.info('The grid_pack flag is set, so I am expecting to create a gridpack in this job')
 
    # Now get a variety of info out of the runArgs
    beamEnergy,random_seed = get_runArgs_info(runArgs)
 
    # Check if process is NLO or LO
    isNLO = my_MGC_instance.isNLO 
 
    # Setup PDF and systematics
    setup_pdf_and_systematic_weights(MADGRAPH_PDFSETTING,my_MGC_instance.runCardDict,isNLO)
 
 
    # temporary fix of makefile, needed for 3.3.1., remove in future
    if isNLO:
        fix_fks_makefile(process_dir=process_dir)
 
    # if f2py not available
    if get_reweight_card(process_dir=process_dir) is not None:
        if shutil.which('f2py') is not None:
            mglog.info('Found f2py, will use it for reweighting')
        else:
            raise RuntimeError('Could not find f2py, needed for reweighting')
        check_reweight_card(process_dir)
 
    global MADGRAPH_COMMAND_STACK
 
    if grid_pack:
        #Running in gridpack mode
        mglog.info('Started generating gridpack at '+str(time.asctime()))
        mglog.warning(' >>>>>> THIS KIND OF JOB SHOULD ONLY BE RUN LOCALLY - NOT IN GRID JOBS <<<<<<')
 
        # Some events required if we specify MadSpin usage!
        my_settings = {'nevents':'1000'}
 
        if isNLO:
            my_settings['req_acc']=str(required_accuracy)
        else:
            # At LO, no events are generated. That means we need to move the MS card aside and back.
            LO_has_madspin = False
            if os.access(f'{process_dir}/Cards/madspin_card.dat',os.R_OK):
                MADGRAPH_COMMAND_STACK += [f'mv {process_dir}/Cards/madspin_card.dat {process_dir}/Cards/madspin_card.tmp.dat']
                os.rename(f'{process_dir}/Cards/madspin_card.dat',f'{process_dir}/Cards/madspin_card.tmp.dat')
                LO_has_madspin = True
            my_settings = {'gridpack':'true'}
        my_MGC_instance.runCardDict.update(my_settings)
    else:
        #Running in on-the-fly mode
        mglog.info('Started generating at '+str(time.asctime()))
 
    mglog.info('Run '+MADGRAPH_RUN_NAME+' will be performed in mode '+str(mode)+' with '+str(njobs)+' jobs in parallel.')
 
    # Ensure that things are set up normally
    if not os.access(process_dir,os.R_OK):
        raise RuntimeError('No process directory found at '+process_dir)
    if not os.access(process_dir+'/bin/generate_events',os.R_OK):
        raise RuntimeError('No generate_events module found in '+process_dir)
 
    mglog.info('For your information, the libraries available are (should include LHAPDF):')
    ls_dir(process_dir+'/lib')
 
    setupFastjet(process_dir=process_dir)
    if bias_module is not None:
        setup_bias_module(bias_module,process_dir)
 
    mglog.info('Now I will hack the make files a bit.  Apologies, but there seems to be no good way around this.')
    shutil.copyfile(process_dir+'/Source/make_opts',process_dir+'/Source/make_opts_old')
    old_opts = open(process_dir+'/Source/make_opts_old','r')
    new_opts = open(process_dir+'/Source/make_opts','w')
    for aline in old_opts:
        if 'FC=g' in aline:
            mglog.info('Configuring the fancy gfortran compiler instead of g77 / f77')
            new_opts.write('  FC=gfortran\n')
        else:
            new_opts.write(aline)
    old_opts.close()
    new_opts.close()
    mglog.info('Make file hacking complete.')
 
    # Change directories
    currdir=os.getcwd()
    os.chdir(process_dir)
    # Record the change
    MADGRAPH_COMMAND_STACK += [ 'cd ${MGaMC_PROCESS_DIR}' ]
 
    # Check the run card
    my_MGC_instance.run_card_consistency_check()
    
 
    # For grid packs we also need to move the systematics program aside
    if grid_pack:
        original_systematics_program = None if 'systematics_program' not in my_MGC_instance.runCardDict else my_MGC_instance.runCardDict['systematics_program']
        my_MGC_instance.runCardDict['systematics_program'] = 'None'
        mglog.info('systematics set to NONE')
 
 
    
    
    
    # Check the param card
    code = check_PMG_updates(process_dir=os.getcwd())
    if requirePMGSettings and code!=0:
        raise RuntimeError('Settings are not compliant with PMG defaults! Please use do_PMG_updates function to get PMG default params.')
 
    # Build up the generate command
    # Use the new-style way of passing things: just --name, everything else in config
    command = [python,'bin/generate_events']
    if isNLO:
        command += ['--name='+MADGRAPH_RUN_NAME]
        mglog.info('Removing Cards/shower_card.dat to ensure we get parton level events only')
        try:
            os.unlink('Cards/shower_card.dat')
        except FileNotFoundError:
            mglog.info('Cannot find Cards/shower_card.dat.')
    else:
        command += [MADGRAPH_RUN_NAME]
    # Set the number of cores to be used
    setNCores(process_dir=os.getcwd(), Ncores=njobs)
    # Special handling for mode 1
    if mode==1:
        mglog.info('Setting up cluster running')
        my_MGC_instance.configCardDict['run_mode'] = 1
        
        if cluster_type=='pbs':
            mglog.info('Modifying bin/internal/cluster.py for PBS cluster running')
            os.system("sed -i \"s:text += prog:text += './'+prog:g\" bin/internal/cluster.py")
    elif mode==2:
        mglog.info('Setting up multi-core running on '+os.environ['ATHENA_CORE_NUMBER']+' cores')
    elif mode==0:
        mglog.info('Setting up serial generation.')
    
    # Writing cards to disk
    my_MGC_instance.write_configCard()
    my_MGC_instance.write_runCard(runArgs=runArgs)
 
    print_cards_from_dir(process_dir=my_MGC_instance.process_dir)
    
    
    generate_prep(process_dir=os.getcwd())
    generate = stack_subprocess(command,stdin=subprocess.PIPE, stderr=subprocess.PIPE if MADGRAPH_CATCH_ERRORS else None)
    (out,err) = generate.communicate()
    error_check(err,generate.returncode)
 
    # Get back to where we came from
    os.chdir(currdir)
    MADGRAPH_COMMAND_STACK += [ 'cd -' ]
 
    if grid_pack:
        # Name dictacted by https://twiki.cern.ch/twiki/bin/viewauth/AtlasProtected/PmgMcSoftware
        # MG version included for traceability (e.g. MG351 for version 3.5.1)
        energy = '%1.1f'%(beamEnergy*2./1000.)
        energy = energy.replace('.0','').replace('.','p')
        gridpack_name='mc_'+energy+'TeV.'+get_physics_short()+'.MG'+get_mg5_version().replace('.','')+'.GRID.tar.gz'
        mglog.info('Tidying up gridpack '+gridpack_name)
 
        # Return the setting for the systematics_program
        my_MGC_instance.runCardDict.update({'systematics_program':original_systematics_program})
        # Write out run Card Dictionary
        my_MGC_instance.write_runCard(runArgs=runArgs)
        
        if not isNLO:
            # At LO, no events are generated. That means we need to move the MS card aside and back.
            if LO_has_madspin:
                MADGRAPH_COMMAND_STACK += [f'mv {process_dir}/Cards/madspin_card.tmp.dat {process_dir}/Cards/madspin_card.dat']
                os.rename(f'{process_dir}/Cards/madspin_card.tmp.dat',f'{process_dir}/Cards/madspin_card.dat')
 
            
            MADGRAPH_COMMAND_STACK += ['cp '+glob.glob(process_dir+'/'+MADGRAPH_RUN_NAME+'_*gridpack.tar.gz')[0]+' '+gridpack_name]
            shutil.copy(glob.glob(process_dir+'/'+MADGRAPH_RUN_NAME+'_*gridpack.tar.gz')[0],gridpack_name)
 
            if gridpack_compile:
                MADGRAPH_COMMAND_STACK += ['mkdir tmp%i/'%os.getpid(),'cd tmp%i/'%os.getpid()]
                os.mkdir('tmp%i/'%os.getpid())
                os.chdir('tmp%i/'%os.getpid())
                mglog.info('untar gridpack')
                untar = stack_subprocess(['tar','xvzf',('../'+gridpack_name)])
                untar.wait()
                mglog.info('compile and clean up')
                MADGRAPH_COMMAND_STACK += ['cd madevent']
                os.chdir('madevent/')
                compilep = stack_subprocess(['./bin/compile'],stderr=subprocess.PIPE if MADGRAPH_CATCH_ERRORS else None)
                (out,err) = compilep.communicate()
                error_check(err,compilep.returncode)
                clean = stack_subprocess(['./bin/clean4grid'],stderr=subprocess.PIPE if MADGRAPH_CATCH_ERRORS else None)
                (out,err) = clean.communicate()
                error_check(err,clean.returncode)
                clean.wait()
                MADGRAPH_COMMAND_STACK += ['cd ..','rm ../'+gridpack_name]
                os.chdir('../')
                mglog.info('remove old tarball')
                os.unlink('../'+gridpack_name)
                mglog.info('Package up new tarball')
                tar = stack_subprocess(['tar','--exclude=SubProcesses/P*/G*/*_results.dat','--exclude=SubProcesses/P*/G*/*.log','--exclude=SubProcesses/P*/G*/*.txt','-cvsf','../'+gridpack_name,'.'])
                tar.wait()
                MADGRAPH_COMMAND_STACK += ['cd ..','rm -r tmp%i/'%os.getpid()]
                os.chdir('../')
                mglog.info('Remove temporary directory')
                shutil.rmtree('tmp%i/'%os.getpid())
                mglog.info('Tidying up complete!')
 
