Close out various resource leaks and usages of uninitialized memory that
were flagged by valgrind. [There's still some more valgrind warnings, but
it's better now... :-/ ]
Also clean up warnings and code formatting.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & valgrind
(h5committest forthcoming)
Corrected use of "SKIP" message in cmake.
Corrections to cmake configuration files (for cmake external projects).
Community suggested changes.
Tested: local linux
Bring Coverity changes into the trunk:
r17877:
Error 266: Uninitialized memspace set to -1. Changed malloc and free to HDmalloc and HDfree. Removed unused dtype var.
r17878:
Error 265: Uninitialized mem_space set to -1. Changed malloc and free to HDmalloc and HDfree.
Error 267: Uninitialized smspace set to -1. Changed malloc and free to HDmalloc and HDfree.
r17879:
Error 242: Uninitialized aid set to -1.
Error 243: Uninitialized sid set to -1.
Uninitialized tid set to -1 for consistency
r17880:
Error 242: reinitialized aid to -1 after close to be ready for reuse.
Error 243: reinitialized sid to -1 after close to be ready for reuse.
reinitialized tid to -1 for consistency after close to be ready for reuse.
r17881:
use valgrind to check there is a memory leak. The fix is to free ptrstr in line 5838 at xml_dump_group() of h5dump.c after it is used. run the valgrind after the fix, no memory leak for that part of the code.
r17882:
Fix Coverity items 256 and 269.
r17883:
Error 222-230: initialized hid_t vars to -1 after close to be ready for reuse.
Also added H5Tclose for tid in gent_bigdims
r17884:
Bug fix (Coverity run2, view 23, dead code)
(this is pair-program done by Albert, Elena and Larry).
Confirmed and fixed the deadcode in hyperslab read branch of function
diff_datasetid.
(Discovered other bad code that diff_datasetid() should be recoded.
Bug 1693 is entered for this.)
r17906:
Fix Coverity item 260.
r17907:
262: Initialized hid_t's dtype, dtype_tmp and file to -1. Initialized H5T_t * dt to NULL.
r17908:
Fix Coverity item 261.
r17909:
Fix Coverity item 248.
r17910:
Revise fix for Coverity item 248.
r17911:
Resolved coverity issues #s 263, 162, 163, 164. All issues in dsets.c. Initialized fid and did hid_t's. filter_corrupt function was returning in the middle of an if statement, bypassing free calls. Updated error handling to free buffers and hid_t's appropriately.
r17912:
(done by Larry and Albert)
Cleanup Coverity view warnings (#231-241) about
using uninitialized variables. Initialized all
of them.
r17913:
Resolved issue 251 and 264. Initialized tid2 to -1 and initialized buffers that were freed in case of an error.
r17914:
Resolved coverity issues 66, 220, and 221:
66: Negative Return assignment ignored
220,221: Initialized hid_t's.
r17915:
Fix Coverity item 247.
r17916:
Fix Coverity item 246.
r17917:
Fix Coverity item 245.
r17918:
Fix Coverity item 244.
r17919:
Coverity Issue #84: Moved asserts in H5T_cmp to the top of the function, and converted them to HDassert. Coverity complaining about using potentially NULL pointer without checking it. Want to see if Coverity will accept Assertions as acceptable checking before using the value.
Tested on:
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/default API=1.8.x,
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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Bring r16846 from revise_chunks branch back to trunk:
Fix broken (for how long?) H5_ASSIGN_OVERFLOW macro to actually detect
overflows during assignments, along with several errors it [now] detected.
Cleaned up a fix minor warnings and/or pieces of code also.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest not needed - multi-platform test performed on branch)
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)
Avoid memory leak when realloc() fails during attempt to get larger
buffer as we are decompressing deflated data.
