def execApbs(vars=None, argv=None):
""" Executes APBS and regulates checking of job status and retrieval of data if job is successfully completed. """
if argv is None:
# i.e. if it is a local run
argv = sys.argv
webRun = False
else:
webRun = True
custom_service_url = None
if vars != None:
if vars.has_key('service_url'):
custom_service_url = vars['service_url']
vars = initRemoteVars(argv)
if custom_service_url != None:
vars['service_url'] = custom_service_url
global service_url
#*argument parser
# command-line arguments
vars['inFile'] = argv[-1]
# parses input file
if(vars['inFile'].find("/")==-1):
directory=""
else:
directory = os.path.dirname(vars['inFile'])+'/'
vars['inFile'] = os.path.basename(vars['inFile'])
nprocs = 1
if not vars.has_key('service_url'):
# find out if it's sequential or parallel
tempFile = open(directory+vars['inFile'], 'r')
version_check_flag = True
for line in tempFile:
# remove whitespace
line=line.strip()
if(line[:5]=='pdime'):
dimension_array = line.split()
nprocs = int(dimension_array[1])*int(dimension_array[2])*int(dimension_array[3])
global parallel_service_url
vars['service_url'] = parallel_service_url
version_check_flag = False
if(line[:5]=='async'):
vars['service_url'] = service_url
version_check_flag = True
break
if version_check_flag:
vars['service_url'] = service_url
tempFile.close()
else:
version_check_flag = True # Enable version checking for custom defined Opal service as well
service_url = vars['service_url']
# Retrieve a reference to the AppServicePort
#*this is also from the path to the service
appServicePort = AppServiceLocator().getAppServicePort(vars['service_url'])
# Set up remote job launch
req = launchJobRequest()
# Checks version compatibility (but currently only works for sequential calculations)
if version_check_flag:
opal_version = AppServicePortTypeSoapBindingSOAP(vars['service_url']).getAppMetadata(getAppMetadataRequest())._usage.split()[-1]
if opal_version != local_version:
stderr.write("WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!\n")
stderr.write("It appears that the remote server version of APBS (%s) does not match\nthe local version (%s)!\n" % (opal_version,local_version))
stderr.write("Proceed at your own risk!!\n")
stderr.write("WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!\n")
if webRun:
return False
if(vars.has_key('argList')):
vars['argList'] = vars['argList'] + " " + vars['inFile']
else:
vars['argList']=vars['inFile']
req._argList = vars['argList']
req._numProcs = nprocs
# append all input files in this manner - in this case we have two of them
inputFiles = []
#*this is where apbs.in is read in
inputFiles.append(ns0.InputFileType_Def('inputFile'))
#*this must be the same as req._argList is defined to be
inputFiles[-1]._name = vars['inFile']
tempFile = open(directory+vars['inFile'], 'r')
inputFiles[-1]._contents = tempFile.read()
tempFile.close()
# this is where the rest of the files to read in are determined
start = False
tempFile = open(directory+vars['inFile'], 'r')
for line in tempFile:
# remove whitespace
line=line.strip()
if(line=="end"):
break
if(start and line.find("#")!=0):
# eliminates lines with just comments
# remove comment
if(line.find("#")!=-1):
line = line[:line.find("#")]
# re-remove whitespace (left after comment removal)
line=line.strip()
# remove everything except file name
count = -1
while line[count]!=' ':
count = count-1
fileName=line[count+1:]
inputFiles.append(ns0.InputFileType_Def('inputFile'))
inputFiles[-1]._name=fileName
tempFile2 = open(directory+fileName, "r")
inputFiles[-1]._contents = tempFile2.read()
tempFile2.close()
if(line=="read"):
start = True
tempFile.close()
# req's inputFile variable is the array of input files created in the lines directly above
req._inputFile = inputFiles
if vars['typeOfRun']=='remote':
appServicePort.launchJob(req)
return [appServicePort, appServicePort.launchJob(req)]
# Launch job, and retrieve job ID
print "Launching remote APBS job"
try:
resp = appServicePort.launchJob(req)
except ZSI.FaultException, errstr:
stderr.write("Error! Failed to execute Opal job. Please send the entire output to the APBS development team.\n")
stderr.write("%s\n" % errstr.fault.AsSoap())
sys.exit(13)
def execApbs(vars=None, argv=None):