        else:
            my_MGC_instance.write_runCard(runArgs=runArgs)
            
            mglog.info('Package up process_dir')
            MADGRAPH_COMMAND_STACK += ['mv '+process_dir+' '+MADGRAPH_GRIDPACK_LOCATION]
            os.rename(process_dir,MADGRAPH_GRIDPACK_LOCATION)
            tar = stack_subprocess(['tar','--exclude=Events/*/*events*gz','--exclude=SubProcesses/P*/G*/log*txt','--exclude=SubProcesses/P*/G*/events.lhe*','--exclude=*/*.o','--exclude=*/*/*.o','--exclude=*/*/*/*.o','--exclude=*/*/*/*/*.o','-czf',gridpack_name,MADGRAPH_GRIDPACK_LOCATION])
            tar.wait()
            MADGRAPH_COMMAND_STACK += ['mv '+MADGRAPH_GRIDPACK_LOCATION+' '+process_dir]
            os.rename(MADGRAPH_GRIDPACK_LOCATION,process_dir)
 
        mglog.info('Gridpack sucessfully created, exiting the transform')
        if hasattr(runArgs,'outputTXTFile'):
            mglog.info('Touching output TXT (LHE) file for the transform')
            open(runArgs.outputTXTFile, 'w').close()
        from AthenaCommon.AppMgr import theApp
        theApp.finalize()
        theApp.exit()
 
    mglog.info('Finished at '+str(time.asctime()))
    return 0
 
 
def generate_from_gridpack(runArgs=None, extlhapath=None, gridpack_compile=None, requirePMGSettings=False):
    global my_MGC_instance # noqa: F824
 
    # Get of info out of the runArgs
    beamEnergy,random_seed = get_runArgs_info(runArgs)
 
    # Just in case
    my_MGC_instance.setup_path_protection()
 
    isNLO = my_MGC_instance.isNLO 
 
    setupFastjet(process_dir=MADGRAPH_GRIDPACK_LOCATION)
 
    # This is hard-coded as a part of MG5_aMC :'(
    gridpack_run_name = 'GridRun_'+str(random_seed)
 
    # Ensure that we only do madspin at the end
    if os.access(MADGRAPH_GRIDPACK_LOCATION+'/Cards/madspin_card.dat',os.R_OK):
        os.rename(MADGRAPH_GRIDPACK_LOCATION+'/Cards/madspin_card.dat',MADGRAPH_GRIDPACK_LOCATION+'/Cards/backup_madspin_card.dat')
        do_madspin=True
    else:
        do_madspin=False
 
    if get_reweight_card(process_dir=MADGRAPH_GRIDPACK_LOCATION) is not None:
        check_reweight_card(MADGRAPH_GRIDPACK_LOCATION)
 
    # Check the param card
    code = check_PMG_updates(process_dir=MADGRAPH_GRIDPACK_LOCATION)
    if requirePMGSettings and code!=0:
        raise RuntimeError('Settings are not compliant with PMG defaults! Please use do_PMG_updates function to get PMG default params.')
 
    # Modify run card, then print
    settings={'iseed':str(random_seed)}
    if not isNLO:
        settings['python_seed']=str(random_seed)
    my_MGC_instance.runCardDict.update(settings)
    
    mglog.info('Generating events from gridpack')
 
    # Ensure that things are set up normally
    if not os.path.exists(MADGRAPH_GRIDPACK_LOCATION):
        raise RuntimeError('Gridpack directory not found at '+MADGRAPH_GRIDPACK_LOCATION)
 
    nevents = my_MGC_instance.runCardDict['nevents']
    mglog.info('>>>> FOUND GRIDPACK <<<<  <- This will be used for generation')
    mglog.info('Generation of '+str(int(nevents))+' events will be performed using the supplied gridpack with random seed '+str(random_seed))
    mglog.info('Started generating events at '+str(time.asctime()))
 
    #Remove addmasses if it's there
    if os.access(MADGRAPH_GRIDPACK_LOCATION+'/bin/internal/addmasses.py',os.R_OK):
        os.remove(MADGRAPH_GRIDPACK_LOCATION+'/bin/internal/addmasses.py')
 
    currdir=os.getcwd()
 
    # Make sure we've set the number of processes appropriately
    setNCores(process_dir=MADGRAPH_GRIDPACK_LOCATION)
 
    # Run the consistency check, print some useful info
    ls_dir(currdir)
    ls_dir(MADGRAPH_GRIDPACK_LOCATION)
 
    # Update the run card according to consistency checks
    my_MGC_instance.run_card_consistency_check()
 
    # Now all done with updates, so print the cards with the final settings
    print_cards_from_dir(process_dir=MADGRAPH_GRIDPACK_LOCATION)
 
    if isNLO:
        #turn off systematics for gridpack generation and store settings for standalone run
        systematics_settings=None
        if my_MGC_instance.runCardDict.get('systematics_program',None) == 'systematics':
            if not my_MGC_instance.runCardDict.get('store_rwgt_info',None):
                raise RuntimeError('Trying to run NLO systematics but reweight info not stored')
            if 'systematics_arguments' in my_MGC_instance.runCardDict:
                systematics_settings=MadGraphControl.MadGraphSystematicsUtils.parse_systematics_arguments(my_MGC_instance.runCardDict['systematics_arguments'])
            else:
                systematics_settings={}
            mglog.info('Turning off systematics for now, running standalone later')
            
            my_MGC_instance.runCardDict['systematics_program'] = 'none'
 
    # Writing run card to disk
    my_MGC_instance.write_runCard(runArgs=runArgs)
    
    global MADGRAPH_COMMAND_STACK
    if not isNLO:
        
        if not os.access(MADGRAPH_GRIDPACK_LOCATION+'/bin/gridrun',os.R_OK):
            mglog.error('/bin/gridrun not found at '+MADGRAPH_GRIDPACK_LOCATION)
            raise RuntimeError('Could not find gridrun executable')
        else:
            mglog.info('Found '+MADGRAPH_GRIDPACK_LOCATION+'/bin/gridrun, starting generation.')
        generate_prep(MADGRAPH_GRIDPACK_LOCATION)
        granularity=1
        mglog.info("Now generating {} events with random seed {} and granularity {}".format(int(nevents),int(random_seed),granularity))
        # not sure whether this is needed but it is done in the old "run.sh" script
        new_ld_path=":".join([os.environ['LD_LIBRARY_PATH'],os.getcwd()+'/'+MADGRAPH_GRIDPACK_LOCATION+'/madevent/lib',os.getcwd()+'/'+MADGRAPH_GRIDPACK_LOCATION+'/HELAS/lib'])
        os.environ['LD_LIBRARY_PATH']=new_ld_path
        MADGRAPH_COMMAND_STACK+=["export LD_LIBRARY_PATH="+":".join(['${LD_LIBRARY_PATH}',new_ld_path])]
        generate = stack_subprocess([python,MADGRAPH_GRIDPACK_LOCATION+'/bin/gridrun',str(int(nevents)),str(int(random_seed)),str(granularity)],stdin=subprocess.PIPE,stderr=subprocess.PIPE if MADGRAPH_CATCH_ERRORS else None)        
        (out,err) = generate.communicate()
        error_check(err,generate.returncode)
        gp_events=MADGRAPH_GRIDPACK_LOCATION+"/Events/GridRun_{}/unweighted_events.lhe.gz".format(int(random_seed))
        if not os.path.exists(gp_events):
            mglog.error('Error in gp generation, did not find events at '+gp_events)
 
        # add reweighting, which is not run automatically from LO GPs
        reweight_card=get_reweight_card(MADGRAPH_GRIDPACK_LOCATION)
        if reweight_card is not None:
            pythonpath_backup=os.environ['PYTHONPATH']
            # workaround as madevent crashes when path to mg in PYTHONPATH
            os.environ['PYTHONPATH']=':'.join([p for p in pythonpath_backup.split(':') if 'madgraph5amc' not in p])
            add_reweighting('GridRun_{}'.format(int(random_seed)))
            os.environ['PYTHONPATH']=pythonpath_backup
 
        shutil.move(gp_events,'events.lhe.gz')
 
    else:
        
        if not os.access(MADGRAPH_GRIDPACK_LOCATION+'/bin/generate_events',os.R_OK):
            raise RuntimeError('Could not find generate_events executable at '+MADGRAPH_GRIDPACK_LOCATION)
        else:
            mglog.info('Found '+MADGRAPH_GRIDPACK_LOCATION+'/bin/generate_events, starting generation.')
 
        ls_dir(MADGRAPH_GRIDPACK_LOCATION+'/Events/')
        if os.access(MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name, os.F_OK):
            mglog.info('Removing '+MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+' directory from gridpack generation')
            MADGRAPH_COMMAND_STACK += ['rm -rf '+MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name]
            shutil.rmtree(MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name)
 
        # Delete events generated when setting up MadSpin during gridpack generation
        if os.access(MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+'_decayed_1', os.F_OK):
            mglog.info('Removing '+MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+'_decayed_1 directory from gridpack generation')
            MADGRAPH_COMMAND_STACK += ['rm -rf '+MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+'_decayed_1']
            shutil.rmtree(MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+'_decayed_1')
 
        ls_dir(MADGRAPH_GRIDPACK_LOCATION+'/Events/')
 
        if not gridpack_compile:
            mglog.info('Copying make_opts from Template')
            shutil.copy(os.environ['MADPATH']+'/Template/LO/Source/make_opts',MADGRAPH_GRIDPACK_LOCATION+'/Source/')
 
            generate_prep(MADGRAPH_GRIDPACK_LOCATION)
            generate = stack_subprocess([python,MADGRAPH_GRIDPACK_LOCATION+'/bin/generate_events','--parton','--nocompile','--only_generation','-f','--name='+gridpack_run_name],stdin=subprocess.PIPE,stderr=subprocess.PIPE if MADGRAPH_CATCH_ERRORS else None)
            (out,err) = generate.communicate()
            error_check(err,generate.returncode)
        else:
            mglog.info('Allowing recompilation of gridpack')
            if os.path.islink(MADGRAPH_GRIDPACK_LOCATION+'/lib/libLHAPDF.a'):
                mglog.info('Unlinking '+MADGRAPH_GRIDPACK_LOCATION+'/lib/libLHAPDF.a')
                os.unlink(MADGRAPH_GRIDPACK_LOCATION+'/lib/libLHAPDF.a')
 
            generate_prep(MADGRAPH_GRIDPACK_LOCATION)
            generate = stack_subprocess([python,MADGRAPH_GRIDPACK_LOCATION+'/bin/generate_events','--parton','--only_generation','-f','--name='+gridpack_run_name],stdin=subprocess.PIPE,stderr=subprocess.PIPE if MADGRAPH_CATCH_ERRORS else None)
            (out,err) = generate.communicate()
            error_check(err,generate.returncode)
    if isNLO and systematics_settings is not None:
        # run systematics
        mglog.info('Running systematics standalone')
        systematics_path=MADGRAPH_GRIDPACK_LOCATION+'/bin/internal/systematics.py'
        events_location=MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+'/events.lhe.gz'
        syst_cmd=[python,systematics_path]+[events_location]*2+["--"+k+"="+systematics_settings[k] for k in systematics_settings]
        mglog.info('running: '+' '.join(syst_cmd))
        systematics = stack_subprocess(syst_cmd)
        systematics.wait()
 
