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hdf5 backend working

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This commit is contained in:
q-posev 2021-03-02 10:55:13 +01:00
parent 472dd5fd91
commit 9cf8d26110
4 changed files with 591 additions and 172 deletions
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12
src/trio.c
View File

@ -129,11 +129,11 @@ trio_exit_code trio_read_nucleus_num(trio_t* file, uint64_t* num) {
case TRIO_TEXT:
return trio_text_read_nucleus_num(file, num);
break;
/*
case TRIO_HDF5:
return trio_hdf5_read_nucleus_num(file, num);
break;
/*
case TRIO_JSON:
return trio_json_read_nucleus_num(file, num);
break;
@ -151,11 +151,11 @@ trio_exit_code trio_write_nucleus_num(trio_t* file, uint64_t num) {
case TRIO_TEXT:
return trio_text_write_nucleus_num(file, num);
break;
/*
case TRIO_HDF5:
return trio_hdf5_write_nucleus_num(file, num);
break;
/*
case TRIO_JSON:
return trio_json_write_nucleus_num(file, num);
break;
@ -195,11 +195,11 @@ trio_exit_code trio_write_nucleus_coord(trio_t* file, double* coord) {
case TRIO_TEXT:
return trio_text_write_nucleus_coord(file, coord);
break;
/*
case TRIO_HDF5:
return trio_hdf5_write_nucleus_coord(file, coord);
break;
/*
case TRIO_JSON:
return trio_json_write_nucleus_coord(file, coord);
break;

380
src/trio.org
View File

@ -251,7 +251,7 @@ trio_t* trio_create(const char* file_name, back_end_t back_end) {
case TRIO_JSON:
rc = trio_json_init(result);
break;
*/
,*/
default:
assert (1 == 0); /* Impossible case */
}
@ -324,11 +324,11 @@ trio_exit_code trio_read_nucleus_num(trio_t* file, uint64_t* num) {
case TRIO_TEXT:
return trio_text_read_nucleus_num(file, num);
break;
/*
case TRIO_HDF5:
return trio_hdf5_read_nucleus_num(file, num);
break;
/*
case TRIO_JSON:
return trio_json_read_nucleus_num(file, num);
break;
@ -346,11 +346,11 @@ trio_exit_code trio_write_nucleus_num(trio_t* file, uint64_t num) {
case TRIO_TEXT:
return trio_text_write_nucleus_num(file, num);
break;
/*
case TRIO_HDF5:
return trio_hdf5_write_nucleus_num(file, num);
break;
/*
case TRIO_JSON:
return trio_json_write_nucleus_num(file, num);
break;
@ -398,11 +398,11 @@ trio_exit_code trio_write_nucleus_coord(trio_t* file, double* coord) {
case TRIO_TEXT:
return trio_text_write_nucleus_coord(file, coord);
break;
/*
case TRIO_HDF5:
return trio_hdf5_write_nucleus_coord(file, coord);
break;
/*
case TRIO_JSON:
return trio_json_write_nucleus_coord(file, coord);
break;
@ -839,6 +839,16 @@ trio_exit_code trio_text_write_nucleus_charge(const trio_t* file, const double*
#+end_src
** HDF5 Back end
*** HDF5 definitions
#+begin_src c :tangle trio_hdf5.c
#define NUCLEUS_GROUP_NAME "nucleus"
#define NUCLEUS_NUM_NAME "nucleus_num"
#define NUCLEUS_CHARGE_NAME "nucleus_charge"
#define NUCLEUS_COORD_NAME "nucleus_coord"
#+end_src
*** HDF5 structures
#+begin_src c :tangle trio_hdf5.h
@ -892,6 +902,58 @@ trio_exit_code trio_hdf5_init(trio_t* file);
#+begin_src c :tangle trio_hdf5.c
/*
* Currently H5LTread_dataset_ is used instead of this function
* but keep it for later if we decide to get rid of the H5LT API
*/
dset_t* trio_hdf5_read_dset_low(const trio_hdf5_t* file, const char *dset_name, void *buf) {
assert (file != NULL);
assert (dset_name != NULL);
assert (buf != NULL);
/*
* Low-level implementation. Involves dealing with all HDF5 handles and dimensions
