class QETask(object):
"""
Base abstract class for 'TaskNameTask' family of classes. It also provides
the interface to launch tasks
All user defined tasks should be derived from this class
setting -- provides access to parallel environment and QE input/output files
"""
def __init__(self, filename = None, configString = None, cleanOutDir = False):
# parallelization parameters
# Default values, see explanations below:
#self.name = 'Launcher'
self._isSerial = True
self._mergedTask = False
self.cleanOutDir = cleanOutDir
QETask.readSetting(self, filename, configString)
def readSetting(self, filename = None, configString = None, \
sectionName = None):
"""
Initializes setting class
"""
configDic = {
'useTorque' : 'False',
'paraTorqueParams': '-l nodes=1:ppn=1',
'serialTorqueParams': '-l nodes=1:ppn=1',
'paraPrefix': '',
'paraPostfix': '',
'serialPrefix': '',
'serialPostfix': '',
'paraRemoteShell': '',
'outdir': None
}
# if filename == None and configString == None:
# configString = ''
# filename = 'config.ini'
if filename == None and configString == None:
self.setting = Setting(configString = "")
else:
self.setting = Setting(filename, configString)
self.setting.section(QETask.name(self), configDic)
if self.setting.get('useTorque') == 'True':
self.setting.set('useTorque', True)
else:
self.setting.set('useTorque', False)
if self.setting.get('useTorque'):
if self.isSerial():
self._torque = QETorque(self.setting.get('serialTorqueParams'))
else:
self._torque = QETorque(self.setting.get('paraTorqueParams'))
# **********************************************************************
# Task subclass specific part:
if hasattr(self, '_type'):
defaultModName = 'QESInput'
modname = self._inputConstructor
#Input = __import__("qeparser." + modname.lower(), globals(), \
# locals(), [modname], -1)
mod_cmd = "from qeparser.%s import %s as Input"%(modname.lower(), modname)
exec(mod_cmd)
from qeparser.qeoutput import QEOutput
if sectionName == None:
name = self.name()
else:
name = sectionName
self.setting.section(name, self._configDic)
# add pointer to setting for input filenames synchronization
#self.input._setting = self.setting
self.output = QEOutput(self.setting, type = self._type)
args = {
'setting': self.setting,
}
if modname == defaultModName:
args['type'] = self._type
if filename != None or configString != None:
self.input = Input(**args)
self.syncSetting()
else:
# add parse:
args['parse'] = False
self.input = Input( **args)
def name(self):
return 'Launcher'
def parse(self):
self.syncSetting()
def syncSetting(self):
"""
Will syncronise QE input file with class Setting for given task (QE input
files may contain multiple input/ouput file names definitions which
can be overriden in this method)
"""
pass
def cleanOutputDir(self, cleanOutDir = None):
"""
Cleans the output directory (directory, where large files, used
for calculation are stored, can be for example 'temp/' or 'scratch/')
"""
# import shutil
if cleanOutDir == None:
cleanOutDir = self.cleanOutDir
# if cleanOutDir == None:
# raise Exception('outDir can not be cleaned, since it was not defined')
if cleanOutDir:
outDir = self.setting.get('outdir')
os.system(self.setting.paraRemoteShell + ' rm -r -f ' + outDir)
os.system(self.setting.paraRemoteShell + ' mkdir ' + outDir)
# if self.setting.useTorque:
#
# else:
# shutil.rmtree(cleanOutDir)
# os.mkdir(cleanOutDir)
# def cmdLine(self):
# """
# returns command string of a given task
# """
# return self._cmdStr
def launch(self, cleanOutDir = False):
"""
Parses input. Launches task. Parses output.