 
    # See if MG5 did the job for us already
    if not os.access('events.lhe.gz',os.R_OK):
        mglog.info('Copying generated events to '+currdir)
        if not os.path.exists(MADGRAPH_GRIDPACK_LOCATION+'Events/'+gridpack_run_name):
            shutil.copy(MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+'/events.lhe.gz','events.lhe.gz')
    else:
        mglog.info('Events were already in place')
 
    ls_dir(currdir)
 
    mglog.info('Moving generated events to be in correct format for arrange_output().')
    mglog.info('Unzipping generated events.')
    unzip = stack_subprocess(['gunzip','-f','events.lhe.gz'])
    unzip.wait()
 
    mglog.info('Moving file over to '+MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+'/unweighted_events.lhe')
    mkdir = stack_subprocess(['mkdir','-p',(MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name)])
    mkdir.wait()
    shutil.move('events.lhe',MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+'/unweighted_events.lhe')
 
    mglog.info('Re-zipping into dataset name '+MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+'/unweighted_events.lhe.gz')
    rezip = stack_subprocess(['gzip',MADGRAPH_GRIDPACK_LOCATION+'/Events/'+gridpack_run_name+'/unweighted_events.lhe'])
    rezip.wait()
 
    os.chdir(currdir)
 
    # Now consider MadSpin:
    if do_madspin:
        # Move card back
        os.rename(MADGRAPH_GRIDPACK_LOCATION+'/Cards/backup_madspin_card.dat',MADGRAPH_GRIDPACK_LOCATION+'/Cards/madspin_card.dat')
        mglog.info('Decaying with MadSpin.')
        add_madspin(process_dir=MADGRAPH_GRIDPACK_LOCATION)
 
    mglog.info('Finished at '+str(time.asctime()))
 
    return 0
 
 
def setupFastjet(process_dir=None):
    global my_MGC_instance # noqa: F824
    
    isNLO = my_MGC_instance.isNLO 
 
    mglog.info('Path to fastjet install dir: '+os.environ['FASTJETPATH'])
    fastjetconfig = os.environ['FASTJETPATH']+'/bin/fastjet-config'
 
    mglog.info('fastjet-config --version:      '+str(subprocess.Popen([fastjetconfig, '--version'],stdout = subprocess.PIPE).stdout.read().strip()))
    mglog.info('fastjet-config --prefix:       '+str(subprocess.Popen([fastjetconfig, '--prefix'],stdout = subprocess.PIPE).stdout.read().strip()))
 
    if not isNLO:
        config_card=process_dir+'/Cards/me5_configuration.txt'
    else:
        config_card=process_dir+'/Cards/amcatnlo_configuration.txt'
 
    oldcard = open(config_card,'r')
    newcard = open(config_card+'.tmp','w')
 
    for line in oldcard:
        if 'fastjet = ' in line:
            newcard.write('fastjet = '+fastjetconfig+'\n')
            mglog.info('Setting fastjet = '+fastjetconfig+' in '+config_card)
        else:
            newcard.write(line)
    oldcard.close()
    newcard.close()
    shutil.move(config_card+'.tmp',config_card)
 
    return
 
def get_runArgs_info(runArgs):
    """This is a temporary function that returns the beam energy and random seed from runArgs, 
    as more functions move to the MGControl class this will not be necessary
    """
    global my_MGC_instance # noqa: F824
    #check if the function has already been called
    if my_MGC_instance.beamEnergy == 0: #if beamEnergy is 0, it hasn't been set yet so we will call the class function.
        my_MGC_instance.get_runArgs_info(runArgs)
    #return the beam energy and the random seeed
    return my_MGC_instance.beamEnergy, my_MGC_instance.random_seed
 
 
def setupLHAPDF(process_dir=None, extlhapath=None, allow_links=True):
    global my_MGC_instance # noqa: F824
 
    isNLO = my_MGC_instance.isNLO 
 
    origLHAPATH=os.environ['LHAPATH']
    origLHAPDF_DATA_PATH=os.environ['LHAPDF_DATA_PATH']
 
    LHAPATH,LHADATAPATH=get_LHAPDF_PATHS()
 
    pdfname=''
    pdfid=-999
 
    
    mydict= my_MGC_instance.runCardDict
    if mydict["pdlabel"].replace("'","") == 'lhapdf':
        #Make local LHAPDF dir
        mglog.info('creating local LHAPDF dir: MGC_LHAPDF/')
        if os.path.islink('MGC_LHAPDF/'):
            os.unlink('MGC_LHAPDF/')
        elif os.path.isdir('MGC_LHAPDF/'):
            shutil.rmtree('MGC_LHAPDF/')
 
        newMGCLHA='MGC_LHAPDF/'
 
        mkdir = subprocess.Popen(['mkdir','-p',newMGCLHA])
        mkdir.wait()
 
        pdfs_used=[ int(x) for x in mydict['lhaid'].replace(' ',',').split(',') ]
        # included systematics pdfs here
        if 'sys_pdf' in mydict:
            sys_pdf=mydict['sys_pdf'].replace('&&',' ').split()
            for s in sys_pdf:
                if s.isdigit():
                    idx=int(s)
                    if idx>1000: # the sys_pdf syntax is such that small numbers are used to specify the subpdf index
                        pdfs_used.append(idx)
                else:
                    pdfs_used.append(s)
        if 'systematics_arguments' in mydict:
            systematics_arguments=MadGraphControl.MadGraphSystematicsUtils.parse_systematics_arguments(mydict['systematics_arguments'])
            if 'pdf' in systematics_arguments:
                sys_pdf=systematics_arguments['pdf'].replace(',',' ').replace('@',' ').split()
                for s in sys_pdf:
                    if s.isdigit():
                        idx=int(s)
                        if idx>1000: # the sys_pdf syntax is such that small numbers are used to specify the subpdf index
                            pdfs_used.append(idx)
                    else:
                        pdfs_used.append(s)
        for pdf in pdfs_used:
            if isinstance(pdf,str) and (pdf.lower()=='errorset' or pdf.lower()=='central'):
                continue
            # new function to get both lhapdf id and name
            pdfid,pdfname=get_lhapdf_id_and_name(pdf)
            mglog.info("Found LHAPDF ID="+str(pdfid)+", name="+pdfname)
 
            if not os.path.exists(newMGCLHA+pdfname) and not os.path.lexists(newMGCLHA+pdfname):
                if not os.path.exists(LHADATAPATH+'/'+pdfname):
                    mglog.warning('PDF not installed at '+LHADATAPATH+'/'+pdfname)
                if allow_links:
                    mglog.info('linking '+LHADATAPATH+'/'+pdfname+' --> '+newMGCLHA+pdfname)
                    os.symlink(LHADATAPATH+'/'+pdfname,newMGCLHA+pdfname)
                else:
                    mglog.info('copying '+LHADATAPATH+'/'+pdfname+' --> '+newMGCLHA+pdfname)
                    shutil.copytree(LHADATAPATH+'/'+pdfname,newMGCLHA+pdfname)
 
        if allow_links:
            mglog.info('linking '+LHADATAPATH+'/pdfsets.index --> '+newMGCLHA+'pdfsets.index')
            os.symlink(LHADATAPATH+'/pdfsets.index',newMGCLHA+'pdfsets.index')
 
            atlasLHADATAPATH=LHADATAPATH.replace('sft.cern.ch/lcg/external/lhapdfsets/current','atlas.cern.ch/repo/sw/Generators/lhapdfsets/current')
            mglog.info('linking '+atlasLHADATAPATH+'/lhapdf.conf --> '+newMGCLHA+'lhapdf.conf')
            os.symlink(atlasLHADATAPATH+'/lhapdf.conf',newMGCLHA+'lhapdf.conf')
        else:
            mglog.info('copying '+LHADATAPATH+'/pdfsets.index --> '+newMGCLHA+'pdfsets.index')
            shutil.copy2(LHADATAPATH+'/pdfsets.index',newMGCLHA+'pdfsets.index')
 
            atlasLHADATAPATH=LHADATAPATH.replace('sft.cern.ch/lcg/external/lhapdfsets/current','atlas.cern.ch/repo/sw/Generators/lhapdfsets/current')
            mglog.info('copying '+atlasLHADATAPATH+'/lhapdf.conf -->'+newMGCLHA+'lhapdf.conf')
            shutil.copy2(atlasLHADATAPATH+'/lhapdf.conf',newMGCLHA+'lhapdf.conf')
 
 
        LHADATAPATH=os.getcwd()+'/MGC_LHAPDF'
 
    else:
        mglog.info('Not using LHAPDF')
        return (LHAPATH,origLHAPATH,origLHAPDF_DATA_PATH)
 
 
    if isNLO:
        os.environ['LHAPDF_DATA_PATH']=LHADATAPATH
 
    mglog.info('Path to LHAPDF install dir: '+LHAPATH)
    mglog.info('Path to LHAPDF data dir: '+LHADATAPATH)
    if not os.path.isdir(LHADATAPATH):
        raise RuntimeError('LHAPDF data dir not accesible: '+LHADATAPATH)
    if not os.path.isdir(LHAPATH):
        raise RuntimeError('LHAPDF path dir not accesible: '+LHAPATH)
 
