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trexio/src/templates_hdf5/templator_hdf5.org
q-posev 7a9d078859 remove append mode
2021-06-02 14:40:23 +02:00

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HDF5 back end

HDF5 back end

Template for HDF5 definitions 

#define $GROUP$_GROUP_NAME          "$group$"
#define $GROUP_NUM$_NAME            "$group_num$"
#define $GROUP_DSET$_NAME           "$group_dset$"

Template for HDF5 structures 

typedef struct trexio_hdf5_s {
trexio_t     parent ;
hid_t      file_id;
hid_t      $group$_group;
const char* file_name;
} trexio_hdf5_t;

Template for HDF5 init/deinit 

trexio_exit_code
trexio_hdf5_init (trexio_t* const file)
{

trexio_hdf5_t* const f = (trexio_hdf5_t*) file;

/* If file doesn't exist, create it */
int f_exists = 0;
struct stat st;

if (stat(file->file_name, &st) == 0) f_exists = 1;

if (f_exists == 1) {

  switch (file->mode) {
  case 'r':
    // reading the existing file -> open as RDONLY
    f->file_id = H5Fopen(file->file_name, H5F_ACC_RDONLY, H5P_DEFAULT);
    break;
  case 'w':
    // writing the existing file -> overwrite it (_TRUNC) [_EXCL | H5F_ACC_DEBUG as an alternative]
    f->file_id = H5Fcreate(file->file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
    break;
  }

} else {

  switch (file->mode) {
  case 'r':
    // reading non-existing file -> error
    return TREXIO_FAILURE;
  case 'w':
    // writing non-existing file -> create it
    f->file_id = H5Fcreate(file->file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
    break;
  }

}

/* Create or open groups in the hdf5 file assuming that they exist if file exists */
switch (file->mode) {
  case 'r':
    f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
    break;
  case 'w':
    f->$group$_group = H5Gcreate(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    break;
}
if (f->$group$_group <= 0L) return TREXIO_INVALID_ID;

return TREXIO_SUCCESS;
}

trexio_exit_code
trexio_hdf5_deinit (trexio_t* const file)
{

trexio_hdf5_t* f = (trexio_hdf5_t*) file;

H5Gclose(f->$group$_group);
f->$group$_group = 0;

H5Fclose(f->file_id);
f->file_id = 0;

return TREXIO_SUCCESS;

}

Template for HDF5 has/read/write a number 

trexio_exit_code
trexio_hdf5_read_$group_num$ (trexio_t* const file, uint64_t* const num)
{

if (file == NULL) return TREXIO_INVALID_ARG_1;
if (num  == NULL) return TREXIO_INVALID_ARG_2;

const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
/* Quit if the dimensioning attribute is missing in the file */
if (H5Aexists(f->$group$_group, $GROUP_NUM$_NAME) == 0) return TREXIO_FAILURE;

/* Read the nucleus_num attribute of nucleus group */
const hid_t num_id = H5Aopen(f->$group$_group, $GROUP_NUM$_NAME, H5P_DEFAULT);
if (num_id <= 0) return TREXIO_INVALID_ID;

const herr_t status = H5Aread(num_id, H5T_NATIVE_UINT64, num);
if (status < 0) return TREXIO_FAILURE;

return TREXIO_SUCCESS;

}
trexio_exit_code
trexio_hdf5_write_$group_num$ (trexio_t* const file, const uint64_t num)
{

if (file == NULL) return TREXIO_INVALID_ARG_1;
if (num  == 0L  ) return TREXIO_INVALID_ARG_2;

trexio_hdf5_t* const f = (trexio_hdf5_t*) file;

if (H5Aexists(f->$group$_group, $GROUP_NUM$_NAME) == 0) {

  /* Write the dimensioning variables */
  const hid_t dtype = H5Tcopy(H5T_NATIVE_UINT64);
  const hid_t dspace = H5Screate(H5S_SCALAR);

  const hid_t num_id = H5Acreate(f->$group$_group, $GROUP_NUM$_NAME, dtype, dspace,
     H5P_DEFAULT, H5P_DEFAULT);
  if (num_id <= 0) {
    H5Sclose(dspace);
    H5Tclose(dtype);
    return TREXIO_INVALID_ID;
  }

  const herr_t status = H5Awrite(num_id, dtype, &(num));
  if (status < 0) {
    H5Aclose(num_id);
    H5Sclose(dspace);
    H5Tclose(dtype);
    return TREXIO_FAILURE;
  }

  H5Sclose(dspace);
  H5Aclose(num_id);
  H5Tclose(dtype);
  return TREXIO_SUCCESS;

