def __init__(self, job_parms, **job_prop):
"""
To support the 2 ways of gamess job creation.
"""
name = "Gamess Job 1"
[self.job_batfile,
self.job_outputfile] = job_prop.get('job_from_file', [None, None])
if self.job_outputfile:
self.job_outputfile = self.job_outputfile.strip('"')
self.gamessJig = job_prop.get('jig', None)
if self.job_batfile:
server_id = job_parms['Server_id']
self.server = ServerManager().getServerById(int(server_id))
if not self.server:
raise ValueError, "The server of %d can't be found." % server_id
SimJob.__init__(self, name, job_parms)
self.edit_cntl = GamessProp()
#Huaicai 7/6/05: try to fix the problem when run a gamess jig coming from mmp file
#and without opening the jig property windows and save it.
if not self.__dict__.has_key('server'):
sManager = ServerManager()
self.server = sManager.getServers()[0]
return
def __init__(self, job_parms, **job_prop):
"""
To support the 2 ways of gamess job creation.
"""
name = "Gamess Job 1"
[self.job_batfile, self.job_outputfile] = job_prop.get('job_from_file', [None, None])
if self.job_outputfile:
self.job_outputfile = self.job_outputfile.strip('"')
self.gamessJig = job_prop.get('jig', None)
if self.job_batfile:
server_id = job_parms['Server_id']
self.server = ServerManager().getServerById(int(server_id))
if not self.server:
raise ValueError, "The server of %d can't be found." % server_id
SimJob.__init__(self, name, job_parms)
self.edit_cntl = GamessProp()
#Huaicai 7/6/05: try to fix the problem when run a gamess jig coming from mmp file
#and without opening the jig property windows and save it.
if not self.__dict__.has_key('server'):
sManager = ServerManager()
self.server = sManager.getServers()[0]
return
class GamessJob(SimJob):
"""
A Gamess job is a setup used to run Gamess simulation.
Two ways exist to create a Gamess Job:
(1). Create a Gamess Jig.
(2). A gamess job coming from a set of existing files
in a particular location.
"""
def __init__(self, job_parms, **job_prop):
"""
To support the 2 ways of gamess job creation.
"""
name = "Gamess Job 1"
[self.job_batfile, self.job_outputfile] = job_prop.get('job_from_file', [None, None])
if self.job_outputfile:
self.job_outputfile = self.job_outputfile.strip('"')
self.gamessJig = job_prop.get('jig', None)
if self.job_batfile:
server_id = job_parms['Server_id']
self.server = ServerManager().getServerById(int(server_id))
if not self.server:
raise ValueError, "The server of %d can't be found." % server_id
SimJob.__init__(self, name, job_parms)
self.edit_cntl = GamessProp()
#Huaicai 7/6/05: try to fix the problem when run a gamess jig coming from mmp file
#and without opening the jig property windows and save it.
if not self.__dict__.has_key('server'):
sManager = ServerManager()
self.server = sManager.getServers()[0]
return
def edit(self):
self.edit_cntl.showDialog(self)
return
def launch(self): # this method should probably exist in the superclass API too [bruce 071216 comment]
"""
Launch GAMESS job.
Returns: 0 = Success
1 = Cancelled
2 = Failed
"""
# Get a unique Job Id and the Job Id directory for this run.
from analysis.GAMESS.JobManager import get_job_manager_job_id_and_dir
### this causes an import cycle.
### FIX - pass in an obj providing this func? or just move this func into SimJob.py?
# [bruce 071216 comment]
job_id, job_id_dir = get_job_manager_job_id_and_dir()
self.Job_id = job_id
self.Status = 'Queued'
basename = self.gamessJig.name + "-" + self.gamessJig.gms_parms_info('_')
# GAMESS Job INP, OUT and BAT files.
self.job_inputfile = os.path.join(job_id_dir, "%s.inp" % basename)
self.job_outputfile = os.path.join(job_id_dir, "%s.out" % basename)
self.job_batfile = os.path.join(job_id_dir, "%s.bat" % basename)
# Write INP file (in ~/Nanorex/JobManager/Job Id subdirectory)
writegms_inpfile(self.job_inputfile, self.gamessJig)
# Create BAT file (in ~/Nanorex/JobManager/Job Id subdirectory)
## writegms_batfile(self.job_batfile, self)
# Open INP file in editor if user checked checkbox in GAMESS jig properties UI.
# if self.edit_cntl.edit_input_file_cbox.isChecked():
# open_file_in_editor(self.job_inputfile)
self.starttime = time.time() # Save the start time for this job.