    # Dealing with LHAPDF
    if extlhapath:
        lhapdfconfig=extlhapath
        if not os.access(lhapdfconfig,os.X_OK):
            raise RuntimeError('Failed to find valid external lhapdf-config at '+lhapdfconfig)
        LHADATAPATH=subprocess.Popen([lhapdfconfig, '--datadir'],stdout = subprocess.PIPE).stdout.read().strip()
        mglog.info('Changing LHAPDF_DATA_PATH to '+LHADATAPATH)
        os.environ['LHAPDF_DATA_PATH']=LHADATAPATH
    else:
        getlhaconfig = subprocess.Popen(['get_files','-data','lhapdf-config'])
        getlhaconfig.wait()
        #Get custom lhapdf-config
        if not os.access(os.getcwd()+'/lhapdf-config',os.X_OK):
            mglog.error('Failed to get lhapdf-config from MadGraphControl')
            return 1
        lhapdfconfig = os.getcwd()+'/lhapdf-config'
 
    mglog.info('lhapdf-config --version:      '+str(subprocess.Popen([lhapdfconfig, '--version'],stdout = subprocess.PIPE).stdout.read().strip()))
    mglog.info('lhapdf-config --prefix:       '+str(subprocess.Popen([lhapdfconfig, '--prefix'],stdout = subprocess.PIPE).stdout.read().strip()))
    mglog.info('lhapdf-config --libdir:       '+str(subprocess.Popen([lhapdfconfig, '--libdir'],stdout = subprocess.PIPE).stdout.read().strip()))
    mglog.info('lhapdf-config --datadir:      '+str(subprocess.Popen([lhapdfconfig, '--datadir'],stdout = subprocess.PIPE).stdout.read().strip()))
    mglog.info('lhapdf-config --pdfsets-path: '+str(subprocess.Popen([lhapdfconfig, '--pdfsets-path'],stdout = subprocess.PIPE).stdout.read().strip()))
 
    
    my_MGC_instance.configCardDict.update({'lhapdf':lhapdfconfig,'lhapdf_py3':lhapdfconfig})
    
    mglog.info('Creating links for LHAPDF')
    if os.path.islink(process_dir+'/lib/PDFsets'):
        os.unlink(process_dir+'/lib/PDFsets')
    elif os.path.isdir(process_dir+'/lib/PDFsets'):
        shutil.rmtree(process_dir+'/lib/PDFsets')
    if allow_links:
        os.symlink(LHADATAPATH,process_dir+'/lib/PDFsets')
    else:
        shutil.copytree(LHADATAPATH,process_dir+'/lib/PDFsets')
    mglog.info('Available PDFs are:')
    mglog.info( sorted( [ x for x in os.listdir(process_dir+'/lib/PDFsets') if ".tar.gz" not in x ] ) )
 
    global MADGRAPH_COMMAND_STACK
    MADGRAPH_COMMAND_STACK += [ '# Copy the LHAPDF files locally' ]
    MADGRAPH_COMMAND_STACK += [ 'cp -r '+os.getcwd()+'/MGC_LHAPDF .' ]
    MADGRAPH_COMMAND_STACK += [ 'cp -r '+process_dir+'/lib/PDFsets ${MGaMC_PROCESS_DIR}/lib/' ]
 
    return (LHAPATH,origLHAPATH,origLHAPDF_DATA_PATH)
 
 
# Function to set the number of cores and the running mode in the run card
def setNCores(process_dir, Ncores=None):
    global my_MGC_instance # noqa: F824
    
    my_Ncores = Ncores
    my_runMode = 2 if 'ATHENA_CORE_NUMBER' in os.environ else 0
    if Ncores is None and 'ATHENA_CORE_NUMBER' in os.environ and int(os.environ['ATHENA_CORE_NUMBER'])>0:
        my_Ncores = int(os.environ['ATHENA_CORE_NUMBER'])
        my_runMode = 2
    if my_Ncores is None:
        mglog.info('Setting up for serial run')
        my_Ncores = 1
    my_MGC_instance.configCardDict.update({'nb_core':my_Ncores,'run_mode':my_runMode,'automatic_html_opening':'False'})
 
 
 
 
 
 
def get_mg5_executable():
    madpath=os.environ['MADPATH']
    if not os.access(madpath+'/bin/mg5_aMC',os.R_OK):
        raise RuntimeError('mg5_aMC executable not found in '+madpath)
    return madpath+'/bin/mg5_aMC'
 
 
def add_lifetimes(process_dir,threshold=None):
    """ Add lifetimes to the generated LHE file.  Should be
    called after generate_events is called.
    """
 
    me_exec=get_mg5_executable()
 
    if len(glob.glob(process_dir+'/Events/*'))<1:
        mglog.error('Process dir '+process_dir+' does not contain events?')
    run = glob.glob(process_dir+'/Events/*')[0].split('/')[-1]
 
    # Note : This slightly clunky implementation is needed for the time being
    # See : https://answers.launchpad.net/mg5amcnlo/+question/267904
 
    tof_c = open('time_of_flight_exec_card','w')
    tof_c.write('launch '+process_dir+''' -i
add_time_of_flight '''+run+((' --threshold='+str(threshold)) if threshold is not None else ''))
    tof_c.close()
 
    mglog.info('Started adding time of flight info '+str(time.asctime()))
 
    generate = stack_subprocess([python,me_exec,'time_of_flight_exec_card'],stdin=subprocess.PIPE,stderr=subprocess.PIPE if MADGRAPH_CATCH_ERRORS else None)
    (out,err) = generate.communicate()
    error_check(err,generate.returncode)
 
    mglog.info('Finished adding time of flight information at '+str(time.asctime()))
 
    # Re-zip the file if needed
    lhe_gz = glob.glob(process_dir+'/Events/*/*lhe.gz')[0]
    if not os.access(lhe_gz,os.R_OK):
        mglog.info('LHE file needs to be zipped')
        lhe = glob.glob(process_dir+'/Events/*/*lhe.gz')[0]
        rezip = stack_subprocess(['gzip',lhe])
        rezip.wait()
        mglog.info('Zipped')
    else:
        mglog.info('LHE file zipped by MadGraph automatically. Nothing to do')
 
    return True
 
 
def add_madspin(madspin_card=None,process_dir=MADGRAPH_GRIDPACK_LOCATION):
    """ Run madspin on the generated LHE file.  Should be
    run when you have inputGeneratorFile set.
    Only requires a simplified process with the same model that you are
    interested in (needed to set up a process directory for MG5_aMC)
    """
 
    me_exec=get_mg5_executable()
 
    if madspin_card is not None:
        shutil.copyfile(madspin_card,process_dir+'/Cards/madspin_card.dat')
 
    if len(glob.glob(process_dir+'/Events/*'))<1:
        mglog.error('Process dir '+process_dir+' does not contain events?')
    proc_dir_list = glob.glob(process_dir+'/Events/*')
    run=None
    for adir in proc_dir_list:
        if 'GridRun_' in adir:
            run=adir.split('/')[-1]
            break
    else:
        run=proc_dir_list[0].split('/')[-1]
 
    # Note : This slightly clunky implementation is needed for the time being
    # See : https://answers.launchpad.net/mg5amcnlo/+question/267904
 
    ms_c = open('madspin_exec_card','w')
    ms_c.write('launch '+process_dir+''' -i
decay_events '''+run)
    ms_c.close()
 
    mglog.info('Started running madspin at '+str(time.asctime()))
 
    generate = stack_subprocess([python,me_exec,'madspin_exec_card'],stdin=subprocess.PIPE,stderr=subprocess.PIPE if MADGRAPH_CATCH_ERRORS else None)
    (out,err) = generate.communicate()
    error_check(err,generate.returncode)
    if len(glob.glob(process_dir+'/Events/'+run+'_decayed_*/')) == 0:
        mglog.error('No '+process_dir+'/Events/'+run+'_decayed_*/ can be found')
        raise RuntimeError('Problem while running MadSpin')
 
    mglog.info('Finished running madspin at '+str(time.asctime()))
 
    # Re-zip the file if needed
    lhe_gz = glob.glob(process_dir+'/Events/*/*lhe.gz')[0]
    if not os.access(lhe_gz,os.R_OK):
        mglog.info('LHE file needs to be zipped')
        lhe = glob.glob(process_dir+'/Events/*/*lhe.gz')[0]
        rezip = stack_subprocess(['gzip',lhe])
        rezip.wait()
        mglog.info('Zipped')
    else:
        mglog.info('LHE file zipped by MadGraph automatically. Nothing to do')
 
 
def madspin_on_lhe(input_LHE,madspin_card,runArgs=None,keep_original=False):
    """ Run MadSpin on an input LHE file. Takes the process
    from the LHE file, so you don't need to have a process directory
    set up in advance. Runs MadSpin and packs the LHE file up appropriately
    Needs runArgs for the file handling"""
    if not os.access(input_LHE,os.R_OK):
        raise RuntimeError('Could not find LHE file '+input_LHE)
    if not os.access(madspin_card,os.R_OK):
        raise RuntimeError('Could not find input MadSpin card '+madspin_card)
    if keep_original:
        shutil.copy(input_LHE,input_LHE+'.original')
        mglog.info('Put backup copy of LHE file at '+input_LHE+'.original')
    # Start writing the card for execution
    madspin_exec_card = open('madspin_exec_card','w')
    madspin_exec_card.write('import '+input_LHE+'\n')
    # Based on the original card
    input_madspin_card = open(madspin_card,'r')
    has_launch = False
    for l in input_madspin_card.readlines():
        commands = l.split('#')[0].split()
        # Skip import of a file name that isn't our file
        if len(commands)>1 and 'import'==commands[0] and not 'model'==commands[1]:
            continue
        # Check for a launch command
        if len(commands)>0 and 'launch' == commands[0]:
            has_launch = True
        madspin_exec_card.write(l.strip()+'\n')
    if not has_launch:
        madspin_exec_card.write('launch\n')
    madspin_exec_card.close()
    input_madspin_card.close()
    # Now get the madspin executable
    madpath=os.environ['MADPATH']
    if not os.access(madpath+'/MadSpin/madspin',os.R_OK):
        raise RuntimeError('madspin executable not found in '+madpath)
    mglog.info('Starting madspin at '+str(time.asctime()))
    generate = stack_subprocess([python,madpath+'/MadSpin/madspin','madspin_exec_card'],stdin=subprocess.PIPE,stderr=subprocess.PIPE if MADGRAPH_CATCH_ERRORS else None)
    (out,err) = generate.communicate()
    error_check(err,generate.returncode)
    mglog.info('Done with madspin at '+str(time.asctime()))
    # Should now have a re-zipped LHE file
    # We now have to do a shortened version of arrange_output below
    # Clean up in case a link or file was already there
    if os.path.exists(os.getcwd()+'/events.lhe'):
        os.remove(os.getcwd()+'/events.lhe')
 
    mglog.info('Unzipping generated events.')
    unzip = stack_subprocess(['gunzip','-f',input_LHE+'.gz'])
    unzip.wait()
 
    mglog.info('Putting a copy in place for the transform.')
    mod_output = open(os.getcwd()+'/events.lhe','w')
 
