fix: Fixing the memory leak issues from #43 for real this time. Also …

…fixing the segfault errors from #43

src/param_id/paramID.py

@@ -2131,6 +2131,13 @@ def run(self):
                         #     rand_survivor_idx = np.random.choice(np.arange(num_elite, num_pop), p=survive_prob)
                         #     param_vals_norm[:, param_idx] = param_vals_norm[:, rand_survivor_idx]
                         #
+
+                        # set the cases with nan cost to have a very large but not nan cost
+                        for idx in range(num_pop):
+                            if np.isnan(cost[idx]):
+                                cost[idx] = 1e25
+                            if cost[idx] > 1e25:
+                                cost[idx] = 1e25
                         survive_prob = cost[num_elite:num_pop]**-1/sum(cost[num_elite:num_pop]**-1)
                         rand_survivor_idxs = np.random.choice(np.arange(num_elite, num_pop),
                                                             size=num_survivors-num_elite, p=survive_prob)
@@ -2468,7 +2475,7 @@ def get_cost_obs_and_pred_from_params(self, param_vals, reset=True,
                     pred_outputs_list.append(pred_outputs)
                 # reset params
                 if reset:
-                    self.sim_helper.reset_and_clear(only_one_exp=only_one_exp)
+                    self.sim_helper.reset_and_clear()
 
             else:
                 # simulation set cost to large,
@@ -2557,7 +2564,7 @@ def get_cost_obs_and_pred_from_params(self, param_vals, reset=True,
 
         return cost, operands_outputs_list, pred_outputs_list
 
-    def get_cost_and_obs_from_params(self, param_vals, reset=True, only_one_exp=1):
+    def get_cost_and_obs_from_params(self, param_vals, reset=True, only_one_exp=-1):
         cost, obs, _ = self.get_cost_obs_and_pred_from_params(param_vals, reset=reset, only_one_exp=only_one_exp)
         return cost, obs
 

src/utilities/opencor_helper.py

@@ -71,9 +71,6 @@ def reset_and_clear(self, only_one_exp=-1):
         # mem = self.process_memory()
         # print(f'memory_pre_clear={mem}')
         self.simulation.reset(True)
-        # if only_one_exp != -1:
-        #     # for some reason if i only do one simulation and then release values there is a seg fault.
-        #     # so here i don't release all values.
         self.simulation.release_all_values()
         self.simulation.clear_results()
         # mem = self.process_memory()
@@ -104,11 +101,11 @@ def get_results(self, variables_list_of_lists, flatten=False):
                 if variable_name == 'time':
                     results[JJ].append(self.tSim)
                 elif variable_name in self.simulation.results().states():
-                    results[JJ].append(self.simulation.results().states()[variable_name].values()[-self.n_steps - 1:])
+                    results[JJ].append(self.simulation.results().states()[variable_name].values()[-self.n_steps - 1:].copy())
                 elif variable_name in self.simulation.results().algebraic():
-                    results[JJ].append(self.simulation.results().algebraic()[variable_name].values()[-self.n_steps-1:])
+                    results[JJ].append(self.simulation.results().algebraic()[variable_name].values()[-self.n_steps-1:].copy())
                 elif variable_name in self.data.constants():
-                    results[JJ].append(self.data.constants()[variable_name])
+                    results[JJ].append(self.data.constants()[variable_name].copy())
                 else:
                     print(f'variable {variable_name} is not a model variable. model variables are')
                     print([name for name in self.simulation.results().states()])