# Validate Gamess Program
r = self._validate_gamess_program()
if r: # Gamess program was not valid.
return 1 # Job Cancelled.
try:
if sys.platform == 'win32': # Windows
return self._launch_pcgamess()
else: # Linux or MacOS
return self._launch_gamess()
except:
print_compact_traceback("Exception happened when run gamess")
return
def _validate_gamess_program(self):
"""
Private method:
Checks that the GAMESS program path exists in the user pref database
and that the file it points to exists. If the GAMESS path does not exist, the
user will be prompted with the file chooser to select the GAMESS executable.
This function does not check whether the GAMESS path is actually GAMESS
or if it is the correct version of GAMESS for this platform (i.e. PC GAMESS for Windows).
Returns: 0 = Valid
1 = Invalid
"""
# Get GAMESS executable path from the user preferences
prefs = preferences.prefs_context()
self.server.program = prefs.get(gmspath_prefs_key)
if not self.server.program:
msg = "The GAMESS executable path is not set.\n"
elif os.path.exists(self.server.program):
return 0
else:
msg = self.server.program + " does not exist.\n"
# GAMESS Prop Dialog is the parent for messagebox and file chooser.
parent = self.edit_cntl
ret = QMessageBox.warning( parent, "GAMESS Executable Path",
msg + "Please select OK to set the location of GAMESS for this computer.",
"&OK", "Cancel", "",
0, 1 )
if ret == 0: # OK
self.server.program = \
get_filename_and_save_in_prefs(parent, gmspath_prefs_key, "Choose GAMESS Executable")
if not self.server.program:
return 1 # Cancelled from file chooser.
# Enable GAMESS Plug-in. Mark 060112.
env.prefs[gamess_enabled_prefs_key] = True
elif ret == 1: # Cancel
return 1
return 0
def _readFromStdout(self):
"""
Slot method to read stdout of the gamess process
"""
#while self.process.canReadLineStdout():
# lineStr = str(self.process.readLineStdout()) + '\n'
# self.outputFile.write(lineStr)
bytes = self.process.readStdout()
self.outputFile.writeBlock(bytes)
return
def startFileWriting(self):
self.fwThread.start()
return
def readOutData(self):
bytes = self.process.readStdout()
if bytes:
self.fwThread.putData(bytes)
return
def processTimeout(self):
if self.process.isRunning():
if not self.progressDialog.isShown() or self.progressDialog.Rejected:
return
msgLabel = self.progressDialog.getMsgLabel()
duration = time.time() - self.stime
elapmsg = "Elapsed Time: " + hhmmss_str(int(duration))
msgLabel.setText(elapmsg)
####bytes = self.process.readStdout()
####if bytes:
#### self.fwThread.putData(bytes)
return
def processDone(self):
#self.fwThread.stop()
self.jobTimer.stop()
if self.process.normalExit():
print "The process is done!"
QDialog.accept(self.progressDialog)
else:
print "The process is cancelled!"
QDialog.reject(self.progressDialog)
return
def _launch_gamess(self):
oldir = os.getcwd() # Save current directory
####self.outputFile = QFile(self.job_outputfile)
####self.outputFile.open( IO_WriteOnly | IO_Append )
jobInputfile = os.path.basename(self.job_inputfile)
jobInputFile = jobInputfile[:-4]
jobOutputfile = self.job_outputfile #os.path.basename(self.job_outputfile)
### Notes: The following way to get the 'bin' works by assuming user didn't change the
### working directory after the atom runs, otherwise it will get problem.
filePath = os.path.dirname(os.path.abspath(sys.argv[0]))
program = os.path.normpath(filePath + '/../bin/rungms')
jobDir = os.path.dirname(self.job_batfile)
os.chdir(jobDir) # Change directory to the GAMESS temp directory.
