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Fix h5repack for variable-length datatyped datasets #3331

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merged 2 commits into from
Aug 2, 2023
Merged

Fix h5repack for variable-length datatyped datasets #3331

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0ca9711
Fix h5repack for variable-length datatyped datasets
jhendersonHDF Aug 2, 2023
b0442ca
Add release note
jhendersonHDF Aug 2, 2023
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13 changes: 12 additions & 1 deletion tools/src/h5repack/h5repack_copy.c
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Original file line number Diff line number Diff line change
Expand Up @@ -653,6 +653,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
int ifil;
int is_ref = 0;
htri_t is_named;
htri_t is_vlen = 0;
hbool_t limit_maxdims;
hsize_t size_dset;
int ret_value = 0;
Expand Down Expand Up @@ -806,6 +807,10 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
if (H5T_REFERENCE == H5Tget_class(ftype_id))
is_ref = 1;

/* early detection of variable-length types */
if ((is_vlen = H5Tdetect_class(ftype_id, H5T_VLEN)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Tdetect_class failed");

/* Check if the datatype is committed */
if ((is_named = H5Tcommitted(ftype_id)) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Tcommitted failed");
Expand All @@ -823,10 +828,16 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
* check if we should use H5Ocopy or not
* if there is a request for filters/layout, we read/write the object
* otherwise we do a copy using H5Ocopy
*
* Note that H5Ocopy is currently unsafe to use for objects that reside in
* or interact with global heaps, such as variable-length datatypes. This
* appears to be due to H5Ocopy not correctly translating in the case where
* these objects move to different global heap addresses in the repacked
* file.
*-------------------------------------------------------------------------
*/
use_h5ocopy = !(options->op_tbl->nelems || options->all_filter == 1 ||
options->all_layout == 1 || is_ref || is_named);
options->all_layout == 1 || is_ref || is_vlen || is_named);

/*
* Check if we are using different source and destination VOL connectors.
Expand Down