"""
# if cleanOutDir == None:
# cleanOutDir = self.cleanOutDir
# if cleanOutDir != None:
# self.cleanOutputDir(cleanOutDir)
#self.input.parse()
self.syncSetting() # sync setting with QE input file
self.input.save()
self.cleanOutputDir(cleanOutDir)
self._run()
self.output.parse(parserList = 'all')
def setSerial(self):
#self._serialThroughMPI = serialThroughMPI
self._isSerial = True
def setParallel(self):
self._isSerial = False
def isSerial(self):
if self._isSerial:
return True
else:
return False
def getPrefix(self) :
if self.isSerial():
# if self._isSerialThroughMPI():
# return ''
# else:
return self.setting.get('serialPrefix')
else:
return self.setting.get('paraPrefix')
def getPostfix(self):
if self.isSerial():
return self.setting.get('serialPostfix')
else:
return self.setting.get('paraPostfix')
def isMerged(self):
return self._mergedTask
def _initCmdLineParams(self):
self._inp = '-inp'
self._devnul = '< /dev/null'
if self.isSerial():
self._inp = '<'
self._devnul = ''
# def _isSerialThroughMPI(self):
# if self.isSerial():
# if self._serialThroughMPI:
# return True
# else:
# return False
def _check(self, x):
"""
Will check the exit status of the program to be executed
"""
signal = x & 0xFF
exitcode = (x >> 8) & 0xFF
if exitcode != 0:
raise Exception("Task " + self.name() + " crashed: check your \
settings!\n" + "Command string: " + self.cmdLine())
def _run(self):
if os.path.exists('CRASH'):
os.remove('CRASH')
outdir = self.setting.get('outdir')
if outdir != None:
os.system(self.setting.paraRemoteShell + ' mkdir -p ' + outdir)
if self.setting.get('useTorque'):
if self.isSerial():
if self.setting.get('serialPrefix') == '':
self._check(os.system(self.cmdLine()))
else:
self._torque.serial(self.cmdLine(), torqueParams = self.setting.serialTorqueParams)
else:
self._torque.serial(self.cmdLine(), torqueParams = self.setting.paraTorqueParams)
else:
self._check(os.system(self.cmdLine()))
# if self.setting.paraPrefix != '' and self.setting.paraPrefix in self.cmdLine():
# if self.setting.useTorque:
# self._torque.serial(self.cmdLine())
# else:
# self._check(os.system(self.cmdLine()))
# else:
# self._check(os.system(self.cmdLine()))
if os.path.exists('CRASH'):
raise Exception("Task " + self.name() + " crashed: 'CRASH' file was discovered")
def _getCmdLine(self, executable, input, output):
self._initCmdLineParams()
return self.getPrefix() + ' ' + executable + " " + self.getPostfix() + \
' ' + self._inp + ' ' + self.setting.get(input) + ' > ' + \
self.setting.get(output) + self._devnul
def _setSetiingInputOutput(self, configDic, filename = None, configString = None, sectionName = None):
"""
Helper method for readSetting()
"""
if sectionName == None:
name = self.name()
else:
name = sectionName
self.setting.section(name, configDic)
self.input = PWInput( self.setting.pwInput ) #self.setting.get('pwInput') )
# add pointer to setting for input filenames synchronization
self.input._setting = self.setting
self.output = QEOutput(self.setting, type='pw')
if filename != None or configString != None:
self.syncSetting()
class QETask(object):
"""
Base abstract class for 'TaskNameTask' family of classes. It also provides
the interface to loumch tasks
All user defined tasks should be derived from this class
setting -- provides access to parallel environment and QE input/output files
"""
def __init__(self, filename = None, configString = None, cleanOutDir = False):
# parallelization parameters
# Default values, see explanations below:
#self.name = 'Launcher'
self._isSerial = True
configDic = {
'useTorque' : 'False',
'paraTorqueParams': '-l nodes=1:ppn=1',
'serialTorqueParams': '-l nodes=1:ppn=1',
'paraPrefix': '',
'paraPostfix': '',
'serialPrefix': '',
'serialPostfix': '',
'paraRemoteShell': '',
'outdir': None
}
