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Merge pull request #166 from mladenivkovic/fix_segfaults_upstream
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explicitly initialize all struct members to solve plethora of issues
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@brittonsmith
brittonsmith committed Jul 21, 2023
2 parents 72be02a + d345f85 commit a59489f
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Showing 3 changed files with 170 additions and 40 deletions.
46 changes: 35 additions & 11 deletions src/clib/initialize_UVbackground_data.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
/
/ Distributed under the terms of the Enzo Public Licence.
/
/ The full license is in the file LICENSE, distributed with this
/ The full license is in the file LICENSE, distributed with this
/ software.
************************************************************************/

Expand All @@ -23,6 +23,30 @@ extern int grackle_verbose;
// function prototypes
int read_dataset(hid_t file_id, char *dset_name, double *buffer);

/**
* Initializes an empty #UVBtable struct with zeros and NULLs.
*/
void initialize_empty_UVBtable_struct(UVBtable *table)
{
table->Nz = 0LL;
table->z = NULL;
table->k24 = NULL;
table->k25 = NULL;
table->k26 = NULL;
table->k27 = NULL;
table->k28 = NULL;
table->k29 = NULL;
table->k30 = NULL;
table->k31 = NULL;
table->piHI = NULL;
table->piHeI = NULL;
table->piHeII = NULL;
table->crsHI = NULL;
table->crsHeII = NULL;
table->crsHeI = NULL;
}


// Initialize UV Background data
int initialize_UVbackground_data(chemistry_data *my_chemistry,
chemistry_data_storage *my_rates)
Expand All @@ -48,7 +72,7 @@ int initialize_UVbackground_data(chemistry_data *my_chemistry,
if (grackle_verbose)
fprintf(stdout, "Reading UV background data from %s.\n",
my_chemistry->grackle_data_file);
file_id = H5Fopen(my_chemistry->grackle_data_file,
file_id = H5Fopen(my_chemistry->grackle_data_file,
H5F_ACC_RDONLY, H5P_DEFAULT);


Expand All @@ -73,7 +97,7 @@ int initialize_UVbackground_data(chemistry_data *my_chemistry,
return FAIL;
}

H5Tclose(memtype);
H5Tclose(memtype);
H5Dclose(dset_id);


Expand Down Expand Up @@ -120,7 +144,7 @@ int initialize_UVbackground_data(chemistry_data *my_chemistry,
my_rates->UVbackground_table.k29 = malloc(Nz * sizeof(double));
my_rates->UVbackground_table.k30 = malloc(Nz * sizeof(double));
my_rates->UVbackground_table.k31 = malloc(Nz * sizeof(double));
}
}

my_rates->UVbackground_table.piHI = malloc(Nz * sizeof(double));
my_rates->UVbackground_table.piHeII = malloc(Nz * sizeof(double));
Expand Down Expand Up @@ -175,41 +199,41 @@ int initialize_UVbackground_data(chemistry_data *my_chemistry,
my_rates->UVbackground_table.k27) ) {
fprintf(stderr, "Error reading dataset '/UVBRates/Chemistry/k27' in %s.\n",
my_chemistry->grackle_data_file);
return FAIL;
return FAIL;
}

// *** k28 ***
if(! read_dataset(file_id, "/UVBRates/Chemistry/k28",
my_rates->UVbackground_table.k28) ) {
fprintf(stderr, "Error reading dataset '/UVBRates/Chemistry/k28' in %s.\n",
my_chemistry->grackle_data_file);
return FAIL;
return FAIL;
}

// *** k29 ***
if(! read_dataset(file_id, "/UVBRates/Chemistry/k29",
my_rates->UVbackground_table.k29) ) {
fprintf(stderr, "Error reading dataset '/UVBRates/Chemistry/k29' in %s.\n",
my_chemistry->grackle_data_file);
return FAIL;
return FAIL;
}

// *** k30 ***
if(! read_dataset(file_id, "/UVBRates/Chemistry/k30",
my_rates->UVbackground_table.k30) ) {
fprintf(stderr, "Error reading dataset '/UVBRates/Chemistry/k30' in %s.\n",
my_chemistry->grackle_data_file);
return FAIL;
return FAIL;
}

