def runMolns(self, data):
self.user_data.set_selected(2)
modelDb = StochKitModelWrapper.get_by_id(data["modelID"])
path = os.path.abspath(os.path.dirname(__file__))
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir=basedir + 'output')
job = ParameterSweepJobWrapper()
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.inData = json.dumps(data)
job.modelName = modelDb.name
job.outData = dataDir
job.status = "Pending"
job.output_stored = False
# # execute cloud task
try:
template_filename = 'parametersweep_template_{0}.py'.format(
data['modelType'])
logging.error(
"parametersweep.runMolns() template_filename={0}".format(
template_filename))
logging.error("*" * 80)
with open(os.path.join(path, template_filename), 'r') as f:
template = f.read()
templateData = {
"name": modelDb.name,
"modelType": modelDb.type,
"species": modelDb.species,
"parameters": modelDb.parameters,
"reactions": modelDb.reactions,
"speciesSelect": data['speciesSelect'],
"maxTime": data['maxTime'],
"increment": data['increment'],
"trajectories": data['trajectories'],
"seed": data['seed'],
"parameterA": data['parameterA'],
"minValueA": data['minValueA'],
"maxValueA": data['maxValueA'],
"stepsA": data['stepsA'],
"logA": data['logA'],
"parameterB": data['parameterB'],
"minValueB": data['minValueB'],
"maxValueB": data['maxValueB'],
"stepsB": data['stepsB'],
"logB": data['logB'],
"variableCount": data['variableCount'],
"isSpatial": modelDb.isSpatial,
"isLocal": False
}
if modelDb.isSpatial:
try:
meshWrapperDb = mesheditor.MeshWrapper.get_by_id(
modelDb.spatial["mesh_wrapper_id"])
except Exception as e:
raise Exception(
"No Mesh file set. Choose one in the Mesh tab of the Model Editor"
)
try:
meshFileObj = fileserver.FileManager.getFile(
self, meshWrapperDb.meshFileId, noFile=False)
templateData["mesh"] = meshFileObj["data"]
except IOError as e:
raise Exception("Mesh file inaccessible. Try another mesh")
templateData[
'reaction_subdomain_assignments'] = modelDb.spatial[
"reactions_subdomain_assignments"]
templateData[
'species_subdomain_assignments'] = modelDb.spatial[
"species_subdomain_assignments"]
templateData[
'species_diffusion_coefficients'] = modelDb.spatial[
"species_diffusion_coefficients"]
templateData['initial_conditions'] = modelDb.spatial[
"initial_conditions"]
templateData['subdomains'] = meshWrapperDb.subdomains
program = os.path.join(dataDir, 'program.py')
with open(program, 'w') as f:
jsonString = json.dumps(templateData, indent=4, sort_keys=True)
# We've got to double escape the strings here cause of how we're substituting the JSON data in a source file
jsonString = jsonString.replace('\\', '\\\\')
f.write(template.replace('___JSON_STRING___', jsonString))
molnsConfigDb = db.GqlQuery(
"SELECT * FROM MolnsConfigWrapper WHERE user_id = :1",
self.user.user_id()).get()
if not molnsConfigDb:
raise Exception("Molns not initialized")
config = molns.MOLNSConfig(config_dir=molnsConfigDb.folder)
result = molns.MOLNSExec.start_job(
['EC2_controller', "python {0}".format(program)], config)
job.resource = "molns"
job.molnsPID = result['id']
job.put()
except Exception as e:
job.status = 'Failed'
job.delete(self)
raise
return job
def runQsub(self, data, cluster_info):
logging.error("*" * 80)
logging.error("parametersweep.runQsub() modelType={0}".format(
data['modelType']))
logging.error("*" * 80)
modelDb = StochKitModelWrapper.get_by_id(data["modelID"])
path = os.path.abspath(os.path.dirname(__file__))
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir=basedir + 'output')
job = ParameterSweepJobWrapper()
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.inData = json.dumps(data)
job.modelName = modelDb.name
job.outData = dataDir
job.status = "Pending"
job.output_stored = False
try:
templateData = {
"name": modelDb.name,
"modelType": modelDb.type,
"species": modelDb.species,
"parameters": modelDb.parameters,
"reactions": modelDb.reactions,
"speciesSelect": data['speciesSelect'],
"maxTime": data['maxTime'],
"increment": data['increment'],
"trajectories": data['trajectories'],
