Memory Leak Fixes

include/all.hxx

@@ -239,7 +239,7 @@ extern void                     listReverseOrder(struct wetting_front** head_ref
 extern bool                     listFindLayer(struct wetting_front* link, int num_layers, double *cum_layer_thickness_cm,
 					      int *lives_in_layer, bool *extends_to_bottom_flag);
 extern struct wetting_front*    listCopy(struct wetting_front* current, struct wetting_front* state_previous=NULL);
-
+extern void listDelete(struct wetting_front* head);
 
 
 

include/bmi_lgar.hxx

@@ -29,7 +29,8 @@ class NotImplemented : public std::logic_error {
 
 class BmiLGAR : public bmi::Bmi {
 public:
-  BmiLGAR() {
+  ~BmiLGAR();
+  BmiLGAR():giuh_ordinates(nullptr), giuh_runoff_queue(nullptr) {
     this->input_var_names[0] = "precipitation_rate";
     this->input_var_names[1] = "potential_evapotranspiration_rate";
     this->input_var_names[2] = "soil_temperature_profile";
@@ -131,6 +132,7 @@ public:
   struct model_state* get_model();
 
 private:
+  void realloc_soil();
   struct model_state* state;
   static const int input_var_name_count  = 3;
   static const int output_var_name_count = 15;

src/bmi_lgar.cxx

@@ -17,6 +17,14 @@
 // default verbosity is set to 'none' other option 'high' or 'low' needs to be specified in the config file
 string verbosity="none";
 
+/**
+ * @brief Delete dynamic arrays allocated in Initialize() and held by this object
+ * 
+ */
+BmiLGAR::~BmiLGAR(){
+  if( giuh_ordinates != nullptr ) delete [] giuh_ordinates;
+  if( giuh_runoff_queue != nullptr ) delete [] giuh_runoff_queue;
+}
 
 /* The `head` pointer stores the address in memory of the first member of the linked list containing
    all the wetting fronts. The contents of struct wetting_front are defined in "all.h" */
@@ -48,6 +56,20 @@ Initialize (std::string config_file)
 
 }
 
+/**
+ * @brief Allocate (or reallocate) storage for soil parameters
+ * 
+ */
+void BmiLGAR::realloc_soil(){
+  if(state->lgar_bmi_params.soil_depth_wetting_fronts != nullptr)
+    delete [] state->lgar_bmi_params.soil_depth_wetting_fronts;
+  if(state->lgar_bmi_params.soil_moisture_wetting_fronts != nullptr)
+    delete [] state->lgar_bmi_params.soil_moisture_wetting_fronts;
+
+  state->lgar_bmi_params.soil_depth_wetting_fronts = new double[state->lgar_bmi_params.num_wetting_fronts];
+  state->lgar_bmi_params.soil_moisture_wetting_fronts = new double[state->lgar_bmi_params.num_wetting_fronts];
+}
+
 /*
   This is the main function calling lgar subroutines for creating, moving, and merging wetting fronts.
   Calls to AET and mass balance module are also happening here
@@ -143,7 +165,10 @@ Update()
       std::cerr<<"BMI Update |Timesteps = "<< state->lgar_bmi_params.timesteps<<", Time [h] = "<<this->state->lgar_bmi_params.time_s / 3600.<<", Subcycle = "<< cycle <<" of "<<subcycles<<std::endl;
     }
 
-    state->state_previous = NULL;
+    if( state->state_previous != NULL ){
+      listDelete(state->state_previous);
+      state->state_previous = NULL;
+    }
     state->state_previous = listCopy(state->head);
 
     // ensure precip and PET are non-negative
@@ -270,7 +295,10 @@ Update()
         listPrint(state->head);
       }
 
-      state->state_previous = NULL;
+      if(state->state_previous != NULL ){
+        listDelete(state->state_previous);
+        state->state_previous = NULL;
+      }
       state->state_previous = listCopy(state->head);
 
       volin_timestep_cm += volin_subtimestep_cm;
@@ -422,8 +450,7 @@ Update()
   state->lgar_bmi_params.num_wetting_fronts = listLength(state->head);
 
