Commit Graph

22902 Commits

Author SHA1 Message Date
Dana Robinson
a7c095d5be
Fix for CVE-2016-4332 (#3406)
This CVE issue was previously listed as fixed (via HDFFV-9950) back in
2016, but with no confirmation test. Now that test files exist for
the 2016 Talos CVE issues, we found that CVE-2016-4332 can raise an
assert in debug builds.

This fix replaces the assert with pointer checks that don't raise
errors or asserts. Since the function is in cleanup code, we do our
best to close and free things, even when presented with partially-
initialized structs.

Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo)
2023-08-21 22:11:56 -05:00
H. Joe Lee
221e727ee2
chore: fix typo (#3405) 2023-08-21 22:09:51 -05:00
jhendersonHDF
5df18802d0
Fix serial to parallel chunked dataset file space allocation bug (#3394) 2023-08-21 22:09:04 -05:00
Allen Byrne
ffde055be2
Update presets, examples uncompress, szip cache (#3391) 2023-08-18 16:01:15 -05:00
jhendersonHDF
81830c1ded
Fix valgrind warning about write of uninitialized bytes in ScaleOffset filter (#3390) 2023-08-18 16:00:43 -05:00
jhendersonHDF
31f4d5aa4e
Fix valgrind warning about write of uninitialized bytes (#3389) 2023-08-18 16:00:10 -05:00
jhendersonHDF
71d98e0706
Fix compile failures with H5C_DO_MEMORY_SANITY_CHECKS enabled (#3388) 2023-08-18 15:59:51 -05:00
jhendersonHDF
98b8fa7469
Fix assertion failure during file close on error (#3387) 2023-08-18 15:59:25 -05:00
Allen Byrne
7025c5f109
restore CI tarball name prefix to match bin/release (#3385) 2023-08-16 08:14:21 -05:00
Allen Byrne
891d00d702
Correct CI settings (#3384)
* Correct CI settings

* Correct plugin file name
2023-08-16 07:33:29 -05:00
Allen Byrne
8c6bc4e250
Correct script (#3377) 2023-08-16 07:32:15 -05:00
Neil Fortner
e5e86912f6
Fix possible performance regression introduced with in-place type conversion in 1.14.2 (#3376) 2023-08-15 08:12:41 -05:00
Neil Fortner
ba2193a270
Add RELEASE.txt notes for recent selection I/O work. (#3374) 2023-08-10 16:15:56 -05:00
Larry Knox
bf68e6eb3a
set H5_PAC_C_MAX_REAL_PRECISION default to 0 when cross sompiling with (#3364)
CMake to fix Fortran build failures.
2023-08-09 15:05:57 -07:00
jhendersonHDF
14eb8f87f4
Work around a testphdf5 failure on Cray MPICH machines (#3361) 2023-08-08 13:02:19 -05:00
vchoi-hdfgroup
291b2f7ae4
Implementation of the mpio driver with selection I/O. (#3222)
* This changes the default selection I/O to on for MPIO.
2023-08-06 22:12:07 -05:00
H. Joe Lee
fb38a8b924
test(parallel): verify FALSE case (#3356) 2023-08-04 22:59:52 -05:00
Allen Byrne
37c60bcea8
Add Fortran ES module to deploy list (#3341)
* Add Fortran ES module to deploy list

* Change fortran mod file export to use a list of names
2023-08-04 16:38:20 -05:00
vchoi-hdfgroup
ede4987b63
Fix for the bug exposed from running test/set_extent.c when selection… (#3319)
* Fix for the bug exposed from running test/set_extent.c when selection I/O is enabled.
This is a fix from Neil.
The test/set_extent.c is modified to test for selection I/O enabled.
2023-08-04 16:36:50 -05:00
jhendersonHDF
915cadb44f
Make h5dump spacing consistent when printing VLEN datatype (#3351) 2023-08-04 09:02:40 -07:00
jhendersonHDF
d6ada85c91
Fix assertion failure in H5D__mpio_collective_filtered_vec_io (#3340) 2023-08-03 16:44:10 -05:00
Aleksandar Jelenak
63b0f152e5
Fix a typo in RELEASE.txt 2023-08-03 11:47:09 -04:00
Sean McBride
07df0d252c
Fixes the last of the -Wextra-semi-stmt warnings (#3326)
* Fixed extra semi warning by adjusting alternative macro definitions

* Find-replace H5E_END_TRY; -> H5E_END_TRY

* Made H5Epush_goto a do-while loop, fixed indentation

* Made GOTOERROR and ERRMSG do-while loops

* Made Hgoto_error and Hgoto_done  do-while loops

* Made vrfy_cint_type and vrfy_ctype  do-while loops

* Made TEST_TYPE_CONTIG and others do-while loops

* Removed extraneous semi-colons

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-08-02 17:46:26 -05:00
Dana Robinson
86ddedf522
Fix CVE-2018-13867 (#3336) 2023-08-02 17:44:19 -05:00
Dana Robinson
11e28fe8b8
Fix CVE-2018-11202 (#3330)
A malformed file could result in chunk index memory leaks. Under most
conditions (i.e., when the --enable-using-memchecker option is NOT
used), this would result in a small memory leak and and infinite loop
and abort when shutting down the library. The infinite loop would be
due to the "free list" package not being able to clear its resources
so the library couldn't shut down. When the "using a memory checker"
option is used, the free lists are disabled so there is just a memory
leak with no abort on library shutdown.

