UNCLASSIFIED
Hi all,
We seem to have tripped a bug in HDF 1.8.14, unless it is an intentional
limitation?
We have a scalar dataset with type VLEN { STRUCT {
double-precision-floating-point, C-string } }. The memory space uses 24 bytes
of storage per element while the file space uses 12 for this format, and so a
"struct(no-opt)" conversion path is selected internally by HDF for reads and
writes.
We initially write 100x { number, string } pairs into the dataset, and that has
no problems.
We then *over-write* with 99x { number, string } pairs. This causes an error
when, having actually completed the write of the new 99x elements internally,
the following code is run from H5Tconv.c:3371...
if(!noop_conv) {
/* For nested VL case, free leftover heap objects
from the deeper level if the length of new data elements is shorter than the
old data elements.*/
if(nested && seq_len < bg_seq_len) {
size_t parent_seq_len;
const uint8_t *tmp;
size_t u;
/* TMP_P is reset each time in the loop because
DST_BASE_SIZE may include some data in addition to VL info. - SLU */
for(u = seq_len; u < bg_seq_len; u++) {
tmp = (uint8_t *)tmp_buf + u *
dst_base_size;
UINT32DECODE(tmp, parent_seq_len);
if(parent_seq_len > 0) {
H5F_addr_decode(dst->shared->u.vlen.f,
&tmp, &(parent_hobjid.addr));
UINT32DECODE(tmp, parent_hobjid.idx);
if(H5HG_remove(dst->shared->u.vlen.f,
dxpl_id, &parent_hobjid) < 0)
HGOTO_ERROR(H5E_DATATYPE,
H5E_WRITEERROR, FAIL, "Unable to remove heap object")
} /* end if */
} /* end for */
} /* end if */
} /* end if */
Conceptually this makes sense that remaining unused elements have their nested
VLEN parts freed. However, the pointer arithmetic for "tmp" points to the start
of the { number, string } PAIR... and so UINT32DECODE fills the parent_seq_len
variable not with the length of the string (the nested VLEN), but with the
first 4 bytes of the floating-point number in the structure. This seems to be a
bug; it seems as if there should be some generic processing here, similar to
how H5T_convert() is called recursively to prepare the write, as there may be
more than one VLEN nested part?
I was wondering whether HDF is currently supposed to support VLEN-STRUCT-VLEN
nested types in scalar datasets?
Thanks in advance,
Mark Hodson
IMPORTANT: This email remains the property of the Department of Defence and is
subject to the jurisdiction of section 70 of the Crimes Act 1914. If you have
received this email in error, you are requested to contact the sender and
delete the email.
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