# print "Current directory is: ", jobDir
executableFile = self.server.program
args = [program, jobInputFile, jobOutputfile, executableFile]#, '01', '1']
self.process = QProcess()
for s in args:
self.process.addArgument(s)
####self.process.setCommunication(QProcess.Stdout)
print "The params for the QProcess run are: ", args
####self.fwThread = _FileWriting(self.outputFile)
self.jobTimer = QTimer(self)
self.progressDialog = JobProgressDialog(self.process, self.Calculation)
self.connect(self.process, SIGNAL('processExited ()'), self.processDone)
#self.connect(self.process, SIGNAL('readyReadStdout()'), self.readOutData)
####self.fwThread.start()
if not self.process.start():
print "The process can't be started."
return 2
self.connect(self.jobTimer, SIGNAL('timeout()'), self.processTimeout)
self.stime = time.time()
self.jobTimer.start(1)
ret = self.progressDialog.exec_()
if ret == QDialog.Accepted:
retValue = 0
else:
retValue = 1
####self.fwThread.wait()
####bytes = self.process.readStdout()
####if bytes:
#####self.outputFile.writeBlock(bytes)
#####self.outputFile.flush()
self.process = None
####self.outputFile.close()
os.chdir(oldir)
self.gamessJig.outputfile = self.job_outputfile
return retValue
def _launch_pcgamess(self):
"""
Run PC GAMESS (Windows only).
PC GAMESS creates 2 output files:
- the DAT file, called "PUNCH", is written to the directory from which
PC GAMESS is started. This is why we chdir to the Gamess temp directory
before we run PC GAMESS.
- the OUT file (aka the log file), which we name jigname.out.
Returns: 0 = Success
1 = Cancelled
2 = Failed
"""
oldir = os.getcwd() # Save current directory
jobDir = os.path.dirname(self.job_batfile)
os.chdir(jobDir) # Change directory to the GAMESS temp directory.
## print "Current directory is: ", jobDir
DATfile = os.path.join(jobDir, "PUNCH")
if os.path.exists(DATfile): # Remove any previous DAT (PUNCH) file.
print "run_pcgamess: Removing DAT file: ", DATfile
os.remove(DATfile)
# Hours wasted testing this undocumented tripe. Here's the deal: When using spawnv
# on Windows, any args that might have spaces must be delimited by double quotes.
# Mark 050530.
#program = "\"" + self.job_batfile + "\""
#args = [program, ]
# Here's the infuriating part. The 2nd arg to spawnv cannot have double quotes, but the
# first arg in args (the program name) must have the double quotes if there is a space in
# self.gms_program.
#print "program = ", program
#print "Spawnv args are %r" % (args,) # this %r remains (see above)
#os.spawnv(os.P_WAIT, self.job_batfile, args)
arg_list = ['-i', self.job_inputfile, '-o', self.job_outputfile]
args = QStringList()
for s in arg_list:
args.append(str(s))
process = QProcess()
process.start(self.server.program, args)
# Blocks for n millisconds until the process has started and started()
# signal is emitted. Returns true if the process was started successfullly.
if not process.waitForStarted(2000):
print "The process can't be started."
return 2
progressDialog = self.showProgress()
progressDialog.show()
i = 55
pInc = True
while process.state() == QProcess.Running:
env.call_qApp_processEvents() #bruce 050908 replaced qApp.processEvents()
if progressDialog.wasCanceled():
process.kill()
os.chdir(oldir)
return 1 # Job cancelled.
progressDialog.setValue(i)
if pInc:
if i < 75: i += 1
else: pInc = False
else:
if i > 55: i -= 1
else: pInc = True
# Do sth here
time.sleep(0.05)
if not process.state() == QProcess.Running:
break
progressDialog.setValue(100)
progressDialog.accept()
os.chdir(oldir)
self.gamessJig.outputfile = self.job_outputfile
return 0 # Success
def showProgress(self, modal = True):
"""
Open the progress dialog to show the current job progress.
"""
#Replace "self.edit_cntl.win" with "None"
#---Huaicai 7/7/05: To fix bug 751, the "win" may be none.
