validateAlignments.py

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#!/usr/bin/env python
#test execute: export CMSSW_BASE=/tmp/CMSSW && ./validateAlignments.py -c defaultCRAFTValidation.ini,test.ini -n -N test
from __future__ import print_function
import os
import sys
import optparse
import datetime
import shutil
import fnmatch

import six
import Alignment.OfflineValidation.TkAlAllInOneTool.configTemplates \
    as configTemplates
import Alignment.OfflineValidation.TkAlAllInOneTool.crabWrapper as crabWrapper
from Alignment.OfflineValidation.TkAlAllInOneTool.TkAlExceptions \
    import AllInOneError
from Alignment.OfflineValidation.TkAlAllInOneTool.helperFunctions \
    import replaceByMap, getCommandOutput2, addIndex
from Alignment.OfflineValidation.TkAlAllInOneTool.betterConfigParser \
    import BetterConfigParser
from Alignment.OfflineValidation.TkAlAllInOneTool.alignment import Alignment

from Alignment.OfflineValidation.TkAlAllInOneTool.genericValidation \
    import GenericValidation, ParallelValidation, ValidationWithComparison, ValidationWithPlots
from Alignment.OfflineValidation.TkAlAllInOneTool.geometryComparison \
    import GeometryComparison
from Alignment.OfflineValidation.TkAlAllInOneTool.offlineValidation \
    import OfflineValidation, OfflineValidationDQM
from Alignment.OfflineValidation.TkAlAllInOneTool.monteCarloValidation \
    import MonteCarloValidation
from Alignment.OfflineValidation.TkAlAllInOneTool.trackSplittingValidation \
    import TrackSplittingValidation
from Alignment.OfflineValidation.TkAlAllInOneTool.zMuMuValidation \
    import ZMuMuValidation
from Alignment.OfflineValidation.TkAlAllInOneTool.primaryVertexValidation \
    import PrimaryVertexValidation
from Alignment.OfflineValidation.TkAlAllInOneTool.preexistingValidation \
    import *
from Alignment.OfflineValidation.TkAlAllInOneTool.plottingOptions \
    import PlottingOptions
import Alignment.OfflineValidation.TkAlAllInOneTool.globalDictionaries \
    as globalDictionaries
from Alignment.OfflineValidation.TkAlAllInOneTool.overlapValidation \
    import OverlapValidation 

####################--- Classes ---############################
class ParallelMergeJob(object):
    
    def __init__(self, _name, _path, _dependency):
        self.name=_name
        self.path=_path
        self.dependencies=_dependency
    def addDependency(self,dependency):
        if isinstance(dependency,list):
            self.dependencies.extend(dependency)
        else:
            self.dependencies.append(dependency)
    def runJob(self, config):
        repMap = {
        "commands": config.getGeneral()["jobmode"].split(",")[1],
        "jobName": self.name,
        "logDir": config.getGeneral()["logdir"],
        "script": self.path,
        "bsub": "/afs/cern.ch/cms/caf/scripts/cmsbsub",
        "conditions": '"' + " && ".join(["ended(" + jobId + ")" for jobId in self.dependencies]) + '"'
        }
        return getCommandOutput2("%(bsub)s %(commands)s "
            "-J %(jobName)s "
            "-o %(logDir)s/%(jobName)s.stdout "
            "-e %(logDir)s/%(jobName)s.stderr "
            "-w %(conditions)s "
            "%(script)s"%repMap)

class ValidationJob(object):

    # these count the jobs of different varieties that are being run
    crabCount = 0
    interactCount = 0
    batchCount = 0
    batchJobIds = []
    jobCount = 0

    def __init__( self, validation, config, options ):
        self.JobId=[]
        if validation[1] == "":
            # intermediate syntax
            valString = validation[0].split( "->" )[0]
            alignments = validation[0].split( "->" )[1]
            # force user to use the normal syntax
            if "->" in validation[0]:
                msg = ("Instead of using the intermediate syntax\n'"
                       +valString.strip()+"-> "+alignments.strip()
                       +":'\nyou have to use the now fully supported syntax \n'"
                       +valString.strip()+": "
                       +alignments.strip()+"'.")
                raise AllInOneError(msg)
        else:
            valString = validation[0]
            alignments = validation[1]
        valString = valString.split()
        self.__valType = valString[0]
        self.__valName = valString[1]
        self.__commandLineOptions = options
        self.__config = config
        self.__preexisting = ("preexisting" in self.__valType)
        if self.__valType[0] == "*":
            self.__valType = self.__valType[1:]
            self.__preexisting = True