    #Removing empty lines in LHE
    nEmpty=0
    with open(input_LHE,'r') as fileobject:
        for line in fileobject:
            if line.strip():
                mod_output.write(line)
            else:
                nEmpty=nEmpty+1
    mod_output.close()
 
    mglog.info('Removed '+str(nEmpty)+' empty lines from LHEF')
 
    # Actually move over the dataset - this first part is horrible...
    if runArgs is None:
        raise RuntimeError('Must provide runArgs to madspin_on_lhe')
 
    outputDS = runArgs.outputTXTFile if hasattr(runArgs,'outputTXTFile') else 'tmp_LHE_events.tar.gz'
 
    mglog.info('Moving file over to '+outputDS.split('.tar.gz')[0]+'.events')
    shutil.move(os.getcwd()+'/events.lhe',outputDS.split('.tar.gz')[0]+'.events')
 
    mglog.info('Re-zipping into dataset name '+outputDS)
    rezip = stack_subprocess(['tar','cvzf',outputDS,outputDS.split('.tar.gz')[0]+'.events'])
    rezip.wait()
 
    # shortening the outputDS in the case of an output TXT file
    if hasattr(runArgs,'outputTXTFile') and runArgs.outputTXTFile is not None:
        outputDS = outputDS.split('.TXT')[0]
    # Do some fixing up for them
    if runArgs is not None:
        mglog.debug('Setting inputGenerator file to '+outputDS)
        runArgs.inputGeneratorFile=outputDS
 
 
def arrange_output(process_dir=MADGRAPH_GRIDPACK_LOCATION,lhe_version=None,saveProcDir=False,runArgs=None,fixEventWeightsForBridgeMode=False):
 
    # NLO is not *really* the question here, we need to know if we should look for weighted or
    #  unweighted events in the output directory.  MadSpin (above) only seems to give weighted
    #  results for now?
    if len(glob.glob(os.path.join(process_dir, 'Events','*')))<1:
        mglog.error('Process dir '+process_dir+' does not contain events?')
    proc_dir_list = glob.glob(os.path.join(process_dir, 'Events', '*'))
    this_run_name=None
    # looping over possible directories to find the right one
    for adir in proc_dir_list:
        if 'decayed' in adir:# skipping '*decayed*' directories produced by MadSpin, will be picked later if they exist
            continue
        else:
            if 'GridRun_' in adir:
                this_run_name=adir
                break # GridRun_* directories have priority
            elif os.path.join(process_dir, 'Events',MADGRAPH_RUN_NAME) in adir:
                this_run_name=adir
    if not os.access(this_run_name,os.R_OK):
        raise RuntimeError('Unable to locate run directory')
 
    hasUnweighted = os.access(this_run_name+'/unweighted_events.lhe.gz',os.R_OK)
 
    hasRunMadSpin=False
    madspinDirs=sorted(glob.glob(this_run_name+'_decayed_*/'))
    if len(madspinDirs):
        hasRunMadSpin=True
    if hasRunMadSpin and not hasUnweighted:
        # check again:
        hasUnweighted = os.access(madspinDirs[-1]+'/unweighted_events.lhe.gz',os.R_OK)
 
    global MADGRAPH_COMMAND_STACK
    if hasRunMadSpin:
        if len(madspinDirs):
            if hasUnweighted:
                # so this is a bit of a mess now...
                # if madspin is run from an NLO grid pack the correct lhe events are at both
                #      madevent/Events/run_01/unweighted_events.lhe.gz
                # and  madevent/Events/run_01_decayed_1/events.lhe.gz
                # so there are unweighted events but not in the madspinDir...
                if os.path.exists(madspinDirs[-1]+'/unweighted_events.lhe.gz'):
                    MADGRAPH_COMMAND_STACK += ['mv '+madspinDirs[-1]+'/unweighted_events.lhe.gz'+' '+this_run_name+'/unweighted_events.lhe.gz']
                    shutil.move(madspinDirs[-1]+'/unweighted_events.lhe.gz',this_run_name+'/unweighted_events.lhe.gz')
                    mglog.info('Moving MadSpin events from '+madspinDirs[-1]+'/unweighted_events.lhe.gz to '+this_run_name+'/unweighted_events.lhe.gz')
                elif os.path.exists(madspinDirs[-1]+'/events.lhe.gz'):
                    MADGRAPH_COMMAND_STACK += ['mv '+madspinDirs[-1]+'/events.lhe.gz'+' '+this_run_name+'/unweighted_events.lhe.gz']
                    shutil.move(madspinDirs[-1]+'/events.lhe.gz',this_run_name+'/unweighted_events.lhe.gz')
                    mglog.info('Moving MadSpin events from '+madspinDirs[-1]+'/events.lhe.gz to '+this_run_name+'/unweighted_events.lhe.gz')
                else:
                    raise RuntimeError('MadSpin was run but can\'t find files :(')
 
            else:
                MADGRAPH_COMMAND_STACK += ['mv '+madspinDirs[-1]+'/events.lhe.gz '+this_run_name+'/events.lhe.gz']
                shutil.move(madspinDirs[-1]+'/events.lhe.gz',this_run_name+'/events.lhe.gz')
                mglog.info('Moving MadSpin events from '+madspinDirs[-1]+'/events.lhe.gz to '+this_run_name+'/events.lhe.gz')
 
        else:
            mglog.error('MadSpin was run but can\'t find output folder '+(this_run_name+'_decayed_1/'))
            raise RuntimeError('MadSpin was run but can\'t find output folder '+(this_run_name+'_decayed_1/'))
 
        if fixEventWeightsForBridgeMode:
            mglog.info("Fixing event weights after MadSpin... initial checks.")
 
            # get the cross section from the undecayed LHE file
            spinmodenone=False
            MGnumevents=-1
            MGintweight=-1
 
            if hasUnweighted:
                eventsfilename="unweighted_events"
            else:
                eventsfilename="events"
            unzip = stack_subprocess(['gunzip','-f',this_run_name+'/%s.lhe.gz' % eventsfilename])
            unzip.wait()
 
            for line in open(process_dir+'/Events/'+MADGRAPH_RUN_NAME+'/%s.lhe'%eventsfilename):
                if "Number of Events" in line:
                    sline=line.split()
                    MGnumevents=int(sline[-1])
                elif "Integrated weight (pb)" in line:
                    sline=line.split()
                    MGintweight=float(sline[-1])
                elif "set spinmode none" in line:
                    spinmodenone=True
                elif "</header>" in line:
                    break
 
            if spinmodenone and MGnumevents>0 and MGintweight>0:
                mglog.info("Fixing event weights after MadSpin... modifying LHE file.")
                newlhe=open(this_run_name+'/%s_fixXS.lhe'%eventsfilename,'w')
                initlinecount=0
                eventlinecount=0
                inInit=False
                inEvent=False
 
                # new default for MG 2.6.1+ (https://its.cern.ch/jira/browse/AGENE-1725)
                # but verified from LHE below.
                event_norm_setting="average" 
 
                for line in open(this_run_name+'/%s.lhe'%eventsfilename):
 
                    newline=line
                    if "<init>" in line:                         
                        inInit=True
                        initlinecount=0
                    elif "</init>" in line:
                        inInit=False
                    elif inInit and initlinecount==0:
                        initlinecount=1
                        # check event_norm setting in LHE file, deteremines how Pythia interprets event weights
                        sline=line.split()
                        if abs(int(sline[-2])) == 3:
                            event_norm_setting="sum"
                        elif abs(int(sline[-2])) == 4:
                            event_norm_setting="average"
                    elif inInit and initlinecount==1:
                        sline=line.split()
                        # update the global XS info
                        relunc=float(sline[1])/float(sline[0])
                        sline[0]=str(MGintweight)                
                        sline[1]=str(float(sline[0])*relunc)     
                        if event_norm_setting=="sum":
                            sline[2]=str(MGintweight/MGnumevents)
                        elif event_norm_setting=="average":
                            sline[2]=str(MGintweight)            
                        newline=' '.join(sline)
                        newline+="\n"
                        initlinecount+=1
                    elif inInit and initlinecount>1:
                        initlinecount+=1
                    elif "<event>" in line:                      
                        inEvent=True
                        eventlinecount=0
                    elif "</event>" in line:
                        inEvent=False
                    elif inEvent and eventlinecount==0:
                        sline=line.split()
                        # next change the per-event weights
                        if event_norm_setting=="sum":
                            sline[2]=str(MGintweight/MGnumevents)
                        elif event_norm_setting=="average":
                            sline[2]=str(MGintweight)            
                        newline=' '.join(sline)
                        newline+="\n"
                        eventlinecount+=1
                    newlhe.write(newline)
                newlhe.close()
 
                mglog.info("Fixing event weights after MadSpin... cleaning up.")
                shutil.copyfile(this_run_name+'/%s.lhe' % eventsfilename,
                                this_run_name+'/%s_badXS.lhe' % eventsfilename)
 
                shutil.move(this_run_name+'/%s_fixXS.lhe' % eventsfilename,
                            this_run_name+'/%s.lhe' % eventsfilename)
 
                rezip = stack_subprocess(['gzip',this_run_name+'/%s.lhe' % eventsfilename])
                rezip.wait()
 
                rezip = stack_subprocess(['gzip',this_run_name+'/%s_badXS.lhe' % eventsfilename])
                rezip.wait()
 
    # Clean up in case a link or file was already there
    if os.path.exists(os.getcwd()+'/events.lhe'):
        os.remove(os.getcwd()+'/events.lhe')
 
    mglog.info('Unzipping generated events.')
    if hasUnweighted:
        unzip = stack_subprocess(['gunzip','-f',this_run_name+'/unweighted_events.lhe.gz'])
        unzip.wait()
    else:
        unzip = stack_subprocess(['gunzip','-f',this_run_name+'/events.lhe.gz'])
        unzip.wait()
 
    mglog.info('Putting a copy in place for the transform.')
    if hasUnweighted:
        orig_input = this_run_name+'/unweighted_events.lhe'
        mod_output = open(os.getcwd()+'/events.lhe','w')
    else:
        orig_input = this_run_name+'/events.lhe'
        mod_output = open(os.getcwd()+'/events.lhe','w')
 