   // allocate new memory based on updated wetting fronts; we could make it conditional i.e. create only if no. of wf are changed
-  state->lgar_bmi_params.soil_depth_wetting_fronts = new double[state->lgar_bmi_params.num_wetting_fronts];
-  state->lgar_bmi_params.soil_moisture_wetting_fronts = new double[state->lgar_bmi_params.num_wetting_fronts];
+  realloc_soil();
 
   // update thickness/depth and soil moisture of wetting fronts (used for state coupling)
   struct wetting_front *current = state->head;
@@ -583,6 +610,30 @@ void BmiLGAR::
 Finalize()
 {
   global_mass_balance();
+  if( state->head != NULL ) listDelete(state->head);
+  if( state->state_previous != NULL ) listDelete(state->state_previous);
+
+  if( state->soil_properties != nullptr ) delete [] state->soil_properties;
+
+  if( state->lgar_bmi_params.soil_depth_wetting_fronts != nullptr ) delete [] state->lgar_bmi_params.soil_depth_wetting_fronts;
+  if( state->lgar_bmi_params.soil_moisture_wetting_fronts != nullptr) delete [] state->lgar_bmi_params.soil_moisture_wetting_fronts;
+
+  if( state->lgar_bmi_params.soil_temperature != nullptr ) delete [] state->lgar_bmi_params.soil_temperature;
+  if( state->lgar_bmi_params.soil_temperature_z != nullptr)  delete [] state->lgar_bmi_params.soil_temperature_z;
+  if( state->lgar_bmi_params.layer_soil_type != nullptr ) delete [] state->lgar_bmi_params.layer_soil_type;
+
+  if( state->lgar_calib_params.theta_e != nullptr ) delete [] state->lgar_calib_params.theta_e;
+  if( state->lgar_calib_params.theta_r != nullptr ) delete [] state->lgar_calib_params.theta_r;
+  if( state->lgar_calib_params.vg_n != nullptr ) delete [] state->lgar_calib_params.vg_n;
+  if( state->lgar_calib_params.vg_alpha != nullptr ) delete [] state->lgar_calib_params.vg_alpha;
+  if( state->lgar_calib_params.Ksat != nullptr ) delete [] state->lgar_calib_params.Ksat;
+
+  if( state->lgar_bmi_params.layer_thickness_cm != nullptr ) delete [] state->lgar_bmi_params.layer_thickness_cm;
+  if( state->lgar_bmi_params.cum_layer_thickness_cm != nullptr ) delete [] state->lgar_bmi_params.cum_layer_thickness_cm;
+  if( state->lgar_bmi_params.giuh_ordinates != nullptr ) delete [] state->lgar_bmi_params.giuh_ordinates;
+  if( state->lgar_bmi_params.frozen_factor != nullptr ) delete [] state->lgar_bmi_params.frozen_factor;
+  if( state->lgar_bmi_input_params != nullptr ) delete state->lgar_bmi_input_params;
+  if( state != nullptr ) delete state;
 }
 
 

src/bmi_main_lgar.cxx

@@ -155,13 +155,15 @@ int main(int argc, char *argv[])
       // write layers data to file
       fprintf(outlayer_fptr,"# Timestep = %d, %s \n", i, time[i].c_str());
       write_state(outlayer_fptr, model_state.get_model()->head);
+      delete [] soil_moisture_wetting_front;
+      delete [] soil_thickness_wetting_front;
     }
 
