| Commit message (Collapse) | Author | Age | Files | Lines |
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Add test dependicies to correct the order of tests - cmake 2.8.4 bug - but also will improve cmake parallel testing.
Tested: local linux, jam
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had the reference count 0. I fixed it by changing the APP_REF parameter of H5I_register from FALSE to TRUE and added a test case in dtypes.c. The changes to configture.in, tools/misc, tools/lib, config, c++/test, Makefile.am, and fortran are only property changes when I merged from the trunk.
Tested on jam. But I tested the same fix in the trunk with h5committest.
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Tested: jam (open_file_pool branch tested with h5committest)
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Bring r20061 from trunk to 1.8 branch:
Bring changes from Coverity branch to trunk:
r19930:
Fix memory leaks involving VL attributes in h5repack and h5diff. The buffers in
copy_attr and diff_attr were not checked for the presence of a vlen before being
freed, and vlen storage was never reclaimed. Added checks and calls to
H5D_vlen_reclaim().
r19933:
Purpose: Fix memory leak in H5L_move_cb()
Description: H5L_move_cb copied the source link using H5O_msg_copy() but freed
it manually using H5MM_xfree(). Since H5O_link_copy allocates the link using
H5FL_MALLOC, this causes the link to be allocated from the free list but is
never put back on the free list when it is freed. This prevents the link free
list from shutting down properly. Modified H5L_move_cb() and H5L_move_dest_cb()
to free the link properly using H5O_msg_free().
r19973:
Fix resource leaks by freeing string created by HD5f2string
r19974:
Issue #345: Inialize buf variable to null
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on Coverity branch)
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Bring r20052 from trunk to 1.8 branch:
Clean up Coverity warnings, and fix some style issues:
r19735:
Fix for memory leak in test/mf found by valgrind.
r19736:
Fix memory leak in h5repack. The buffer in copy_objects, when copying the
entire dataset at once, was not checked for the presence of a vlen, and vlen
storage was never reclaimed. Added check and call to H5D_vlen_reclaim().
r19772:
Change H5assert() to
if (H5T_VLEN != src->shared->type || H5T_VLEN != dst->shared->type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a H5T_VLEN datatype")
r19774:
removed unused priv.
r19775:
removed unused variables
r19778:
Fix memory leak comparing for variable length data types.
r19834:
Fixed memory leaks found by valgrind. Memory errors remain for another day.
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on branch)
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Description:
When using the scale-offset filter with floating point data or fill values, big
endian machines would save some metadata in the wrong byte order. This caused
such datasets to yield incorrect data when read on little endian machines.
Fixed the scale-offset filter to always save this metadata in the right byte order (i.e. little endian).
Tested: jam, amani, heiwa (h5committedt); fedora, linew
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H5Oset(get)_comment_by_name. It's related to bug 2130.
Tested on jam because I've tested the same change to the trunk with h5committest.
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because Neil prefers to it for fill value test. I
updated the data files, too.
Tested on linew and jam.
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cross_read.c and updated the data files from BE, LE, and VMS. This is the test for bug 2131 that dataset of FLOAT with scale-offset filter can't be read across BE and LE.
Tested on jam and linew.
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macro use for checking libtype.
Tested: Windows
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programs. Added BUILT_AS_STATIC_LIBRARY define to set the windows import/export defines correctly for static libraries.
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m4 to version 1.4.15.
Tested with h5committest on amani, jam and heiwa.
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big.c:
Changed the test to run Huge Dataset (tens of GB), Xtra large dataset(4GB big),
Large dataset (2GB big), or merely 1GB big, depending on if the file system
supports sparse file or if it supports larger than 32bigs I/O.
H5FDstdio.c:
Removed an incorrect condition that whether STDIO VFD supports
larger than 32bits I/O depends on the support of fseeko. Windows does not
use that. Instead, it uses _fseeki64 to support larger than 32bits I/O.
Tested: h5committest, jam (serial).
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of H5Znbit.c in H5Z_nbit_compress -
"*buffer_size = j + 1;" was mistakenly taken out by someone. It is necessary to update the new size. I
put it back and made 2 test cases for integer and float to verify the correct dataset size.