    #Removing empty lines and bad comments in LHE
    #and check for existence of weights
    initrwgt=None
    nEmpty=0
    lhe_weights=[]
    with open(orig_input,'r') as fileobject:
        for line in fileobject:
            if line.strip():
                # search for bad characters (neccessary until at least MG5 2.8.1)
                newline=line
                if '#' not in newline:
                    newline=newline
                elif '>' not in newline[ newline.find('#'): ]:
                    newline=newline
                else:
                    mglog.info('Found bad LHE line with an XML mark in a comment: "'+newline.strip()+'"')
                    newline=newline[:newline.find('#')]+'#'+ (newline[newline.find('#'):].replace('>','-'))
                # check for weightnames that should exist, simplify nominal weight names
                if initrwgt is False:
                    pass
                elif "</initrwgt>" in newline:
                    initrwgt=False
                elif "<initrwgt>" in newline:
                    initrwgt=True
                elif initrwgt is not None:
                    newline=newline.replace('_DYNSCALE-1','')
                    if '</weight>' in newline:
                        iend=newline.find('</weight>')
                        istart=newline[:iend].rfind('>')
                        lhe_weights+=[newline[istart+1:iend].strip()]
                mod_output.write(newline)           
            else:
                nEmpty=nEmpty+1
    mod_output.close()
    mglog.info('Removed '+str(nEmpty)+' empty lines from LHEF')
    
    mglog.info("The following  "+str(len(lhe_weights))+" weights have been written to the LHE file: "+",".join(lhe_weights))
    expected_weights=get_expected_reweight_names(get_reweight_card(process_dir))
    expected_weights+=get_expected_systematic_names(MADGRAPH_PDFSETTING)
    mglog.info("Checking whether the following expected weights are in LHE file: "+",".join(expected_weights))
    for w in expected_weights:
        if w not in lhe_weights:
            raise RuntimeError("Did not find expected weight "+w+" in lhe file. Did the reweight or systematics module crash?")
    mglog.info("Found all required weights!")
    
    if lhe_version:
        mod_output2 = open(os.getcwd()+'/events.lhe','r')
        test=mod_output2.readline()
        if 'version="' in test:
            mglog.info('Applying LHE version hack')
            final_file = open(os.getcwd()+'/events.lhe.copy','w')
            final_file.write('<LesHouchesEvents version="%i.0">\n'%lhe_version)
            shutil.copyfileobj(mod_output2, final_file)
            final_file.close()
            shutil.copy(os.getcwd()+'/events.lhe.copy',os.getcwd()+'/events.lhe')
            # Clean up after ourselves
            os.remove(os.getcwd()+'/events.lhe.copy')
        mod_output2.close()
 
    # Actually move over the dataset
    if runArgs is None:
        raise RuntimeError('Must provide runArgs to arrange_output')
 
    if hasattr(runArgs,'outputTXTFile'):
        outputDS = runArgs.outputTXTFile
    else:
        outputDS = 'tmp_LHE_events.tar.gz'
 
    mglog.info('Moving file over to '+outputDS.split('.tar.gz')[0]+'.events')
 
    shutil.move(os.getcwd()+'/events.lhe',outputDS.split('.tar.gz')[0]+'.events')
 
    mglog.info('Re-zipping into dataset name '+outputDS)
    rezip = stack_subprocess(['tar','cvzf',outputDS,outputDS.split('.tar.gz')[0]+'.events'])
    rezip.wait()
 
    if not saveProcDir:
        mglog.info('Removing the process directory')
        shutil.rmtree(process_dir,ignore_errors=True)
 
        if os.path.isdir('MGC_LHAPDF/'):
            shutil.rmtree('MGC_LHAPDF/',ignore_errors=True)
 
    # shortening the outputDS in the case of an output TXT file
    if hasattr(runArgs,'outputTXTFile') and runArgs.outputTXTFile is not None:
        outputDS = outputDS.split('.TXT')[0]
    # Do some fixing up for them
    if runArgs is not None:
        mglog.debug('Setting inputGenerator file to '+outputDS)
        runArgs.inputGeneratorFile=outputDS
 
    mglog.info('All done with output arranging!')
    return outputDS
 
def get_expected_reweight_names(reweight_card_loc):
    if reweight_card_loc is None:
        return []
    names=[]
    f_rw=open(reweight_card_loc)
    for line in f_rw:
        if 'launch' not in line:
            continue
        match=re.match(r'launch.*--rwgt_info\s*=\s*(\S+).*',line.strip())
        if len(match.groups())!=1:
            raise RuntimeError('Unexpected format of reweight card in line'+line)
        else:
            names+=[match.group(1)]
    f_rw.close()
    return names
 
def get_expected_systematic_names(syst_setting):
    names=[]
    if syst_setting is None or 'central_pdf' not in syst_setting:
        mglog.warning("Systematics have not been defined via base fragment or 'MADGRAPH_PDFSETTING', cannot check for expected weights")
        return []
    if 'pdf_variations' in syst_setting and isinstance(syst_setting['pdf_variations'],list):
        names+=[MadGraphControl.MadGraphSystematicsUtils.SYSTEMATICS_WEIGHT_INFO%{'mur':1.0,'muf':1.0,'pdf':syst_setting['central_pdf']}]
        for pdf in syst_setting['pdf_variations']:
            names+=[MadGraphControl.MadGraphSystematicsUtils.SYSTEMATICS_WEIGHT_INFO%{'mur':1.0,'muf':1.0,'pdf':pdf+1}]
    if 'alternative_pdfs' in syst_setting and isinstance(syst_setting['alternative_pdfs'],list):
        for pdf in syst_setting['alternative_pdfs']:
            names+=[MadGraphControl.MadGraphSystematicsUtils.SYSTEMATICS_WEIGHT_INFO%{'mur':1.0,'muf':1.0,'pdf':pdf}]
    if 'scale_variations' in syst_setting and isinstance(syst_setting['scale_variations'],list):
        for mur in syst_setting['scale_variations']:
            for muf in syst_setting['scale_variations']:
                names+=[MadGraphControl.MadGraphSystematicsUtils.SYSTEMATICS_WEIGHT_INFO%{'mur':mur,'muf':muf,'pdf':syst_setting['central_pdf']}]
    return names
 
def setup_bias_module(bias_module,process_dir):
    run_card = process_dir+'/Cards/run_card.dat'
    if isinstance(bias_module,tuple):
        mglog.info('Using bias module '+bias_module[0])
        the_run_card = open(run_card,'r')
        for line in the_run_card:
            if 'bias_module' in line and not bias_module[0] in line:
                raise RuntimeError('You need to add the bias module '+bias_module[0]+' to the run card to actually run it')
        the_run_card.close()
        if len(bias_module)!=3:
            raise RuntimeError('Please give a 3-tuple of strings containing bias module name, bias module, and makefile. Alternatively, give path to bias module tarball.')
        bias_module_newpath=process_dir+'/Source/BIAS/'+bias_module[0]
        os.makedirs(bias_module_newpath)
        bias_module_file=open(bias_module_newpath+'/'+bias_module[0]+'.f','w')
        bias_module_file.write(bias_module[1])
        bias_module_file.close()
        bias_module_make_file=open(bias_module_newpath+'/Makefile','w')
        bias_module_make_file.write(bias_module[2])
        bias_module_make_file.close()
    else:
        mglog.info('Using bias module '+bias_module)
        bias_module_name=bias_module.split('/')[-1].replace('.gz','')
        bias_module_name=bias_module_name.replace('.tar','')
        the_run_card = open(run_card,'r')
        for line in the_run_card:
            if 'bias_module' in line and bias_module_name not in line:
                raise RuntimeError('You need to add the bias module '+bias_module_name+' to the run card to actually run it')
        the_run_card.close()
 
        if os.path.exists(bias_module+'.tar.gz'):
            bias_module_path=bias_module+'.tar.gz'
        elif os.path.exists(bias_module+'.gz'):
            bias_module_path=bias_module+'.gz'
        elif os.path.exists(bias_module):
            bias_module_path=bias_module
        else:
            mglog.error('Did not find bias module '+bias_module+' , this path should point to folder or tarball.  Alternatively give a tuple of strings containing module name, module, and makefile')
            return 1
        bias_module_newpath=process_dir+'/Source/BIAS/'+bias_module_path.split('/')[-1]
        mglog.info('Copying bias module into place: '+bias_module_newpath)
        shutil.copy(bias_module_path,bias_module_newpath)
        mglog.info('Unpacking bias module')
        if bias_module_newpath.endswith('.tar.gz'):
            untar = stack_subprocess(['tar','xvzf',bias_module_newpath,'--directory='+process_dir+'/Source/BIAS/'])
            untar.wait()
        elif bias_module_path.endswith('.gz'):
            gunzip = stack_subprocess(['gunzip',bias_module_newpath])
            gunzip.wait()
 
 
def get_reweight_card(process_dir=MADGRAPH_GRIDPACK_LOCATION):
    if os.access(process_dir+'/Cards/reweight_card.dat',os.R_OK):
        return process_dir+'/Cards/reweight_card.dat'
    return None
 