        # workaround for intermediate parallel version
        if self.__valType == "offlineParallel":
            print ("offlineParallel and offline are now the same.  To run an offline parallel validation,\n"
                   "just set parallelJobs to something > 1.  There is no reason to call it offlineParallel anymore.")
            self.__valType = "offline"            
        section = self.__valType + ":" + self.__valName
        if not self.__config.has_section( section ):
            raise AllInOneError("Validation '%s' of type '%s' is requested in"
                                  " '[validation]' section, but is not defined."
                                  "\nYou have to add a '[%s]' section."
                                  %( self.__valName, self.__valType, section ))
        self.validation = self.__getValidation( self.__valType, self.__valName,
                                                alignments, self.__config,
                                                options )

    def __getValidation( self, valType, name, alignments, config, options ):
        if valType == "compare":
            alignmentsList = alignments.split( "," )
            firstAlignList = alignmentsList[0].split()
            firstAlignName = firstAlignList[0].strip()
            if firstAlignName == "IDEAL":
                raise AllInOneError("'IDEAL' has to be the second (reference)"
                                      " alignment in 'compare <val_name>: "
                                      "<alignment> <reference>'.")
            if len( firstAlignList ) > 1:
                firstRun = firstAlignList[1]
            else:
                raise AllInOneError("Have to provide a run number for geometry comparison")
            firstAlign = Alignment( firstAlignName, self.__config, firstRun )
            firstAlignName = firstAlign.name
            secondAlignList = alignmentsList[1].split()
            secondAlignName = secondAlignList[0].strip()
            if secondAlignName == "IDEAL":
                secondAlign = secondAlignName
            else:
                if len( secondAlignList ) > 1:
                    secondRun = secondAlignList[1]
                else:
                    raise AllInOneError("Have to provide a run number for geometry comparison")
                secondAlign = Alignment( secondAlignName, self.__config,
                                         secondRun )
                secondAlignName = secondAlign.name
                
            validation = GeometryComparison( name, firstAlign, secondAlign,
                                             self.__config,
                                             self.__commandLineOptions.getImages)
        elif valType == "offline":
            validation = OfflineValidation( name, 
                Alignment( alignments.strip(), self.__config ), self.__config )
        elif valType == "preexistingoffline":
            validation = PreexistingOfflineValidation(name, self.__config)
        elif valType == "offlineDQM":
            validation = OfflineValidationDQM( name, 
                Alignment( alignments.strip(), self.__config ), self.__config )
        elif valType == "mcValidate":
            validation = MonteCarloValidation( name, 
                Alignment( alignments.strip(), self.__config ), self.__config )
        elif valType == "preexistingmcValidate":
            validation = PreexistingMonteCarloValidation(name, self.__config)
        elif valType == "split":
            validation = TrackSplittingValidation( name, 
                Alignment( alignments.strip(), self.__config ), self.__config )
        elif valType == "preexistingsplit":
            validation = PreexistingTrackSplittingValidation(name, self.__config)
        elif valType == "zmumu":
            validation = ZMuMuValidation( name, 
                Alignment( alignments.strip(), self.__config ), self.__config )
        elif valType == "primaryvertex":
            validation = PrimaryVertexValidation( name, 
                Alignment( alignments.strip(), self.__config ), self.__config )
        elif valType == "preexistingprimaryvertex":
            validation = PreexistingPrimaryVertexValidation(name, self.__config)
        elif valType == "overlap":
            validation = OverlapValidation( name,
                Alignment( alignments.strip(), self.__config ), self.__config )
        else:
            raise AllInOneError("Unknown validation mode '%s'"%valType)

        return validation

    def __createJob( self, jobMode, outpath ):
        """This private method creates the needed files for the validation job.
           """
        self.validation.createConfiguration( outpath )
        if self.__preexisting:
            return
        self.__scripts = sum([addIndex(script, self.validation.NJobs) for script in self.validation.createScript( outpath )], [])
        if jobMode.split( ',' )[0] == "crab":
            self.validation.createCrabCfg( outpath )
        return None