The chunk index resources are now correctly cleaned up when reading
misparsed files and valgrind confirms no memory leaks.
2023-08-02 13:59:26 -07:00
jhendersonHDF
f5c3963c18
Fix h5repack for variable-length datatyped datasets (#3331) 2023-08-02 13:19:21 -07:00
Allen Byrne
8e9c281cf1
A couple of documentation items to fix (#3332) 2023-08-02 13:16:26 -07:00
Allen Byrne
7ed8dd7813
Windows runtime items go into the bin folder (#3320) 2023-08-02 09:29:20 -07:00
Larry Knox
0d3617135b
Update files to skip list and ignore_words_list (#3321)
* Update files to skip list and ignore_words_list for codespell to not
check files generated by autotools.  Autotools generate misspellings
that can't be fixed in HDF5 code.
2023-08-02 08:39:56 -05:00
Sean McBride
2b0badb90e
Made HGOTO_ERROR a do-while loop (#3308)
* Made HGOTO_ERROR a do-while loop
2023-08-02 08:39:15 -05:00
Allen Byrne
56451503c5
Fix loading plugin fails with missing directory GH issue #3248 (#3315) 2023-08-01 23:16:11 -05:00
jhendersonHDF
74352dfda8
Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314) 2023-08-01 23:14:32 -05:00
jhendersonHDF
a78863a82c
Fix incorrect error check in H5Ofill.c for undefined fill values (#3312) 2023-08-01 23:14:02 -05:00
jhendersonHDF
b1e07c74fd
Switch parallel compression to use vector I/O (#3245)
Updates parallel compression feature to use vector I/O instead of
creating and passing down MPI derived types to VFD
2023-08-01 23:01:01 -05:00
Dana Robinson
f62feaef31
Update README.md w/ 1.4.3 info (#3318) 2023-08-01 10:21:13 -07:00
Dana Robinson
354491a8f4
Update release schedule (#3317)
* Move 1.12.3 to November
* Add 1.14.3 in October
2023-08-01 10:16:39 -07:00
H. Joe Lee
0ff29e7d85
Remove py-pip from h5py action (#3265) 2023-07-27 07:46:53 -07:00
H. Joe Lee
85d216634a
chore: fix typo - persent -> present (#3273) 2023-07-25 10:47:08 -07:00
Sean McBride
553e1cd311
Another round of fixing -Wextra-semi-stmt warnings (#3264)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-07-24 16:18:04 -05:00
H. Joe Lee
e0083c48e9
chore: fix grammar - get hang -> get hung (#3272) 2023-07-24 14:44:02 -05:00
Jan-Willem Blokland
8853687933
CMake: (fix) Threads dependency (#3267)
- If the HDF5 library has been build with either thread-safety or
  subfiling VFD feature on it will have an additional dependency
  on a threading library. This dependency has been added to the
  hdf-config.cmake.in file.
2023-07-24 14:43:43 -05:00
H. Joe Lee
fe7e027db6
chore: make VRFY output consistent (#3268) 2023-07-24 12:02:10 -05:00
Jan-Willem Blokland
adb3a173f1
ROS3: (fix) Replaced HDfprintf (#3266)
- Replaced the HDfprintf() functions by fprintf() to be consistent
  with other parts of the library.
2023-07-24 11:21:23 -05:00
Scot Breitenfeld
1706355ee1
removed the use of encoded single apostrophe (#3261)
* removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read

* updated sanitizer paragraph
* fixed brief description for H5Fget_info
2023-07-20 09:01:58 -05:00
Sean McBride
b68988d2d2
Fixed some -Wunused-variable warnings and one Wsometimes-uninitialized warning (#3260) 2023-07-20 07:57:54 -05:00
Dana Robinson
5f0d1439f7
Move 1.12.3 release to October (#3263) 2023-07-19 19:56:29 -07:00
Allen Byrne
800edda078
Option changed but not all references (#3252)
* Option changed but not all references

* remove quotes from binary var
2023-07-18 17:27:12 -05:00
Scot Breitenfeld
7670d1b753
changed the scope of #ifdef DOXYGEN to now include H5D multi-functions (#3254) 2023-07-18 17:26:38 -05:00
Allen Byrne
a04fd783cb
Update DEFAULT_API_VERSION documentation for CMake (#3255)
* Update DEFAULT_API_VERSION documentation for CMake

* Fix hint

---------

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2023-07-18 17:26:01 -05:00
jhendersonHDF
59a0d8baef
Fix warning in H5C__UPDATE_STATS_FOR_DIRTY_PIN macro (#3259)
Add braces to H5C__UPDATE_STATS_FOR_DIRTY_PIN macro to fix warning
causing Werror Release builds to fail
2023-07-18 12:42:03 -07:00