 
def check_reweight_card(process_dir=MADGRAPH_GRIDPACK_LOCATION):
    reweight_card=get_reweight_card(process_dir=process_dir)
    shutil.move(reweight_card,reweight_card+'.old')
    oldcard = open(reweight_card+'.old','r')
    newcard = open(reweight_card,'w')
    changed = False
    info_expression=r'launch.*--rwgt_info\s*=\s*(\S+).*'
    name_expression=info_expression.replace('info','name')
    goodname_expression=r'^[A-Za-z0-9_\-.]+$'
    for line in oldcard:
        # we are only interested in the 'launch' line
        if not line.strip().startswith('launch') :
            newcard.write(line)
        else:
            rwgt_name_match=re.match(name_expression,line.strip())
            rwgt_info_match=re.match(info_expression,line.strip())
            if rwgt_name_match is None and rwgt_info_match is None:
                raise RuntimeError('Every reweighting should have a --rwgt_info (see https://cp3.irmp.ucl.ac.be/projects/madgraph/wiki/Reweight), please update your reweight_card accordingly. Line to fix: '+line)
            for match in [rwgt_info_match,rwgt_name_match]:
                if match is None:
                    continue
                if len(match.groups())!=1:
                    raise RuntimeError('Unexpected format of reweight card in line: '+line)
                if not re.match(goodname_expression,match.group(1)):
                    raise RuntimeError('No special character in reweighting info/name, only allowing '+goodname_expression)
            if rwgt_info_match is not None:
                newcard.write(line)
            elif rwgt_name_match is not None:
                newcard.write(line.strip()+' --rwgt_info={0}\n'.format(rwgt_name_match.group(1)))
                changed=True
    if changed:
        mglog.info('Updated reweight_card')
    newcard.close()
    oldcard.close()
 
 
def update_lhe_file(lhe_file_old,param_card_old=None,lhe_file_new=None,masses={},delete_old_lhe=True):
    """Build a new LHE file from an old one and an updated param card.
    The masses of some particles can be changed via the masses dictionary.  No particles that appear in the events
    may have their masses changed.
    If the param card is provided, the decay block in the LHE file will be replaced with the one in the param card.
    By default, the old LHE file is removed.
    If None is provided as a new LHE file name, the new file will replace the old one."""
    # If we want to just use a temp file, then put in a little temp holder
    lhe_file_new_tmp = lhe_file_new if lhe_file_new is not None else lhe_file_old+'.tmp'
    # Make sure the LHE file is there
    if not os.access(lhe_file_old,os.R_OK):
        raise RuntimeError('Could not access old LHE file at '+str(lhe_file_old)+'. Please check the file location.')
    # Grab the old param card
    if param_card_old is not None:
        paramcard = subprocess.Popen(['get_files','-data',param_card_old])
        paramcard.wait()
        if not os.access(param_card_old,os.R_OK):
            raise RuntimeError('Could not get param card '+param_card_old)
    # Don't overwrite old param cards
    if os.access(lhe_file_new_tmp,os.R_OK):
        raise RuntimeError('Old file at'+str(lhe_file_new_tmp)+' in the current directory. Dont want to clobber it. Please move it first.')
 
    newlhe = open(lhe_file_new_tmp,'w')
    blockName = None
    decayEdit = False
    eventRead = False
    particles_in_events = []
    # Decay block ends with </slha>
 
    with open(lhe_file_old,'r') as fileobject:
        for line in fileobject:
            if decayEdit and '</slha>' not in line:
                continue
            if decayEdit and '</slha>' in line:
                decayEdit = False
            if line.strip().upper().startswith('BLOCK') or line.strip().upper().startswith('DECAY')\
                        and len(line.strip().split()) > 1:
                pos = 0 if line.strip().startswith('DECAY') else 1
                blockName = line.strip().upper().split()[pos]
 
            akey = None
            if blockName != 'DECAY' and len(line.strip().split()) > 0:
                akey = line.strip().split()[0]
            elif blockName == 'DECAY' and len(line.strip().split()) > 1:
                akey = line.strip().split()[1]
 
            # Replace the masses with those in the dictionary
            if akey is not None and blockName == 'MASS'  and akey in masses:
                newlhe.write('   '+akey+'    '+str(masses[akey])+'  # \n')
                mglog.info('   '+akey+'    '+str(masses[akey])+'  #')
                decayEdit = False
                continue
 
            # Replace the entire decay section of the LHE file with the one from the param card
            if blockName == 'DECAY' and param_card_old is not None:
                # We are now reading the decay blocks!  Take them from the param card
                oldparam = open(param_card_old,'r')
                newDecays = False
                for old_line in oldparam.readlines():
                    newBlockName = None
                    if old_line.strip().upper().startswith('DECAY') and len(old_line.strip().split()) > 1:
                        newBlockName = line.strip().upper().split()[pos]
                    if newDecays:
                        newlhe.write(old_line)
                    elif newBlockName == 'DECAY':
                        newDecays = True
                        newlhe.write(old_line)
                oldparam.close()
                # Done adding the decays
                decayEdit = True
                blockName = None
                continue
 
            # Keep a record of the particles that are in the events
            if not eventRead and '<event>' in line:
                eventRead = True
            if eventRead:
                if len(line.split())==11:
                    aparticle = line.split()[0]
                    if aparticle not in particles_in_events:
                        particles_in_events += [aparticle]
 
            # Otherwise write the line again
            newlhe.write(line)
 
    # Check that none of the particles that we were setting the masses of appear in the LHE events
    for akey in masses:
        if akey in particles_in_events:
            mglog.error('Attempted to change mass of a particle that was in an LHE event!  This is not allowed!')
            return -1
 
    # Close up and return
    newlhe.close()
 
    # Move the new file to the old file location
    if lhe_file_new is None:
        os.remove(lhe_file_old)
        shutil.move(lhe_file_new_tmp,lhe_file_old)
        lhe_file_new_tmp = lhe_file_old
    # Delete the old file if requested
    elif delete_old_lhe:
        os.remove(lhe_file_old)
 
    return lhe_file_new_tmp
 
 
 
def print_cards_from_dir(process_dir=MADGRAPH_GRIDPACK_LOCATION):
    card_dir=process_dir+'/Cards/'
    print_cards(proc_card=card_dir+'proc_card_mg5.dat',run_card=card_dir+'run_card.dat',param_card=card_dir+'param_card.dat',\
                madspin_card=card_dir+'madspin_card.dat',reweight_card=card_dir+'reweight_card.dat',warn_on_missing=False)
 
 
def print_cards(proc_card='proc_card_mg5.dat',run_card=None,param_card=None,madspin_card=None,reweight_card=None,warn_on_missing=True):
    if os.access(proc_card,os.R_OK):
        mglog.info("proc_card:")
        procCard = subprocess.Popen(['cat',proc_card])
        procCard.wait()
    elif warn_on_missing:
        mglog.warning('No proc_card: '+proc_card+' found')
 
    if run_card is not None and os.access(run_card,os.R_OK):
        mglog.info("run_card:")
        runCard = subprocess.Popen(['cat',run_card])
        runCard.wait()
    elif run_card is not None and warn_on_missing:
        mglog.warning('No run_card: '+run_card+' found')
    else:
        mglog.info('Default run card in use')
 
    if param_card is not None and os.access(param_card,os.R_OK):
        mglog.info("param_card:")
        paramCard = subprocess.Popen(['cat',param_card])
        paramCard.wait()
    elif param_card is not None and warn_on_missing:
        mglog.warning('No param_card: '+param_card+' found')
    else:
        mglog.info('Default param card in use')
 
    if madspin_card is not None and os.access(madspin_card,os.R_OK):
        mglog.info("madspin_card:")
        madspinCard = subprocess.Popen(['cat',madspin_card])
        madspinCard.wait()
    elif madspin_card is not None and warn_on_missing:
        mglog.warning('No madspin_card: '+madspin_card+' found')
    else:
        mglog.info('No madspin card in use')
 
    if reweight_card is not None and os.access(reweight_card,os.R_OK):
        mglog.info("reweight_card:")
        madspinCard = subprocess.Popen(['cat',reweight_card])
        madspinCard.wait()
    elif reweight_card is not None and warn_on_missing:
        mglog.warning('No reweight_card: '+reweight_card+' found')
    else:
        mglog.info('No reweight card in use')
 
 
def is_gen_from_gridpack():
    """ Simple function for checking if there is a grid pack.
    Relies on the specific location of the unpacked gridpack (madevent)
    which is here set as a global variable. The gridpack is untarred by
    the transform (Gen_tf.py) and no sign is sent to the job itself
    that there is a gridpack in use except the file's existence"""
    if os.access(MADGRAPH_GRIDPACK_LOCATION,os.R_OK):
        mglog.info('Located input grid pack area')
        return True
    return False
 
 
 
def modify_run_card(run_card_input=None,run_card_backup=None,process_dir=MADGRAPH_GRIDPACK_LOCATION,runArgs=None,settings={},skipBaseFragment=False):
    """Build a new run_card.dat from an existing one.
    This function can get a fresh runcard from DATAPATH or start from the process directory.
    Settings is a dictionary of keys (no spaces needed) and values to replace.
    """
 
    global my_MGC_instance # noqa: F824
    # my_MGC_instance.getRunCardDict(card_loc=process_dir+'/Cards/run_card.dat')
    my_MGC_instance.runCardDict.update(settings)
    # my_MGC_instance.write_runCard()
    
    # Operate on lower case settings, and choose the capitalization MG5 has as the default (or all lower case)
    settings_lower = {}
    for s in list(settings.keys()):
        settings_lower[s.lower()] = settings[s]
 
    # Check for the default run card location
    if run_card_input is None:
        run_card_input=get_default_runcard(process_dir)
    elif run_card_input is not None and not os.access(run_card_input,os.R_OK):
        runcard = subprocess.Popen(['get_files','-data',run_card_input])
        runcard.wait()
        if not os.access(run_card_input,os.R_OK):
            raise RuntimeError('Could not get run card '+run_card_input)
 
    # guess NLO
    isNLO = my_MGC_instance.isNLO 
    # add gobal PDF and scale uncertainty config to extras, except PDF or weights for syscal config are explictly set
    if not skipBaseFragment:
        setup_pdf_and_systematic_weights(MADGRAPH_PDFSETTING,settings_lower,isNLO)
 
    # Get some info out of the runArgs
    if runArgs is not None:
        beamEnergy,rand_seed = get_runArgs_info(runArgs)
        if 'iseed' not in settings_lower:
            settings_lower['iseed']=rand_seed
        if not isNLO and 'python_seed' not in settings_lower:
            settings_lower['python_seed']=rand_seed
        if 'beamenergy' in settings_lower:
            mglog.warning('Do not set beam energy in MG settings. The variables are ebeam1 and ebeam2. Will use your setting of '+str(settings_lower['beamenergy']))
            beamEnergy=settings_lower['beamenergy']
            settings_lower.pop('beamenergy')
        if 'ebeam1' not in settings_lower:
            settings_lower['ebeam1']=beamEnergy
        if 'ebeam2' not in settings_lower:
            settings_lower['ebeam2']=beamEnergy
    # Make sure nevents is an integer
    if 'nevents' in settings_lower:
        settings_lower['nevents'] = int(settings_lower['nevents'])
        