if filename == None and configString == None:
filename = 'config.ini'
self.setting = Setting(filename, configString)
self.setting.section(QETask.name(self), configDic)
self.cleanOutDir = cleanOutDir
if self.setting.get('useTorque') == 'True':
self.setting.set('useTorque', True)
else:
self.setting.set('useTorque', False)
if self.setting.get('useTorque'):
if self.isSerial():
self._torque = QETorque(self.setting.get('serialTorqueParams'))
else:
self._torque = QETorque(self.setting.get('paraTorqueParams'))
def name(self):
return 'Launcher'
def _check(self, x):
"""
Will check the exit status of the program to be executed
"""
signal = x & 0xFF
exitcode = (x >> 8) & 0xFF
if exitcode != 0:
raise Exception("Task " + self.name() + " crashed: check your settings" + "Command string:" + self.cmdLine())
def _run(self):
if os.path.exists('CRASH'):
os.remove('CRASH')
outdir = self.setting.get('outdir')
if outdir != None:
os.system(self.setting.paraRemoteShell + ' mkdir -p ' + outdir)
if self.setting.get('useTorque'):
if self.isSerial():
if self.setting.get('serialPrefix') == '':
self._check(os.system(self.cmdLine()))
else:
self._torque.serial(self.cmdLine(), torqueParams = self.setting.serialTorqueParams)
else:
self._torque.serial(self.cmdLine(), torqueParams = self.setting.paraTorqueParams)
else:
self._check(os.system(self.cmdLine()))
# if self.setting.paraPrefix != '' and self.setting.paraPrefix in self.cmdLine():
# if self.setting.useTorque:
# self._torque.serial(self.cmdLine())
# else:
# self._check(os.system(self.cmdLine()))
# else:
# self._check(os.system(self.cmdLine()))
if os.path.exists('CRASH'):
raise Exception("Task " + self.name() + " crashed: 'CRASH' file was discovered")
def syncSetting(self):
"""
Will syncronise QE input file with class Setting for given task (QE input
files may contain multiple input/ouput file names definitions which
can be overriden in this method)
"""
pass
def cleanOutputDir(self, cleanOutDir = None):
"""
Cleans the output directory (directory, where large files, used
for calculation are stored, can be for example 'temp/' or 'scratch/')
"""
# import shutil
if cleanOutDir == None:
cleanOutDir = self.cleanOutDir
# if cleanOutDir == None:
# raise Exception('outDir can not be cleaned, since it was not defined')
if cleanOutDir:
outDir = self.setting.get('outdir')
os.system(self.setting.paraRemoteShell + ' rm -r -f ' + outDir)
os.system(self.setting.paraRemoteShell + ' mkdir ' + outDir)
# if self.setting.useTorque:
#
# else:
# shutil.rmtree(cleanOutDir)
# os.mkdir(cleanOutDir)
# def cmdLine(self):
# """
# returns command string of a given task
# """
# return self._cmdStr
def launch(self, cleanOutDir = False):
"""
Parses input. Launches task. Parses output.
"""
# if cleanOutDir == None:
# cleanOutDir = self.cleanOutDir
# if cleanOutDir != None:
# self.cleanOutputDir(cleanOutDir)
self.input.parse()
self.syncSetting() # sync setting with QE input file
self.input.save()
self.cleanOutputDir(cleanOutDir)
self._run()
self.output.parse(parserList = 'all')
def setSerial(self):
#self._serialThroughMPI = serialThroughMPI
self._isSerial = True
def setParallel(self):
self._isSerial = False
def isSerial(self):
if self._isSerial:
return True
else:
return False
def getPrefix(self) :
if self.isSerial():
# if self._isSerialThroughMPI():
# return ''
# else:
return self.setting.get('serialPrefix')
else:
return self.setting.get('paraPrefix')
def getPostfix(self):
if self.isSerial():
return self.setting.get('serialPostfix')
else:
return self.setting.get('paraPostfix')
def _initCmdLineParams(self):
self._inp = '-inp'
self._devnul = '< /dev/null'
if self.isSerial():
self._inp = '<'
self._devnul = ''
# def _isSerialThroughMPI(self):
# if self.isSerial():
# if self._serialThroughMPI:
# return True
# else:
# return False
def _getCmdLine(self, executable, input, output):
