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provide dimensions and decouple dataset read/write from parent group

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This commit is contained in:
q-posev 2021-03-04 14:03:34 +01:00
parent 88d2808200
commit aee737fa23
5 changed files with 100 additions and 150 deletions
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10
src/trexio.c
View File

@ -183,6 +183,9 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
int64_t dim_coord = nucleus_num*3; int64_t dim_coord = nucleus_num*3;
if (dim_coord < 0) return TREXIO_FAILURE; if (dim_coord < 0) return TREXIO_FAILURE;
int rank = 2;
uint64_t dims[2] = {nucleus_num, 3};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
@ -190,7 +193,7 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
break; break;
case TREXIO_HDF5: case TREXIO_HDF5:
return trexio_hdf5_read_nucleus_coord(file, coord); return trexio_hdf5_read_nucleus_coord(file, coord, rank, dims);
break; break;
/* /*
case TREXIO_JSON: case TREXIO_JSON:
@ -213,6 +216,9 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
int64_t dim_coord = nucleus_num*3; int64_t dim_coord = nucleus_num*3;
if (dim_coord < 0) return TREXIO_FAILURE; if (dim_coord < 0) return TREXIO_FAILURE;
int rank = 2;
uint64_t dims[2] = {nucleus_num, 3};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
@ -220,7 +226,7 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
break; break;
case TREXIO_HDF5: case TREXIO_HDF5:
return trexio_hdf5_write_nucleus_coord(file, coord); return trexio_hdf5_write_nucleus_coord(file, coord, rank, dims);
break; break;
/* /*
case TREXIO_JSON: case TREXIO_JSON:

10
src/trexio.org
View File

@ -345,6 +345,9 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
int64_t dim_coord = nucleus_num*3; int64_t dim_coord = nucleus_num*3;
if (dim_coord < 0) return TREXIO_FAILURE; if (dim_coord < 0) return TREXIO_FAILURE;
int rank = 2;
uint64_t dims[2] = {nucleus_num, 3};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
@ -352,7 +355,7 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
break; break;
case TREXIO_HDF5: case TREXIO_HDF5:
return trexio_hdf5_read_nucleus_coord(file, coord); return trexio_hdf5_read_nucleus_coord(file, coord, rank, dims);
break; break;
/* /*
case TREXIO_JSON: case TREXIO_JSON:
@ -375,6 +378,9 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
int64_t dim_coord = nucleus_num*3; int64_t dim_coord = nucleus_num*3;
if (dim_coord < 0) return TREXIO_FAILURE; if (dim_coord < 0) return TREXIO_FAILURE;
int rank = 2;
uint64_t dims[2] = {nucleus_num, 3};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
@ -382,7 +388,7 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
break; break;
case TREXIO_HDF5: case TREXIO_HDF5:
return trexio_hdf5_write_nucleus_coord(file, coord); return trexio_hdf5_write_nucleus_coord(file, coord, rank, dims);
break; break;
/* /*
case TREXIO_JSON: case TREXIO_JSON:

111
src/trexio_hdf5.c
View File

@ -406,113 +406,82 @@ trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint6
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }
trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord) { trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims) {
assert (file != NULL); assert (file != NULL);
assert (coord != NULL); assert (coord != NULL);
/*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
if (nucleus == NULL) return TREXIO_FAILURE;
assert (nucleus->coord != NULL);*/
/* Allocate and read nucleus_coord array */
h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
assert (nucleus != NULL);
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
assert (rc == TREXIO_SUCCESS);
assert (nucleus->num > 0L);
nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
assert (nucleus->coord != NULL);
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
herr_t status;
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
status = H5LTread_dataset_double(f->nucleus_group,
NUCLEUS_COORD_NAME,
nucleus->coord);
assert (status >= 0);
for (size_t i=0 ; i<3*nucleus->num ; i++) { uint64_t nucleus_num;
coord[i] = nucleus->coord[i]; 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};
for (int i=0; i<rank; i++){
assert (ddims[i] == dims[i]);
} }
trexio_hdf5_free_nucleus(nucleus); 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 */
herr_t status = H5LTread_dataset_double(f->nucleus_group,
NUCLEUS_COORD_NAME,
nucleus_coord);
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;
} }
trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord) { trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims) {
assert (file != NULL); assert (file != NULL);
assert (coord != NULL); assert (coord != NULL);
/*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file); uint64_t nucleus_num;
if (nucleus == NULL) return TREXIO_FAILURE; trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
assert (nucleus->coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
nucleus->coord[i] = coord[i];
}
trexio_exit_code rc = trexio_hdf5_write_nucleus((trexio_hdf5_t*) file, nucleus);
assert (rc == TREXIO_SUCCESS);*/
h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
assert (nucleus != NULL);
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
assert (rc == TREXIO_SUCCESS); assert (rc == TREXIO_SUCCESS);
assert (nucleus->num > 0L); assert (nucleus_num > 0L);
nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double)); double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
assert (nucleus->coord != NULL); assert (nucleus_coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) { for (size_t i=0 ; i<3*nucleus_num ; i++) {
nucleus->coord[i] = coord[i]; nucleus_coord[i] = coord[i];
} }
trexio_hdf5_t* f = (trexio_hdf5_t*) file; trexio_hdf5_t* f = (trexio_hdf5_t*) file;
hid_t dset_id, dspace, dtype;
herr_t status; herr_t status;
int coord_rank = 2;
const hsize_t coord_dims[2] = {nucleus->num, 3};
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,
coord_rank, coord_dims, nucleus->coord); rank, (hsize_t*) dims, nucleus_coord);
assert (status >= 0); assert (status >= 0);
} else { } else {
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);
dspace = H5Dget_space(dset_id);
assert (dspace > 0);
dtype = H5Dget_type(dset_id);
assert (dtype > 0);
int rrank; status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus_coord);
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); assert (status >= 0);
H5Sclose(dspace);
H5Tclose(dtype);
H5Dclose(dset_id); H5Dclose(dset_id);
} }
trexio_hdf5_free_nucleus(nucleus); free(nucleus_coord);
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }

4
src/trexio_hdf5.h
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@ -91,7 +91,7 @@ typedef struct four_index_s {
trexio_exit_code trexio_hdf5_read_nucleus_num(const trexio_t* file, uint64_t* num); trexio_exit_code trexio_hdf5_read_nucleus_num(const trexio_t* file, uint64_t* num);
trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint64_t num); trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint64_t num);
trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord); trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims);
trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord); trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims);
#endif #endif

115
src/trexio_hdf5.org
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@ -564,118 +564,87 @@ trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint6
The ~coord~ array is assumed allocated with the appropriate size. The ~coord~ array is assumed allocated with the appropriate size.
#+begin_src c :tangle trexio_hdf5.h #+begin_src c :tangle trexio_hdf5.h
trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord); trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims);
trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord); trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims);
#+end_src #+end_src
#+begin_src c :tangle trexio_hdf5.c #+begin_src c :tangle trexio_hdf5.c
trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord) { trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims) {
assert (file != NULL); assert (file != NULL);
assert (coord != NULL); assert (coord != NULL);
/*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
if (nucleus == NULL) return TREXIO_FAILURE;
assert (nucleus->coord != NULL);*/
/* Allocate and read nucleus_coord array */
h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
assert (nucleus != NULL);
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
assert (rc == TREXIO_SUCCESS);
assert (nucleus->num > 0L);
nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
assert (nucleus->coord != NULL);
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
herr_t status;
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
status = H5LTread_dataset_double(f->nucleus_group,
NUCLEUS_COORD_NAME,
nucleus->coord);
assert (status >= 0);
for (size_t i=0 ; i<3*nucleus->num ; i++) { uint64_t nucleus_num;
coord[i] = nucleus->coord[i]; 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};
for (int i=0; i<rank; i++){
assert (ddims[i] == dims[i]);
} }
trexio_hdf5_free_nucleus(nucleus); 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 */
herr_t status = H5LTread_dataset_double(f->nucleus_group,
NUCLEUS_COORD_NAME,
nucleus_coord);
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;
} }
trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord) { trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims) {
assert (file != NULL); assert (file != NULL);
assert (coord != NULL); assert (coord != NULL);
/*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file); uint64_t nucleus_num;
if (nucleus == NULL) return TREXIO_FAILURE; trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
assert (nucleus->coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
nucleus->coord[i] = coord[i];
}
trexio_exit_code rc = trexio_hdf5_write_nucleus((trexio_hdf5_t*) file, nucleus);
assert (rc == TREXIO_SUCCESS);*/
h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
assert (nucleus != NULL);
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
assert (rc == TREXIO_SUCCESS); assert (rc == TREXIO_SUCCESS);
assert (nucleus->num > 0L); assert (nucleus_num > 0L);
nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double)); double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
assert (nucleus->coord != NULL); assert (nucleus_coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) { for (size_t i=0 ; i<3*nucleus_num ; i++) {
nucleus->coord[i] = coord[i]; nucleus_coord[i] = coord[i];
} }
trexio_hdf5_t* f = (trexio_hdf5_t*) file; trexio_hdf5_t* f = (trexio_hdf5_t*) file;
hid_t dset_id, dspace, dtype;
herr_t status; herr_t status;
int coord_rank = 2;
const hsize_t coord_dims[2] = {nucleus->num, 3};
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,
coord_rank, coord_dims, nucleus->coord); rank, (hsize_t*) dims, nucleus_coord);
assert (status >= 0); assert (status >= 0);
} else { } else {
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);
dspace = H5Dget_space(dset_id);
assert (dspace > 0);
dtype = H5Dget_type(dset_id);
assert (dtype > 0);
int rrank; status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus_coord);
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); assert (status >= 0);
H5Sclose(dspace);
H5Tclose(dtype);
H5Dclose(dset_id); H5Dclose(dset_id);
} }
trexio_hdf5_free_nucleus(nucleus); free(nucleus_coord);
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }