Merge pull request #290 from MetaCell/feature/263_avoid_kernel_crash

Feature/263 avoid kernel crash

Author: filippomc

netpyne_ui/netpyne_geppetto.py

@@ -100,9 +100,10 @@ def simulateNetPyNEModelInGeppetto(self, args):
                     self.geppetto_model = self.model_interpreter.getGeppettoModel(sim)
                     netpyne_model = sim
 
-                else:  # single cpu computation
+                else:
                     logging.info("Starting simulation")
-                    if not 'usePrevInst' in args or not args['usePrevInst']:
+
+                    if not args.get('usePrevInst', False):
                         logging.debug('Instantiating single thread simulation')
                         netpyne_model = self.instantiateNetPyNEModel()
                         self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model)
@@ -163,7 +164,8 @@ def remove(dictionary):
                 wake_up_geppetto = False
                 if all([args[option] for option in ['loadNetParams', 'loadSimCfg', 'loadSimData', 'loadNet']]):
                     wake_up_geppetto = True
-                    if self.doIhaveInstOrSimData()['haveInstance']: sim.clearAll()
+                    if self.doIhaveInstOrSimData()['haveInstance']:
+                        sim.clearAll()
                     sim.initialize()
                     sim.loadAll(args['jsonModelFolder'])
                     self.netParams = sim.net.params
@@ -173,7 +175,8 @@ def remove(dictionary):
                 else:
                     if args['loadNet']:
                         wake_up_geppetto = True
-                        if self.doIhaveInstOrSimData()['haveInstance']: sim.clearAll()
+                        if self.doIhaveInstOrSimData()['haveInstance']:
+                            sim.clearAll()
                         sim.initialize()
                         sim.loadNet(args['jsonModelFolder'])
 
@@ -191,7 +194,8 @@ def remove(dictionary):
                         remove(self.simConfig.todict())
 
                     if args['loadNetParams']:
-                        if self.doIhaveInstOrSimData()['haveInstance']: sim.clearAll()
+                        if self.doIhaveInstOrSimData()['haveInstance']:
+                            sim.clearAll()
                         sim.loadNetParams(args['jsonModelFolder'])
                         self.netParams = sim.net.params
                         remove(self.netParams.todict())
@@ -218,6 +222,11 @@ def importModel(self, modelParameters):
         :param modelParameters:
         :return:
         """
+        if self.doIhaveInstOrSimData()['haveInstance']:
+            # TODO: this must be integrated into the general lifecycle of "model change -> simulate"
+            #   Shouldn't be specific to Import
+            sim.clearAll()
+
         try:
             # Get Current dir
             owd = os.getcwd()
@@ -226,27 +235,30 @@ def importModel(self, modelParameters):
 
             with redirect_stdout(sys.__stdout__):
                 # NetParams
-                netParamsPath = str(modelParameters["netParamsPath"])
-                sys.path.append(netParamsPath)
-                os.chdir(netParamsPath)
+                net_params_path = str(modelParameters["netParamsPath"])
+                sys.path.append(net_params_path)
+                os.chdir(net_params_path)
                 # Import Module
-                netParamsModuleName = importlib.import_module(str(modelParameters["netParamsModuleName"]))
+                net_params_module_name = importlib.import_module(str(modelParameters["netParamsModuleName"]))
                 # Import Model attributes
-                self.netParams = getattr(netParamsModuleName, str(modelParameters["netParamsVariable"]))
+                self.netParams = getattr(net_params_module_name, str(modelParameters["netParamsVariable"]))
 
                 for key, value in self.netParams.cellParams.items():
                     if hasattr(value, 'todict'):
                         self.netParams.cellParams[key] = value.todict()
 
                 # SimConfig
-                simConfigPath = str(modelParameters["simConfigPath"])
-                sys.path.append(simConfigPath)
-                os.chdir(simConfigPath)
+                sim_config_path = str(modelParameters["simConfigPath"])
+                sys.path.append(sim_config_path)
+                os.chdir(sim_config_path)
                 # Import Module
-                simConfigModuleName = importlib.import_module(str(modelParameters["simConfigModuleName"]))
+                sim_config_module_name = importlib.import_module(str(modelParameters["simConfigModuleName"]))
                 # Import Model attributes
-                self.simConfig = getattr(simConfigModuleName, str(modelParameters["simConfigVariable"]))
+                self.simConfig = getattr(sim_config_module_name, str(modelParameters["simConfigVariable"]))
 
+                # TODO: when should sim.initialize be called?
+                #   Only on import or better before every simulation or network instantiation?
+                sim.initialize()
             return utils.getJSONReply()
         except:
             return utils.getJSONError("Error while importing the NetPyNE model", sys.exc_info())
@@ -319,7 +331,6 @@ def importNeuroML(self, modelParams):
             return utils.getJSONError("Error while exporting the NetPyNE model", sys.exc_info())
 
     def deleteModel(self, modelParams):
-
         try:
             with redirect_stdout(sys.__stdout__):
                 self.netParams = specs.NetParams()
@@ -332,8 +343,8 @@ def deleteModel(self, modelParams):
         try:
             # This function fails is some keys don't exists
             # sim.clearAll()
+            # TODO: as part of #264 we should remove the method and use clearAll intstead
             self.clearSim()
-
         except:
             pass
 
@@ -357,7 +368,11 @@ def simulateNetPyNEModel(self):
             sim.saveData()
         return sim
 
-    def doIhaveInstOrSimData(self):  # return [bool, bool] telling if we have an instance and simulated data
+    def doIhaveInstOrSimData(self):
+        """ Telling if we have an instance or simulated data.
+
+        return [bool, bool]
+        """
         with redirect_stdout(sys.__stdout__):
             out = [False, False]
             if hasattr(sim, 'net'):

webapp/components/topbar/menuConfiguration.js

@@ -325,6 +325,8 @@ export const getModelMenu = (props) => (
       label: TOPBAR_CONSTANTS.SIMULATE,
       action: {
         handlerAction: 'redux',
+        // TODO: (#263) this logic causes issues by potentially simulating
+        //  old instance with modified netParams and simConfig
         parameters: [props.modelState === MODEL_STATE.NOT_INSTANTIATED ? createAndSimulateNetwork : simulateNetwork],
       },
     },

webapp/redux/middleware/middleware.js

@@ -1,8 +1,7 @@
 import {
   UPDATE_CARDS, CREATE_NETWORK, CREATE_SIMULATE_NETWORK, PYTHON_CALL, SIMULATE_NETWORK, SHOW_NETWORK,
-  editModel, EDIT_MODEL, LOAD_TUTORIAL, RESET_MODEL, setDefaultWidgets,
+  editModel, EDIT_MODEL, LOAD_TUTORIAL, RESET_MODEL,
 } from '../actions/general';
-import FLEXLAYOUT_DEFAULT_STATE from '../../components/layout/defaultLayout';
 import { openBackendErrorDialog } from '../actions/errors';
 import { closeDrawerDialogBox } from '../actions/drawer';
 import Utils from '../../Utils';
@@ -68,7 +67,7 @@ export default (store) => (next) => (action) => {
       break;
     }
     case SIMULATE_NETWORK:
-      simulateNetwork({ parallelSimulation: false, usePrevInst: true }).then(toNetworkCallback(false), pythonErrorCallback);
+      simulateNetwork({ parallelSimulation: false, usePrevInst: false }).then(toNetworkCallback(false), pythonErrorCallback);
       break;
     case PYTHON_CALL: {
       const callback = (response) => {