    def createJob(self):
        """This is the method called to create the job files."""
        self.__createJob( self.validation.jobmode,
                          os.path.abspath( self.__commandLineOptions.Name) )

    def runJob( self ):
        if self.__preexisting:
            if self.validation.jobid:
                self.batchJobIds.append(self.validation.jobid)
            log = ">             " + self.validation.name + " is already validated."
            print(log)
            return log
        else:
            if self.validation.jobid:
                print("jobid {} will be ignored, since the validation {} is not preexisting".format(self.validation.jobid, self.validation.name))

        general = self.__config.getGeneral()
        log = ""
        for script in self.__scripts:
            name = os.path.splitext( os.path.basename( script) )[0]
            ValidationJob.jobCount += 1
            if self.__commandLineOptions.dryRun:
                print("%s would run: %s"%( name, os.path.basename( script) ))
                continue
            log = ">             Validating "+name
            print(">             Validating "+name)
            if self.validation.jobmode == "interactive":
                log += getCommandOutput2( script )
                ValidationJob.interactCount += 1
            elif self.validation.jobmode.split(",")[0] == "lxBatch":
                repMap = { 
                    "commands": self.validation.jobmode.split(",")[1],
                    "logDir": general["logdir"],
                    "jobName": name,
                    "script": script,
                    "bsub": "/afs/cern.ch/cms/caf/scripts/cmsbsub"
                    }
                for ext in ("stdout", "stderr", "stdout.gz", "stderr.gz"):
                    oldlog = "%(logDir)s/%(jobName)s."%repMap + ext
                    if os.path.exists(oldlog):
                        os.remove(oldlog)
                bsubOut=getCommandOutput2("%(bsub)s %(commands)s "
                                          "-J %(jobName)s "
                                          "-o %(logDir)s/%(jobName)s.stdout "
                                          "-e %(logDir)s/%(jobName)s.stderr "
                                          "%(script)s"%repMap)
                #Attention: here it is assumed that bsub returns a string
                #containing a job id like <123456789>
                jobid=bsubOut.split("<")[1].split(">")[0]
                self.JobId.append(jobid)
                ValidationJob.batchJobIds.append(jobid)
                log+=bsubOut
                ValidationJob.batchCount += 1
            elif self.validation.jobmode.split( "," )[0] == "crab":
                os.chdir( general["logdir"] )
                crabName = "crab." + os.path.basename( script )[:-3]
                theCrab = crabWrapper.CrabWrapper()
                options = { "-create": "",
                            "-cfg": crabName + ".cfg",
                            "-submit": "" }
                try:
                    theCrab.run( options )
                except AllInOneError as e:
                    print("crab:", str(e).split("\n")[0])
                    exit(1)
                ValidationJob.crabCount += 1

            else:
                raise AllInOneError("Unknown 'jobmode'!\n"
                                      "Please change this parameter either in "
                                      "the [general] or in the ["
                                      + self.__valType + ":" + self.__valName
                                      + "] section to one of the following "
                                      "values:\n"
                                      "\tinteractive\n\tlxBatch, -q <queue>\n"
                                      "\tcrab, -q <queue>")

        return log

    def getValidation( self ):
        return self.validation

    @property
    def needsproxy(self):
        return self.validation.needsproxy and not self.__preexisting and not self.__commandLineOptions.dryRun


####################--- Functions ---############################
def createMergeScript( path, validations, options ):
    if(len(validations) == 0):
        raise AllInOneError("Cowardly refusing to merge nothing!")

    config = validations[0].config
    repMap = config.getGeneral()
    repMap.update({
            "DownloadData":"",
            "CompareAlignments":"",
            "RunValidationPlots":"",
            "CMSSW_BASE": os.environ["CMSSW_BASE"],
            "SCRAM_ARCH": os.environ["SCRAM_ARCH"],
            "CMSSW_RELEASE_BASE": os.environ["CMSSW_RELEASE_BASE"],
            })

    comparisonLists = {} # directory of lists containing the validations that are comparable
    for validation in validations:
        for referenceName in validation.filesToCompare:
            validationtype = type(validation)
            if issubclass(validationtype, PreexistingValidation):
                #find the actual validationtype
                for parentclass in validationtype.mro():
                    if not issubclass(parentclass, PreexistingValidation):
                        validationtype = parentclass
                        break
            key = (validationtype, referenceName)
            if key in comparisonLists:
                comparisonLists[key].append(validation)
            else:
                comparisonLists[key] = [validation]

