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Merge pull request #22 from TREX-CoE/change_h5rw_datasets

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hdf5_read/write_dset decoupled from the parent group
This commit is contained in:
Evgeny Posenitskiy 2021-03-05 08:59:44 +01:00 committed by GitHub
commit e88a228bb5
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GPG Key ID: 4AEE18F83AFDEB23
8 changed files with 211 additions and 96 deletions
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38
src/trexio.c
View File

@ -81,8 +81,12 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
break; break;
*/ */
} }
if (rc != TREXIO_SUCCESS) return NULL;
if (rc != TREXIO_SUCCESS) {
free(result->file_name);
free(result);
return NULL;
}
/* File locking */ /* File locking */
@ -96,17 +100,19 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
case TREXIO_HDF5: case TREXIO_HDF5:
rc = TREXIO_SUCCESS; rc = TREXIO_SUCCESS;
/*
rc = trexio_hdf5_lock(result);
break; break;
/*
case TREXIO_JSON: case TREXIO_JSON:
rc = trexio_json_lock(result); rc = trexio_json_lock(result);
break; break;
*/ */
} }
if (rc != TREXIO_SUCCESS) return NULL;
if (rc != TREXIO_SUCCESS) {
free(result->file_name);
free(result);
return NULL;
}
return result; return result;
} }
@ -137,10 +143,11 @@ trexio_exit_code trexio_close(trexio_t* file) {
} }
if (rc != TREXIO_SUCCESS) { if (rc != TREXIO_SUCCESS) {
free(file->file_name);
free(file);
return TREXIO_FAILURE; return TREXIO_FAILURE;
} }
/* File unlocking */ /* File unlocking */
rc = TREXIO_FAILURE; rc = TREXIO_FAILURE;
@ -153,17 +160,13 @@ trexio_exit_code trexio_close(trexio_t* file) {
case TREXIO_HDF5: case TREXIO_HDF5:
rc = TREXIO_SUCCESS; rc = TREXIO_SUCCESS;
/*
rc = trexio_hdf5_unlock(file);
break; break;
/*
case TREXIO_JSON: case TREXIO_JSON:
rc = trexio_json_unlock(file); rc = trexio_json_unlock(file);
break; break;
*/ */
} }
if (rc != TREXIO_SUCCESS) return TREXIO_FAILURE;
/* Terminate front end */ /* Terminate front end */
@ -171,10 +174,11 @@ trexio_exit_code trexio_close(trexio_t* file) {
file->file_name = NULL; file->file_name = NULL;
int irc = pthread_mutex_destroy( &(file->thread_lock) ); int irc = pthread_mutex_destroy( &(file->thread_lock) );
free(file); free(file);
if (irc != 0) return TREXIO_ERRNO; if (irc != 0) return TREXIO_ERRNO;
if (rc != TREXIO_SUCCESS) return TREXIO_FAILURE;
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }
@ -244,6 +248,9 @@ 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;
uint32_t rank = 2;
uint64_t dims[2] = {nucleus_num, 3};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
@ -251,7 +258,7 @@ 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:
@ -274,6 +281,9 @@ 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;
uint32_t rank = 2;
uint64_t dims[2] = {nucleus_num, 3};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
@ -281,7 +291,7 @@ 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:

2
src/trexio.h
View File

@ -22,6 +22,8 @@ typedef int32_t trexio_exit_code;
#define TREXIO_END ( (trexio_exit_code) 10 ) #define TREXIO_END ( (trexio_exit_code) 10 )
#define TREXIO_READONLY ( (trexio_exit_code) 11 ) #define TREXIO_READONLY ( (trexio_exit_code) 11 )
#define TREXIO_ERRNO ( (trexio_exit_code) 12 ) #define TREXIO_ERRNO ( (trexio_exit_code) 12 )
#define TREXIO_INVALID_ID ( (trexio_exit_code) 20 )
#define TREXIO_INVALID_NUM ( (trexio_exit_code) 21 )
typedef int32_t back_end_t; typedef int32_t back_end_t;

