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Sealed up memory leaks
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This commit overhauls deallocation in both gridded and non-gridded modes.
In ST_main.c
* Added a boolean parameter to deallocate_Globals.
* Wrapped some of the variables in an if statement dependent on the parameter. I did this because in gridded mode these pointers do not allocate any memory, but in non-gridded mode they do.

In sxw.c:
* Removed free_sxw_memory, _deallocate_memory, and load_sxw_memory
* I removed free_sxw_memory because it overcomplicated the code. It's only call was in free_all_sxw_memory, so I combined them to make the code more readable.
* I removed load_sxw_memory because it is depreciated, and referenced free_sxw_memory which I had already deleted.
* I removed _deallocate_memory because it was redundant and unused.
* In free_all_sxw_memory I went through each struct and deallocated every pointer to ensure no memory is leaked.
* I did NOT delete SXW->f_files because it is never actually allocated memory. The previous call to Mem_Free(SXW->f_files.in) worked because it pointed to another variable which is allocated, but calling the function multiple times in gridded mode revealed that it is unnecessary.

In ST_grid.c:
* Added a few additional pointers to _free_grid_memory.
* Added a loop which loads in a cell, then calls the non-gridded mode deallocation function. This reduces code reuse.
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chaukap committed Jun 17, 2019
1 parent be91251 commit 010e678
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Showing 3 changed files with 41 additions and 66 deletions.
12 changes: 11 additions & 1 deletion ST_grid.c
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Original file line number Diff line number Diff line change
Expand Up @@ -326,7 +326,7 @@ void parm_free_memory(void);

//from ST_main.c
void Plot_Initialize(void);
void deallocate_Globals(void);
void deallocate_Globals(Bool isGriddedMode);

//functions from ST_stats.c
void stat_Collect(Int year);
Expand Down Expand Up @@ -1646,10 +1646,20 @@ static void _free_grid_memory(void)
for(i = 0; i < grid_Rows; ++i){
for(j = 0; j < grid_Cols; ++j){
Mem_Free(gridCells[i][j].mySpeciesInit.species_seed_avail);
Mem_Free(gridCells[i][j].mySeedDispersal->prob);
Mem_Free(gridCells[i][j].mySeedDispersal);
Mem_Free(gridCells[i][j].someKillage);
Mem_Free(gridCells[i][j].mySoils.lyr);

/* Use deallocate_Globals from ST_main to deallocate global variables,
and free_all_sxw_memory from sxw to deallocate SXW variables. */
load_cell(i,j);
deallocate_Globals(TRUE);
free_all_sxw_memory();
unload_cell();
}
}

for(i = 0; i < grid_Rows; ++i){
Mem_Free(gridCells[i]);
}
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19 changes: 11 additions & 8 deletions ST_main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ extern Bool* _SomeKillage;
/***********************************************************/
void Plot_Initialize( void);
void allocate_Globals(void);
void deallocate_Globals(void);
void deallocate_Globals(Bool isGriddedMode);

static void usage(void) {
char *s ="STEPPE plant community dynamics (SGS-LTER Jan-04).\n"
Expand Down Expand Up @@ -329,7 +329,7 @@ int main(int argc, char **argv) {
SW_CTL_clear_model(TRUE); // de-allocate all memory
free_all_sxw_memory();

deallocate_Globals();
deallocate_Globals(FALSE);

printf("\nend program\n");
fprintf(progfp, "\n");
Expand Down Expand Up @@ -424,15 +424,18 @@ void allocate_Globals(void){
}

/* Deallocates the global variables */
void deallocate_Globals(void){
void deallocate_Globals(Bool isGriddedMode){
GrpIndex rg;
SppIndex sp;
Mem_Free(Env);
Mem_Free(Succulent);
Mem_Free(Globals);
Mem_Free(Plot);
Mem_Free(_SomeKillage);

if(!isGriddedMode){
Mem_Free(Env);
Mem_Free(Succulent);
Mem_Free(Globals);
Mem_Free(Plot);
Mem_Free(_SomeKillage);
}

/* Free Species */
ForEachSpecies(sp){
/* Start by freeing any pointers in the Species struct */
Expand Down
76 changes: 19 additions & 57 deletions sxw.c
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Original file line number Diff line number Diff line change
Expand Up @@ -136,11 +136,7 @@ static void _make_swc_array(void);
static void SXW_SW_Setup_Echo(void);
static void SXW_Reinit(char* SOILWAT_file);

//these last four functions are to be used in ST_grid.c
void load_sxw_memory( RealD * grid_roots_max, RealD* grid_rootsXphen, RealD* grid_roots_active, RealD* grid_roots_active_rel, RealD* grid_roots_active_sum, RealD* grid_phen, RealD* grid_prod_bmass, RealD* grid_prod_pctlive );
void save_sxw_memory( RealD * grid_roots_max, RealD* grid_rootsXphen, RealD* grid_roots_active, RealD* grid_roots_active_rel, RealD* grid_roots_active_sum, RealD* grid_phen, RealD* grid_prod_bmass, RealD* grid_prod_pctlive );
void free_sxw_memory( void );
void _deallocate_memory(void);
SXW_t* getSXW(void);
SXW_resourceType* getSXWResources(void);
transp_t* getTranspWindow(void);
Expand Down Expand Up @@ -449,18 +445,6 @@ transp_t* getTranspWindow(void){
return transp_window;
}