// *** k31 ***
if(! read_dataset(file_id, "/UVBRates/Chemistry/k31",
my_rates->UVbackground_table.k31) ) {
fprintf(stderr, "Error reading dataset '/UVBRates/Chemistry/k31' in %s.\n",
my_chemistry->grackle_data_file);
return FAIL;
return FAIL;
}

}

// *** piHI ***
Expand Down Expand Up @@ -334,7 +358,7 @@ int read_dataset(hid_t file_id, char *dset_name, double *buffer) {
fprintf(stderr, "Failed to read dataset 'z'.\n");
return FAIL;
}

H5Dclose(dset_id);

return SUCCESS;
Expand Down
130 changes: 108 additions & 22 deletions src/clib/initialize_chemistry_data.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
/
/ Distributed under the terms of the Enzo Public Licence.
/
/ The full license is in the file LICENSE, distributed with this
/ The full license is in the file LICENSE, distributed with this
/ software.
************************************************************************/

Expand Down Expand Up @@ -46,9 +46,11 @@ int initialize_UVbackground_data(chemistry_data *my_chemistry,

int local_free_chemistry_data(chemistry_data *my_chemistry, chemistry_data_storage *my_rates);

int initialize_rates(chemistry_data *my_chemistry, chemistry_data_storage *my_rates, code_units *my_units,
int initialize_rates(chemistry_data *my_chemistry, chemistry_data_storage *my_rates, code_units *my_units,
double co_length_units, double co_density_units);

void initialize_empty_UVBtable_struct(UVBtable *table);

static void show_version(FILE *fp)
{
grackle_version gversion = get_grackle_version();
Expand All @@ -59,11 +61,108 @@ static void show_version(FILE *fp)
fprintf (fp, "\n");
}

/**
* Initializes an empty #chemistry_data_storage struct with zeros and NULLs.
*/
void initialize_empty_chemistry_data_storage_struct(chemistry_data_storage *my_rates)
{
my_rates->k1 = NULL;
my_rates->k2 = NULL;
my_rates->k3 = NULL;
my_rates->k4 = NULL;
my_rates->k5 = NULL;
my_rates->k6 = NULL;
my_rates->k7 = NULL;
my_rates->k8 = NULL;
my_rates->k9 = NULL;
my_rates->k10 = NULL;
my_rates->k11 = NULL;
my_rates->k12 = NULL;
my_rates->k13 = NULL;
my_rates->k14 = NULL;
my_rates->k15 = NULL;
my_rates->k16 = NULL;
my_rates->k17 = NULL;
my_rates->k18 = NULL;
my_rates->k19 = NULL;
my_rates->k20 = NULL;
my_rates->k21 = NULL;
my_rates->k22 = NULL;
my_rates->k23 = NULL;
my_rates->k13dd = NULL;
my_rates->k24 = 0.;
my_rates->k25 = 0.;
my_rates->k26 = 0.;
my_rates->k27 = 0.;
my_rates->k28 = 0.;
my_rates->k29 = 0.;
my_rates->k30 = 0.;
my_rates->k31 = 0.;
my_rates->k50 = NULL;
my_rates->k51 = NULL;
my_rates->k52 = NULL;
my_rates->k53 = NULL;
my_rates->k54 = NULL;
my_rates->k55 = NULL;
my_rates->k56 = NULL;
my_rates->k57 = NULL;
my_rates->k58 = NULL;
my_rates->h2dust = NULL;
my_rates->n_cr_n = NULL;
my_rates->n_cr_d1 = NULL;
my_rates->n_cr_d2 = NULL;
my_rates->ceHI = NULL;
my_rates->ceHeI = NULL;
my_rates->ceHeII = NULL;
my_rates->ciHI = NULL;
my_rates->ciHeI = NULL;
my_rates->ciHeIS = NULL;
my_rates->ciHeII = NULL;
my_rates->reHII = NULL;
my_rates->reHeII1 = NULL;
my_rates->reHeII2 = NULL;
my_rates->reHeIII = NULL;
my_rates->brem = NULL;
my_rates->comp = 0.;
my_rates->comp_xray = 0.;
my_rates->temp_xray = 0.;
my_rates->piHI = 0.;
my_rates->piHeI = 0.;
my_rates->piHeII = 0.;
my_rates->crsHI = 0.;
my_rates->crsHeI = 0.;
my_rates->crsHeII = 0.;
my_rates->hyd01k = NULL;
my_rates->h2k01 = NULL;
my_rates->vibh = NULL;
my_rates->roth = NULL;
my_rates->rotl = NULL;
my_rates->GP99LowDensityLimit = NULL;
my_rates->GP99HighDensityLimit = NULL;
my_rates->GAHI = NULL;
my_rates->GAH2 = NULL;
my_rates->GAHe = NULL;
my_rates->GAHp = NULL;
my_rates->GAel = NULL;
my_rates->H2LTE = NULL;
my_rates->HDlte = NULL;
my_rates->HDlow = NULL;
my_rates->cieco = NULL;
my_rates->gammah = 0.;
my_rates->regr = NULL;
my_rates->gamma_isrf = 0.;
my_rates->gas_grain = NULL;
my_rates->cloudy_data_new = -1;
}

