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better error handling for HDF5

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This commit is contained in:
q-posev 2021-12-10 16:49:31 +01:00
parent 32192f53aa
commit 070ef06818
1 changed files with 82 additions and 22 deletions
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104
src/templates_hdf5/templator_hdf5.org
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@ -262,7 +262,7 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
@ -317,7 +317,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const $group_dset_dtype$*
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
@ -406,8 +406,20 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
if ( H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) != 1 ) {
hid_t dspace = H5Screate_simple(h5_rank, chunk_dims, maxdims);
if (dspace < 0) return TREXIO_INVALID_ID;
hid_t prop = H5Pcreate(H5P_DATASET_CREATE);
if (prop < 0) {
H5Sclose(dspace);
return TREXIO_INVALID_ID;
}
herr_t status = H5Pset_chunk(prop, h5_rank, chunk_dims);
if (status < 0) {
H5Sclose(dspace);
H5Pclose(prop);
return TREXIO_INVALID_ID;
}
hid_t dset_id = H5Dcreate(f->$group$_group,
$GROUP_DSET$_NAME,
@ -416,19 +428,21 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
H5P_DEFAULT,
prop,
H5P_DEFAULT);
if (dset_id < 0) {
H5Sclose(dspace);
H5Pclose(prop);
return TREXIO_INVALID_ID;
}
assert(dset_id >= 0);
status = H5Dwrite(dset_id, H5T_NATIVE_INT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, index_sparse);
/*const herr_t status = H5LTmake_dataset(f->$group$_group,
$GROUP_DSET$_NAME,
(int) rank, (const hsize_t*) dims,
H5T_$GROUP_DSET_H5_DTYPE$,
$group_dset$);
if (status < 0) return TREXIO_FAILURE;*/
status = H5Dwrite(dset_id,
H5T_NATIVE_INT32,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
index_sparse);
H5Sclose(dspace);
H5Pclose(prop);
H5Dclose(dset_id);
H5Sclose(dspace);
if (status < 0) return TREXIO_FAILURE;
} else {
@ -436,6 +450,11 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
if (dset_id <= 0) return TREXIO_INVALID_ID;
hid_t fspace = H5Dget_space(dset_id);
if (fspace < 0) {
H5Dclose(dset_id);
return TREXIO_INVALID_ID;
}
hsize_t offset[1] = {(hsize_t) offset_file * $group_dset_rank$};
// allocate space for the dimensions to be read
@ -447,26 +466,46 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
// extend the dset size
herr_t status = H5Dset_extent(dset_id, ddims);
if (status < 0) {
H5Sclose(fspace);
H5Dclose(dset_id);
return TREXIO_INVALID_ID;
}
// close and reopen the file dataspace to take into account the extension
H5Sclose(fspace);
fspace = H5Dget_space(dset_id);
if (fspace < 0) {
H5Dclose(dset_id);
return TREXIO_INVALID_ID;
}
// select hyperslab to be written using chunk_dims and offset values
status = H5Sselect_hyperslab(fspace, H5S_SELECT_SET, offset, NULL, chunk_dims, NULL);
if (status < 0) {
H5Sclose(fspace);
H5Dclose(dset_id);
return TREXIO_INVALID_ID;
}
// create memory dataspace to write from
hid_t dspace = H5Screate_simple(h5_rank, chunk_dims, NULL);
if (dspace < 0) {
H5Sclose(fspace);
H5Sclose(dspace);
H5Dclose(dset_id);
return TREXIO_INVALID_ID;
}
status = H5Dwrite(dset_id,
H5T_NATIVE_INT32,
dspace, fspace, H5P_DEFAULT,
index_sparse);
assert(status >= 0);
H5Dclose(dset_id);
H5Sclose(dspace);
H5Sclose(fspace);
if (status < 0) return TREXIO_FAILURE;
}
return TREXIO_SUCCESS;
@ -496,20 +535,24 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file,
// get the dataspace of the dataset
hid_t fspace_id = H5Dget_space(dset_id);
if (fspace_id < 0) {
H5Dclose(dset_id);
return TREXIO_INVALID_ID;
}
// TODO: check for possible overflow HERE ?
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
/* get dims of the dset stored 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)
,*/
*/
hsize_t ddims[1] = {0};
int rrank = H5Sget_simple_extent_dims(fspace_id, ddims, NULL);
hsize_t max_offset = offset[0] + count[0];
int eof_reachable = 0;
// if max_offset exceed current dim of the dset => EOF
if (max_offset > ddims[0]) {
eof_reachable = 1;
// lower the value of count to reduce the number of elements which will be read
@ -519,15 +562,28 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file,
}
herr_t status = H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, offset, NULL, count, NULL);
if (status < 0) {
H5Sclose(fspace_id);
H5Dclose(dset_id);
return TREXIO_INVALID_ID;
}
hid_t memspace_id = H5Screate_simple(1, count, NULL);
if (memspace_id < 0) {
H5Sclose(fspace_id);
H5Dclose(dset_id);
return TREXIO_INVALID_ID;
}
status = H5Dread(dset_id, H5T_NATIVE_INT32, memspace_id, fspace_id, H5P_DEFAULT, index_read);
status = H5Dread(dset_id,
H5T_NATIVE_INT32,
memspace_id, fspace_id, H5P_DEFAULT,
index_read);
H5Sclose(fspace_id);
H5Sclose(memspace_id);
H5Dclose(dset_id);
assert (status >= 0);
if (status < 0) return TREXIO_FAILURE;
if (eof_reachable == 1) return TREXIO_END;
@ -549,6 +605,10 @@ trexio_hdf5_read_$group_dset$_size (trexio_t* const file, int64_t* const size_ma
if (dset_id <= 0) return TREXIO_INVALID_ID;
hid_t fspace_id = H5Dget_space(dset_id);
if (fspace_id < 0) {
H5Dclose(dset_id);
return TREXIO_INVALID_ID;
}
// allocate space for the dimensions to be read
hsize_t ddims[1] = {0};