Commit Graph

2226 Commits

Author SHA1 Message Date
H. Joe Lee
d920a45413
Fix ifx unused variable hdferr warning. (#3568) 2023-09-22 08:45:50 -05:00
Scot Breitenfeld
08e115b7d8
Added new Fortran API wrappers (#3511)
* Added new wrappers for
h5get_free_list_sizes_f
H5Sselect_intersect_block_f
H5Sselect_shape_same_f
h5pget_no_selection_io_cause_f
h5pget_mpio_no_collective_cause_f
H5Lvisit_by_name_f
H5Lvisit_f
H5Fget_info_f
h5dwrite_chunk_f
h5dread_chunk_f

* added h5pget_file_space_page_size_f, h5pset_file_space_page_size_f, h5pget_file_space_strategy_f, h5pset_file_space_strategy_f, h5info tests

* added fortran tests

* Update tH5F.F90
2023-09-07 17:25:07 -05:00
jhendersonHDF
0b24f40b0f
Fix Subfiling VFD IOC assignment bug (#3456) 2023-09-01 09:59:28 -07:00
Neil Fortner
1d79445a1d
Remove extraneous "33" in RELEASE.txt (#3425) 2023-08-24 10:43:36 -07:00
jhendersonHDF
216d2191c7
Skip atomicity tests for OpenMPI major versions < 5 (#3421) 2023-08-24 08:54:13 -07:00
Neil Fortner
b155ec5b10
Add RELEASE.txt entry for compound performance regression fix (#3376) (#3416) 2023-08-23 16:49:51 -05:00
Alex
0b2e11d5c0
Fix Heap-buffer-overflow WRITE in H5MM_memcpy (#3368) 2023-08-23 12:35:06 -07:00
Allen Byrne
e1602a287b
Re-enable SZIP default to ON in CMake (#3414)
The Autotools were handled in a separate commit
2023-08-23 12:32:09 -07:00
Dana Robinson
81fc47cc06
Enable szip by default in Autotools (#3412)
Since libaec is so prevalent and BSD-licensed for both encode and
decode, we build the szip filter by default when the szip or aec
libraries are found.
2023-08-23 08:21:33 -07:00
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
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
98b8fa7469
Fix assertion failure during file close on error (#3387) 2023-08-18 15:59:25 -05:00
Neil Fortner
ba2193a270
Add RELEASE.txt notes for recent selection I/O work. (#3374) 2023-08-10 16:15:56 -05:00
jhendersonHDF
14eb8f87f4
Work around a testphdf5 failure on Cray MPICH machines (#3361) 2023-08-08 13:02:19 -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
Aleksandar Jelenak
63b0f152e5
Fix a typo in RELEASE.txt 2023-08-03 11:47:09 -04:00
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
56451503c5
Fix loading plugin fails with missing directory GH issue #3248 (#3315) 2023-08-01 23:16:11 -05:00
jhendersonHDF
a78863a82c
Fix incorrect error check in H5Ofill.c for undefined fill values (#3312) 2023-08-01 23:14:02 -05:00
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
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
Mark Kittisopikul
426a7f82f6
Avoid truncating at null byte when copying to std::string (#3083)
---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-07-15 23:31:57 -05:00
Jan-Willem Blokland
305ac88865
ROS3: (feature) Temporary security credentials (#3030)
- Implemented support for AWS temporary security credentials.
  For this kind of credentials also a session/security token
  should be included in the request by adding the
  x-amz-security-token header.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-07-14 15:15:11 -05:00
jhendersonHDF
26059fc7ab
Subfiling VFD source cleanup (#3241)
* Subfiling VFD source cleanup

Modularize Subfiling CMake code into separate CMakeLists.txt file

Update Mercury util code to latest version and update Copyright

Generate mercury_util_config.h header file instead of using
pre-generated file

Remove unnecessary Mercury functionality

Fix minor warning in Subfiling VFD code

* Remove Mercury headers from Autotools publicly-distributed header list
2023-07-13 12:19:02 -05:00
jhendersonHDF
f5ca9237a2
Fix assertion failure when attempting to use IOC VFD directly (#3187) 2023-06-27 21:36:12 -07:00
Larry Knox
7e3c100755
Fix #1978 h5vers usage message. (#3162)
Update Platforms Tested in RELEASE.txt.
2023-06-20 16:57:43 -07:00
H. Joe Lee
a37795d8b9
chore: fix grammar (#3150)
* chore: fix grammar
2023-06-16 12:43:26 -07:00
Jan-Willem Blokland
8135cc280c
CMake: (feature) ROS3 and cmake config file. (#3146)
- Added a cmake variable to the hdf5-config.cmake file which
  indicate if the library has been build with or without the
  read-only S3 functionality.
2023-06-16 07:34:06 -07:00
Dana Robinson
fcdd0ab9dc
Revert long double checks (#3133)
* Revert "Remove long double conversion work-arounds (#3097)"

This reverts commit 1e1dac1dac.

* Update comments to reflect newer systems
2023-06-15 09:13:22 -07:00
Allen Byrne
75bcd68e7c
Add note for issue 3056 (#3117) 2023-06-13 16:12:14 -07:00
Dana Robinson
d4605919f9
Remove H5detect and H5make_libsettings (#3104)
Removes H5detect and H5make_libsettings from the build and replaces
their functionality with things that don't affect cross-compiling.