Tested on:
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (kagiso)
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Description: Removed PABLO from the source
Solution:
Platforms tested: arabica with 64-bit, copper with parallel,
heping with GNU C and C++ and PGI fortran (but
I disabled hl, there is some weird problem only
on heping: F9XMODFLAG is not
propagated to the Makefile files
Misc. update:
Purpose:
HDF5 now supports SZIP with no encoder.
Description:
SZIP can be configured to have both encoder and decoder or just to have the decoder. HDF5 can now query the configuration of any filter, and will throw errors if users try to write using a filter with encoding disabled.
Solution:
Added H5Zget_filter_info function, changed API for H5Pget_filter and H5P_get_filter_by_id. See SZIP RFC.
Platforms tested:
Copper (fortran, C++, parallel), Sleipnir (C++), Arabica (fortran, C++), Verbena (fortran, C++)
Misc. update:
Code cleanup & minor optimization
Description:
Re-work the way interface initialization routines are specified in the
library to avoid the overhead of checking for them in routines where there is
no interface initialization routine. This cleans up warnings with gcc 3.4,
reduces the library binary size a bit (about 2-3%) and should speedup the
library's execution slightly.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/gcc34
h5committest
Code cleanup
Description:
Clean up lots of warnings based on those reported from the SGI compilers
as well as gcc.
Platforms tested:
SGI O3900, IRIX64 6.5 (Cheryl's SGI machine)
FreeBSD 4.9 (sleipnir) w/ & w/o parallel
h5committest
Code cleanup/new features
Description:
Switch over to a new style for registering filters with the library -
instead passing in an ID, a string and a callback function to H5Zregister,
the client should pass in a single pointer to a H5Z_claass_t struct which
contains the ID, the description string and all the function callbacks as
fields.
Added support for a new "can apply" callback for each filter, which is
called when a dataset is created to check whether the parameters for that
filter apply correctly to the combination of the datatype and the chunk size
(i.e. dataspace) for the dataset.
Added support for a new "set local" callback for each filter, which
is called when a dataset is created (after the "can apply" filter callback)
and sets filter parameters that are specific to that particular dataset.
Switched the filters we ship over to use the new H5Z_class_t struct for
their internal registrations and also added "set local" callbacks to the
szip and shuffle filters and a "can apply" callback to the szip filter.
Lots of other code cleanups, etc. also
Solution:
Platforms tested:
FreeBSD 4.8 (sleipnir) w/szip
Linux 2.4 (sleipnir) w/szip
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel
Misc. update:
Code cleanup
Description:
Added lots of comments to existing filters, so they are easier to understand
and use as examples for future filters. Cleaned up various bits of code, etc.
Solution:
Platforms tested:
FreeBSD 4.8 (sleipnir)
IRIX64 6.5 (modi4) w/parallel
Misc. update:
Code cleanup/new feature.
Description:
Split FUNC_LEAVE into API and non-API specific versions. This allows a
solution to compiling this branch with C++, as well as reducing the size
of the binaries produced.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
Code Cleanup & New Feature
Description:
H5config.h.in:
Removed H5_HAVE_COMPRESSION & H5_HAVE_FILTER_GZIP flags.
Added H5_HAVE_FILTER_DEFLATE flag.
H5Z.c:
H5Zprivate.h:
H5Zpublic.h:
Switched from using H5_HAVE_COMPRESSION flag in favor of
H5_HAVE_FILTER_DEFLATE.
Added H5Zunregister & H5Zfilter_avail API functions.
Changed a numeric constant (256) to a symbolic constant
(H5Z_FILTER_RESERVED).
Automatically add the shuffling filter to the list of available filters
(when it is enabled).
Moved prototypes for H5Z_filter_deflate & H5Z_filter_shuffle from the
public header into the private header.
H5Zdeflate.c:
Switched from using H5_HAVE_COMPRESSION & H5_HAVE_FILTER_GZIP flags in
favor of H5_HAVE_FILTER_DEFLATE.
Cleaned up formatting & error reporting a bit.
H5Zshuffle.c:
Rewrote shuffling algorithm to be more efficient.
Added error checking & reporting.