    # introduced to merge individual validation outputs separately
    #  -> avoids problems with merge script
    repMap["doMerge"] = "mergeRetCode=0\n"
    repMap["rmUnmerged"] = ("if [[ mergeRetCode -eq 0 ]]; then\n"
                            "    echo -e \\n\"Merging succeeded, removing original files.\"\n")
    repMap["beforeMerge"] = ""
    repMap["mergeParallelFilePrefixes"] = ""
    repMap["createResultsDirectory"]=""
    

    anythingToMerge = []
    
    
    #prepare dictionary containing handle objects for parallel merge batch jobs
    if options.mergeOfflineParallel:
        parallelMergeObjects={}
    for (validationType, referencename), validations in six.iteritems(comparisonLists):
        for validation in validations:
            #parallel merging
            if (isinstance(validation, PreexistingValidation)
                or validation.NJobs == 1
                or not isinstance(validation, ParallelValidation)):
                    continue
            if options.mergeOfflineParallel and validationType.valType=='offline' and validation.jobmode.split(",")[0]=="lxBatch":
                repMapTemp=repMap.copy()
                if validationType not in anythingToMerge:
                    anythingToMerge += [validationType]
                    #create init script
                    fileName="TkAlMergeInit"
                    filePath = os.path.join(path, fileName+".sh")
                    theFile = open( filePath, "w" )
                    repMapTemp["createResultsDirectory"]="#!/bin/bash"
                    repMapTemp["createResultsDirectory"]+=replaceByMap(configTemplates.createResultsDirectoryTemplate, repMapTemp)
                    theFile.write( replaceByMap( configTemplates.createResultsDirectoryTemplate, repMapTemp ) )
                    theFile.close()
                    os.chmod(filePath,0o755)
                    #create handle
                    parallelMergeObjects["init"]=ParallelMergeJob(fileName, filePath,[])
                    #clear 'create result directory' code
                    repMapTemp["createResultsDirectory"]=""
                
                #edit repMapTmp as necessary:
                #fill contents of mergeParallelResults
                repMapTemp["beforeMerge"] += validationType.doInitMerge()
                repMapTemp["doMerge"] += '\n\n\n\necho -e "\n\nMerging results from %s jobs with alignment %s"\n\n' % (validationType.valType,validation.alignmentToValidate.name)
                repMapTemp["doMerge"] += validation.doMerge()
                for f in validation.getRepMap()["outputFiles"]:
                    longName = os.path.join("/eos/cms/store/group/alca_trackeralign/AlignmentValidation/",
                                            validation.getRepMap()["eosdir"], f)
                    repMapTemp["rmUnmerged"] += "    rm "+longName+"\n"
                
                repMapTemp["rmUnmerged"] += ("else\n"
                             "    echo -e \\n\"WARNING: Merging failed, unmerged"
                             " files won't be deleted.\\n"
                             "(Ignore this warning if merging was done earlier)\"\n"
                             "fi\n")
                
                #fill mergeParallelResults area of mergeTemplate
                repMapTemp["DownloadData"] = replaceByMap( configTemplates.mergeParallelResults, repMapTemp )
                #fill runValidationPlots area of mergeTemplate
                repMapTemp["RunValidationPlots"] = validationType.doRunPlots(validations)
                
                #create script file
                fileName="TkAlMergeOfflineValidation"+validation.name+validation.alignmentToValidate.name
                filePath = os.path.join(path, fileName+".sh")
                theFile = open( filePath, "w" )
                theFile.write( replaceByMap( configTemplates.mergeParallelOfflineTemplate, repMapTemp ) )
                theFile.close()
                os.chmod(filePath,0o755)
                #create handle object
                if "parallel" in parallelMergeObjects:
                    parallelMergeObjects["parallel"].append(ParallelMergeJob(fileName, filePath,[]))
                else:
                    parallelMergeObjects["parallel"]=[ParallelMergeJob(fileName, filePath,[])]
                continue
                