#Feel awkward for the design of our code.
simProgressDialog = QProgressDialog()
simProgressDialog.setModal(True)
simProgressDialog.setObjectName("progressDialog")
simProgressDialog.setWindowIcon(geticon('ui/border/MainWindow'))
if self.Calculation == 'Energy':
simProgressDialog.setWindowTitle("Calculating Energy ...Please Wait")
else:
simProgressDialog.setWindowTitle("Optimizing ...Please Wait")
progBar = QProgressBar(simProgressDialog)
progBar.setMaximum(0)
progBar.setMinimum(0)
progBar.setValue(0)
progBar.setTextVisible(False)
simProgressDialog.setBar(progBar)
simProgressDialog.setAutoReset(False)
simProgressDialog.setAutoClose(False)
return simProgressDialog
# Added by Mark 050919 for bug #915. Not used yet.
def _job_cancelation_confirmed(self):
ret = QMessageBox.warning( None, "Confirm",
"Please confirm you want to abort the GAMESS simulation.\n",
"Confirm",
"Cancel",
"",
1, # The "default" button, when user presses Enter or Return (1 = Cancel)
1) # Escape (1= Cancel)
if ret == 0: # Confirmed
print "CONFIRMED"
return True
else:
print "CANCELLED"
return False
pass # end of class GamessJob
class GamessJob(SimJob):
"""
A Gamess job is a setup used to run Gamess simulation.
Two ways exist to create a Gamess Job:
(1). Create a Gamess Jig.
(2). A gamess job coming from a set of existing files
in a particular location.
"""
def __init__(self, job_parms, **job_prop):
"""
To support the 2 ways of gamess job creation.
"""
name = "Gamess Job 1"
[self.job_batfile,
self.job_outputfile] = job_prop.get('job_from_file', [None, None])
if self.job_outputfile:
self.job_outputfile = self.job_outputfile.strip('"')
self.gamessJig = job_prop.get('jig', None)
if self.job_batfile:
server_id = job_parms['Server_id']
self.server = ServerManager().getServerById(int(server_id))
if not self.server:
raise ValueError, "The server of %d can't be found." % server_id
SimJob.__init__(self, name, job_parms)
self.edit_cntl = GamessProp()
#Huaicai 7/6/05: try to fix the problem when run a gamess jig coming from mmp file
#and without opening the jig property windows and save it.
if not self.__dict__.has_key('server'):
sManager = ServerManager()
self.server = sManager.getServers()[0]
return
def edit(self):
self.edit_cntl.showDialog(self)
return
def launch(
self
): # this method should probably exist in the superclass API too [bruce 071216 comment]
"""
Launch GAMESS job.
Returns: 0 = Success
1 = Cancelled
2 = Failed
"""
# Get a unique Job Id and the Job Id directory for this run.
from analysis.GAMESS.JobManager import get_job_manager_job_id_and_dir
### this causes an import cycle.
### FIX - pass in an obj providing this func? or just move this func into SimJob.py?
# [bruce 071216 comment]
job_id, job_id_dir = get_job_manager_job_id_and_dir()
self.Job_id = job_id
self.Status = 'Queued'
basename = self.gamessJig.name + "-" + self.gamessJig.gms_parms_info(
'_')
# GAMESS Job INP, OUT and BAT files.
self.job_inputfile = os.path.join(job_id_dir, "%s.inp" % basename)
self.job_outputfile = os.path.join(job_id_dir, "%s.out" % basename)
self.job_batfile = os.path.join(job_id_dir, "%s.bat" % basename)
# Write INP file (in ~/Nanorex/JobManager/Job Id subdirectory)
writegms_inpfile(self.job_inputfile, self.gamessJig)
# Create BAT file (in ~/Nanorex/JobManager/Job Id subdirectory)
## writegms_batfile(self.job_batfile, self)
# Open INP file in editor if user checked checkbox in GAMESS jig properties UI.
# if self.edit_cntl.edit_input_file_cbox.isChecked():
# open_file_in_editor(self.job_inputfile)
self.starttime = time.time() # Save the start time for this job.
# Validate Gamess Program
r = self._validate_gamess_program()
if r: # Gamess program was not valid.
return 1 # Job Cancelled.
try:
if sys.platform == 'win32': # Windows
return self._launch_pcgamess()
else: # Linux or MacOS
return self._launch_gamess()
except:
print_compact_traceback("Exception happened when run gamess")
return
def _validate_gamess_program(self):
"""
Private method:
Checks that the GAMESS program path exists in the user pref database
and that the file it points to exists. If the GAMESS path does not exist, the
user will be prompted with the file chooser to select the GAMESS executable.
