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adapt HDF5 back end to be generated for an arbitrary number of indices

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q-posev 2021-12-10 16:02:38 +01:00
parent 9f5ee463e1
commit 1c16b75992
2 changed files with 15 additions and 18 deletions
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4
src/templates_front/templator_front.org
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@ -2476,7 +2476,7 @@ trexio_read_$group_dset$(trexio_t* const file,
// shift indices to be one-based if Fortran API is used
if (file->one_based) {
// if EOF is reached - shift only indices that have been read, not an entire buffer
uint64_t index_size = (rc == TREXIO_END) ? (4UL*eof_read_size) : (4UL*buffer_size) ;
uint64_t index_size = (rc == TREXIO_END) ? (rank*eof_read_size) : (rank*buffer_size) ;
for (uint64_t i=0; i<index_size; ++i){
index_sparse[i] += 1;
}
@ -2548,7 +2548,7 @@ trexio_write_$group_dset$(trexio_t* const file,
// shift indices to be zero-based if Fortran API is used
if (file->one_based) {
uint64_t index_size = 4UL*buffer_size;
uint64_t index_size = rank * buffer_size;
index_sparse_p = CALLOC(index_size, int32_t);
if (index_sparse_p == NULL) return TREXIO_ALLOCATION_FAILED;

29
src/templates_hdf5/templator_hdf5.org
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@ -399,16 +399,15 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
const uint32_t rank = 1; // 4;
const hsize_t chunk_dims[1] = {size*4}; //[4] = {size, size, size, size};
// TODO: generator
hsize_t maxdims[1] = {H5S_UNLIMITED}; // [4] = {H5S_UNLIMITED, H5S_UNLIMITED, H5S_UNLIMITED, H5S_UNLIMITED};
const uint32_t h5_rank = 1;
const hsize_t chunk_dims[1] = {size * $group_dset_rank$};
const hsize_t maxdims[1] = {H5S_UNLIMITED};
if ( H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) != 1 ) {
hid_t dspace = H5Screate_simple(rank, chunk_dims, maxdims);
hid_t dspace = H5Screate_simple(h5_rank, chunk_dims, maxdims);
hid_t prop = H5Pcreate(H5P_DATASET_CREATE);
herr_t status = H5Pset_chunk(prop, rank, chunk_dims);
herr_t status = H5Pset_chunk(prop, h5_rank, chunk_dims);
hid_t dset_id = H5Dcreate(f->$group$_group,
$GROUP_DSET$_NAME,
@ -436,9 +435,8 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (dset_id <= 0) return TREXIO_INVALID_ID;
hid_t fspace = H5Dget_space(dset_id);
hsize_t offset[1] = {(hsize_t) offset_file*4}; //[4] = {offset_file, offset_file, offset_file, offset_file};
hsize_t offset[1] = {(hsize_t) offset_file * $group_dset_rank$};
// allocate space for the dimensions to be read
hsize_t ddims[1] = {0};
@ -455,7 +453,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
fspace = H5Dget_space(dset_id);
status = H5Sselect_hyperslab(fspace, H5S_SELECT_SET, offset, NULL, chunk_dims, NULL);
hid_t dspace = H5Screate_simple(rank, chunk_dims, NULL);
hid_t dspace = H5Screate_simple(h5_rank, chunk_dims, NULL);
status = H5Dwrite(dset_id,
H5T_NATIVE_INT32,
@ -472,7 +470,6 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
}
return TREXIO_SUCCESS;
}
#+end_src
@ -501,8 +498,8 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file,
hid_t fspace_id = H5Dget_space(dset_id);
// TODO: check for possible overflow HERE ?
hsize_t offset[1] = {(hsize_t) offset_file*4};
hsize_t count[1] = {(hsize_t) size*4};
hsize_t offset[1] = {(hsize_t) offset_file * $group_dset_rank$};
hsize_t count[1] = {(hsize_t) size * $group_dset_rank$};
/* get dimensions of the dataset in the file to check whether reading with user-provided chunk size
will reach end of the dataset (i.e. EOF in TEXT back end)
@ -518,7 +515,7 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file,
// lower the value of count to reduce the number of elements which will be read
count[0] -= max_offset - ddims[0];
// modify the eof_read_size accordingly
*eof_read_size = (uint64_t) (count[0] / 4UL);
*eof_read_size = (uint64_t) (count[0] / $group_dset_rank$UL);
}
herr_t status = H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, offset, NULL, count, NULL);
@ -562,11 +559,11 @@ trexio_hdf5_read_$group_dset$_size (trexio_t* const file, int64_t* const size_ma
H5Dclose(dset_id);
H5Sclose(fspace_id);
int mod_4 = (int) (ddims[0] % 4);
int mod_$group_dset_rank$ = (int) (ddims[0] % $group_dset_rank$);
if (mod_4 != 0) return TREXIO_FAILURE;
if (mod_$group_dset_rank$ != 0) return TREXIO_FAILURE;
*size_max = ((int64_t) ddims[0]) / 4L;
*size_max = ((int64_t) ddims[0]) / $group_dset_rank$L;
return TREXIO_SUCCESS;
}