def runQsub(self, data, cluster_info): logging.error("*" * 80) logging.error("simulate.runQsub() modelType={0}".format( data['execType'])) logging.error("*" * 80) modelDb = StochKitModelWrapper.get_by_id(int(data["id"])) path = os.path.abspath(os.path.dirname(__file__)) basedir = path + '/../' dataDir = tempfile.mkdtemp(dir=basedir + 'output') job = SpatialJobWrapper() 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" job.is_spatial = True try: templateData = { "name": modelDb.name, "modelType": modelDb.type, "species": modelDb.species, "parameters": modelDb.parameters, "reactions": modelDb.reactions, # "speciesSelect": data['speciesSelect'], "speciesSelect": data['selections'], # "maxTime": data['maxTime'], "maxTime": data['time'], "increment": data['increment'], # "trajectories": data['trajectories'], "trajectories": data['realizations'], "seed": data['seed'], "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['execType'] == "stochastic": job.qsubHandle = pickle.dumps( parametersweep_qsub.stochastic( templateData, cluster_info, not_full_parameter_sweep=True)) elif data['execType'] == "deterministic": job.qsubHandle = pickle.dumps( parametersweep_qsub.deterministic( templateData, cluster_info, not_full_parameter_sweep=True)) elif data['execType'] == "spatial": job.qsubHandle = pickle.dumps( parametersweep_qsub.spatial( templateData, cluster_info, not_full_parameter_sweep=True)) # 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("simulate.runQsub() modelType={0}".format(data['execType'])) logging.error("*" * 80) modelDb = StochKitModelWrapper.get_by_id(int(data["id"])) path = os.path.abspath(os.path.dirname(__file__)) basedir = path + '/../' dataDir = tempfile.mkdtemp(dir=basedir + 'output') job = SpatialJobWrapper() 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" job.is_spatial = True try: templateData = { "name": modelDb.name, "modelType": modelDb.type, "species": modelDb.species, "parameters": modelDb.parameters, "reactions": modelDb.reactions, # "speciesSelect": data['speciesSelect'], "speciesSelect": data['selections'], # "maxTime": data['maxTime'], "maxTime": data['time'], "increment": data['increment'], # "trajectories": data['trajectories'], "trajectories": data['realizations'], "seed": data['seed'], "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['execType'] == "stochastic": job.qsubHandle = pickle.dumps(parametersweep_qsub.stochastic(templateData, cluster_info, not_full_parameter_sweep=True)) elif data['execType'] == "deterministic": job.qsubHandle = pickle.dumps(parametersweep_qsub.deterministic(templateData, cluster_info, not_full_parameter_sweep=True)) elif data['execType'] == "spatial": job.qsubHandle = pickle.dumps(parametersweep_qsub.spatial(templateData, cluster_info, not_full_parameter_sweep=True))# 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