*/
dset_t* dset = (dset_t*) malloc(sizeof(dset_t));
assert (dset != NULL);
dset->dset_id = H5Dopen(file->nucleus_group,
dset_name,
H5P_DEFAULT);
assert (dset->dset_id > 0);
/*
* Get dataspace, datatype and dimensions
* dspace and dtype handles created below have to be closed when not used
*/
dset->dspace_id = H5Dget_space(dset->dset_id);
assert (dset->dspace_id > 0);
dset->dtype_id = H5Dget_type(dset->dset_id);
assert (dset->dtype_id > 0);
/* Check dimensions. Usefull, but then additional parameters
* ranks and dims[] have to be passed to the function
int rrank;
const int rank = 1;
hsize_t dims[1] = {0};
rrank = H5Sget_simple_extent_dims(nucleus->h5_charge->dspace_id,
dims, NULL);
assert (rrank == rank);
for (int i=0; i<rank; i++){
assert (dims[i] > 0);
}
*/
herr_t status;
status = H5Dread(dset->dset_id, dset->dtype_id,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
buf);
assert (status >= 0);
return dset;
}
trio_exit_code trio_hdf5_init(trio_t* file) {
trio_hdf5_t* f = (trio_hdf5_t*) file;
@ -911,18 +973,13 @@ trio_exit_code trio_hdf5_init(trio_t* file) {
}
/* Create groups in the hdf5 file */
const char* nucleus_group_name = "nucleus";
//const char* electron_group_name = "electron";
if (f_ishere == 0){
f->nucleus_group = H5Gcreate(f->file_id, nucleus_group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//f->electron_group = H5Gcreate(f->file_id, electron_group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
} else {
f->nucleus_group = H5Gopen(f->file_id, nucleus_group_name, H5P_DEFAULT);
//f->electron_group = H5Gopen(f->file_id, electron_group_name, H5P_DEFAULT);
f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
//f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT);
}
/* not sure if assert statement here makes sence
H5Gcreate will raise its own H5 error if somethings is wrong*/
assert (f->nucleus_group > 0L);
//assert (f->electron_group > 0L);
@ -948,6 +1005,10 @@ trio_exit_code trio_hdf5_finalize(trio_t* file) {
H5Gclose(f->electron_group);
f->electron_group = 0;
*/
H5Fclose(f->file_id);
f->file_id = 0;
return TRIO_SUCCESS;
}
#+end_src
@ -969,14 +1030,16 @@ h5nucleus_t* trio_hdf5_read_nucleus(const trio_hdf5_t* file) {
nucleus->h5_coord = NULL;
nucleus->h5_charge = NULL;
/* Try to open the file. If HDF5 cannot open, return */
/* Check that the file was opened/created correctly, return */
if (file->file_id < 0) return nucleus;
/* Quit if the dimensioning attribute is missing in the file */
if (H5Aexists(file->nucleus_group, NUCLEUS_NUM_NAME) == 0) return nucleus;
herr_t status;
/* Read the nucleus_num attribute of nucleus group */
const char *num_name = "nucleus_num";
hid_t num_id;
num_id = H5Aopen(file->nucleus_group, num_name, H5P_DEFAULT);
num_id = H5Aopen(file->nucleus_group, NUCLEUS_NUM_NAME, H5P_DEFAULT);
assert (num_id > 0);
status = H5Aread(num_id, H5T_NATIVE_ULLONG, &(nucleus->num));
@ -986,85 +1049,152 @@ h5nucleus_t* trio_hdf5_read_nucleus(const trio_hdf5_t* file) {
nucleus->charge = (double*) calloc(nucleus->num, sizeof(double));
assert (nucleus->charge != NULL);
/*
* High-level H5LT API. No need to deal with dataspaces and datatypes
*/
/*
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
status = H5LTread_dataset_double(file->nucleus_group,