"seed": data['seed'],
"parameterA": data['parameterA'],
"minValueA": data['minValueA'],
"maxValueA": data['maxValueA'],
"stepsA": data['stepsA'],
"logA": data['logA'],
"parameterB": data['parameterB'],
"minValueB": data['minValueB'],
"maxValueB": data['maxValueB'],
"stepsB": data['stepsB'],
"logB": data['logB'],
"variableCount": data['variableCount'],
"isSpatial": modelDb.isSpatial,
"isLocal": True
}
if modelDb.isSpatial:
try:
meshWrapperDb = mesheditor.MeshWrapper.get_by_id(
modelDb.spatial["mesh_wrapper_id"])
except Exception as e:
logging.exception(e)
logging.error(
"No Mesh file set. Choose one in the Mesh tab of the Model Editor"
)
raise Exception(
"No Mesh file set. Choose one in the Mesh tab of the Model Editor"
)
try:
meshFileObj = fileserver.FileManager.getFile(
self, meshWrapperDb.meshFileId, noFile=False)
templateData["mesh"] = meshFileObj["data"]
except IOError as e:
logging.exception(e)
logging.error("Mesh file inaccessible. Try another mesh")
raise Exception("Mesh file inaccessible. Try another mesh")
templateData[
'reaction_subdomain_assignments'] = modelDb.spatial[
"reactions_subdomain_assignments"]
templateData[
'species_subdomain_assignments'] = modelDb.spatial[
"species_subdomain_assignments"]
templateData[
'species_diffusion_coefficients'] = modelDb.spatial[
"species_diffusion_coefficients"]
templateData['initial_conditions'] = modelDb.spatial[
"initial_conditions"]
templateData['subdomains'] = meshWrapperDb.subdomains
if data['modelType'] == "stochastic":
job.qsubHandle = pickle.dumps(
parametersweep_qsub.stochastic(templateData, cluster_info))
elif data['modelType'] == "deterministic":
job.qsubHandle = pickle.dumps(
parametersweep_qsub.deterministic(templateData,
cluster_info))
elif data['modelType'] == "spatial":
job.qsubHandle = pickle.dumps(
parametersweep_qsub.spatial(templateData, cluster_info))
else:
raise Exception(
"Trying to runQsub on unsupported modelType {0}".format(
data['modelType']))
job.resource = "qsub"
job.put()
except Exception as e:
logging.exception(e)
job.status = 'Failed'
job.delete(self)
raise
return job
def runQsub(self, data, cluster_info):
logging.error("*"*80)
logging.error("parametersweep.runQsub() modelType={0}".format(data['modelType']))
logging.error("*"*80)
modelDb = StochKitModelWrapper.get_by_id(data["modelID"])
path = os.path.abspath(os.path.dirname(__file__))
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir = basedir + 'output')
job = ParameterSweepJobWrapper()
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.inData = json.dumps(data)
job.modelName = modelDb.name
job.outData = dataDir
job.status = "Pending"
job.output_stored = False
try:
templateData = {
"name" : modelDb.name,
"modelType" : modelDb.type,
"species" : modelDb.species,
"parameters" : modelDb.parameters,
"reactions" : modelDb.reactions,
"speciesSelect" : data['speciesSelect'],
"maxTime" : data['maxTime'],
"increment" : data['increment'],
"trajectories" : data['trajectories'],
"seed" : data['seed'],
"parameterA" : data['parameterA'],
"minValueA" : data['minValueA'],
"maxValueA" : data['maxValueA'],
"stepsA" : data['stepsA'],
"logA" : data['logA'],
"parameterB" : data['parameterB'],
"minValueB" : data['minValueB'],
"maxValueB" : data['maxValueB'],
"stepsB" : data['stepsB'],
"logB" : data['logB'],
"variableCount" : data['variableCount'],
"isSpatial" : modelDb.isSpatial,
"isLocal" : True
}
if modelDb.isSpatial:
try:
meshWrapperDb = mesheditor.MeshWrapper.get_by_id(modelDb.spatial["mesh_wrapper_id"])
except Exception as e:
logging.exception(e)
logging.error("No Mesh file set. Choose one in the Mesh tab of the Model Editor")
raise Exception("No Mesh file set. Choose one in the Mesh tab of the Model Editor")
try:
meshFileObj = fileserver.FileManager.getFile(self, meshWrapperDb.meshFileId, noFile = False)
templateData["mesh"] = meshFileObj["data"]
except IOError as e:
logging.exception(e)
logging.error("Mesh file inaccessible. Try another mesh")
raise Exception("Mesh file inaccessible. Try another mesh")