                
            else:
                if validationType not in anythingToMerge:
                    anythingToMerge += [validationType]
                    repMap["doMerge"] += '\n\n\n\necho -e "\n\nMerging results from %s jobs"\n\n' % validationType.valType
                    repMap["beforeMerge"] += validationType.doInitMerge()
                repMap["doMerge"] += validation.doMerge()
                for f in validation.getRepMap()["outputFiles"]:
                    longName = os.path.join("/eos/cms/store/group/alca_trackeralign/AlignmentValidation/",
                                            validation.getRepMap()["eosdir"], f)
                    repMap["rmUnmerged"] += "    rm "+longName+"\n"
                
                
    
    repMap["rmUnmerged"] += ("else\n"
                             "    echo -e \\n\"WARNING: Merging failed, unmerged"
                             " files won't be deleted.\\n"
                             "(Ignore this warning if merging was done earlier)\"\n"
                             "fi\n")
    
    
    
    if anythingToMerge:
        repMap["DownloadData"] += replaceByMap( configTemplates.mergeParallelResults, repMap )
    else:
        repMap["DownloadData"] = ""

    repMap["RunValidationPlots"] = ""
    for (validationType, referencename), validations in six.iteritems(comparisonLists):
        if issubclass(validationType, ValidationWithPlots):
            repMap["RunValidationPlots"] += validationType.doRunPlots(validations)

    repMap["CompareAlignments"] = "#run comparisons"
    for (validationType, referencename), validations in six.iteritems(comparisonLists):
        if issubclass(validationType, ValidationWithComparison):
            repMap["CompareAlignments"] += validationType.doComparison(validations)
    
    #if user wants to merge parallely and if there are valid parallel scripts, create handle for plotting job and set merge script name accordingly
    if options.mergeOfflineParallel and parallelMergeObjects!={}:
        parallelMergeObjects["continue"]=ParallelMergeJob("TkAlMergeFinal",os.path.join(path, "TkAlMergeFinal.sh"),[])
        filePath = os.path.join(path, "TkAlMergeFinal.sh")
    #if not merging parallel, add code to create results directory and set merge script name accordingly
    else:
        repMap["createResultsDirectory"]=replaceByMap(configTemplates.createResultsDirectoryTemplate, repMap)
        filePath = os.path.join(path, "TkAlMerge.sh")
    
    
    #filePath = os.path.join(path, "TkAlMerge.sh")
    theFile = open( filePath, "w" )
    theFile.write( replaceByMap( configTemplates.mergeTemplate, repMap ) )
    theFile.close()
    os.chmod(filePath,0o755)
    
    if options.mergeOfflineParallel:
        return {'TkAlMerge.sh':filePath, 'parallelMergeObjects':parallelMergeObjects}
    else:
        return filePath
    
def loadTemplates( config ):
    if config.has_section("alternateTemplates"):
        for templateName in config.options("alternateTemplates"):
            if templateName == "AutoAlternates":
                continue
            newTemplateName = config.get("alternateTemplates", templateName )
            #print "replacing default %s template by %s"%( templateName, newTemplateName)
            configTemplates.alternateTemplate(templateName, newTemplateName)

    
####################--- Main ---############################
def main(argv = None):
    if argv == None:
       argv = sys.argv[1:]
    optParser = optparse.OptionParser()
    optParser.description = """All-in-one Alignment Validation.
This will run various validation procedures either on batch queues or interactively.
If no name is given (-N parameter) a name containing time and date is created automatically.
To merge the outcome of all validation procedures run TkAlMerge.sh in your validation's directory.
"""
    optParser.add_option("-n", "--dryRun", dest="dryRun", action="store_true", default=False,
                         help="create all scripts and cfg File but do not start jobs (default=False)")
    optParser.add_option( "--getImages", dest="getImages", action="store_true", default=True,
                          help="get all Images created during the process (default= True)")
    defaultConfig = "TkAlConfig.ini"
    optParser.add_option("-c", "--config", dest="config", default = defaultConfig,
                         help="configuration to use (default TkAlConfig.ini) this can be a comma-seperated list of all .ini file you want to merge", metavar="CONFIG")
    optParser.add_option("-N", "--Name", dest="Name",
                         help="Name of this validation (default: alignmentValidation_DATE_TIME)", metavar="NAME")
    optParser.add_option("-r", "--restrictTo", dest="restrictTo",
                         help="restrict validations to given modes (comma seperated) (default: no restriction)", metavar="RESTRICTTO")
    optParser.add_option("-s", "--status", dest="crabStatus", action="store_true", default = False,
                         help="get the status of the crab jobs", metavar="STATUS")
    optParser.add_option("-d", "--debug", dest="debugMode", action="store_true",
                         default = False,
                         help="run the tool to get full traceback of errors",
                         metavar="DEBUG")
    optParser.add_option("-m", "--autoMerge", dest="autoMerge", action="store_true", default = False,
                         help="submit TkAlMerge.sh to run automatically when all jobs have finished (default=False)."
                              " Works only for batch jobs")
    optParser.add_option("--mergeOfflineParallel", dest="mergeOfflineParallel", action="store_true", default = False,
                         help="Enable parallel merging of offline data. Best used with -m option. Only works with lxBatch-jobmode", metavar="MERGE_PARALLEL")