int local_initialize_chemistry_data(chemistry_data *my_chemistry,
chemistry_data_storage *my_rates,
code_units *my_units)
{

/* Better safe than sorry: Initialize everything to NULL/0 */
initialize_empty_chemistry_data_storage_struct(my_rates);

if (grackle_verbose) {
show_version(stdout);
fprintf(stdout, "Initializing grackle data.\n");
Expand Down Expand Up @@ -133,7 +232,7 @@ int local_initialize_chemistry_data(chemistry_data *my_chemistry,
# endif

/* Only allow a units to be one with proper coordinates. */
if (my_units->comoving_coordinates == FALSE &&
if (my_units->comoving_coordinates == FALSE &&
my_units->a_units != 1.0) {
fprintf(stderr, "ERROR: a_units must be 1.0 if comoving_coordinates is 0.\n");
return FAIL;
Expand All @@ -151,6 +250,9 @@ int local_initialize_chemistry_data(chemistry_data *my_chemistry,
if (my_chemistry->h2_on_dust > 0 || my_chemistry->dust_chemistry > 0 || my_chemistry->dust_recombination_cooling > 0) {
my_rates->gas_grain = malloc(my_chemistry->NumberOfTemperatureBins * sizeof(double));
my_rates->regr = malloc(my_chemistry->NumberOfTemperatureBins * sizeof(double));
} else {
my_rates->gas_grain = NULL;
my_rates->regr = NULL;
}

double co_length_units, co_density_units;
Expand Down Expand Up @@ -191,23 +293,7 @@ int local_initialize_chemistry_data(chemistry_data *my_chemistry,
}

/* Initialize UV Background data. */
my_rates->UVbackground_table.Nz = 0;
my_rates->UVbackground_table.z = NULL;
my_rates->UVbackground_table.k24 = NULL;
my_rates->UVbackground_table.k25 = NULL;
my_rates->UVbackground_table.k26 = NULL;
my_rates->UVbackground_table.k27 = NULL;
my_rates->UVbackground_table.k28 = NULL;
my_rates->UVbackground_table.k29 = NULL;
my_rates->UVbackground_table.k30 = NULL;
my_rates->UVbackground_table.k31 = NULL;
my_rates->UVbackground_table.piHI = NULL;
my_rates->UVbackground_table.piHeII = NULL;
my_rates->UVbackground_table.piHeI = NULL;
my_rates->UVbackground_table.crsHI = NULL;
my_rates->UVbackground_table.crsHeII = NULL;
my_rates->UVbackground_table.crsHeI = NULL;

initialize_empty_UVBtable_struct(&(my_rates->UVbackground_table));
if (initialize_UVbackground_data(my_chemistry, my_rates) == FAIL) {
fprintf(stderr, "Error in initialize_UVbackground_data.\n");
return FAIL;
Expand Down Expand Up @@ -373,7 +459,7 @@ int local_free_chemistry_data(chemistry_data *my_chemistry,

_free_cloudy_data(&my_rates->cloudy_primordial, my_chemistry, /* primordial */ 1);
_free_cloudy_data(&my_rates->cloudy_metal, my_chemistry, /* primordial */ 0);

