def _readMoreXML(self, xmlNode):
"""
Function to read the portion of the xml input that belongs to this
specialized class and initialize variables based on the input received.
@ In, xmlNode, xml.etree.ElementTree.Element, XML element node that represents the portion of the input that belongs to this class
@ Out, None
"""
DateBase._readMoreXML(self, xmlNode)
# Check if database directory exist, otherwise create it
if '~' in self.databaseDir:
self.databaseDir = copy.copy(os.path.expanduser(self.databaseDir))
# Determine RELATIVE location for HDF5.
# - if a full path is given, accept it as given, else ...
if not os.path.isabs(self.databaseDir):
# use working dir as base
self.databaseDir = os.path.join(self.workingDir, self.databaseDir)
self.databaseDir = os.path.normpath(self.databaseDir)
utils.makeDir(self.databaseDir)
self.raiseADebug('Database Directory is:', self.databaseDir)
# Check if a filename has been provided
# if yes, we assume the user wants to load the data from there
# or update it
#try:
self.filename = xmlNode.attrib.get('filename', self.name + '.h5')
if 'readMode' not in xmlNode.attrib.keys():
self.raiseAnError(
IOError,
'No "readMode" attribute was specified for hdf5 database',
self.name)
self.readMode = xmlNode.attrib['readMode'].strip().lower()
readModes = ['read', 'overwrite']
if self.readMode not in readModes:
self.raiseAnError(IOError, 'readMode attribute for hdf5 database',
self.name, 'is not recognized:', self.readMode,
'. Options are:', readModes)
self.raiseADebug('HDF5 Read Mode is "' + self.readMode + '".')
fullpath = os.path.join(self.databaseDir, self.filename)
if os.path.isfile(fullpath):
if self.readMode == 'read':
self.exist = True
elif self.readMode == 'overwrite':
self.exist = False
self.database = h5Data(self.name, self.databaseDir,
self.messageHandler, self.filename,
self.exist)
else:
#file does not exist in path
if self.readMode == 'read':
self.raiseAWarning(
'Requested to read from database, but it does not exist at:',
fullpath, '; continuing without reading...')
self.exist = False
self.database = h5Data(self.name, self.databaseDir,
self.messageHandler, self.filename,
self.exist)
self.raiseAMessage('Database is located at:', fullpath)
def __readRunInfo(self,xmlNode,runInfoSkip,xmlFilename):
"""
Method that reads the xml input file for the RunInfo block
@ In, xmlNode, xml.etree.Element, the xml node that belongs to Simulation
@ In, runInfoSkip, string, the runInfo step to skip
@ In, xmlFilename, string, xml input file name
@ Out, None
"""
if 'verbosity' in xmlNode.attrib.keys():
self.verbosity = xmlNode.attrib['verbosity']
self.raiseAMessage('Global verbosity level is "',self.verbosity,'"',verbosity='quiet')
for element in xmlNode:
if element.tag in runInfoSkip:
self.raiseAWarning("Skipped element ",element.tag)
elif element.tag == 'printInput':
text = element.text.strip() if element.text is not None else ''
#extension fixing
if len(text) >= 4 and text[-4:].lower() == '.xml':
text = text[:-4]
# if the user asked to not print input instead of leaving off tag, respect it
if text.lower() in utils.stringsThatMeanFalse():
self.runInfoDict['printInput'] = False
# if the user didn't provide a name, provide a default
elif len(text)<1:
self.runInfoDict['printInput'] = 'duplicated_input.xml'
# otherwise, use the user-provided name
else:
self.runInfoDict['printInput'] = text+'.xml'
elif element.tag == 'WorkingDir':
# first store the cwd, the "CallDir"
self.runInfoDict['CallDir'] = os.getcwd()
# then get the requested "WorkingDir"
tempName = element.text
if '~' in tempName:
tempName = os.path.expanduser(tempName)
if os.path.isabs(tempName):
self.runInfoDict['WorkingDir'] = tempName
elif "runRelative" in element.attrib:
self.runInfoDict['WorkingDir'] = os.path.abspath(tempName)
else:
if xmlFilename == None:
self.raiseAnError(IOError,'Relative working directory requested but xmlFilename is None.')
