Description:
Previously, there was no versioning for H5Z_class_t. This prevented applications
written for 1.6 using custom filters from being able to use the 1.8 library.
There is now an H5Z_class1_t and H5Z_class2_t to enable compatibility. H5Zregister is
*not* versioned, it determines which version of the struct has been passed in by the
value of the first field (id or version, both are ints).
Tested: jam, linew, smirom (h5committest), jam (--with-default-api-version=v16)
Description:
When writing data to a dataset, the data transform was performed after type conversion.
This caused an error if the file type was non-native. This has been changed so data
transforms are always performed on the memory type.
Tested: jam, linew. smirom (h5committest)
Description:
h5repack previously would not take named datatypes into consideration when copying
datasets and attributes. This would cause extra anonymous datatypes in the target file
at best, and cause errors halfway through the repacking at worst. h5repack should now
always handle named datatypes correctly. Named datatypes are also now converted to the
native type when -n is given.
Tested: jam, linew, smirom (h5committest)
- Updated bin/reconfigure to use latest version of automake (1.10.2).
Regenerated Makefile.in's by running bin/reconfigure.
- Added libtool version numbers to c++, fortran, hl, hl c++, and hl fortran
libraries.
Tested:
jam, liberty, smirom
Added a Make target of check-all-install to test the correctness of
installing via the prefix= or $DESTDIR options.
Platforms tested:
h5committested and jam serial mode. Then test check-all-install by hand.
- h5diff new flag, -c, --compare, list objects that are not comparable.
PVN - 2009/4/2 - 1368
- h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2
Description:
The H5L interface was not marked as uninitialized when H5L_term_interface was
called. This caused the interface to not initialize itself later on. This
prevented external links from working after calling H5close, because they were
never re-registered.
Tested: jam, smirom, linew (h5committest)
Description:
Versions of the library between 1.3.0 and 1.6.3 have a bug which prevents them
from opening any file that does not have the root group's symbol table
information cached in the root group's entry in the superblock. Prior to 1.8
this was not an issue as this information was always cached. However, 1.8.0
stopped writing this information (which is not required by the file format
specification), and these older versions can therefore not read files created or
last written by versions 1.8.0 to 1.8.2. This fix modifies the library to once
again add this information to the superblock (when using the old file format).
Tested: jam, linew, smirom (h5committest)
Description:
Changed Skip list package to use a deterministic skip list. This allows the
skip list package to avoid calling rand() and srand(), even on machines without
rand_r(). There is no longer a p-value or maximum level for skip lists.
Tested: jam, smirom, linew (h5committest)
Description:
Previously, H5Lcopy and H5Lmove would (through H5L_move) improperly apply the
"create intermediate groups" property to the source path traversal, and not the
destination. Fixed it to apply the property to the destination and not the
source. Also fixed H5Lcreate_ud to reject internal link classes without
throwing an assertion.
Tested: linew, jam, smirom (h5committtest)
#1402 (B1) h5repack does not preserve creation order indexing.
ISSUE : h5repack does not handle group creation order flags.
ACTION: call H5P(g)(s)et_link_creation_order functions when handling groups, add new groups with these flags to the test generation program, and verify results in the test program.
TEST: in the test program, function that compares property lists, added code to verify groups
DOCS: Added the note to RELEASE.txt: "h5repack now handles group creation order. PVN - 2009/4/2 - 1402".
Description:
Due to a bug in H5F_super_read, every time a file with a user block was opened
it would grow by the size of the user block. The bug has been fixed, and
comments have been added to clarify when an eoa address should be relative and
when it should be absolute.
Tested:
jam, linew (h5committest)
#1047 (B1) The h5lt info routines are returning data in transposed form. ISSUE : the dimension array of the function h5ltget_dataset_info_f was not transposed (because of C-FORTRAN storage order, the FORTRAN function calls the C function with the same name). SOLUTION: transpose the array. ACTION: add a test case.
added the note
Fortran High-Level APIs:
------
- Lite: The h5ltget_dataset_info_f function (gets information about a dataset)
was not correctly returning the dimension array (PVN - 2009/3/23)
tested: linux
Description:
Some files apparently exist in the wild which have corrupt symbol table messages
on the root group. These files can be opened by 1.6 (which uses the cached
information in the superblock) but not by 1.8. This patch fixes 1.8 and 1.9 so
they can now open these files, and will correct them if necessary. Also fix
some potential (rare) problems with array datatype versions.