GRACKLE_FREE(my_rates->UVbackground_table.z);
GRACKLE_FREE(my_rates->UVbackground_table.k24);
GRACKLE_FREE(my_rates->UVbackground_table.k25);
Expand All @@ -391,7 +477,7 @@ int local_free_chemistry_data(chemistry_data *my_chemistry,
GRACKLE_FREE(my_rates->UVbackground_table.piHeII);
GRACKLE_FREE(my_rates->UVbackground_table.piHeI);

if (my_chemistry->self_shielding_method > 0){
if (my_chemistry->self_shielding_method > 0){
GRACKLE_FREE(my_rates->UVbackground_table.crsHI);
GRACKLE_FREE(my_rates->UVbackground_table.crsHeII);
GRACKLE_FREE(my_rates->UVbackground_table.crsHeI);
Expand Down
34 changes: 27 additions & 7 deletions src/clib/initialize_cloudy_data.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
/
/ Distributed under the terms of the Enzo Public Licence.
/
/ The full license is in the file LICENSE, distributed with this
/ The full license is in the file LICENSE, distributed with this
/ software.
************************************************************************/

Expand All @@ -24,6 +24,21 @@

extern int grackle_verbose;


/**
* Initializes an empty #cloudy_data struct with zeros and NULLs.
*/
void initialize_empty_cloudy_data_struct(cloudy_data *my_cloudy)
{
my_cloudy->grid_rank = 0LL;
my_cloudy->grid_dimension = NULL;
my_cloudy->grid_parameters = NULL;
my_cloudy->heating_data = NULL;
my_cloudy->cooling_data = NULL;
my_cloudy->mmw_data = NULL;
my_cloudy->data_size = 0LL;
}

// Initialize Cloudy cooling data
int initialize_cloudy_data(chemistry_data *my_chemistry,
chemistry_data_storage *my_rates,
Expand All @@ -38,17 +53,23 @@ int initialize_cloudy_data(chemistry_data *my_chemistry,
char parameter_name[MAX_LINE_LENGTH];

// Initialize things needed even if cloudy cooling is not used.
initialize_empty_cloudy_data_struct(my_cloudy);

my_cloudy->grid_parameters = malloc(CLOUDY_MAX_DIMENSION * sizeof(double));
my_cloudy->grid_parameters = malloc(CLOUDY_MAX_DIMENSION * sizeof(double *));
my_cloudy->grid_dimension = malloc(CLOUDY_MAX_DIMENSION * sizeof(long long));
for (q = 0;q < CLOUDY_MAX_DIMENSION;q++) {
my_cloudy->grid_dimension[q] = 0;
my_cloudy->grid_dimension[q] = 0LL;
my_cloudy->grid_parameters[q] = NULL;
}

// Zero arrays if cloudy cooling not used.

if (read_data == 0) {
my_cloudy->grid_rank = 0;
my_cloudy->heating_data = NULL;
my_cloudy->cooling_data = NULL;
my_cloudy->mmw_data = NULL;
my_cloudy->data_size = 0LL;
return SUCCESS;
}

Expand Down Expand Up @@ -81,12 +102,11 @@ int initialize_cloudy_data(chemistry_data *my_chemistry,
(POW(tbase1,3) * dbase1);

// Read cooling data in from hdf5 file.

hid_t file_id, dset_id, attr_id;
hid_t file_id, dset_id, attr_id;
herr_t status;
herr_t h5_error = -1;

file_id = H5Fopen(my_chemistry->grackle_data_file,
file_id = H5Fopen(my_chemistry->grackle_data_file,
H5F_ACC_RDONLY, H5P_DEFAULT);

if (H5Aexists(file_id, "old_style")) {
Expand Down Expand Up @@ -167,7 +187,7 @@ int initialize_cloudy_data(chemistry_data *my_chemistry,

attr_id = H5Aopen_name(dset_id, parameter_name);
if (attr_id == h5_error) {
fprintf(stderr,"Failed to open %s attribute in Cooling dataset.\n",
fprintf(stderr,"Failed to open %s attribute in Cooling dataset.\n",
parameter_name);
return FAIL;
}
Expand Down

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