"nucleus_charge",
nucleus->charge)
*/
/*
* Low-level implementation. Involves dealing with all HDF5 handles and dimensions
*/
nucleus->h5_charge = (dset_t*) malloc(sizeof(dset_t));
assert (nucleus->h5_charge != NULL);
nucleus->h5_charge->dset_id = H5Dopen(file->nucleus_group,
"nucleus_charge",
H5P_DEFAULT);
assert (nucleus->h5_charge->dset_id > 0);
/*
* Get dataspace, datatype and dimensions
* dspace and dtype handles created below have to be closed when not used
*/
nucleus->h5_charge->dspace_id = H5Dget_space(nucleus->h5_charge->dset_id);
assert (nucleus->h5_charge->dspace_id > 0);
nucleus->h5_charge->dtype_id = H5Dget_type(nucleus->h5_charge->dset_id);
assert (nucleus->h5_charge->dtype_id > 0);
int rrank;
const int rank = 1;
hsize_t dims[1] = {0};
rrank = H5Sget_simple_extent_dims(nucleus->h5_charge->dspace_id,
dims, NULL);
assert (rrank == rank);
for (int i=0; i<rank; i++){
assert (dims[i] > 0);
}
status = H5Dread(nucleus->h5_charge->dset_id, nucleus->h5_charge->dtype_id,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
NUCLEUS_CHARGE_NAME,
nucleus->charge);
assert (status >= 0);
/* Allocate and read nucleus_coord array */
nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
assert (nucleus->coord != NULL);
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
status = H5LTread_dataset_double(file->nucleus_group,
"nucleus_coord",
NUCLEUS_COORD_NAME,
nucleus->coord);
assert (status >= 0);
/* Print arrays */
/*
for (size_t i=0 ; i<nucleus->num ; i++) {
printf("%lf \n", nucleus->charge[i]);
}
for (size_t i=0 ; i<3*nucleus->num ; i++) {
printf("%lf \n", nucleus->coord[i]);
}
/* Low-level read. Do not forget to close the associated IDs (dset,dtype,dspace)
* when not used anymore, see below. Note how this function is similar to H5LTread_dataset_double
*/
/*
nucleus->h5_coord = trio_hdf5_read_dset_low(file, NUCLEUS_COORD_NAME,
nucleus->coord);
H5Sclose(nucleus->h5_coord->dspace_id);
H5Tclose(nucleus->h5_coord->dtype_id);
H5Dclose(nucleus->h5_coord->dset_id);
*/
H5Aclose(num_id);
H5Sclose(nucleus->h5_charge->dspace_id);
H5Tclose(nucleus->h5_charge->dtype_id);
H5Dclose(nucleus->h5_charge->dset_id);
H5Fclose(file->file_id);
return nucleus;
}
trio_exit_code trio_hdf5_write_nucleus(const trio_hdf5_t* file, h5nucleus_t* nucleus) {
assert (nucleus != NULL);
assert (file != NULL);
assert (nucleus != NULL);
// TODO
return TRIO_FAILURE;
herr_t status;
hid_t dspace, dtype;
hid_t attr_id;
dtype = H5Tcopy(H5T_NATIVE_ULLONG);
/* Write the dimensioning variables */
if (H5Aexists(file->nucleus_group, NUCLEUS_NUM_NAME) == 0) {
dspace = H5Screate(H5S_SCALAR);
attr_id = H5Acreate(file->nucleus_group, NUCLEUS_NUM_NAME, dtype, dspace,
H5P_DEFAULT, H5P_DEFAULT);
assert (attr_id > 0);
/* High-level routine does not work for some reason
* status = H5LTset_attribute_ulong (file->nucleus_group, "nucleus", NUCLEUS_NUM_NAME,
* &(nucleus->num), 1);
*/
} else {
attr_id = H5Aopen(file->nucleus_group, NUCLEUS_NUM_NAME, H5P_DEFAULT);
assert (attr_id > 0);
}
status = H5Awrite(attr_id, dtype, &(nucleus->num));
assert (status >= 0);
H5Aclose(attr_id);
/* Write arrays */
hid_t dset_id;
int charge_rank = 1;
const hsize_t charge_dims[1] = {nucleus->num};
if ( H5LTfind_dataset(file->nucleus_group, NUCLEUS_CHARGE_NAME) != 1) {
status = H5LTmake_dataset_double (file->nucleus_group, NUCLEUS_CHARGE_NAME,