} else {

  uint64_t infile_num;
  trexio_exit_code rc = trexio_hdf5_read_$group_num$(file, &(infile_num));
  if (rc != TREXIO_SUCCESS) return rc;

  if (infile_num != num) {

    if (infile_num != 0) {

return TREXIO_NUM_ALREADY_EXISTS;

    } else {

const hid_t dtype = H5Tcopy(H5T_NATIVE_UINT64);
const hid_t num_id = H5Aopen(f->$group$_group, $GROUP_NUM$_NAME, H5P_DEFAULT);
if (num_id <= 0) return TREXIO_INVALID_ID;

const herr_t status = H5Awrite(num_id, dtype, &(num));
if (status < 0) return TREXIO_FAILURE;

H5Aclose(num_id);
H5Tclose(dtype);
    }
  }
  return TREXIO_SUCCESS;
}

}
trexio_exit_code
trexio_hdf5_has_$group_num$ (trexio_t* const file)
{

if (file == NULL) return TREXIO_INVALID_ARG_1;

const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;

htri_t status = H5Aexists(f->$group$_group, $GROUP_NUM$_NAME);
/* H5Aexists returns positive value if attribute exists, 0 if does not, negative if error */
if (status > 0){
  return TREXIO_SUCCESS;
} else if (status == 0) {
  return TREXIO_HAS_NOT;
} else {
  return TREXIO_FAILURE;
}

}

Template for HDF5 has/read/write a dataset 

trexio_exit_code
trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $group_dset$,
	       const uint32_t rank, const uint64_t* dims)
{

if (file == NULL) return TREXIO_INVALID_ARG_1;
if ($group_dset$  == NULL) return TREXIO_INVALID_ARG_2;

const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;

herr_t status;
int rrank;
// get the rank of the dataset in a file
status = H5LTget_dataset_ndims (f->$group$_group, $GROUP_DSET$_NAME, &rrank);

if (status < 0) return TREXIO_FAILURE;

if (rrank != (int) rank) return TREXIO_INVALID_ARG_3;

// open the dataset to get its dimensions
hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (dset_id <= 0) return TREXIO_INVALID_ID;

// allocate space for the dimensions to be read
hsize_t* ddims = CALLOC( (int) rank, 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;
}

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(f->$group$_group,
    $GROUP_DSET$_NAME,
    H5T_NATIVE_$GROUP_DSET_H5_DTYPE$,
    $group_dset$);
if (status < 0) return TREXIO_FAILURE;

return TREXIO_SUCCESS;
}
trexio_exit_code
trexio_hdf5_write_$group_dset$ (trexio_t* const file, const $group_dset_dtype$* $group_dset$,
		const uint32_t rank, const uint64_t* dims)
{

if (file == NULL) return TREXIO_INVALID_ARG_1;
if ($group_dset$  == NULL) return TREXIO_INVALID_ARG_2;

trexio_exit_code rc;
uint64_t $group_dset_dim$;
// error handling for rc is added by the generator
rc = trexio_hdf5_read_$group_dset_dim$(file, &($group_dset_dim$));
if ($group_dset_dim$ == 0L) return TREXIO_INVALID_NUM;

trexio_hdf5_t* f = (trexio_hdf5_t*) file;

if ( H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) != 1 ) {

 const herr_t status = H5LTmake_dataset(f->$group$_group,
		   $GROUP_DSET$_NAME,
		   (int) rank, (const hsize_t*) dims,
		   H5T_NATIVE_$GROUP_DSET_H5_DTYPE$,
		   $group_dset$);
 if (status < 0) return TREXIO_FAILURE;

} else {

 hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
 if (dset_id <= 0) return TREXIO_INVALID_ID;

 const herr_t status = H5Dwrite(dset_id,
	   H5T_NATIVE_$GROUP_DSET_H5_DTYPE$,
	   H5S_ALL, H5S_ALL, H5P_DEFAULT,
	   $group_dset$);

 H5Dclose(dset_id);
 if (status < 0) return TREXIO_FAILURE;

}

return TREXIO_SUCCESS;

}
trexio_exit_code
trexio_hdf5_has_$group_dset$ (trexio_t* const file)
{

if (file == NULL) return TREXIO_INVALID_ARG_1;

trexio_hdf5_t* f = (trexio_hdf5_t*) file;

herr_t status = H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME);
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
 return TREXIO_SUCCESS;
} else if (status == 0) {
 return TREXIO_HAS_NOT;
} else {
 return TREXIO_FAILURE;
}

}