Tested on jam, heiwa, and amani.
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a) Add comments to test_4() in test/external.c about the name "/ link".
b) Fix one memory leak in src/H5Lexternal.c: free memory pointed to by tmp_env_prefix for HDF5_EXT_PREFIX case.
3. Made changes for bug #1930 as in rev #19783, #19781 in trunk.
4. Made corresponding CMake changes as in rev #19782 in trunk.
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Add additional error checking to catch erroneous user input.
Description:
Attempting to retrieve a links's name by index in the case
where the link is external and the file that the object is
located in doesn't exist was causing a segmentation fault
(in production) and an assertion failure (in debug).
The segfault wasn't occuring until the metadata accumulator
attempted a write, so I've added error checking higher in
the pipeline in H5O_protect (where there was previously just
an assert) to catch this. I've also added additional asserts
in the H5F layer where there were none.
Additionally, I added another case to the links.c test to
test that this fails gracefully instead of segfaulting or
asserting out.
Tested:
h5committest and gandalf (mac os x)
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Tested: local linux
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Tested: local linux
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CTestConfig.ctest
Added MemCheck Ignore tests for repeated tools tests
Added Debug flag for windows
Bring r19702 from trunk
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to convert some values from long
double to (unsigned) long and from (unsigned) long to long double. I added tests in configure.in
to detect these algorithms. Before I can figure out them, I disable the tests in dt_arith.c.
Tested on jam, heiwa, amani, IBM Power6 Linux machine in Holland (huygens.sara.nl).
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error stack
printing on and off.
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Bring r19668 from trunk to 1.8 branch:
Do some extra range-checking on H5Pset_elink_acc_flags() calls.
Clean up some minor compiler warnings also.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(too minor to require h5committest)
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Bring r19654 from trunk to 1.8 branch:
Bring Coverity revisions from branch back to trunk, and clean up some other
misc. compiler warnings also.
r19500:
Fix coverity items 1446 and 1447. Moved up calls to memset in test_cont in
ohdr.c so the test never tries to close uninitialized locations.
r19501:
Fix coverity items 1398-1445. Various uninitialized variable errors in fheap.c.
r19502:
Fixed coverity issue 579 and some additional warnings in the file as well.
r19503:
Bug fix: This fix addressed the "RESOURCE_LEAK" problems #789 and 790, run 26
r19504:
minor mods to try to keep coverity from flagging false positives.
r19505:
Fixed coverity issues 566 - 571. Declared variables that are passed to functions that use them as arrays to be arrays of size 1.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug, production & parallel
(h5committested on coverity branch)
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Remove shared library check around ws2_32.lib linking in test library. Issue on windows static builds.
Tested: windows
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- Fix a bug in each of the metadata accumulator source and test code
Description:
- In accum.c test file, switch dxpl_id used in H5F_accum_*
function calls to H5P_DATASET_XFER_DEFAULT (instead of
H5AC_dxpl_id), to fix compilation on windows.
- Changed boundary checking from <= to < when checking
if a read from disk with overlapping dirty metadata in the
accumulator has the read ending such that it aligns exactly
with the dirty accumulator (line 234 of H5Faccum.c).
Tested:
- h5committested
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Bring metadata accumulator fixes and tests into 1.8
Description:
Changes consist of addition of tests for H5Faccum.c source code,
as well as some fixes that address some discovered bugs in the
metadata accumulator on several corner cases.
Tested:
h5committested
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Bring r19587 from trunk to 1.8 branch:
Address issue with object headers being created getting evicted from
the metadata cache cache before they are completely initialized. This is
done by pinning the object header in the cache until it is completely
initialized and attached to a group.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/64-amd64 2.6 (amani) 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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
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application uses -DH5_USE_16_API
with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2
set through H5Eset_auto. I changed the structure H5E_auto_t. I added a IS_DEDAULT flag in
it. Both H5Eprint1/2 are the default now. If the user sets his/her own printing function.
Then a call to H5Eget_auto1/2 will have to match H5Eset_auto1/2.
Tested on heiwa, jam, and amani.