charge_rank, charge_dims, nucleus->charge);
assert (status >= 0);
} else {
dset_id = H5Dopen(file->nucleus_group, NUCLEUS_CHARGE_NAME, H5P_DEFAULT);
assert (dset_id > 0);
dspace = H5Dget_space(dset_id);
assert (dspace > 0);
dtype = H5Dget_type(dset_id);
assert (dtype > 0);
int rrank;
hsize_t dims[1] = {0};
rrank = H5Sget_simple_extent_dims(dspace,
dims, NULL);
assert (rrank == charge_rank);
// disabling asserts like this allows to overwrite _num variable
for (int i=0; i<rrank; i++){
assert (dims[i] == charge_dims[i]);
}
status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus->charge);
assert (status >= 0);
H5Sclose(dspace);
H5Tclose(dtype);
H5Dclose(dset_id);
}
int coord_rank = 2;
const hsize_t coord_dims[2] = {nucleus->num, 3};
if ( H5LTfind_dataset(file->nucleus_group, NUCLEUS_COORD_NAME) != 1) {
status = H5LTmake_dataset_double (file->nucleus_group, NUCLEUS_COORD_NAME,
coord_rank, coord_dims, nucleus->coord);
assert (status >= 0);
} else {
dset_id = H5Dopen(file->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
assert (dset_id > 0);
dspace = H5Dget_space(dset_id);
assert (dspace > 0);
dtype = H5Dget_type(dset_id);
assert (dtype > 0);
int rrank;
hsize_t dims[2] = {0, 0};
rrank = H5Sget_simple_extent_dims(dspace,
dims, NULL);
assert (rrank == coord_rank);
for (int i=0; i<rrank; i++){
assert (dims[i] == coord_dims[i]);
}
status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus->coord);
assert (status >= 0);
H5Sclose(dspace);
H5Tclose(dtype);
H5Dclose(dset_id);
}
return TRIO_SUCCESS;
}
#+end_src
*** Free memory
@ -1094,7 +1224,77 @@ trio_exit_code trio_hdf5_free_nucleus(h5nucleus_t* nucleus) {
}
#+end_src
*** TODO Read/Write the num attribute
*** Read/Write the num attribute
#+begin_src c :tangle trio_hdf5.h
trio_exit_code trio_hdf5_read_nucleus_num(const trio_t* file, uint64_t* num);
trio_exit_code trio_hdf5_write_nucleus_num(const trio_t* file, const uint64_t num);
#+end_src
#+begin_src c :tangle trio_hdf5.c
trio_exit_code trio_hdf5_read_nucleus_num(const trio_t* file, uint64_t* num) {
assert (file != NULL);
assert (num != NULL);
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
if (nucleus == NULL) {
return TRIO_FAILURE;
}
/**/ *num = nucleus->num;
trio_hdf5_free_nucleus(nucleus);
return TRIO_SUCCESS;
}
trio_exit_code trio_hdf5_write_nucleus_num(const trio_t* file, const uint64_t num) {
assert (file != NULL);
assert (num > 0L);
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
assert (nucleus != NULL);
if (nucleus->num != num) {
if (nucleus->num != 0) {
printf("%ld -> %ld %s \n", num, nucleus->num,
"This variable alreasy exists. Overwriting it is not supported");
trio_hdf5_free_nucleus(nucleus);
return TRIO_FAILURE;
}
nucleus->num = num;
if (nucleus->charge != NULL) free(nucleus->charge);
nucleus->charge = NULL;
nucleus->charge = (double*) calloc(num, sizeof(double));
assert (nucleus->charge != NULL);
if (nucleus->coord != NULL) free(nucleus->coord );
nucleus->coord = NULL;
nucleus->coord = (double*) calloc(3*num, sizeof(double));
assert (nucleus->coord != NULL);
} else {
nucleus->num = num;
}
trio_exit_code rc = trio_hdf5_write_nucleus((trio_hdf5_t*) file, nucleus);
assert (rc == TRIO_SUCCESS);
trio_hdf5_free_nucleus(nucleus);
return TRIO_SUCCESS;
}
#+end_src