templateData['reaction_subdomain_assignments'] = modelDb.spatial["reactions_subdomain_assignments"]
templateData['species_subdomain_assignments'] = modelDb.spatial["species_subdomain_assignments"]
templateData['species_diffusion_coefficients'] = modelDb.spatial["species_diffusion_coefficients"]
templateData['initial_conditions'] = modelDb.spatial["initial_conditions"]
templateData['subdomains'] = meshWrapperDb.subdomains
if data['modelType'] == "stochastic":
job.qsubHandle = pickle.dumps(parametersweep_qsub.stochastic(templateData, cluster_info))
elif data['modelType'] == "deterministic":
job.qsubHandle = pickle.dumps(parametersweep_qsub.deterministic(templateData, cluster_info))
elif data['modelType'] == "spatial":
job.qsubHandle = pickle.dumps(parametersweep_qsub.spatial(templateData, cluster_info))
else:
raise Exception("Trying to runQsub on unsupported modelType {0}".format(data['modelType']))
job.resource = "qsub"
job.put()
except Exception as e:
logging.exception(e)
job.status='Failed'
job.delete(self)
raise
return job
def runMolns(self, data):
modelDb = StochKitModelWrapper.get_by_id(data["modelID"])
path = os.path.abspath(os.path.dirname(__file__))
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir = basedir + 'output')
job = ParameterSweepJobWrapper()
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.inData = json.dumps(data)
job.modelName = modelDb.name
job.outData = dataDir
job.status = "Pending"
job.output_stored = False
# # execute cloud task
try:
with open(os.path.join(path, 'parametersweep_template.py'), 'r') as f:
template = f.read()
templateData = {
"name" : modelDb.name,
"modelType" : modelDb.type,
"species" : modelDb.species,
"parameters" : modelDb.parameters,
"reactions" : modelDb.reactions,
"speciesSelect" : data['speciesSelect'],
"maxTime" : data['maxTime'],
"increment" : data['increment'],
"trajectories" : data['trajectories'],
"seed" : data['seed'],
"parameterA" : data['parameterA'],
"minValueA" : data['minValueA'],
"maxValueA" : data['maxValueA'],
"stepsA" : data['stepsA'],
"logA" : data['logA'],
"parameterB" : data['parameterB'],
"minValueB" : data['minValueB'],
"maxValueB" : data['maxValueB'],
"stepsB" : data['stepsB'],
"logB" : data['logB'],
"variableCount" : data['variableCount'],
"isSpatial" : modelDb.isSpatial,
"isLocal" : False
}
if modelDb.isSpatial:
try:
meshWrapperDb = mesheditor.MeshWrapper.get_by_id(modelDb.spatial["mesh_wrapper_id"])
except Exception as e:
raise Exception("No Mesh file set. Choose one in the Mesh tab of the Model Editor")
try:
meshFileObj = fileserver.FileManager.getFile(self, meshWrapperDb.meshFileId, noFile = False)
templateData["mesh"] = meshFileObj["data"]
except IOError as e:
raise Exception("Mesh file inaccessible. Try another mesh")
templateData['reaction_subdomain_assignments'] = modelDb.spatial["reactions_subdomain_assignments"]
templateData['species_subdomain_assignments'] = modelDb.spatial["species_subdomain_assignments"]
templateData['species_diffusion_coefficients'] = modelDb.spatial["species_diffusion_coefficients"]
templateData['initial_conditions'] = modelDb.spatial["initial_conditions"]
templateData['subdomains'] = meshWrapperDb.subdomains
program = os.path.join(dataDir, 'program.py')
with open(program, 'w') as f:
jsonString = json.dumps(templateData, indent = 4, sort_keys = True)
# We've got to double escape the strings here cause of how we're substituting the JSON data in a source file
jsonString = jsonString.replace('\\', '\\\\')
f.write(template.replace('___JSON_STRING___', jsonString))
molnsConfigDb = db.GqlQuery("SELECT * FROM MolnsConfigWrapper WHERE user_id = :1", self.user.user_id()).get()
if not molnsConfigDb:
raise Exception("Molns not initialized")
config = molns.MOLNSConfig(config_dir=molnsConfigDb.folder)
result = molns.MOLNSExec.start_job(['EC2_controller', "python {0}".format(program)], config)
job.resource = "molns"
job.molnsPID = result['id']
job.put()
except Exception as e:
job.status='Failed'
job.delete(self)
raise
return job