self._initCmdLineParams()
return self.getPrefix() + ' ' + executable + " " + self.getPostfix() + \
' ' + self._inp + ' ' + self.setting.get(input) + ' > ' + \
self.setting.get(output) + self._devnul
class QETask(object):
"""
Base abstract class for 'TaskNameTask' family of classes. It also provides
the interface to launch tasks
All user defined tasks should be derived from this class
setting -- provides access to parallel environment and QE input/output files
"""
def __init__(self, filename=None, configString=None, cleanOutDir=False):
# parallelization parameters
# Default values, see explanations below:
#self.name = 'Launcher'
self._isSerial = True
self._mergedTask = False
self.cleanOutDir = cleanOutDir
QETask.readSetting(self, filename, configString)
def readSetting(self, filename = None, configString = None, \
sectionName = None):
"""
Initializes setting class
"""
configDic = {
'useTorque': 'False',
'paraTorqueParams': '-l nodes=1:ppn=1',
'serialTorqueParams': '-l nodes=1:ppn=1',
'paraPrefix': '',
'paraPostfix': '',
'serialPrefix': '',
'serialPostfix': '',
'paraRemoteShell': '',
'outdir': None
}
# if filename == None and configString == None:
# configString = ''
# filename = 'config.ini'
if filename == None and configString == None:
self.setting = Setting(configString="")
else:
self.setting = Setting(filename, configString)
self.setting.section(QETask.name(self), configDic)
if self.setting.get('useTorque') == 'True':
self.setting.set('useTorque', True)
else:
self.setting.set('useTorque', False)
if self.setting.get('useTorque'):
if self.isSerial():
self._torque = QETorque(self.setting.get('serialTorqueParams'))
else:
self._torque = QETorque(self.setting.get('paraTorqueParams'))
# **********************************************************************
# Task subclass specific part:
if hasattr(self, '_type'):
defaultModName = 'QESInput'
modname = self._inputConstructor
#Input = __import__("qeparser." + modname.lower(), globals(), \
# locals(), [modname], -1)
mod_cmd = "from qeparser.%s import %s as Input" % (modname.lower(),
modname)
exec(mod_cmd)
from qeparser.qeoutput import QEOutput
if sectionName == None:
name = self.name()
else:
name = sectionName
self.setting.section(name, self._configDic)
# add pointer to setting for input filenames synchronization
#self.input._setting = self.setting
self.output = QEOutput(self.setting, type=self._type)
args = {
'setting': self.setting,
}
if modname == defaultModName:
args['type'] = self._type
if filename != None or configString != None:
self.input = Input(**args)
self.syncSetting()
else:
# add parse:
args['parse'] = False
self.input = Input(**args)
def name(self):
return 'Launcher'
def parse(self):
self.syncSetting()
def syncSetting(self):
"""
Will syncronise QE input file with class Setting for given task (QE input
files may contain multiple input/ouput file names definitions which
can be overriden in this method)
"""
pass
def cleanOutputDir(self, cleanOutDir=None):
"""
Cleans the output directory (directory, where large files, used
for calculation are stored, can be for example 'temp/' or 'scratch/')
"""
# import shutil
if cleanOutDir == None:
cleanOutDir = self.cleanOutDir
# if cleanOutDir == None:
# raise Exception('outDir can not be cleaned, since it was not defined')
if cleanOutDir:
outDir = self.setting.get('outdir')
os.system(self.setting.paraRemoteShell + ' rm -r -f ' + outDir)
os.system(self.setting.paraRemoteShell + ' mkdir ' + outDir)
# if self.setting.useTorque:
#
# else:
# shutil.rmtree(cleanOutDir)
# os.mkdir(cleanOutDir)
# def cmdLine(self):
# """
# returns command string of a given task
# """
# return self._cmdStr
def launch(self, cleanOutDir=False):
"""
Parses input. Launches task. Parses output.