    # Normalise custom_fcts early so the rewritten run_card uses the full path
    if 'custom_fcts' in settings_lower and settings_lower['custom_fcts']:
        raw_name = str(settings_lower['custom_fcts']).split()[0]
        # Determine jobConfig directory
        if runArgs is not None and hasattr(runArgs, 'jobConfig'):
            cfgdir = runArgs.jobConfig[0] if isinstance(runArgs.jobConfig, (list, tuple)) else runArgs.jobConfig
            # Build full path and make absolute
            full_path = os.path.join(cfgdir, raw_name)
            settings_lower['custom_fcts'] = os.path.abspath(full_path)
            print(f"Using custom function(s), specified in custom_fcts with path: {settings_lower['custom_fcts']}")
        else:
            # For internal tests, where jobConfig is not set
            settings_lower['custom_fcts'] = os.path.abspath(raw_name)
 
    mglog.info('Modifying run card located at '+run_card_input)
    if run_card_backup is not None:
        mglog.info('Keeping backup of original run card at '+run_card_backup)
        run_card_old = run_card_backup
    else:
        run_card_old = run_card_input+'.old_to_be_deleted'
    mglog.debug('Modifying runcard settings: '+str(settings_lower))
    if os.path.isfile(run_card_old):
        os.unlink(run_card_old) # delete old backup
    os.rename(run_card_input, run_card_old) # change name of original card
 
    oldCard = open(run_card_old, 'r')
    newCard = open(process_dir+'/Cards/run_card.dat', 'w')
    used_settings = []
    for line in iter(oldCard):
        if not line.strip().startswith('#'): # line commented out
            command = line.split('!', 1)[0]
            comment = line.split('!', 1)[1] if '!' in line else ''
            if '=' in command:
                setting = command.split('=')[-1] #.strip()
                stripped_setting = setting.strip()
                oldValue = '='.join(command.split('=')[:-1])
                if stripped_setting.lower() in settings_lower:
                    # if setting set to 'None' it will be removed from run_card
                    if settings_lower[stripped_setting.lower()] is None:
                        line=''
                        mglog.info('Removing '+stripped_setting+'.')
                        used_settings += [ stripped_setting.lower() ]
                    else:
                        if stripped_setting.lower() == 'custom_fcts':
                            # Overwrite completely to avoid duplicating in custom_fcts, else MadGraph will crash
                            line = ' '+str(settings_lower[stripped_setting.lower()])+' = '+setting
                            if comment != '':
                                line += '  !'+comment
                        else:
                            line = oldValue.replace(oldValue.strip(), str(settings_lower[stripped_setting.lower()]))+'='+setting
                            if comment != '':
                                line += '  !' + comment
                        mglog.info('Setting '+stripped_setting+' = '+str(settings_lower[stripped_setting.lower()]))
                        used_settings += [ stripped_setting.lower() ]
        newCard.write(line.strip()+'\n')
    
    # Check whether mcatnlo_delta is applied to setup pythia8 path
    if 'mcatnlo_delta' in settings_lower:       
        if settings_lower['mcatnlo_delta'] == 'True':
            modify_config_card(process_dir=process_dir,settings={'pythia8_path':os.getenv("PY8PATH")})
 
        
    # Clean up unused options
    for asetting in settings_lower:
        if asetting in used_settings:
            continue
        if settings_lower[asetting] is None:
            continue
        mglog.info('Option '+asetting+' was not in the default run_card (normal for hidden options).  Adding by hand a setting to '+str(settings_lower[asetting]) )
        newCard.write( ' '+str(settings_lower[asetting])+'   = '+str(asetting)+'\n')
    # close files
    oldCard.close()
    newCard.close()
    mglog.info('Finished modification of run card.')
    if run_card_backup is None:
        os.unlink(run_card_old)
 
 
def modify_config_card(config_card_backup=None,process_dir=MADGRAPH_GRIDPACK_LOCATION,settings={},set_commented=True):
    """Build a new configuration from an existing one.
    This function can get a fresh runcard from DATAPATH or start from the process directory.
    Settings is a dictionary of keys (no spaces needed) and values to replace.
    """
    global my_MGC_instance # noqa: F824
    
    my_MGC_instance.configCardDict.update(settings)
    # Check for the default config card location
    config_card = my_MGC_instance.config_path 
 
    # The format is similar to the run card, but backwards
    mglog.info('Modifying config card located at '+config_card)
    if config_card_backup is not None:
        mglog.info('Keeping backup of original config card at '+config_card_backup)
        config_card_old = config_card_backup
    else:
        config_card_old = config_card+'.old_to_be_deleted'
    mglog.debug('Modifying config card settings: '+str(settings))
    if os.path.isfile(config_card_old):
        os.unlink(config_card_old) # delete old backup
    os.rename(config_card, config_card_old) # change name of original card
 
    oldCard = open(config_card_old, 'r')
    newCard = open(config_card, 'w')
    used_settings = []
    for line in iter(oldCard):
        lmod = line if set_commented else line.split('#')[0]
        if '=' in lmod:
            modified = False
            for setting in settings:
                if setting not in lmod:
                    continue
                # Assume we hit
                mglog.info('Setting '+setting.strip()+' to '+str(settings[setting]))
                newCard.write(' '+str(setting.strip())+' = '+str(settings[setting])+'\n')
                used_settings += [ setting.strip() ]
                modified = True
                break
            if modified:
                continue
        newCard.write(line)
 
    # Clean up unused options
    for asetting in settings:
        if asetting in used_settings:
            continue
        if settings[asetting] is None:
            continue
        mglog.warning('Option '+asetting+' was not in the default config card.  Adding by hand a setting to '+str(settings[asetting]) )
        newCard.write(' '+str(asetting)+' = '+str(settings[asetting])+'\n')
    # close files
    oldCard.close()
    newCard.close()
    mglog.info('Finished modification of config card.')
    if config_card_backup is None:
        os.unlink(config_card_old)
 
 
 
def get_cluster_type():
    global my_MGC_instance # noqa: F824
    if 'cluster_type' in my_MGC_instance.configCardDict:
        return my_MGC_instance.configCardDict['cluster_type']
    else:
        return None
    
 
 
 
def add_reweighting(run_name,reweight_card=None,process_dir=MADGRAPH_GRIDPACK_LOCATION):
    mglog.info('Running reweighting module on existing events')
    if reweight_card is not None:
        mglog.info('Copying new reweight card from '+reweight_card)
        shutil.move(reweight_card,process_dir+'/Cards/reweight_card.dat')
    reweight_cmd='{}/bin/madevent reweight {} -f'.format(process_dir,run_name)
    reweight = stack_subprocess([python]+reweight_cmd.split(),stdin=subprocess.PIPE,stderr=subprocess.PIPE if MADGRAPH_CATCH_ERRORS else None)
    (out,err) = reweight.communicate()
    error_check(err,reweight.returncode)
    mglog.info('Finished reweighting')
 
 
 
 
def ls_dir(directory):
    mglog.info('For your information, ls of '+directory+':')
    mglog.info( sorted( os.listdir( directory ) ) )
 
# Final import of some code used in these functions
import MadGraphControl.MadGraphSystematicsUtils
 
# To be removed once we moved past MG5 3.3.1
def fix_fks_makefile(process_dir):
    makefile_fks=process_dir+'/SubProcesses/makefile_fks_dir'
    mglog.info('Fixing '+makefile_fks)
    shutil.move(makefile_fks,makefile_fks+'_orig')
    fin=open(makefile_fks+'_orig')
    fout=open(makefile_fks,'w')
    edit=False
    for line in fin:
        if 'FKSParams.mod' in line:
            fout.write(line.replace('FKSParams.mod','FKSParams.o'))
            edit=True
        elif edit and 'driver_mintFO' in line:
            fout.write('driver_mintFO.o: weight_lines.o mint_module.o FKSParams.o\n')
        elif edit and 'genps_fks.o' in line:
            fout.write('genps_fks.o: mint_module.o FKSParams.o\n')
        elif edit and 'test_soft_col_limits' in line:
            fout.write(line)
            fout.write('madfks_plot.o: mint_module.o\n')
            fout.write('cluster.o: weight_lines.o\n')
        else:
            fout.write(line)
    fin.close()
    fout.close()
 
#==================================================================================
# this function is called during build_run card to check the consistency of user-provided arguments with the inlude
# and throw errors, warnings, or corrects the input as is appropriate
def setup_pdf_and_systematic_weights(the_base_fragment,extras,isNLO):
    
    global my_MGC_instance # noqa: F824
    
    
    list = []
    tmp_dict = {}
    for k in extras:
        k_clean=k.lower().replace("'",'').replace('"','')
        if k_clean!=k and k_clean in systematics_run_card_options(isNLO):
            list.append(k)
            tmp_dict[k_clean] = extras[k]
    # Removing systematics with incorrect formatting 
    for o in list:
        if o in extras:
            extras.pop(o,None)
    # Adding cleaned up systematics into dictionary
    extras.update(tmp_dict)
    
    if my_MGC_instance.base_fragment_setup_check(the_base_fragment,extras,isNLO):
        return
    # if something is set that contradicts the base fragment: bad!
    for o in systematics_run_card_options(isNLO):
        if o in extras:
            mglog.warning('You tried to set "'+str(o)+'" by hand, but you should trust the base fragment with the following options: '+', '.join(systematics_run_card_options(isNLO)))
            mglog.info('We will update "'+str(o))
 
    new_settings=get_pdf_and_systematic_settings(the_base_fragment,isNLO)
    
    user_set_extras=dict(extras)
    for s in new_settings:
        if s is not None:
            extras[s]=new_settings[s]
 
    
    mglog.info('PDF and scale settings were set as follows:')
    for p in systematics_run_card_options(isNLO):
        user_set='not set'
        if p in user_set_extras:
            user_set=str(user_set_extras[p])
        new_value='not set'
        if p in extras:
            new_value=str(extras[p])   
        mglog.info('MadGraphUtils set '+str(p)+' to "'+new_value+'", was set to "'+user_set+'"')