This function does not check whether the GAMESS path is actually GAMESS
or if it is the correct version of GAMESS for this platform (i.e. PC GAMESS for Windows).
Returns: 0 = Valid
1 = Invalid
"""
# Get GAMESS executable path from the user preferences
prefs = preferences.prefs_context()
self.server.program = prefs.get(gmspath_prefs_key)
if not self.server.program:
msg = "The GAMESS executable path is not set.\n"
elif os.path.exists(self.server.program):
return 0
else:
msg = self.server.program + " does not exist.\n"
# GAMESS Prop Dialog is the parent for messagebox and file chooser.
parent = self.edit_cntl
ret = QMessageBox.warning(
parent, "GAMESS Executable Path", msg +
"Please select OK to set the location of GAMESS for this computer.",
"&OK", "Cancel", "", 0, 1)
if ret == 0: # OK
self.server.program = \
get_filename_and_save_in_prefs(parent, gmspath_prefs_key, "Choose GAMESS Executable")
if not self.server.program:
return 1 # Cancelled from file chooser.
# Enable GAMESS Plug-in. Mark 060112.
env.prefs[gamess_enabled_prefs_key] = True
elif ret == 1: # Cancel
return 1
return 0
def _readFromStdout(self):
"""
Slot method to read stdout of the gamess process
"""
#while self.process.canReadLineStdout():
# lineStr = str(self.process.readLineStdout()) + '\n'
# self.outputFile.write(lineStr)
bytes = self.process.readStdout()
self.outputFile.writeBlock(bytes)
return
def startFileWriting(self):
self.fwThread.start()
return
def readOutData(self):
bytes = self.process.readStdout()
if bytes:
self.fwThread.putData(bytes)
return
def processTimeout(self):
if self.process.isRunning():
if not self.progressDialog.isShown(
) or self.progressDialog.Rejected:
return
msgLabel = self.progressDialog.getMsgLabel()
duration = time.time() - self.stime
elapmsg = "Elapsed Time: " + hhmmss_str(int(duration))
msgLabel.setText(elapmsg)
####bytes = self.process.readStdout()
####if bytes:
#### self.fwThread.putData(bytes)
return
def processDone(self):
#self.fwThread.stop()
self.jobTimer.stop()
if self.process.normalExit():
print "The process is done!"
QDialog.accept(self.progressDialog)
else:
print "The process is cancelled!"
QDialog.reject(self.progressDialog)
return
def _launch_gamess(self):
oldir = os.getcwd() # Save current directory
####self.outputFile = QFile(self.job_outputfile)
####self.outputFile.open( IO_WriteOnly | IO_Append )
jobInputfile = os.path.basename(self.job_inputfile)
jobInputFile = jobInputfile[:-4]
jobOutputfile = self.job_outputfile #os.path.basename(self.job_outputfile)
### Notes: The following way to get the 'bin' works by assuming user didn't change the
### working directory after the atom runs, otherwise it will get problem.
filePath = os.path.dirname(os.path.abspath(sys.argv[0]))
program = os.path.normpath(filePath + '/../bin/rungms')
jobDir = os.path.dirname(self.job_batfile)
os.chdir(jobDir) # Change directory to the GAMESS temp directory.
# print "Current directory is: ", jobDir
executableFile = self.server.program
args = [program, jobInputFile, jobOutputfile,
executableFile] #, '01', '1']
self.process = QProcess()
for s in args:
self.process.addArgument(s)
####self.process.setCommunication(QProcess.Stdout)
print "The params for the QProcess run are: ", args
####self.fwThread = _FileWriting(self.outputFile)
self.jobTimer = QTimer(self)
self.progressDialog = JobProgressDialog(self.process, self.Calculation)
self.connect(self.process, SIGNAL('processExited ()'),
self.processDone)
#self.connect(self.process, SIGNAL('readyReadStdout()'), self.readOutData)
####self.fwThread.start()
if not self.process.start():
print "The process can't be started."
return 2
self.connect(self.jobTimer, SIGNAL('timeout()'), self.processTimeout)
self.stime = time.time()
self.jobTimer.start(1)
ret = self.progressDialog.exec_()
if ret == QDialog.Accepted:
retValue = 0
else:
retValue = 1
####self.fwThread.wait()
####bytes = self.process.readStdout()
####if bytes:
#####self.outputFile.writeBlock(bytes)
#####self.outputFile.flush()
self.process = None
####self.outputFile.close()
os.chdir(oldir)
self.gamessJig.outputfile = self.job_outputfile
return retValue
def _launch_pcgamess(self):
"""
Run PC GAMESS (Windows only).
