Clean up code and eliminate resource leaks. Also avoid "null" I/O when
chunk doesn't exist and we can skip it.
Tested on:
Mac OS X/32 10.5.6 (amazon)
(too minor to require h5committest)
Clean up (i.e. remove) more internal calls to H5E_clear_stack(), along with
some other minor code cleanups.
Tested on:
Mac OS X/32 10.5.6 (amazon)
(too minor to require 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 This field has been replaced by "nbytes_max" and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)
on disk, the library still loaded it in the cache, which is redundant. I changed it to bypass the
cache and added a test in dsets.c.
Tested on jam and smirom.
Eliminate some more calls to H5E_clear_stack() from within library code.
Clean up some warnings & comments also.
Tested on:
Mac OS X/32 10.5.6 (amazon)
(Too minor to require h5committest)
Correct error introduced in r16353 with layout version, and add test
so it gets caught earlier.
Tested on:
FreeBSD/32 6.3 (duty)
Too minor to require h5committest
Rename H5O_msg_read_real -> H5O_msg_read_oh, to be more consistent with
other routines in library.
Move H5O_msg_read_oh and H5O_msg_exists_oh from package to private
header file, so other routines in library can use them.
Tested on:
FreeBSD/32 6.3 (duty)
Too minor to require 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)
Changed max macro in earray.c to avoid Windows conflict.
Changed if(test) to assert(test) in H5FDcore.c - H5FD_core_open()
Tested on:
Windows: XP32, XP64, Vista32, Vista64
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)
Refactor internal address encode/decode routines slightly, to allow for
more flexible use.
Tested on:
Mac OS X/32 (amazon)
FreeBSD/32 (duty)
(too minor to require 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)
Bring r16353 back from revise_chunks branch:
Refactor internal layout information, making it easier to add another
type of chunk index.
Tested on:
FreeBSD/32 6.3 (duty)
(other platforms tested with original patch)
Description: H5Tinsert will now detect when a compound type that was previously
not packed becomes packed due to out of offset order insertion of a member.
H5Tinsert will now attempt to keep members sorted by offset order. This should
improve performance of H5Tinsert in all cases due to the fact that it no longer
needs to check every other member for overlapping, and should improve
performance of H5Tpack and possibly type conversion when compounds are packed
out of order.
Tested: jam, smirom (h5committest)
Code Cleanup
Description:
- Pulled out repetitive cache stats code into its own new macro.
- Converted HDasserts in cache stats macros to if / HGOTO_ERROR statments
in order to keep code consistent.
Tested:
jam, smirom, liberty
Improvement
Description:
Modified the warning messages from the Version mismatch checking to suggest
the users to try recompiling or checking the shared lib setting.
Platforms tested:
Tested in Jam only since it was just a simple text string changes.
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)
Bring r16305 back from revise_chunks branch:
Add detection of C99 "designated initializers" to configure script and
use new H5_HAVE_C99_DESIGNATED_INITIALIZER macro to conditionally compile
default layout variables in src/H5Pdcpl.c
Also, minor code cleanups, etc.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(Other platforms tested on branch)
Adding code to maintain a min_clean_fraction in the cache in serial mode.
Description:
The metadata cache now has the ability to maintain a min_clean_fraction
when in serial mode. The default initial cache size has been changed
from 1MB to 2MB, and the default min_clean_fraction has been set at 30%.
This check-in includes modifications to H5C.c to support maintaining a
min_clean_size, including the addition of clean_index_size and
dirty_index_size trackers, modifications to the H5C_make_space_in_cache
algorithm, as well as associated test code and additional statistics
tracking variables.
Maintaining the min_clean_fraction addresses the possibility of
experiencing a "metadata blizzard" when the cache gets completely
full with dirty entries. Upon having to make space, the cache would
previously need to flush every single entry in the cache before coming
across a clean entry which could be evicted. This resulted in unnecessary
flushing of oftentimes hot entries in the cache. Maintaining the
min_clean_fraction ensures that, when space is needed, clean entries
are more readily available to evict.
Tested:
jam, smirom, linew (h5committest)
Description: Added H5Pset/get_elink_cb to allow the user to specify a callback
function to be called whenever an external link is traversed. Added
H5Pset/get_elink_acc_flags to allow the user to specify the file access flags
to use to open the target file of an external link. All these properties are set on a LAPL.
Tested: jam, linew, smirom (h5committest)
Bring revision 16278 back from revise_chunks branch:
Update layout information in DCPL to unify all information in one
underlying property and switch to using H5O_layout_t for storing it, which
simplifies things considerably.
Also, fix many compiler warnings.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(Original patch tested on many machines)
new test program: It adds tests for several ranks, use of fill value or not, compression, different fill value allocation times, use of different storage layouts, and external files
tested: windows, linux
to the beginning of the file. Otherwise, the file might be re-extended later on Open VMS.
Also updated the return value for the HDlseek to be more appropriate.
Tested 1.8 on Open VMS.
Bug fix (#1357)
Description:
Three filters have not assigned correct value to one value-result argument, "buf_size". N-bit, szip, and scale offset filter have had this problem.
However, I don't think this problem has been making buffer overrun because those filters were informing the caller that the "buf", another value-result argument, is smaller than it actually is. If there was actual buffer overrun, I believe another problem exists although I don't know.
Tested:
jam, smirom, linew
Although all test were passed, I'm concerned about valgrind memcheck error. There can be another miscommunication between filter and the caller.
Moved v1 B-tree debugging routines into separate module and thinned
out header files a bit.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
On Open VMS, if the last read or write put the file pointer beyond the current file size
(it happens when an object is deleted), the file can be extended when it's truncated.
Tested v1.8 on VMS.
Bug Fix
Description:
Resolved issues with broken sanity checks that were failing when the 'b2'
debugging package was enabled (v2 b-tree debugging):
- Fixed outdated assertions that would not compile. They now compile
and function correctly.
- Removed too far outdated assertions that would require too much
unnecessary refactoring of code in order to satisfy their
initial purpose.
- Re-enabled b2 debugging package when "--enable-debug=all" is
specified on the configure line.
Tested:
jam, smirom, linew
