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dummy write and smart read

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This commit is contained in:
q-posev 2021-03-04 15:02:23 +01:00
parent aee737fa23
commit e52cfbafea
2 changed files with 47 additions and 59 deletions
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52
src/trexio_hdf5.c
View File

@ -411,34 +411,37 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
assert (file != NULL); assert (file != NULL);
assert (coord != NULL); assert (coord != NULL);
uint64_t nucleus_num; trexio_hdf5_t* f = (trexio_hdf5_t*) file;
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
assert (rc == TREXIO_SUCCESS);
assert (nucleus_num > 0L);
uint64_t ddims[2] = {nucleus_num, 3}; herr_t status;
int rrank;
status = H5LTget_dataset_ndims (f->nucleus_group, NUCLEUS_COORD_NAME,
&rrank);
assert (status >= 0);
assert (rrank == rank);
hsize_t* ddims = (hsize_t*) calloc(rrank, sizeof(hsize_t));
hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
assert (dset_id > 0);
status = H5LDget_dset_dims(dset_id, ddims);
assert (status >= 0);
H5Dclose(dset_id);
//uint64_t ddims[2] = {nucleus_num, 3};
for (int i=0; i<rank; i++){ for (int i=0; i<rank; i++){
assert (ddims[i] == dims[i]); assert (ddims[i] == dims[i]);
} }
double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
assert (nucleus_coord != NULL);
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
/* High-level H5LT API. No need to deal with dataspaces and datatypes */ /* High-level H5LT API. No need to deal with dataspaces and datatypes */
herr_t status = H5LTread_dataset_double(f->nucleus_group, status = H5LTread_dataset_double(f->nucleus_group,
NUCLEUS_COORD_NAME, NUCLEUS_COORD_NAME,
nucleus_coord); coord);
assert (status >= 0); assert (status >= 0);
for (size_t i=0 ; i<3*nucleus_num ; i++) {
coord[i] = nucleus_coord[i];
}
free(nucleus_coord);
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }
@ -453,20 +456,13 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
assert (rc == TREXIO_SUCCESS); assert (rc == TREXIO_SUCCESS);
assert (nucleus_num > 0L); assert (nucleus_num > 0L);
double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
assert (nucleus_coord != NULL);
for (size_t i=0 ; i<3*nucleus_num ; i++) {
nucleus_coord[i] = coord[i];
}
trexio_hdf5_t* f = (trexio_hdf5_t*) file; trexio_hdf5_t* f = (trexio_hdf5_t*) file;
herr_t status; herr_t status;
if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) { if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) {
status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME, status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME,
rank, (hsize_t*) dims, nucleus_coord); rank, (hsize_t*) dims, coord);
assert (status >= 0); assert (status >= 0);
} else { } else {
@ -474,14 +470,12 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT); hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
assert (dset_id > 0); assert (dset_id > 0);
status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus_coord); status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, coord);
assert (status >= 0); assert (status >= 0);
H5Dclose(dset_id); H5Dclose(dset_id);
} }
free(nucleus_coord);
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }

54
src/trexio_hdf5.org
View File

@ -36,7 +36,7 @@
#include "trexio_hdf5.h" #include "trexio_hdf5.h"
#+end_src #+end_src
* HDF5 Back end * HDF5 Back end
** HDF5 definitions ** HDF5 definitions
@ -574,34 +574,37 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
assert (file != NULL); assert (file != NULL);
assert (coord != NULL); assert (coord != NULL);
uint64_t nucleus_num; trexio_hdf5_t* f = (trexio_hdf5_t*) file;
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
assert (rc == TREXIO_SUCCESS);
assert (nucleus_num > 0L);
uint64_t ddims[2] = {nucleus_num, 3}; herr_t status;
int rrank;
status = H5LTget_dataset_ndims (f->nucleus_group, NUCLEUS_COORD_NAME,
&rrank);
assert (status >= 0);
assert (rrank == rank);
hsize_t* ddims = (hsize_t*) calloc(rrank, sizeof(hsize_t));
hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
assert (dset_id > 0);
status = H5LDget_dset_dims(dset_id, ddims);
assert (status >= 0);
H5Dclose(dset_id);
//uint64_t ddims[2] = {nucleus_num, 3};
for (int i=0; i<rank; i++){ for (int i=0; i<rank; i++){
assert (ddims[i] == dims[i]); assert (ddims[i] == dims[i]);
} }
double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
assert (nucleus_coord != NULL);
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
/* High-level H5LT API. No need to deal with dataspaces and datatypes */ /* High-level H5LT API. No need to deal with dataspaces and datatypes */
herr_t status = H5LTread_dataset_double(f->nucleus_group, status = H5LTread_dataset_double(f->nucleus_group,
NUCLEUS_COORD_NAME, NUCLEUS_COORD_NAME,
nucleus_coord); coord);
assert (status >= 0); assert (status >= 0);
for (size_t i=0 ; i<3*nucleus_num ; i++) {
coord[i] = nucleus_coord[i];
}
free(nucleus_coord);
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }
@ -616,20 +619,13 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
assert (rc == TREXIO_SUCCESS); assert (rc == TREXIO_SUCCESS);
assert (nucleus_num > 0L); assert (nucleus_num > 0L);
double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
assert (nucleus_coord != NULL);
for (size_t i=0 ; i<3*nucleus_num ; i++) {
nucleus_coord[i] = coord[i];
}
trexio_hdf5_t* f = (trexio_hdf5_t*) file; trexio_hdf5_t* f = (trexio_hdf5_t*) file;
herr_t status; herr_t status;
if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) { if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) {
status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME, status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME,
rank, (hsize_t*) dims, nucleus_coord); rank, (hsize_t*) dims, coord);
assert (status >= 0); assert (status >= 0);
} else { } else {
@ -637,14 +633,12 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT); hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
assert (dset_id > 0); assert (dset_id > 0);
status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus_coord); status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, coord);
assert (status >= 0); assert (status >= 0);
H5Dclose(dset_id); H5Dclose(dset_id);
} }
free(nucleus_coord);
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }