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Fix for the bug exposed from running test/set_extent.c when selection… #3319

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merged 10 commits into from
Aug 4, 2023
Merged

Fix for the bug exposed from running test/set_extent.c when selection… #3319

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9652a3e
Fix for the bug exposed from running test/set_extent.c when selection…
vchoi-hdfgroup Aug 1, 2023
4757aa1
Correct spelling errors.
vchoi-hdfgroup Aug 1, 2023
49f45e4
Committing clang-format changes
github-actions[bot] Aug 1, 2023
7de6747
Merge branch 'develop' into extent_bug_develop
vchoi-hdfgroup Aug 2, 2023
86f9650
Update H5Dscatgath.c
vchoi-hdfgroup Aug 2, 2023
7343375
Fix based on the PR review comment.
vchoi-hdfgroup Aug 3, 2023
f362e30
Committing clang-format changes
github-actions[bot] Aug 3, 2023
f6cd3f1
Merge branch 'HDFGroup:develop' into extent_bug_develop
vchoi-hdfgroup Aug 3, 2023
5e8ec6f
Merge branch 'HDFGroup:develop' into extent_bug_develop
vchoi-hdfgroup Aug 3, 2023
5ec6f18
Fix as suggested in PR review.
vchoi-hdfgroup Aug 4, 2023
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44 changes: 32 additions & 12 deletions src/H5Dchunk.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2731,11 +2731,20 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
}
} /* end if */
else if (!skip_missing_chunks) {
/* Set up nonexistent dataset info for (fill value) read from nonexistent chunk */
nonexistent_dset_info.layout_io_info.contig_piece_info = chunk_info;
nonexistent_dset_info.file_space = chunk_info->fspace;
nonexistent_dset_info.mem_space = chunk_info->mspace;
nonexistent_dset_info.nelmts = chunk_info->piece_points;

/* Set request_nelmts. This is not normally set by the upper layers because selection I/O
* usually does not use strip mining (H5D__scatgath_write), and instead allocates buffers
* large enough for the entire I/O. Set request_nelmts to be large enough for all selected
* elements in this chunk because it must be at least that large */
nonexistent_dset_info.type_info.request_nelmts = nonexistent_dset_info.nelmts;

/* Perform the actual read operation from the nonexistent chunk
*/
nonexistent_dset_info.file_space = chunk_info->fspace;
nonexistent_dset_info.mem_space = chunk_info->mspace;
nonexistent_dset_info.nelmts = chunk_info->piece_points;
if ((dset_info->io_ops.single_read)(&nonexistent_io_info, &nonexistent_dset_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed");
} /* end if */
Expand Down Expand Up @@ -2866,9 +2875,10 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)

/* Perform the actual read operation */
assert(chk_io_info->count == 1);
chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
chk_io_info->dsets_info[0].layout_io_info.contig_piece_info = chunk_info;
chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
if ((dset_info->io_ops.single_read)(chk_io_info, &chk_io_info->dsets_info[0]) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed");

Expand Down Expand Up @@ -3055,10 +3065,19 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
/* Set up the storage buffer information for this chunk */
cpt_store.compact.buf = chunk;

/* Set up compact dataset info for write to cached chunk */
cpt_dset_info.layout_io_info.contig_piece_info = chunk_info;
cpt_dset_info.file_space = chunk_info->fspace;
cpt_dset_info.mem_space = chunk_info->mspace;
cpt_dset_info.nelmts = chunk_info->piece_points;

/* Set request_nelmts. This is not normally set by the upper layers because selection I/O
* usually does not use strip mining (H5D__scatgath_write), and instead allocates buffers
* large enough for the entire I/O. Set request_nelmts to be large enough for all selected
* elements in this chunk because it must be at least that large */
cpt_dset_info.type_info.request_nelmts = cpt_dset_info.nelmts;

/* Perform the actual write operation */
cpt_dset_info.file_space = chunk_info->fspace;
cpt_dset_info.mem_space = chunk_info->mspace;
cpt_dset_info.nelmts = chunk_info->piece_points;
if ((dset_info->io_ops.single_write)(&cpt_io_info, &cpt_dset_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed");

Expand Down Expand Up @@ -3253,9 +3272,10 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)

/* Perform the actual write operation */
assert(chk_io_info->count == 1);
chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
chk_io_info->dsets_info[0].layout_io_info.contig_piece_info = chunk_info;
chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
if ((dset_info->io_ops.single_write)(chk_io_info, &chk_io_info->dsets_info[0]) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed");

Expand Down
5 changes: 3 additions & 2 deletions src/H5Dcompact.c
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Original file line number Diff line number Diff line change
Expand Up @@ -233,8 +233,9 @@ H5D__compact_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo)
{
FUNC_ENTER_PACKAGE_NOERR

dinfo->store->compact.buf = dinfo->dset->shared->layout.storage.u.compact.buf;
dinfo->store->compact.dirty = &dinfo->dset->shared->layout.storage.u.compact.dirty;
dinfo->store->compact.buf = dinfo->dset->shared->layout.storage.u.compact.buf;
dinfo->store->compact.dirty = &dinfo->dset->shared->layout.storage.u.compact.dirty;
dinfo->layout_io_info.contig_piece_info = NULL;

/* Disable selection I/O */
io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
Expand Down
3 changes: 3 additions & 0 deletions src/H5Defl.c
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Original file line number Diff line number Diff line change
Expand Up @@ -198,6 +198,9 @@ H5D__efl_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo)

H5MM_memcpy(&dinfo->store->efl, &(dinfo->dset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));

/* No "pieces" selected */
dinfo->layout_io_info.contig_piece_info = NULL;

/* Disable selection I/O */
io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
io_info->no_selection_io_cause |= H5D_SEL_IO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET;
Expand Down
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