"""
# if cleanOutDir == None:
# cleanOutDir = self.cleanOutDir
# if cleanOutDir != None:
# self.cleanOutputDir(cleanOutDir)
#self.input.parse()
self.syncSetting() # sync setting with QE input file
self.input.save()
self.cleanOutputDir(cleanOutDir)
self._run()
self.output.parse(parserList='all')
def setSerial(self):
#self._serialThroughMPI = serialThroughMPI
self._isSerial = True
def setParallel(self):
self._isSerial = False
def isSerial(self):
if self._isSerial:
return True
else:
return False
def getPrefix(self):
if self.isSerial():
# if self._isSerialThroughMPI():
# return ''
# else:
return self.setting.get('serialPrefix')
else:
return self.setting.get('paraPrefix')
def getPostfix(self):
if self.isSerial():
return self.setting.get('serialPostfix')
else:
return self.setting.get('paraPostfix')
def isMerged(self):
return self._mergedTask
def _initCmdLineParams(self):
self._inp = '-inp'
self._devnul = '< /dev/null'
if self.isSerial():
self._inp = '<'
self._devnul = ''
# def _isSerialThroughMPI(self):
# if self.isSerial():
# if self._serialThroughMPI:
# return True
# else:
# return False
def _check(self, x):
"""
Will check the exit status of the program to be executed
"""
signal = x & 0xFF
exitcode = (x >> 8) & 0xFF
if exitcode != 0:
raise Exception("Task " + self.name() + " crashed: check your \
settings!\n" + "Command string: " + self.cmdLine())
def _run(self):
if os.path.exists('CRASH'):
os.remove('CRASH')
outdir = self.setting.get('outdir')
if outdir != None:
os.system(self.setting.paraRemoteShell + ' mkdir -p ' + outdir)
if self.setting.get('useTorque'):
if self.isSerial():
if self.setting.get('serialPrefix') == '':
self._check(os.system(self.cmdLine()))
else:
self._torque.serial(
self.cmdLine(),
torqueParams=self.setting.serialTorqueParams)
else:
self._torque.serial(self.cmdLine(),
torqueParams=self.setting.paraTorqueParams)
else:
self._check(os.system(self.cmdLine()))
# if self.setting.paraPrefix != '' and self.setting.paraPrefix in self.cmdLine():
# if self.setting.useTorque:
# self._torque.serial(self.cmdLine())
# else:
# self._check(os.system(self.cmdLine()))
# else:
# self._check(os.system(self.cmdLine()))
if os.path.exists('CRASH'):
raise Exception("Task " + self.name() +
" crashed: 'CRASH' file was discovered")
def _getCmdLine(self, executable, input, output):
self._initCmdLineParams()
return self.getPrefix() + ' ' + executable + " " + self.getPostfix() + \
' ' + self._inp + ' ' + self.setting.get(input) + ' > ' + \
self.setting.get(output) + self._devnul
def _setSettingInputOutput(self,
configDic,
filename=None,
configString=None,
sectionName=None):
"""
Helper method for readSetting()
"""
if sectionName == None:
name = self.name()
else:
name = sectionName
self.setting.section(name, configDic)
self.input = PWInput(
self.setting.pwInput) #self.setting.get('pwInput') )
# add pointer to setting for input filenames synchronization
self.input._setting = self.setting
self.output = QEOutput(self.setting, type='pw')
if filename != None or configString != None:
self.syncSetting()
class QETask(object):
"""
Base abstract class for 'TaskNameTask' family of classes. It also provides
the interface to loumch tasks
All user defined tasks should be derived from this class
setting -- provides access to parallel environment and QE input/output files
"""
def __init__(self, filename=None, configString=None, cleanOutDir=False):
# parallelization parameters
# Default values, see explanations below:
#self.name = 'Launcher'
self._isSerial = True
configDic = {
'useTorque': 'False',
'paraTorqueParams': '-l nodes=1:ppn=1',
'serialTorqueParams': '-l nodes=1:ppn=1',
'paraPrefix': '',
'paraPostfix': '',
'serialPrefix': '',
'serialPostfix': '',
'paraRemoteShell': '',
'outdir': None
}
if filename == None and configString == None:
filename = 'config.ini'
self.setting = Setting(filename, configString)
self.setting.section(QETask.name(self), configDic)