*** Read/Write the coord attribute
@ -1102,19 +1302,19 @@ trio_exit_code trio_hdf5_free_nucleus(h5nucleus_t* nucleus) {
#+begin_src c :tangle trio_hdf5.h
trio_exit_code trio_hdf5_read_nucleus_coord(const trio_t* file, double* coord);
// TODO
//trio_exit_code trio_hdf5_write_nucleus_coord(const trio_t* file, const double* coord);
trio_exit_code trio_hdf5_write_nucleus_coord(const trio_t* file, const double* coord);
#+end_src
#+begin_src c :tangle trio_hdf5.c
trio_exit_code trio_hdf5_read_nucleus_coord(const trio_t* file, double* coord) {
assert (file != NULL);
assert (coord != NULL);
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
if (nucleus == NULL) return TRIO_FAILURE;
assert (coord != NULL);
assert (nucleus->coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
coord[i] = nucleus->coord[i];
@ -1126,11 +1326,27 @@ trio_exit_code trio_hdf5_read_nucleus_coord(const trio_t* file, double* coord) {
trio_exit_code trio_hdf5_write_nucleus_coord(const trio_t* file, const double* coord) {
assert (file != NULL);
assert (coord != NULL);
// TODO
return TRIO_FAILURE;
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
if (nucleus == NULL) return TRIO_FAILURE;
assert (nucleus->coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
nucleus->coord[i] = coord[i];
}
trio_exit_code rc = trio_hdf5_write_nucleus((trio_hdf5_t*) file, nucleus);
assert (rc == TRIO_SUCCESS);
trio_hdf5_free_nucleus(nucleus);
return TRIO_SUCCESS;
}
#+end_src
*** TODO Read/Write the charge attribute

345
src/trio_hdf5.c
View File

@ -7,6 +7,62 @@
#include "trio_hdf5.h"
#define NUCLEUS_GROUP_NAME "nucleus"
#define NUCLEUS_NUM_NAME "nucleus_num"
#define NUCLEUS_CHARGE_NAME "nucleus_charge"
#define NUCLEUS_COORD_NAME "nucleus_coord"
/*
* Currently H5LTread_dataset_ is used instead of this function
* but keep it for later if we decide to get rid of the H5LT API
*/
dset_t* trio_hdf5_read_dset_low(const trio_hdf5_t* file, const char *dset_name, void *buf) {
assert (file != NULL);
assert (dset_name != NULL);
assert (buf != NULL);
/*
* Low-level implementation. Involves dealing with all HDF5 handles and dimensions
*/
dset_t* dset = (dset_t*) malloc(sizeof(dset_t));
assert (dset != NULL);
dset->dset_id = H5Dopen(file->nucleus_group,
dset_name,
H5P_DEFAULT);
assert (dset->dset_id > 0);
/*
* Get dataspace, datatype and dimensions
* dspace and dtype handles created below have to be closed when not used
*/
dset->dspace_id = H5Dget_space(dset->dset_id);
assert (dset->dspace_id > 0);
dset->dtype_id = H5Dget_type(dset->dset_id);
assert (dset->dtype_id > 0);
/* Check dimensions. Usefull, but then additional parameters
* ranks and dims[] have to be passed to the function
int rrank;
const int rank = 1;
hsize_t dims[1] = {0};
rrank = H5Sget_simple_extent_dims(nucleus->h5_charge->dspace_id,
dims, NULL);
assert (rrank == rank);
for (int i=0; i<rank; i++){
assert (dims[i] > 0);
}
*/
herr_t status;
status = H5Dread(dset->dset_id, dset->dtype_id,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
buf);
assert (status >= 0);
return dset;
}
trio_exit_code trio_hdf5_init(trio_t* file) {
trio_hdf5_t* f = (trio_hdf5_t*) file;
@ -26,18 +82,13 @@ trio_exit_code trio_hdf5_init(trio_t* file) {
}
/* Create groups in the hdf5 file */
const char* nucleus_group_name = "nucleus";
//const char* electron_group_name = "electron";