def runLocal(self, data):
self.user_data.set_selected(0)
logging.error("*"*80)
logging.error("parametersweep.runLocal() modelType={0}".format(data['modelType']))
logging.error("*"*80)
modelDb = StochKitModelWrapper.get_by_id(data["modelID"])
path = os.path.abspath(os.path.dirname(__file__))
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir = basedir + 'output')
job = ParameterSweepJobWrapper()
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.inData = json.dumps(data)
job.modelName = modelDb.name
job.outData = dataDir
job.status = "Pending"
job.output_stored = False
# # execute local task
try:
template_filename = 'parametersweep_template_{0}.py'.format(data['modelType'])
logging.error("parametersweep.runLocal() template_filename={0}".format(template_filename))
logging.error("*"*80)
with open(os.path.join(path,template_filename ), 'r') as f:
template = f.read()
templateData = {
"name" : modelDb.name,
"modelType" : modelDb.type,
"species" : modelDb.species,
"parameters" : modelDb.parameters,
"reactions" : modelDb.reactions,
"speciesSelect" : data['speciesSelect'],
"maxTime" : data['maxTime'],
"increment" : data['increment'],
"trajectories" : data['trajectories'],
"seed" : data['seed'],
"parameterA" : data['parameterA'],
"minValueA" : data['minValueA'],
"maxValueA" : data['maxValueA'],
"stepsA" : data['stepsA'],
"logA" : data['logA'],
"parameterB" : data['parameterB'],
"minValueB" : data['minValueB'],
"maxValueB" : data['maxValueB'],
"stepsB" : data['stepsB'],
"logB" : data['logB'],
"variableCount" : data['variableCount'],
"isSpatial" : modelDb.isSpatial,
"isLocal" : True
}
if modelDb.isSpatial:
try:
meshWrapperDb = mesheditor.MeshWrapper.get_by_id(modelDb.spatial["mesh_wrapper_id"])
except Exception as e:
logging.exception(e)
logging.error("No Mesh file set. Choose one in the Mesh tab of the Model Editor")
raise Exception("No Mesh file set. Choose one in the Mesh tab of the Model Editor")
try:
meshFileObj = fileserver.FileManager.getFile(self, meshWrapperDb.meshFileId, noFile = False)
templateData["mesh"] = meshFileObj["data"]
except IOError as e:
logging.exception(e)
logging.error("Mesh file inaccessible. Try another mesh")
raise Exception("Mesh file inaccessible. Try another mesh")
templateData['reaction_subdomain_assignments'] = modelDb.spatial["reactions_subdomain_assignments"]
templateData['species_subdomain_assignments'] = modelDb.spatial["species_subdomain_assignments"]
templateData['species_diffusion_coefficients'] = modelDb.spatial["species_diffusion_coefficients"]
templateData['initial_conditions'] = modelDb.spatial["initial_conditions"]
templateData['subdomains'] = meshWrapperDb.subdomains
program = os.path.join(dataDir, 'stochss_parametersweep_program.py')
with open(program, 'w') as f:
jsonString = json.dumps(templateData, indent = 4, sort_keys = True)
# We've got to double escape the strings here cause of how we're substituting the JSON data in a source file
jsonString = jsonString.replace('\\', '\\\\')
f.write(template.replace('___JSON_STRING___', jsonString))
#? molnsConfigDb = db.GqlQuery("SELECT * FROM MolnsConfigWrapper WHERE user_id = :1", self.user.user_id()).get()
#? if not molnsConfigDb:
#? raise Exception("Molns not initialized")
#?
#? config = molns.MOLNSConfig(config_dir=molnsConfigDb.folder)
#? result = molns.MOLNSExec.start_job(['EC2_controller', "python {0}".format(program)], config)
cmd = "python {0}".format(program)
logging.info('parametersweep.runLocal(): cmd={0}'.format(cmd))
logging.info('*'*80)
exstring = '{0}/backend/wrapper.py {1}/stdout {1}/stderr {1}/return_code {2}'.format(basedir, dataDir, cmd)
logging.info('parametersweep.runLocal(): exstring={0}'.format(exstring))
logging.info('*'*80)
handle = subprocess.Popen(exstring.split(), preexec_fn=os.setsid)
job.pid = handle.pid
logging.info("parametersweep.runLocal() job started pid={0}".format(job.pid))
logging.info('*'*80)
job.resource = "local"
job.put()
except Exception as e:
logging.exception(e)
job.status='Failed'
job.delete(self)
raise
return job