    (options, args) = optParser.parse_args(argv)

    if not options.restrictTo == None:
        options.restrictTo = options.restrictTo.split(",")

    options.config = [ os.path.abspath( iniFile ) for iniFile in \
                       options.config.split( "," ) ]
    config = BetterConfigParser()
    outputIniFileSet = set( config.read( options.config ) )
    failedIniFiles = [ iniFile for iniFile in options.config if iniFile not in outputIniFileSet ]

    # Check for missing ini file
    if options.config == [ os.path.abspath( defaultConfig ) ]:
        if ( not options.crabStatus ) and \
               ( not os.path.exists( defaultConfig ) ):
                raise AllInOneError( "Default 'ini' file '%s' not found!\n"
                                       "You can specify another name with the "
                                       "command line option '-c'/'--config'."
                                       %( defaultConfig ))
    else:
        for iniFile in failedIniFiles:
            if not os.path.exists( iniFile ):
                raise AllInOneError( "'%s' does not exist. Please check for "
                                       "typos in the filename passed to the "
                                       "'-c'/'--config' option!"
                                       %( iniFile ))
            else:
                raise AllInOneError(( "'%s' does exist, but parsing of the "
                                       "content failed!" ) % iniFile)

    # get the job name
    if options.Name == None:
        if not options.crabStatus:
            options.Name = "alignmentValidation_%s"%(datetime.datetime.now().strftime("%y%m%d_%H%M%S"))
        else:
            existingValDirs = fnmatch.filter( os.walk( '.' ).next()[1],
                                              "alignmentValidation_*" )
            if len( existingValDirs ) > 0:
                options.Name = existingValDirs[-1]
            else:
                print("Cannot guess last working directory!")
                print ( "Please use the parameter '-N' or '--Name' to specify "
                        "the task for which you want a status report." )
                return 1

    # set output path
    outPath = os.path.abspath( options.Name )

    # Check status of submitted jobs and return
    if options.crabStatus:
        os.chdir( outPath )
        crabLogDirs = fnmatch.filter( os.walk('.').next()[1], "crab.*" )
        if len( crabLogDirs ) == 0:
            print("Found no crab tasks for job name '%s'"%( options.Name ))
            return 1
        theCrab = crabWrapper.CrabWrapper()
        for crabLogDir in crabLogDirs:
            print()
            print("*" + "=" * 78 + "*")
            print ( "| Status report and output retrieval for:"
                    + " " * (77 - len( "Status report and output retrieval for:" ) )
                    + "|" )
            taskName = crabLogDir.replace( "crab.", "" )
            print("| " + taskName + " " * (77 - len( taskName ) ) + "|")
            print("*" + "=" * 78 + "*")
            print()
            crabOptions = { "-getoutput":"",
                            "-c": crabLogDir }
            try:
                theCrab.run( crabOptions )
            except AllInOneError as e:
                print("crab:  No output retrieved for this task.")
            crabOptions = { "-status": "",
                            "-c": crabLogDir }
            theCrab.run( crabOptions )
        return

    general = config.getGeneral()
    config.set("internals","workdir",os.path.join(general["workdir"],options.Name) )
    config.set("internals","scriptsdir",outPath)
    config.set("general","datadir",os.path.join(general["datadir"],options.Name) )
    config.set("general","logdir",os.path.join(general["logdir"],options.Name) )
    config.set("general","eosdir",os.path.join("AlignmentValidation", general["eosdir"], options.Name) )

    if not os.path.exists( outPath ):
        os.makedirs( outPath )
    elif not os.path.isdir( outPath ):
        raise AllInOneError("the file %s is in the way rename the Job or move it away"%outPath)