self.cleanOutDir = cleanOutDir
if self.setting.get('useTorque') == 'True':
self.setting.set('useTorque', True)
else:
self.setting.set('useTorque', False)
if self.setting.get('useTorque'):
if self.isSerial():
self._torque = QETorque(self.setting.get('serialTorqueParams'))
else:
self._torque = QETorque(self.setting.get('paraTorqueParams'))
def name(self):
return 'Launcher'
def _check(self, x):
"""
Will check the exit status of the program to be executed
"""
signal = x & 0xFF
exitcode = (x >> 8) & 0xFF
if exitcode != 0:
raise Exception("Task " + self.name() +
" crashed: check your settings" +
"Command string:" + self.cmdLine())
def _run(self):
if os.path.exists('CRASH'):
os.remove('CRASH')
outdir = self.setting.get('outdir')
if outdir != None:
os.system(self.setting.paraRemoteShell + ' mkdir -p ' + outdir)
if self.setting.get('useTorque'):
if self.isSerial():
if self.setting.get('serialPrefix') == '':
self._check(os.system(self.cmdLine()))
else:
self._torque.serial(
self.cmdLine(),
torqueParams=self.setting.serialTorqueParams)
else:
self._torque.serial(self.cmdLine(),
torqueParams=self.setting.paraTorqueParams)
else:
self._check(os.system(self.cmdLine()))
# if self.setting.paraPrefix != '' and self.setting.paraPrefix in self.cmdLine():
# if self.setting.useTorque:
# self._torque.serial(self.cmdLine())
# else:
# self._check(os.system(self.cmdLine()))
# else:
# self._check(os.system(self.cmdLine()))
if os.path.exists('CRASH'):
raise Exception("Task " + self.name() +
" crashed: 'CRASH' file was discovered")
def syncSetting(self):
"""
Will syncronise QE input file with class Setting for given task (QE input
files may contain multiple input/ouput file names definitions which
can be overriden in this method)
"""
pass
def cleanOutputDir(self, cleanOutDir=None):
"""
Cleans the output directory (directory, where large files, used
for calculation are stored, can be for example 'temp/' or 'scratch/')
"""
# import shutil
if cleanOutDir == None:
cleanOutDir = self.cleanOutDir
# if cleanOutDir == None:
# raise Exception('outDir can not be cleaned, since it was not defined')
if cleanOutDir:
outDir = self.setting.get('outdir')
os.system(self.setting.paraRemoteShell + ' rm -r -f ' + outDir)
os.system(self.setting.paraRemoteShell + ' mkdir ' + outDir)
# if self.setting.useTorque:
#
# else:
# shutil.rmtree(cleanOutDir)
# os.mkdir(cleanOutDir)
# def cmdLine(self):
# """
# returns command string of a given task
# """
# return self._cmdStr
def launch(self, cleanOutDir=False):
"""
Parses input. Launches task. Parses output.
"""
# if cleanOutDir == None:
# cleanOutDir = self.cleanOutDir
# if cleanOutDir != None:
# self.cleanOutputDir(cleanOutDir)
self.input.parse()
self.syncSetting() # sync setting with QE input file
self.input.save()
self.cleanOutputDir(cleanOutDir)
self._run()
self.output.parse(parserList='all')
def setSerial(self):
#self._serialThroughMPI = serialThroughMPI
self._isSerial = True
def setParallel(self):
self._isSerial = False
def isSerial(self):
if self._isSerial:
return True
else:
return False
def getPrefix(self):
if self.isSerial():
# if self._isSerialThroughMPI():
# return ''
# else:
return self.setting.get('serialPrefix')
else:
return self.setting.get('paraPrefix')
def getPostfix(self):
if self.isSerial():
return self.setting.get('serialPostfix')
else:
return self.setting.get('paraPostfix')
def _initCmdLineParams(self):
self._inp = '-inp'
self._devnul = '< /dev/null'
if self.isSerial():
self._inp = '<'
self._devnul = ''
# def _isSerialThroughMPI(self):
# if self.isSerial():
# if self._serialThroughMPI:
# return True
# else:
# return False
def _getCmdLine(self, executable, input, output):
self._initCmdLineParams()
return self.getPrefix() + ' ' + executable + " " + self.getPostfix() + \
' ' + self._inp + ' ' + self.setting.get(input) + ' > ' + \
self.setting.get(output) + self._devnul