/* Deallocate any sxw local pointers. When running the non-gridded mode
* there is no need to call this since we only have one transp_window variable */
void _deallocate_memory(void){
Mem_Free(transp_window->ratios);
Mem_Free(transp_window->transp);
Mem_Free(transp_window->SoS_array);
Mem_Free(transp_window);

Mem_Free(SXW);
Mem_Free(SXWResources);
}

/* Shallow copy variables into the local sxw variables. */
void copy_sxw_variables(SXW_t* newSXW, SXW_resourceType* newSXWResources, transp_t* newTransp_window){
SXW = newSXW;
Expand Down Expand Up @@ -1139,26 +1123,13 @@ int getNTranspLayers(int veg_prod_type) {
void free_all_sxw_memory( void ) {
int k;

free_sxw_memory();
Mem_Free(SXW->f_files);
Mem_Free(SXW->f_roots);
Mem_Free(SXW->f_phen);
Mem_Free(SXW->f_bvt);
Mem_Free(SXW->f_prod);
Mem_Free(SXW->f_watin);

Mem_Free(SXW->transpTotal);
ForEachVegType(k) {
Mem_Free(SXW->transpVeg[k]);
}

//Mem_Free(SXW->sum_dSWA_repartitioned); // required for `_SWA_contribution_by_group`

Mem_Free(SXW->swc);
}
/* Free transp_window */
Mem_Free(transp_window->ratios);
Mem_Free(transp_window->transp);
Mem_Free(transp_window->SoS_array);
Mem_Free(transp_window);

/***********************************************************/
void free_sxw_memory( void ) {
/* Free SXWResources memory */
Mem_Free(SXWResources->_roots_max);
Mem_Free(SXWResources->_rootsXphen);
Mem_Free(SXWResources->_roots_active);
Expand All @@ -1167,29 +1138,20 @@ void free_sxw_memory( void ) {
Mem_Free(SXWResources->_phen);
Mem_Free(SXWResources->_prod_bmass);
Mem_Free(SXWResources->_prod_pctlive);
}
Mem_Free(SXWResources);

/***********************************************************/
void load_sxw_memory( RealD* grid_roots_max, RealD* grid_rootsXphen, RealD* grid_roots_active, RealD* grid_roots_active_rel, RealD* grid_roots_active_sum, RealD* grid_phen, RealD* grid_prod_bmass, RealD* grid_prod_pctlive ) {
//load memory from the grid
free_sxw_memory();
SXWResources->_roots_max = Mem_Calloc(SXW->NGrps * SXW->NTrLyrs, sizeof(RealD), "load_sxw_memory()");
SXWResources->_rootsXphen = Mem_Calloc(SXW->NGrps * SXW->NPds * SXW->NTrLyrs, sizeof(RealD), "load_sxw_memory()");
SXWResources->_roots_active = Mem_Calloc(SXW->NGrps * SXW->NPds * SXW->NTrLyrs, sizeof(RealD), "load_sxw_memory()");
SXWResources->_roots_active_rel = Mem_Calloc(SXW->NGrps * SXW->NPds * SXW->NTrLyrs, sizeof(RealD), "load_sxw_memory()");
SXWResources->_roots_active_sum = Mem_Calloc(4 * SXW->NPds * SXW->NTrLyrs, sizeof(RealD), "load_sxw_memory()");
SXWResources->_phen = Mem_Calloc(SXW->NGrps * MAX_MONTHS, sizeof(RealD), "load_sxw_memory()");
SXWResources->_prod_bmass = Mem_Calloc(SXW->NGrps * MAX_MONTHS, sizeof(RealD), "load_sxw_memory()");
SXWResources->_prod_pctlive = Mem_Calloc(SXW->NGrps * MAX_MONTHS, sizeof(RealD), "load_sxw_memory()");

memcpy(SXWResources->_roots_max, grid_roots_max, SXW->NGrps * SXW->NTrLyrs * sizeof(RealD));
memcpy(SXWResources->_rootsXphen, grid_rootsXphen, SXW->NGrps * SXW->NPds * SXW->NTrLyrs * sizeof(RealD));
memcpy(SXWResources->_roots_active, grid_roots_active, SXW->NGrps * SXW->NPds * SXW->NTrLyrs * sizeof(RealD));
memcpy(SXWResources->_roots_active_rel, grid_roots_active_rel, SXW->NGrps * SXW->NPds * SXW->NTrLyrs * sizeof(RealD));
memcpy(SXWResources->_roots_active_sum, grid_roots_active_sum, 4 * SXW->NPds * SXW->NTrLyrs * sizeof(RealD));
memcpy(SXWResources->_phen, grid_phen, SXW->NGrps * MAX_MONTHS * sizeof(RealD));
memcpy(SXWResources->_prod_bmass, grid_prod_bmass, SXW->NGrps * MAX_MONTHS * sizeof(RealD));
memcpy(SXWResources->_prod_pctlive, grid_prod_pctlive, SXW->NGrps * MAX_MONTHS * sizeof(RealD));
/* Free SXW */
Mem_Free(SXW->f_roots);
Mem_Free(SXW->f_phen);
Mem_Free(SXW->f_bvt);
Mem_Free(SXW->f_prod);
Mem_Free(SXW->f_watin);
Mem_Free(SXW->transpTotal);
ForEachVegType(k) {
Mem_Free(SXW->transpVeg[k]);
}
Mem_Free(SXW->swc);
Mem_Free(SXW);
}

/***********************************************************/
Expand Down

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@chaukap
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