The property change in configure.in, config, tools/misc, tools/lib, c++/test, fortran, and
Makefile.am came from the merge of the trunk library change.
--This line, and th se below, will be ignored--
_M .
M test/testerror.sh.in
M test/err_compat.c
M test/testfiles/err_compat_1
_M configure.in
M src/H5Epkg.h
M src/H5E.c
M src/H5Eint.c
M src/H5Edeprec.c
_M tools/misc
_M tools/lib
_M config
_M c++/test
_M Makefile.am
_M fortran
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Add configurefile command to copy CTestCustom to build folder.
Bring r19527 back from trunk
Tested: local linux
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will fail instead of H5Dclose
when the chunk cache is disabled and the mandatory filter fails.
Tested on jam - simple change.
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match return.
Bring r19520 back from trunk
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Correct script comment in testh5diff.sh
Bring r19509 back from trunk
Tested: Windows Cygwin
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unresolved issues - r19441 and 19466.
Bug 1707 is that H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with
the 1.8 library to compile.
Tested on jam - backing out, simple.
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Bring r19472 from trunk to the 1.8 branch:
Create a new, more streamlined method of generating I/O sequences when
there is only a single block defined by a hyperslab. This improves the
performance of Ger Van Diepen's (LOFAR team) benchmark by about 20%.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committested on trunk)
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Description:
The AIX platform does not install the lib*.so for some reason but libhdf5.a
acts like a shared library. Until we can find out how to fix this, patch
up tetlibinfo.sh to not look for an lib*.so in AIX. (Note the test results
look wierd as it says libhdf5.a passed and skipped.)
Tested: NCSA BP for both enable and disable-shared.
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script and OPTION HDF5_TEST_VFD
Tested: local linux
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Big.c was included by mistake.
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tested on jam and amani, heiwa hasn't finished yet.
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Description:
In an AIX 6.1 system, configure --enable-shared could not build a shared
HDF5 library. The problem was because the version of config.guess was too
old to recongnize AIX 6.X and also configure.in had a local fix which did
not recognize AIX 6.X.
Solution:
1. Mike McGreevy updated bin/config.guess to handle AIX 6.X.
2 Albert fixed configure.in to recognize AIX 6.X.
Note that though HDF5 can build shared lib for AIX 6.X systems
but it still could not install the proper library as in AIX 5.X
systems. Also, bin/config.sub should be updated too.
Tested: BP which is the AIX 6.1 system that exposed this problem.
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has been removed. According to the official description of DESTDIR by Gnu at
http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is
prepended to the normal and complete install path that it precedes for the
purpose of installing in a temporary directory which is useful for building
rpms and other packages. The '/' after ${DESTDIR} will be followed by another
'/' at the beginning of the normal install path. When DESTDIR is empty the
path then begins with '//', which is incorrect and causes problems at least for
Cygwin.
The change made in config/commence.am affects many Makefile.*s when bin/reconfigure
is run. EXAMPLEDIRs had to be corrected individually.
Also the scripts to run examples after they are installed have checks added to see
that the fortran and c++ directories are present before trying to run the scripts
in them.
Tested with h5committest on amani, heiwa and jam.
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Bring r19402 from trunk to 1.8 branch:
Correct Bz#1968 (Problem when opening new format file with
H5F_LIBVER_EARLIEST) by initializing symbol table leaf information in a
more universal way. Also cleaned up other superblock initialization a
little bit while I'm here.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
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Bring r19398 from trunk to 1.8 branch:
Clean up the internal usage H5I_dec_ref() to eliminate the sequence of
flags that has been creeping in.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
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Bring r19396 from trunk to 1.8 branch:
Bring back various modifications to the v2 B-trees that were introduced
in the revise_chunks branch but aren't dependent on any file format or API
changes.
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 (amani) 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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
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Description:
When merging r19386 from the trunk calls to H5AC_ignore_tags were not removed.
This has been corrected.
Tested: Fedora
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file pointer
Description:
The fractal heap header structure keeps a pointer to the file associated with
it. However, it is possible for that file pointer to be closed while the
header is still in cache (through the shared file pointer). Previously, the
header's file pointer was not updated and subsequently pointed to an invalid
file structure. Modified fractal heap code to update the file pointer every
time the header is accessed.