PC GAMESS creates 2 output files:
- the DAT file, called "PUNCH", is written to the directory from which
PC GAMESS is started. This is why we chdir to the Gamess temp directory
before we run PC GAMESS.
- the OUT file (aka the log file), which we name jigname.out.
Returns: 0 = Success
1 = Cancelled
2 = Failed
"""
oldir = os.getcwd() # Save current directory
jobDir = os.path.dirname(self.job_batfile)
os.chdir(jobDir) # Change directory to the GAMESS temp directory.
## print "Current directory is: ", jobDir
DATfile = os.path.join(jobDir, "PUNCH")
if os.path.exists(DATfile): # Remove any previous DAT (PUNCH) file.
print "run_pcgamess: Removing DAT file: ", DATfile
os.remove(DATfile)
# Hours wasted testing this undocumented tripe. Here's the deal: When using spawnv
# on Windows, any args that might have spaces must be delimited by double quotes.
# Mark 050530.
#program = "\"" + self.job_batfile + "\""
#args = [program, ]
# Here's the infuriating part. The 2nd arg to spawnv cannot have double quotes, but the
# first arg in args (the program name) must have the double quotes if there is a space in
# self.gms_program.
#print "program = ", program
#print "Spawnv args are %r" % (args,) # this %r remains (see above)
#os.spawnv(os.P_WAIT, self.job_batfile, args)
arg_list = ['-i', self.job_inputfile, '-o', self.job_outputfile]
args = QStringList()
for s in arg_list:
args.append(str(s))
process = QProcess()
process.start(self.server.program, args)
# Blocks for n millisconds until the process has started and started()
# signal is emitted. Returns true if the process was started successfullly.
if not process.waitForStarted(2000):
print "The process can't be started."
return 2
progressDialog = self.showProgress()
progressDialog.show()
i = 55
pInc = True
while process.state() == QProcess.Running:
env.call_qApp_processEvents(
) #bruce 050908 replaced qApp.processEvents()
if progressDialog.wasCanceled():
process.kill()
os.chdir(oldir)
return 1 # Job cancelled.
progressDialog.setValue(i)
if pInc:
if i < 75: i += 1
else: pInc = False
else:
if i > 55: i -= 1
else: pInc = True
# Do sth here
time.sleep(0.05)
if not process.state() == QProcess.Running:
break
progressDialog.setValue(100)
progressDialog.accept()
os.chdir(oldir)
self.gamessJig.outputfile = self.job_outputfile
return 0 # Success
def showProgress(self, modal=True):
"""
Open the progress dialog to show the current job progress.
"""
#Replace "self.edit_cntl.win" with "None"
#---Huaicai 7/7/05: To fix bug 751, the "win" may be none.
#Feel awkward for the design of our code.
simProgressDialog = QProgressDialog()
simProgressDialog.setModal(True)
simProgressDialog.setObjectName("progressDialog")
simProgressDialog.setWindowIcon(geticon('ui/border/MainWindow'))
if self.Calculation == 'Energy':
simProgressDialog.setWindowTitle(
"Calculating Energy ...Please Wait")
else:
simProgressDialog.setWindowTitle("Optimizing ...Please Wait")
progBar = QProgressBar(simProgressDialog)
progBar.setMaximum(0)
progBar.setMinimum(0)
progBar.setValue(0)
progBar.setTextVisible(False)
simProgressDialog.setBar(progBar)
simProgressDialog.setAutoReset(False)
simProgressDialog.setAutoClose(False)
return simProgressDialog
# Added by Mark 050919 for bug #915. Not used yet.
def _job_cancelation_confirmed(self):
ret = QMessageBox.warning(
None,
"Confirm",
"Please confirm you want to abort the GAMESS simulation.\n",
"Confirm",
"Cancel",
"",
1, # The "default" button, when user presses Enter or Return (1 = Cancel)
1) # Escape (1= Cancel)
if ret == 0: # Confirmed
print "CONFIRMED"
return True
else:
print "CANCELLED"
return False
pass # end of class GamessJob