Tested: jam (parallel; h5committest not working on linew or smirom)
When reading the compression parameter keyword, the compression type read flag was incorrectly set to read, removed this line of code
in->configOptionVector[COMPRESS] = 1;
Modified one configuration file to have the COMPRESSION-TYPE GZIP
Keyword.
Entered a bug description fix of
- h5import: By selecting a compression type, a big endian byte order was being
selected (PVN - 2009/11/3)
tested: linux
Bug Fix
Description:
Fixing BZ #1381. The --includedir=DIR configure option, which is used to
spceify installation location of C header files, did not work correctly as
the path was hard-coded into config/commence.am. I'm presuming this is
because an older version of automake didn't know where to put C header
files. In any case, removing this line now defaults the includedir to the
same directory that it is currently hard-coded to, and also fixes the
configure flag which allows for customization of this value.
Tested:
jam, liberty
Bug Fix
Description:
Removing the code from configure which strips the '-g' flag from CFLAGS
when in production mode. The current default CFLAGS in production mode
does not include '-g', as intended, but we should allow users to
override this and enable '-g' by setting the CFLAGS environment
variable if desired. Note that this applies to FCFLAGS and CXXFLAGS
as well.
Tested:
kagiso, linew, liberty
Description:
In some situations it was possible for the fill value to not be written to parts
of a chunked dataset, particularly when extending and/or shrinking. Prior to
the fix for the chunk cache (1015) these bugs would have been exceedingly rare.
Tested: jam, smirom, linew (h5committest)
Description:
The meaning of the "nbytes" field in H5D_rdcc_t was not clear, and some places
assumed it was the maximum size of the chunk cache, while some assumed it was
the current size of the chunk cache. The end result was that only 1 chunk could
be held in cache at a time. This field has been replaced by "nbytes_max" and
"nbytes_used". Performance of cached I/O should improve greatly.
Tested: jam, smirom (h5committest)
file handles.
Description:
An attribute's "oloc" field which specifies the file it resides in was located
in the attribute's "shared" structure. So when an attribute was opened multiple
times all of the handles for that attribute pointed to the same file id, even if
different file id's were used to open the different handles for the attribute.
The "oloc" has been moved to the top level H5A_t struct.
Tested: jam, smirom (h5committest)
Description:
Since the new object header format, it has been possible for a situation to be
created where none of the messages are large enough to hold a continuation
message and there are no null messages to merge with. This makes it impossible
to add a new object header chunk. This case will now be handled by moving every
message in the last chunk to the newly allocated one, except for null messages
which are deleted.
Tested: jam, smirom (h5committest)
Description:
When an attribute was created with a datatype or dataspace that was shared in
the same object header that the attribute was in, the attribute could not be
deleted. Changes made to ensure that the attribute can be deleted both when the
attribute is in the object header and when it is shared in the heap. Object
header message decode routines now take an "open_oh" parameter to enable them to
avoid opening the same object header twice.
Tested: jam, smirom (h5committest)
Description:
Attribute object copy routines have been moved from H5Oattr.c to H5Aint.c.
These routines are now shared between compact and densely stored attributes.
New routines written to support the copying of dense attributes. This patch wasmostly written by Peter Cao.
Tested: jam, smirom (h5committest)
Description: When attempting to copy an object with a message shared in its own
object header, the library attempts to protect the same object header twice.
Previously, it was possible for the object header to be protected with write
access in one or both of these protects, which would be illegal. The library
should now always protect with read only access in this case. The conditions
for fixing incorrect datatype versions have been made weaker to support this
change. The version will only be corrected if the object header the datatype
is in is modified.
Tested: jam, smirom (h5committest)
Description: H5Tset_order will now properly reject H5T_ORDER_NONE for most
datatypes. Previously this could cause major problems as the file could not be
flushed.
Tested: jam, smirom (h5committest)
Description:
If a compound type was packed except for some extra space at the end, H5Tpack
would not modify the type and the extra space would remain. Changed
H5T_is_packed to fix this behaviour.
Tested: jam, smirom (h5committest - linew down)
svn merge
Description:
merging revision 16290 from trunk to 1.8
(revision 16290 contains the code that maintains a min_clean_fraction
of the metadata cache in serial).
Tested:
smirom, jam
chunk size as the same size of the size of the hyperslab used to read the chunks.
The size of the hyperslabs are defined as the size of each dimension or a
predefined constant, whatever is smaller. This assures that the chunk
read fits in the chunk cache. (PVN - 2008/11/21)
- H5Dset_extent: when shrinking dimensions, some chunks were not deleted.
(PVN - 2009/01/8)