   }
 
   // do final mass balance
   model_state.global_mass_balance();
-
+  model_state.Finalize();
   if (outdata_fptr) {
     fclose(outdata_fptr);
     fclose(outlayer_fptr);

src/lgar.cxx

@@ -643,6 +643,7 @@ extern void InitFromConfigFile(string config_file, struct model_state *state)
     }
   }
   else {
+    //NJF FIXME these arrays should be allocated based on num_cells_temp...
     state->lgar_bmi_params.soil_temperature   = new double[1]();
     state->lgar_bmi_params.soil_temperature_z = new double[1]();
     state->lgar_bmi_params.num_cells_temp     = 1;
@@ -1117,6 +1118,8 @@ extern void lgar_move_wetting_fronts(double timestep_h, double *volin_cm, int wf
 	double theta_below = 0.0;
 
 	new_mass += layer_thickness * (theta - theta_below);
+  //NJF theta_below is always 0, so all delta_thetas are always 0...
+  //does this really need a dynamic array in this case???
 	delta_thetas[k] = theta_below;
 	delta_thickness[k] = layer_thickness;
       }
@@ -1134,7 +1137,9 @@ extern void lgar_move_wetting_fronts(double timestep_h, double *volin_cm, int wf
       double theta_new = lgar_theta_mass_balance(layer_num, soil_num, psi_cm, new_mass, prior_mass, AET_demand_cm,
 						 delta_thetas, delta_thickness, soil_type, soil_properties);
       actual_ET_demand = *AET_demand_cm;
-
+      //done with delta_thetas and delta_thickness, cleanup memory
+      free(delta_thetas);
+      free(delta_thickness);
       current->theta = fmax(theta_r, fmin(theta_new, theta_e));
 
       double Se = calc_Se_from_theta(current->theta,theta_e,theta_r);
@@ -1276,7 +1281,9 @@ extern void lgar_move_wetting_fronts(double timestep_h, double *volin_cm, int wf
 	double theta_new = lgar_theta_mass_balance(layer_num, soil_num, psi_cm, new_mass, prior_mass, AET_demand_cm,
 						   delta_thetas, delta_thickness, soil_type, soil_properties);
   actual_ET_demand = *AET_demand_cm;
-
+  //done with delta_thetas and delta_thickness, cleanup memory
+  free(delta_thetas);
+  free(delta_thickness);
 	current->theta = fmax(theta_r, fmin(theta_new, theta_e));
 
       }

src/linked_list.cxx

@@ -26,6 +26,20 @@
 //___________________________________________________________
 
 
+/*###########################################################*/
+/* listDelete() - deletes memory allocated to a linked list  */
+/* This function must be called on any list to deallocate    */
+/* the dynamic memory used in creating and manipultating the */
+/* list. (added by NJF)                                                     */
+/*###########################################################*/
+extern void listDelete(struct wetting_front* head)
+{
+  if( head != NULL ){
+    struct wetting_front *next = head->next;
+    free( head );
+    listDelete(next);
+  }
+}
 
 /*#########################################################*/
 /* listPrint() - prints a linked list to screen             */
@@ -240,7 +254,7 @@ extern struct wetting_front* listDeleteFront(int front_num, struct wetting_front
     previous = current->next;
 
   }
-
+  if( current != NULL ) free( current );
   current = previous;
 
   while(previous != NULL) { // decrement all front numbers

src/main.cxx

@@ -435,6 +435,7 @@ for(time_step_num=0;time_step_num<num_time_steps;time_step_num++)
       printf(" ************ time step %d ******** \n",time_step_num);
     }
 
+    if( state_previous != NULL ) listDelete(state_previous);
     state_previous = NULL;
     state_previous = listCopy(head);
 
@@ -542,6 +543,7 @@ for(time_step_num=0;time_step_num<num_time_steps;time_step_num++)
 	lgar_create_surfacial_front(&ponded_depth_cm, &volin_timestep_cm, dry_depth, theta1, soil_type_by_layer, soil_properties, cum_layer_thickness_cm, nint, time_step_h);
 
 	//listPrint();
+  if( state_previous != NULL ) listDelete(state_previous);
 	state_previous = NULL;
 	state_previous = listCopy(head);