""" Executes APBS and regulates checking of job status and retrieval of data if job is successfully completed. """
if argv is None:
# i.e. if it is a local run
argv = sys.argv
webRun = False
else:
webRun = True
custom_service_url = None
if vars != None:
if vars.has_key('service_url'):
custom_service_url = vars['service_url']
vars = initRemoteVars(argv)
if custom_service_url != None:
vars['service_url'] = custom_service_url
global service_url
#*argument parser
# command-line arguments
vars['inFile'] = argv[-1]
# parses input file
if (vars['inFile'].find("/") == -1):
directory = ""
else:
directory = os.path.dirname(vars['inFile']) + '/'
vars['inFile'] = os.path.basename(vars['inFile'])
nprocs = 1
if not vars.has_key('service_url'):
# find out if it's sequential or parallel
tempFile = open(directory + vars['inFile'], 'r')
version_check_flag = True
for line in tempFile:
# remove whitespace
line = line.strip()
if (line[:5] == 'pdime'):
dimension_array = line.split()
nprocs = int(dimension_array[1]) * int(
dimension_array[2]) * int(dimension_array[3])
global parallel_service_url
vars['service_url'] = parallel_service_url
version_check_flag = False
if (line[:5] == 'async'):
vars['service_url'] = service_url
version_check_flag = True
break
if version_check_flag:
vars['service_url'] = service_url
tempFile.close()
else:
version_check_flag = True # Enable version checking for custom defined Opal service as well
service_url = vars['service_url']
# Retrieve a reference to the AppServicePort
#*this is also from the path to the service
appServicePort = AppServiceLocator().getAppServicePort(vars['service_url'])
# Set up remote job launch
req = launchJobRequest()
# Checks version compatibility (but currently only works for sequential calculations)
if version_check_flag:
opal_version = AppServicePortTypeSoapBindingSOAP(
vars['service_url']).getAppMetadata(
getAppMetadataRequest())._usage.split()[-1]
if opal_version != local_version:
stderr.write(
"WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!\n"
)
stderr.write(
"It appears that the remote server version of APBS (%s) does not match\nthe local version (%s)!\n"
% (opal_version, local_version))
stderr.write("Proceed at your own risk!!\n")
stderr.write(
"WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!\n"
)
if webRun:
return False
if (vars.has_key('argList')):
vars['argList'] = vars['argList'] + " " + vars['inFile']
else:
vars['argList'] = vars['inFile']
req._argList = vars['argList']
req._numProcs = nprocs
# append all input files in this manner - in this case we have two of them
inputFiles = []
#*this is where apbs.in is read in
inputFiles.append(ns0.InputFileType_Def('inputFile'))
#*this must be the same as req._argList is defined to be
inputFiles[-1]._name = vars['inFile']
tempFile = open(directory + vars['inFile'], 'r')
inputFiles[-1]._contents = tempFile.read()
tempFile.close()
# this is where the rest of the files to read in are determined
start = False
tempFile = open(directory + vars['inFile'], 'r')
for line in tempFile:
# remove whitespace
line = line.strip()
if (line == "end"):
break
if (start and line.find("#") != 0):
# eliminates lines with just comments
# remove comment
if (line.find("#") != -1):
line = line[:line.find("#")]
# re-remove whitespace (left after comment removal)
line = line.strip()
# remove everything except file name
count = -1
while line[count] != ' ':
count = count - 1
fileName = line[count + 1:]
inputFiles.append(ns0.InputFileType_Def('inputFile'))
inputFiles[-1]._name = fileName
tempFile2 = open(directory + fileName, "r")
inputFiles[-1]._contents = tempFile2.read()
tempFile2.close()
if (line == "read"):
start = True
tempFile.close()
# req's inputFile variable is the array of input files created in the lines directly above
req._inputFile = inputFiles
if vars['typeOfRun'] == 'remote':
appServicePort.launchJob(req)
return [appServicePort, appServicePort.launchJob(req)]
# Launch job, and retrieve job ID
print "Launching remote APBS job"
try:
resp = appServicePort.launchJob(req)
except ZSI.FaultException, errstr:
stderr.write(
"Error! Failed to execute Opal job. Please send the entire output to the APBS development team.\n"
)
stderr.write("%s\n" % errstr.fault.AsSoap())
sys.exit(13)