H5detect --> floating-point types are now detected on library load
H5make_libsettings --> Moved functionality to a new H5build_settings.c template file
2023-06-13 08:16:41 -07:00
Dana Robinson
1e1dac1dac
Remove long double conversion work-arounds (#3097)
Several options and public symbols that were provided to paper
      over non-standard long double conversions between signed/unsigned
      long and long long values were removed from the Autotools and
      CMake. These were added twenty years ago, when C99 and 64-bit
      platforms were less common and are no longer needed.

      Autotools:
        --enable-dconv-accuracy

      CMake:
        HDF5_WANT_DATA_ACCURACY

      H5pubconf.h symbols:
        H5_WANT_DATA_ACCURACY
        H5_LDOUBLE_TO_LONG_SPECIAL
        H5_LONG_TO_LDOUBLE_SPECIAL
        H5_LDOUBLE_TO_LLONG_ACCURATE
        H5_LLONG_TO_LDOUBLE_CORRECT
        H5_DISABLE_SOME_LDOUBLE_CONV
2023-06-12 14:12:57 -07:00
Dana Robinson
a1a9526b14
Address memory issues when copying empty enums (#3088)
When copying an empty enum type (including implicitly, as when an enum
is contained in a compound type), the library would allocate 0-size
blocks of memory and attempt to memcpy 0 bytes from NULL pointers, which
are undefined behavior. In debug mode, the library would raise an
assert in H5MM.

The library now avoid undefined memory operations when copying empty
enum types and a test that copies empty enums has been added.
2023-06-12 12:14:25 -07:00
Scot Breitenfeld
66cee72768
Print out the VOL connector being used in the ASYNC test (#3016)
* Print out the VOL connector being used in the ASYNC test
* Add h5pget_vol_cap_flags_f with test
2023-06-05 09:59:51 -07:00
jhendersonHDF
79bb60c3f6
API test updates (#3018)
* Remove macros from api tests (#2929)
* Remove macros and undefined callbacks (#2959)
* Remove remaining macros from H5_api_tests_disabled.h (#2968)
* Put some vol capability checks in testpar tests and remove remaining warnings (#2995)
* API tests datatype generation cleanup
* Clean up API tests' random datatype generation and fix bug with enum
datatype generation
* Init parallel API tests with MPI_THREAD_MULTIPLE
* HDF5 API tests - Check VOL connector registration
* Determine whether a VOL connector failed to load before running API
tests
* Cleanup some usages of H5VL_CAP_FLAG_CREATION_ORDER in API tests
* Remove some now-unused macros from H5_api_tests_disabled.h
* Enable HDF5 API tests by default
* Implement CMake option to install HDF5 API tests
* Check for invalid AAPL from H5Acreate
* Enable building of VOL connectors alongside HDF5 in CMake
* Prepend CMake VOL URL option indices with 0s so they come in order
* Don't turn on API tests by default yet
* Document VOL connector FetchContent functionality
* Add release note for API test updates
* Only install testing library if API tests are installed
* Fix grammar
2023-05-26 13:29:02 -07:00
Dana Robinson
b50225e8b2
Add release note for #2999 (#3009) 2023-05-25 07:53:15 -07:00
Allen Byrne
8186a8ded0
Fix plugin cache variable name (#2988)
* Fix plugin cache variable name
* Prefix plugin project local variables
2023-05-22 18:04:48 -05:00
Dana Robinson
5c2e434dc6
Fix 'datatype' misspellings ('dataype') (#2984) 2023-05-19 09:05:23 -07:00
Allen Byrne
dc3ef6055f
Change defaults of standard filters. (#2927) 2023-05-18 16:05:20 -05:00
Larry Knox
6e5c4a5c58
Remove version specific examples from README_HPC. (#2613) (#2975) 2023-05-17 17:38:59 -05:00
Allen Byrne
4b228ec6af
Fix CMake generator expression syntax (#2909) 2023-05-05 15:57:40 -05:00
Allen Byrne
2c3797d7bd
remove obsolete SZIP find module (#2901) 2023-05-05 09:07:16 -07:00
Scot Breitenfeld
654dd01525
Force lowercase Fortran module file names (#2891)
* fixed args in execvp for h5fuse

* Force lowercase Fortran module file names for Cray compilers
2023-05-03 22:03:58 -05:00
jhendersonHDF
25a8ba9fde
Add RELEASE.txt entry for API tests (#2889) 2023-05-03 14:11:38 -07:00
Scot Breitenfeld
a0340338e5
Add Fortran Selection IO APIs (#2864)
new selection IO fortran APIs with tests
2023-05-01 15:21:47 -07:00
Dana Robinson
265494b5b9
Remove "the the" from comments and docs (#2865) 2023-05-01 09:06:39 -07:00
Neil Fortner
3236fb79ce
Implement selection I/O with type conversion (#2823)
Initial implementation of selection I/O with type conversion.  Allows
Parallel collective I/O with type conversion, as long as selection I/O
is enabled.
2023-04-28 16:58:25 -07:00