44
src/trexio.org
View File

@ -79,6 +79,8 @@ typedef int32_t trexio_exit_code;
#define TREXIO_END ( (trexio_exit_code) 10 ) #define TREXIO_END ( (trexio_exit_code) 10 )
#define TREXIO_READONLY ( (trexio_exit_code) 11 ) #define TREXIO_READONLY ( (trexio_exit_code) 11 )
#define TREXIO_ERRNO ( (trexio_exit_code) 12 ) #define TREXIO_ERRNO ( (trexio_exit_code) 12 )
#define TREXIO_INVALID_ID ( (trexio_exit_code) 20 )
#define TREXIO_INVALID_NUM ( (trexio_exit_code) 21 )
#+end_src #+end_src
** Back ends ** Back ends
@ -219,8 +221,12 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
break; break;
,*/ ,*/
} }
if (rc != TREXIO_SUCCESS) return NULL;
if (rc != TREXIO_SUCCESS) {
free(result->file_name);
free(result);
return NULL;
}
/* File locking */ /* File locking */
@ -234,17 +240,19 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
case TREXIO_HDF5: case TREXIO_HDF5:
rc = TREXIO_SUCCESS; rc = TREXIO_SUCCESS;
/*
rc = trexio_hdf5_lock(result);
break; break;
/*
case TREXIO_JSON: case TREXIO_JSON:
rc = trexio_json_lock(result); rc = trexio_json_lock(result);
break; break;
,*/ */
} }
if (rc != TREXIO_SUCCESS) return NULL;
if (rc != TREXIO_SUCCESS) {
free(result->file_name);
free(result);
return NULL;
}
return result; return result;
} }
@ -283,10 +291,11 @@ trexio_exit_code trexio_close(trexio_t* file) {
} }
if (rc != TREXIO_SUCCESS) { if (rc != TREXIO_SUCCESS) {
free(file->file_name);
free(file);
return TREXIO_FAILURE; return TREXIO_FAILURE;
} }
/* File unlocking */ /* File unlocking */
rc = TREXIO_FAILURE; rc = TREXIO_FAILURE;
@ -299,17 +308,13 @@ trexio_exit_code trexio_close(trexio_t* file) {
case TREXIO_HDF5: case TREXIO_HDF5:
rc = TREXIO_SUCCESS; rc = TREXIO_SUCCESS;
/*
rc = trexio_hdf5_unlock(file);
break; break;
/*
case TREXIO_JSON: case TREXIO_JSON:
rc = trexio_json_unlock(file); rc = trexio_json_unlock(file);
break; break;
,*/ */
} }
if (rc != TREXIO_SUCCESS) return TREXIO_FAILURE;
/* Terminate front end */ /* Terminate front end */
@ -317,10 +322,11 @@ trexio_exit_code trexio_close(trexio_t* file) {
file->file_name = NULL; file->file_name = NULL;
int irc = pthread_mutex_destroy( &(file->thread_lock) ); int irc = pthread_mutex_destroy( &(file->thread_lock) );
free(file); free(file);
if (irc != 0) return TREXIO_ERRNO; if (irc != 0) return TREXIO_ERRNO;
if (rc != TREXIO_SUCCESS) return TREXIO_FAILURE;
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }
@ -407,6 +413,9 @@ 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;
uint32_t rank = 2;
uint64_t dims[2] = {nucleus_num, 3};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
@ -414,7 +423,7 @@ 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:
@ -437,6 +446,9 @@ 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;
uint32_t rank = 2;
uint64_t dims[2] = {nucleus_num, 3};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
@ -444,7 +456,7 @@ 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:

81
src/trexio_hdf5.c
View File

@ -402,43 +402,88 @@ 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 uint32_t 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); trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (nucleus == NULL) return TREXIO_FAILURE; herr_t status;
assert (nucleus->coord != NULL); int rrank;
// get the rank of the dataset in a file
status = H5LTget_dataset_ndims (f->nucleus_group, NUCLEUS_COORD_NAME,
&rrank);
for (size_t i=0 ; i<3*nucleus->num ; i++) { if (status < 0) return TREXIO_FAILURE;
coord[i] = nucleus->coord[i];
if (rrank != (int) rank) return TREXIO_INVALID_ARG_3;
// open the dataset to get its dimensions
hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
if (dset_id <= 0) return TREXIO_INVALID_ID;
// allocate space for the dimensions to be read
hsize_t* ddims = (hsize_t*) calloc( (int) rank, sizeof(hsize_t));
if (ddims == NULL) return TREXIO_FAILURE;
// read dimensions from the existing dataset
status = H5LDget_dset_dims(dset_id, ddims);
H5Dclose(dset_id);
if (status < 0) {
free(ddims);
return TREXIO_FAILURE;
} }
trexio_hdf5_free_nucleus(nucleus); for (uint32_t i=0; i<rank; i++){
if (ddims[i] != dims[i]) {
free(ddims);
return TREXIO_INVALID_ARG_4;
}
}
free(ddims);
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
status = H5LTread_dataset_double(f->nucleus_group,
NUCLEUS_COORD_NAME,
coord);
if (status < 0) return TREXIO_FAILURE;
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 uint32_t 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;
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
if (rc != TREXIO_SUCCESS) return rc;
if (nucleus_num <= 0L) return TREXIO_INVALID_NUM;
if (nucleus == NULL) return TREXIO_FAILURE; trexio_hdf5_t* f = (trexio_hdf5_t*) file;
assert (nucleus->coord != NULL);
herr_t status;
if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) {
status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME,
(int) rank, (hsize_t*) dims, coord);
if (status < 0) return TREXIO_FAILURE;
} else {
hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
if (dset_id <= 0) return TREXIO_INVALID_ID;
status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, coord);
H5Dclose(dset_id);
if (status < 0) return TREXIO_FAILURE;
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);
trexio_hdf5_free_nucleus(nucleus);
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }

4
src/trexio_hdf5.h
View File

@ -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 uint32_t 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 uint32_t rank, const uint64_t* dims);
#endif #endif

85
src/trexio_hdf5.org
View File

@ -560,49 +560,94 @@ 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 uint32_t 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 uint32_t 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 uint32_t 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); trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (nucleus == NULL) return TREXIO_FAILURE; herr_t status;
assert (nucleus->coord != NULL); int rrank;
// get the rank of the dataset in a file
status = H5LTget_dataset_ndims (f->nucleus_group, NUCLEUS_COORD_NAME,
&rrank);
for (size_t i=0 ; i<3*nucleus->num ; i++) { if (status < 0) return TREXIO_FAILURE;
coord[i] = nucleus->coord[i];
if (rrank != (int) rank) return TREXIO_INVALID_ARG_3;
// open the dataset to get its dimensions
hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
if (dset_id <= 0) return TREXIO_INVALID_ID;
// allocate space for the dimensions to be read
hsize_t* ddims = (hsize_t*) calloc( (int) rank, sizeof(hsize_t));
if (ddims == NULL) return TREXIO_FAILURE;
// read dimensions from the existing dataset
status = H5LDget_dset_dims(dset_id, ddims);
H5Dclose(dset_id);
if (status < 0) {
free(ddims);
return TREXIO_FAILURE;
} }
trexio_hdf5_free_nucleus(nucleus); for (uint32_t i=0; i<rank; i++){
if (ddims[i] != dims[i]) {
free(ddims);
return TREXIO_INVALID_ARG_4;
}
}
free(ddims);
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
status = H5LTread_dataset_double(f->nucleus_group,
NUCLEUS_COORD_NAME,
coord);
if (status < 0) return TREXIO_FAILURE;
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 uint32_t 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;
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
if (rc != TREXIO_SUCCESS) return rc;
if (nucleus_num <= 0L) return TREXIO_INVALID_NUM;
if (nucleus == NULL) return TREXIO_FAILURE; trexio_hdf5_t* f = (trexio_hdf5_t*) file;
assert (nucleus->coord != NULL);
herr_t status;
if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) {
status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME,
(int) rank, (hsize_t*) dims, coord);
if (status < 0) return TREXIO_FAILURE;
} else {
hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
if (dset_id <= 0) return TREXIO_INVALID_ID;
status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, coord);
H5Dclose(dset_id);
if (status < 0) return TREXIO_FAILURE;
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);
trexio_hdf5_free_nucleus(nucleus);
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }

2
src/trexio_text.c
View File

@ -448,7 +448,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
if (file->parent.mode == 'w') { if (file->parent.mode == 'w') {
rdm->file = fopen(file_name,"a"); rdm->file = fopen(file_name,"a");
} else { } else {
rdm->file = fopen(file_name,""); rdm->file = fopen(file_name,"r");
} }
free(file_name); free(file_name);
file->rdm = rdm ; file->rdm = rdm ;

3
src/trexio_text.org
View File

@ -99,6 +99,7 @@ typedef struct trexio_text_s {
#+end_src #+end_src
*** Init/deinit functions
#+begin_src c :tangle trexio_text.h #+begin_src c :tangle trexio_text.h
trexio_exit_code trexio_text_init(trexio_t* file); trexio_exit_code trexio_text_init(trexio_t* file);
@ -634,7 +635,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
if (file->parent.mode == 'w') { if (file->parent.mode == 'w') {
rdm->file = fopen(file_name,"a"); rdm->file = fopen(file_name,"a");
} else { } else {
rdm->file = fopen(file_name,""); rdm->file = fopen(file_name,"r");
} }
free(file_name); free(file_name);
file->rdm = rdm ; file->rdm = rdm ;