if (f_ishere == 0){
f->nucleus_group = H5Gcreate(f->file_id, nucleus_group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//f->electron_group = H5Gcreate(f->file_id, electron_group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
} else {
f->nucleus_group = H5Gopen(f->file_id, nucleus_group_name, H5P_DEFAULT);
//f->electron_group = H5Gopen(f->file_id, electron_group_name, H5P_DEFAULT);
f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
//f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT);
}
/* not sure if assert statement here makes sence
H5Gcreate will raise its own H5 error if somethings is wrong*/
assert (f->nucleus_group > 0L);
//assert (f->electron_group > 0L);
@ -55,6 +106,10 @@ trio_exit_code trio_hdf5_finalize(trio_t* file) {
H5Gclose(f->electron_group);
f->electron_group = 0;
*/
H5Fclose(f->file_id);
f->file_id = 0;
return TRIO_SUCCESS;
}
@ -70,14 +125,16 @@ h5nucleus_t* trio_hdf5_read_nucleus(const trio_hdf5_t* file) {
nucleus->h5_coord = NULL;
nucleus->h5_charge = NULL;
/* Try to open the file. If HDF5 cannot open, return */
/* Check that the file was opened/created correctly, return */
if (file->file_id < 0) return nucleus;
/* Quit if the dimensioning attribute is missing in the file */
if (H5Aexists(file->nucleus_group, NUCLEUS_NUM_NAME) == 0) return nucleus;
herr_t status;
/* Read the nucleus_num attribute of nucleus group */
const char *num_name = "nucleus_num";
hid_t num_id;
num_id = H5Aopen(file->nucleus_group, num_name, H5P_DEFAULT);
num_id = H5Aopen(file->nucleus_group, NUCLEUS_NUM_NAME, H5P_DEFAULT);
assert (num_id > 0);
status = H5Aread(num_id, H5T_NATIVE_ULLONG, &(nucleus->num));
@ -87,84 +144,150 @@ h5nucleus_t* trio_hdf5_read_nucleus(const trio_hdf5_t* file) {
nucleus->charge = (double*) calloc(nucleus->num, sizeof(double));
assert (nucleus->charge != NULL);
/*
* High-level H5LT API. No need to deal with dataspaces and datatypes
*/
/*
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
status = H5LTread_dataset_double(file->nucleus_group,
"nucleus_charge",
nucleus->charge)
*/
/*
* Low-level implementation. Involves dealing with all HDF5 handles and dimensions
*/
nucleus->h5_charge = (dset_t*) malloc(sizeof(dset_t));
assert (nucleus->h5_charge != NULL);
nucleus->h5_charge->dset_id = H5Dopen(file->nucleus_group,
"nucleus_charge",
H5P_DEFAULT);
assert (nucleus->h5_charge->dset_id > 0);
/*
* Get dataspace, datatype and dimensions
* dspace and dtype handles created below have to be closed when not used
*/
nucleus->h5_charge->dspace_id = H5Dget_space(nucleus->h5_charge->dset_id);
assert (nucleus->h5_charge->dspace_id > 0);
nucleus->h5_charge->dtype_id = H5Dget_type(nucleus->h5_charge->dset_id);
assert (nucleus->h5_charge->dtype_id > 0);
int rrank;
const int rank = 1;
hsize_t dims[1] = {0};
rrank = H5Sget_simple_extent_dims(nucleus->h5_charge->dspace_id,
dims, NULL);
assert (rrank == rank);
for (int i=0; i<rank; i++){
assert (dims[i] > 0);
}
status = H5Dread(nucleus->h5_charge->dset_id, nucleus->h5_charge->dtype_id,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
NUCLEUS_CHARGE_NAME,
nucleus->charge);
assert (status >= 0);
/* Allocate and read nucleus_coord array */
nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
assert (nucleus->coord != NULL);
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
status = H5LTread_dataset_double(file->nucleus_group,
"nucleus_coord",
NUCLEUS_COORD_NAME,
nucleus->coord);
assert (status >= 0);
/* Print arrays */
/*
for (size_t i=0 ; i<nucleus->num ; i++) {
printf("%lf \n", nucleus->charge[i]);
}
for (size_t i=0 ; i<3*nucleus->num ; i++) {
printf("%lf \n", nucleus->coord[i]);
}
/* Low-level read. Do not forget to close the associated IDs (dset,dtype,dspace)
* when not used anymore, see below. Note how this function is similar to H5LTread_dataset_double
*/
/*
nucleus->h5_coord = trio_hdf5_read_dset_low(file, NUCLEUS_COORD_NAME,
nucleus->coord);
H5Sclose(nucleus->h5_coord->dspace_id);
H5Tclose(nucleus->h5_coord->dtype_id);
H5Dclose(nucleus->h5_coord->dset_id);
*/
H5Aclose(num_id);
H5Sclose(nucleus->h5_charge->dspace_id);
H5Tclose(nucleus->h5_charge->dtype_id);
H5Dclose(nucleus->h5_charge->dset_id);
H5Fclose(file->file_id);
return nucleus;
}
trio_exit_code trio_hdf5_write_nucleus(const trio_hdf5_t* file, h5nucleus_t* nucleus) {
assert (nucleus != NULL);
assert (file != NULL);
assert (nucleus != NULL);
// TODO
return TRIO_FAILURE;
herr_t status;
hid_t dspace, dtype;
hid_t attr_id;
dtype = H5Tcopy(H5T_NATIVE_ULLONG);
/* Write the dimensioning variables */
if (H5Aexists(file->nucleus_group, NUCLEUS_NUM_NAME) == 0) {
dspace = H5Screate(H5S_SCALAR);
attr_id = H5Acreate(file->nucleus_group, NUCLEUS_NUM_NAME, dtype, dspace,
H5P_DEFAULT, H5P_DEFAULT);
assert (attr_id > 0);
/* High-level routine does not work for some reason
* status = H5LTset_attribute_ulong (file->nucleus_group, "nucleus", NUCLEUS_NUM_NAME,
* &(nucleus->num), 1);
*/
} else {
attr_id = H5Aopen(file->nucleus_group, NUCLEUS_NUM_NAME, H5P_DEFAULT);
assert (attr_id > 0);
}
status = H5Awrite(attr_id, dtype, &(nucleus->num));
assert (status >= 0);
H5Aclose(attr_id);
/* Write arrays */
hid_t dset_id;
int charge_rank = 1;
const hsize_t charge_dims[1] = {nucleus->num};
if ( H5LTfind_dataset(file->nucleus_group, NUCLEUS_CHARGE_NAME) != 1) {
status = H5LTmake_dataset_double (file->nucleus_group, NUCLEUS_CHARGE_NAME,
charge_rank, charge_dims, nucleus->charge);
assert (status >= 0);
} else {
dset_id = H5Dopen(file->nucleus_group, NUCLEUS_CHARGE_NAME, H5P_DEFAULT);
assert (dset_id > 0);
dspace = H5Dget_space(dset_id);
assert (dspace > 0);
dtype = H5Dget_type(dset_id);
assert (dtype > 0);
int rrank;
hsize_t dims[1] = {0};
rrank = H5Sget_simple_extent_dims(dspace,
dims, NULL);
assert (rrank == charge_rank);
// disabling asserts like this allows to overwrite _num variable
for (int i=0; i<rrank; i++){
assert (dims[i] == charge_dims[i]);
}
status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus->charge);
assert (status >= 0);
H5Sclose(dspace);
H5Tclose(dtype);
H5Dclose(dset_id);
}
int coord_rank = 2;
const hsize_t coord_dims[2] = {nucleus->num, 3};
if ( H5LTfind_dataset(file->nucleus_group, NUCLEUS_COORD_NAME) != 1) {
status = H5LTmake_dataset_double (file->nucleus_group, NUCLEUS_COORD_NAME,
coord_rank, coord_dims, nucleus->coord);
assert (status >= 0);
} else {
dset_id = H5Dopen(file->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
assert (dset_id > 0);
dspace = H5Dget_space(dset_id);
assert (dspace > 0);
dtype = H5Dget_type(dset_id);
assert (dtype > 0);
int rrank;
hsize_t dims[2] = {0, 0};
rrank = H5Sget_simple_extent_dims(dspace,
dims, NULL);
assert (rrank == coord_rank);
for (int i=0; i<rrank; i++){
assert (dims[i] == coord_dims[i]);
}
status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus->coord);
assert (status >= 0);
H5Sclose(dspace);
H5Tclose(dtype);
H5Dclose(dset_id);
}
return TRIO_SUCCESS;
}
trio_exit_code trio_hdf5_free_nucleus(h5nucleus_t* nucleus) {
@ -188,14 +311,77 @@ trio_exit_code trio_hdf5_free_nucleus(h5nucleus_t* nucleus) {
return TRIO_SUCCESS;
}
trio_exit_code trio_hdf5_read_nucleus_num(const trio_t* file, uint64_t* num) {
assert (file != NULL);
assert (num != NULL);
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
if (nucleus == NULL) {
return TRIO_FAILURE;
}
/**/ *num = nucleus->num;
trio_hdf5_free_nucleus(nucleus);
return TRIO_SUCCESS;
}
trio_exit_code trio_hdf5_write_nucleus_num(const trio_t* file, const uint64_t num) {
assert (file != NULL);
assert (num > 0L);
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
assert (nucleus != NULL);
if (nucleus->num != num) {
if (nucleus->num != 0) {
printf("%ld -> %ld %s \n", num, nucleus->num,
"This variable alreasy exists. Overwriting it is not supported");
trio_hdf5_free_nucleus(nucleus);
return TRIO_FAILURE;
}
nucleus->num = num;
if (nucleus->charge != NULL) free(nucleus->charge);
nucleus->charge = NULL;
nucleus->charge = (double*) calloc(num, sizeof(double));
assert (nucleus->charge != NULL);
if (nucleus->coord != NULL) free(nucleus->coord );
nucleus->coord = NULL;
nucleus->coord = (double*) calloc(3*num, sizeof(double));
assert (nucleus->coord != NULL);
} else {
nucleus->num = num;
}
trio_exit_code rc = trio_hdf5_write_nucleus((trio_hdf5_t*) file, nucleus);
assert (rc == TRIO_SUCCESS);
trio_hdf5_free_nucleus(nucleus);
return TRIO_SUCCESS;
}
trio_exit_code trio_hdf5_read_nucleus_coord(const trio_t* file, double* coord) {
assert (file != NULL);
assert (coord != NULL);
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
if (nucleus == NULL) return TRIO_FAILURE;
assert (coord != NULL);
assert (nucleus->coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
coord[i] = nucleus->coord[i];
@ -207,8 +393,23 @@ trio_exit_code trio_hdf5_read_nucleus_coord(const trio_t* file, double* coord) {
trio_exit_code trio_hdf5_write_nucleus_coord(const trio_t* file, const double* coord) {
assert (file != NULL);
assert (coord != NULL);
// TODO
return TRIO_FAILURE;
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
if (nucleus == NULL) return TRIO_FAILURE;
assert (nucleus->coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
nucleus->coord[i] = coord[i];
}
trio_exit_code rc = trio_hdf5_write_nucleus((trio_hdf5_t*) file, nucleus);
assert (rc == TRIO_SUCCESS);
trio_hdf5_free_nucleus(nucleus);
return TRIO_SUCCESS;
}

6
src/trio_hdf5.h
View File

@ -62,8 +62,10 @@ trio_exit_code trio_hdf5_init(trio_t* file);
trio_exit_code trio_hdf5_finalize(trio_t* file);
trio_exit_code trio_hdf5_read_nucleus_num(const trio_t* file, uint64_t* num);
trio_exit_code trio_hdf5_write_nucleus_num(const trio_t* file, const uint64_t num);
trio_exit_code trio_hdf5_read_nucleus_coord(const trio_t* file, double* coord);
// TODO
//trio_exit_code trio_hdf5_write_nucleus_coord(const trio_t* file, const double* coord);
trio_exit_code trio_hdf5_write_nucleus_coord(const trio_t* file, const double* coord);
#endif