Tested: jam, linew, amani (h5committest)
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and m4 to version 1.4.14. Also added m4 directory for m4 macros according to autoconf suggestion.
Tested with h5committest on amani, jam, and heiwa, and on linew.
-This line, and those below, will be ignored--
M hdf5_1_8/test/Makefile.in
A hdf5_1_8/m4
AM hdf5_1_8/m4/ltsugar.m4
AM hdf5_1_8/m4/libtool.m4
AM hdf5_1_8/m4/ltversion.m4
AM hdf5_1_8/m4/lt~obsolete.m4
AM hdf5_1_8/m4/ltoptions.m4
M hdf5_1_8/configure
M hdf5_1_8/Makefile.in
M hdf5_1_8/testpar/Makefile.in
M hdf5_1_8/configure.in
M hdf5_1_8/src/Makefile.in
M hdf5_1_8/tools/Makefile.in
M hdf5_1_8/tools/misc/Makefile.in
M hdf5_1_8/tools/h5dump/Makefile.in
M hdf5_1_8/tools/h5repack/Makefile.in
M hdf5_1_8/tools/h5jam/Makefile.in
M hdf5_1_8/tools/h5diff/Makefile.in
M hdf5_1_8/tools/lib/Makefile.in
M hdf5_1_8/tools/h5copy/Makefile.in
M hdf5_1_8/tools/h5import/Makefile.in
M hdf5_1_8/tools/h5stat/Makefile.in
M hdf5_1_8/tools/h5ls/Makefile.in
M hdf5_1_8/hl/test/Makefile.in
M hdf5_1_8/hl/tools/Makefile.in
M hdf5_1_8/hl/tools/gif2h5/Makefile.in
M hdf5_1_8/hl/Makefile.in
M hdf5_1_8/hl/src/Makefile.in
M hdf5_1_8/hl/c++/test/Makefile.in
M hdf5_1_8/hl/c++/Makefile.in
M hdf5_1_8/hl/c++/src/Makefile.in
M hdf5_1_8/hl/c++/examples/Makefile.in
M hdf5_1_8/hl/fortran/test/Makefile.in
M hdf5_1_8/hl/fortran/Makefile.in
M hdf5_1_8/hl/fortran/src/Makefile.in
M hdf5_1_8/hl/fortran/examples/Makefile.in
M hdf5_1_8/hl/examples/Makefile.in
M hdf5_1_8/config/commence.am
M hdf5_1_8/MANIFEST
M hdf5_1_8/c++/test/Makefile.in
M hdf5_1_8/c++/Makefile.in
M hdf5_1_8/c++/src/Makefile.in
M hdf5_1_8/c++/examples/Makefile.in
M hdf5_1_8/bin/ltmain.sh
M hdf5_1_8/bin/reconfigure
M hdf5_1_8/perform/Makefile.in
M hdf5_1_8/fortran/test/Makefile.in
M hdf5_1_8/fortran/testpar/Makefile.in
M hdf5_1_8/fortran/Makefile.in
M hdf5_1_8/fortran/src/Makefile.in
M hdf5_1_8/fortran/examples/Makefile.in
M hdf5_1_8/aclocal.m4
M hdf5_1_8/examples/Makefile.in
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Add windows threads support to HDF5.
Description:
Added calls to the windows threads library to the H5TS layer, and wrapped
most calls to either pthreads or windows threads library with portable
H5TS-style defines. Modified tests to use portable function definitions
as well.
This can be configured via CMake with the HDF5_ENABLE_THREADSAFE
option, and should work on windows vista and later operating systems.
Tested:
h5committest, plus threadsafe with pthreads on jam and amani,
and tested on a Windows Vista VM with threadsafe using windows threads.
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couldn't close (bug 1260). The fix releases all resources and closes
the dataset but returns a failure.
Tested with h5committest - jam, heiwa, amani.
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be set. This is to
avoid H5Eclose_stack clearing the default stack. Please see bug 1799.
Tested on jam - simple change.
The changes to configure.in, tools/lib, config, c++/test, Makefile.am, and fortran
are only property changes from the merge.
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