Added standard Pablo information.
Added standard function header comment.
Added FUNC_ENTER & FUNC_LEAVE macros.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir)
Update, Bug Fix, and Feature Add
Description:
- Updated how AC_{ENABLE,WITH} help messages were being generated.
Autoconf now gives you an AC_HELP_STRING macro to use to create
them.
- Fixed the problem with Linux LFS on RedHat 7.3 machines. It wasn't
finding getdents64(), so we can't rely on that being present
anymore...
- Added GPFS detection and setting.
- Updated how compression is specified. It's no longer necessary to
test for HAVE_ZLIB_H, HAVE_LIBZ, and HAVE_COMPRESS2. The one macro
{H5_}HAVE_COMPRESSION takes care of all of these.
Solution:
Changed the check for Linux LFS from looking for getdents() to
looking at the version number of the kernel (using the uname -r
command). You can still override with the --enable-linux-lfs switch
if you really believe that your <2.4 kernel has LFS support.
Platforms tested:
Linux (2.2 and 2.4)
Bug fix.
Description:
The chunking code was using internal allocation routines to put blocks on
a free list for reuse, instead of using the system allocation routines (ie.
malloc, free, etc.). This causes problems when user filters attempt to
allocate/free chunks for their algorithm's use.
Solution:
Switched the chunking code back to using the system allocation routines,
we can address performance issues with them if it becomes a real problem.
Platforms tested:
Linux 2.2.x (eirene) && IRIX64 6.5 (modi4)
Code cleanup
Description:
Broke the FUNC_ENTER macro into several macros, with more specialized
uses (which followup mail will describe). This was designed to move
most/all of the checks which could be done at compile time to that point,
instead of needlessly performing them (over & over :-) at run-time.
This reduces the library's size (and thus staticly linked binaries) and
has a minor speedup effect also.
Platforms tested:
IRIX64 6.5 (modi4) with parallel & FORTRAN enabled, and additional testing
on FreeBSD and Solaris immediately after the checkin.
Code cleanup (sorta)
Description:
When the first versions of the HDF5 library were designed, I remembered
vividly the difficulties of porting code from a 32-bit platform to a 16-bit
platform and asked that people use intn & uintn instead of int & unsigned
int, respectively. However, in hindsight, this was overkill and
unnecessary since we weren't going to be porting the HDF5 library to
16-bit architectures.
Currently, the extra uintn & intn typedefs are causing problems for users
who'd like to include both the HDF5 and HDF4 header files in one source
module (like Kent's h4toh5 library).
Solution:
Changed the uintn & intn's to unsigned and int's respectively.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Update
Description:
Changed
#include <hdf_file.h>
construct to
#include "hdf_file.h"
so that the GNU compiler can more easily pick up the dependencies
which it places in the .depend and Dependencies files. Also
regenerated the Dependencies to go along with this.
Platforms tested:
Linux
Code cleanup.
Description:
Fixed _lots_ (I mean _tons_) of warnings spit out by the gcc with the
extra warnings. Including a few show-stoppers for compression on IRIX
machines.
Solution:
Changed lots of variables' types to more sensible and consistent types,
more range-checking, more variable typecasts, etc.
Platforms tested:
FreeBSD 4.2 (hawkwind), IRIX64-64 (modi4)
Redo of a patch
Description:
As Quincey pointed out, the parameters are only ``UNUSED'' if we
can't find libz.a.
Solution:
I changed it to conditionally put the UNUSED in there...
Platforms tested:
Linux
Fixed a read-uninitialized-memory error that resulted in the
file containing small amounts (<8 bytes each) of uninitialized
data. These padding areas (which are never read by hdf5) are
initialized to zero now.
./MANIFEST
./src/H5Z.c
./src/H5Zdeflate.c [NEW]
./src/H5Zprivate.h
./src/H5Zpublic.h
./src/Makefile.in
The zlib filter was moved to a separate file but is still
automatically defined.