    # replace default templates by the ones specified in the "alternateTemplates" section
    loadTemplates( config )

    #save backup configuration file
    backupConfigFile = open( os.path.join( outPath, "usedConfiguration.ini" ) , "w"  )
    config.write( backupConfigFile )

    #copy proxy, if there is one
    try:
        proxyexists = int(getCommandOutput2("voms-proxy-info --timeleft")) > 10
    except RuntimeError:
        proxyexists = False

    if proxyexists:
        shutil.copyfile(getCommandOutput2("voms-proxy-info --path").strip(), os.path.join(outPath, ".user_proxy"))

    validations = []
    for validation in config.items("validation"):
        alignmentList = [validation[1]]
        validationsToAdd = [(validation[0],alignment) \
                                for alignment in alignmentList]
        validations.extend(validationsToAdd)
    jobs = [ ValidationJob( validation, config, options) \
                 for validation in validations ]
    for job in jobs:
        if job.needsproxy and not proxyexists:
            raise AllInOneError("At least one job needs a grid proxy, please init one.")
    map( lambda job: job.createJob(), jobs )
    validations = [ job.getValidation() for job in jobs ]

    if options.mergeOfflineParallel:
        parallelMergeObjects=createMergeScript(outPath, validations, options)['parallelMergeObjects']
    else:
        createMergeScript(outPath, validations, options)


    print()
    map( lambda job: job.runJob(), jobs )

    if options.autoMerge and ValidationJob.jobCount == ValidationJob.batchCount and config.getGeneral()["jobmode"].split(",")[0] == "lxBatch":
        print(">             Automatically merging jobs when they have ended")
        # if everything is done as batch job, also submit TkAlMerge.sh to be run
        # after the jobs have finished
        
        #if parallel merge scripts: manage dependencies
        if options.mergeOfflineParallel and parallelMergeObjects!={}:
            initID=parallelMergeObjects["init"].runJob(config).split("<")[1].split(">")[0]
            parallelIDs=[]
            for parallelMergeScript in parallelMergeObjects["parallel"]:
                parallelMergeScript.addDependency(initID)
                for job in jobs:
                    if isinstance(job.validation, OfflineValidation) and "TkAlMerge"+job.validation.alignmentToValidate.name==parallelMergeScript.name:
                        parallelMergeScript.addDependency(job.JobId)
                parallelIDs.append(parallelMergeScript.runJob(config).split("<")[1].split(">")[0])
            parallelMergeObjects["continue"].addDependency(parallelIDs)
            parallelMergeObjects["continue"].addDependency(ValidationJob.batchJobIds)
            parallelMergeObjects["continue"].runJob(config)
            
            
        
    
        else:
            repMap = {
                "commands": config.getGeneral()["jobmode"].split(",")[1],
                "jobName": "TkAlMerge",
                "logDir": config.getGeneral()["logdir"],
                "script": "TkAlMerge.sh",
                "bsub": "/afs/cern.ch/cms/caf/scripts/cmsbsub",
                "conditions": '"' + " && ".join(["ended(" + jobId + ")" for jobId in ValidationJob.batchJobIds]) + '"'
                }
            for ext in ("stdout", "stderr", "stdout.gz", "stderr.gz"):
                oldlog = "%(logDir)s/%(jobName)s."%repMap + ext
                if os.path.exists(oldlog):
                    os.remove(oldlog)

            #issue job
            getCommandOutput2("%(bsub)s %(commands)s "
                            "-o %(logDir)s/%(jobName)s.stdout "
                            "-e %(logDir)s/%(jobName)s.stderr "
                            "-w %(conditions)s "
                            "%(logDir)s/%(script)s"%repMap)

if __name__ == "__main__":        
    # main(["-n","-N","test","-c","defaultCRAFTValidation.ini,latestObjects.ini","--getImages"])
    if "-d" in sys.argv[1:] or "--debug" in sys.argv[1:]:
        main()
    else:
        try:
            main()
        except AllInOneError as e:
            print("\nAll-In-One Tool:", str(e))
            exit(1)