# store location of the input
xmlDirectory = os.path.dirname(os.path.abspath(xmlFilename))
self.runInfoDict['InputDir'] = xmlDirectory
rawRelativeWorkingDir = element.text.strip()
# working dir is file location + relative working dir
self.runInfoDict['WorkingDir'] = os.path.join(xmlDirectory,rawRelativeWorkingDir)
utils.makeDir(self.runInfoDict['WorkingDir'])
elif element.tag == 'maxQueueSize':
try:
self.runInfoDict['maxQueueSize'] = int(element.text)
except ValueError:
self.raiseAnError('Value give for RunInfo.maxQueueSize could not be converted to integer: {}'.format(element.text))
elif element.tag == 'RemoteRunCommand':
tempName = element.text
if '~' in tempName:
tempName = os.path.expanduser(tempName)
if os.path.isabs(tempName):
self.runInfoDict['RemoteRunCommand'] = tempName
else:
self.runInfoDict['RemoteRunCommand'] = os.path.abspath(os.path.join(self.runInfoDict['FrameworkDir'],tempName))
elif element.tag == 'NodeParameter':
self.runInfoDict['NodeParameter'] = element.text.strip()
elif element.tag == 'MPIExec':
self.runInfoDict['MPIExec'] = element.text.strip()
elif element.tag == 'JobName':
self.runInfoDict['JobName' ] = element.text.strip()
elif element.tag == 'ParallelCommand':
self.runInfoDict['ParallelCommand' ] = element.text.strip()
elif element.tag == 'queueingSoftware':
self.runInfoDict['queueingSoftware' ] = element.text.strip()
elif element.tag == 'ThreadingCommand':
self.runInfoDict['ThreadingCommand' ] = element.text.strip()
elif element.tag == 'NumThreads':
self.runInfoDict['NumThreads' ] = int(element.text)
elif element.tag == 'totalNumCoresUsed':
self.runInfoDict['totalNumCoresUsed' ] = int(element.text)
elif element.tag == 'NumMPI':
self.runInfoDict['NumMPI' ] = int(element.text)
elif element.tag == 'internalParallel':
self.runInfoDict['internalParallel' ] = utils.interpretBoolean(element.text)
elif element.tag == 'batchSize':
self.runInfoDict['batchSize' ] = int(element.text)
elif element.tag.lower() == 'maxqueuesize':
self.runInfoDict['maxQueueSize' ] = int(element.text)
elif element.tag == 'MaxLogFileSize':
self.runInfoDict['MaxLogFileSize' ] = int(element.text)
elif element.tag == 'precommand':
self.runInfoDict['precommand' ] = element.text
elif element.tag == 'postcommand':
self.runInfoDict['postcommand' ] = element.text
elif element.tag == 'deleteOutExtension':
self.runInfoDict['deleteOutExtension'] = element.text.strip().split(',')
elif element.tag == 'delSucLogFiles' :
if element.text.lower() in utils.stringsThatMeanTrue():
self.runInfoDict['delSucLogFiles' ] = True
else:
self.runInfoDict['delSucLogFiles' ] = False
elif element.tag == 'logfileBuffer':
self.runInfoDict['logfileBuffer'] = utils.convertMultipleToBytes(element.text.lower())
elif element.tag == 'clusterParameters':
self.runInfoDict['clusterParameters'].extend(splitCommand(element.text)) #extend to allow adding parameters at different points.
elif element.tag == 'mode' :
self.runInfoDict['mode'] = element.text.strip().lower()
#parallel environment
if self.runInfoDict['mode'] in self.__modeHandlerDict:
self.__modeHandler = self.__modeHandlerDict[self.runInfoDict['mode']](self.messageHandler)
self.__modeHandler.XMLread(element)
else:
self.raiseAnError(IOError,"Unknown mode "+self.runInfoDict['mode'])
elif element.tag == 'expectedTime':
self.runInfoDict['expectedTime' ] = element.text.strip()
elif element.tag == 'Sequence':
for stepName in element.text.split(','):
self.stepSequenceList.append(stepName.strip())
elif element.tag == 'DefaultInputFile':
self.runInfoDict['DefaultInputFile'] = element.text.strip()
elif element.tag == 'CustomMode' :
modeName = element.text.strip()
modeClass = element.attrib["class"]
modeFile = element.attrib["file"]
#XXX This depends on if the working directory has been set yet.
# So switching the order of WorkingDir and CustomMode can
# cause different results.
modeFile = modeFile.replace("%BASE_WORKING_DIR%",self.runInfoDict['WorkingDir'])
modeFile = modeFile.replace("%FRAMEWORK_DIR%",self.runInfoDict['FrameworkDir'])
modeDir, modeFilename = os.path.split(modeFile)
if modeFilename.endswith(".py"):
modeModulename = modeFilename[:-3]
else:
modeModulename = modeFilename
os.sys.path.append(modeDir)
module = __import__(modeModulename)
if modeName in self.__modeHandlerDict:
self.raiseAWarning("duplicate mode definition " + modeName)
self.__modeHandlerDict[modeName] = module.__dict__[modeClass]
else:
self.raiseAnError(IOError,'RunInfo element "'+element.tag +'" unknown!')