Commit Graph

22402 Commits

Author SHA1 Message Date
jhendersonHDF
c75b4af1a2 Add initial version of HDF5 API tests (#2877) 2023-05-03 13:26:57 -05:00
Larry Knox
75d64819b0
Redo remove selection I/O test from testphdf5 in CMake #2860. (#2874) (#2884) 2023-05-03 12:37:05 -05:00
Larry Knox
85b5e8e7da
Update so numbers for hdf5 1.14.1 release. (#2881) 2023-05-03 12:36:47 -05:00
Larry Knox
271b0fbb8c
Sync 2 new develop prs to hdf5_1_14 (#2879)
* Add bin directory to make distclean (#2872)

This allows h5cc to be cleaned up

* Fixed test failure for when REAL is promoted via a compiler flag (#2873)

---------

Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
2023-05-02 16:06:16 -05:00
Dana Robinson
6eb021b68a
Sync with develop (#2871) 2023-05-01 22:25:48 -07:00
Allen Byrne
da46fdbf50
Add daily test create binary workflow for prior day (#2862) 2023-05-01 08:54:04 -07:00
Allen Byrne
e22750f7b8
add new presets (#2861) 2023-05-01 08:53:12 -07:00
jhendersonHDF
88d78fb508
Allow H5P_DEFAULT in H5Pget_vol_cap_flags and H5Pget_vol_id (#2807) (#2815) 2023-04-30 13:15:51 -07:00
Allen Byrne
a5a0d2beca
Correct compression install files (#2846) 2023-04-30 13:14:30 -07:00
Dana Robinson
a150e5fc25
Sync with develop (#2849)
Cherry pick of

ea7dfcd (Change Powershell to PowerShell in docs)

to

4497feb (Update H5Dget_space_status bug note to reference 1.14.0)
2023-04-28 13:37:04 -07:00
jhendersonHDF
f82f056d7b
Fix hdfeos5 workflow concurrency conflicts (#2804) (#2826) 2023-04-26 15:39:21 -07:00
jhendersonHDF
0312137b00
Fix ROS3 VFD anonymous credential usage with h5dump and h5ls (#2798) (#2800) 2023-04-24 09:12:00 -07:00
Allen Byrne
5c8c9ce925
Correct CMake option defaults - deprecate szip for libaec (#2786) 2023-04-24 09:11:26 -07:00
Dana Robinson
7707859279
Merge with develop (#2790) 2023-04-21 23:25:12 -07:00
Dave Allured
a4371b6fce
H5Spoint.c: Comment fix (#2783)
Comment here should be "point", not "hyperslab".
2023-04-20 16:51:25 -05:00
Larry Knox
f909e6e83f
Add new version of COPYING_LBNL_HDF5. (#2775) 2023-04-18 13:07:06 -07:00
Allen Byrne
becd452562
Add no subsets option to h5diff like h5dump (#2759) 2023-04-18 11:21:34 -07:00
glennsong09
298d7218d5
Clean up memory allocated when reading messages in H5Dlayout on error (#2769) 2023-04-17 19:10:15 -07:00
jhendersonHDF
84d9885fd7
Check for invalid AAPL in H5Aopen (#2712) (#2770) 2023-04-17 15:11:16 -07:00
Dana Robinson
9a07981148
Remove author and date from RELEASE.txt entries (#2751) 2023-04-16 12:28:40 -07:00
jhendersonHDF
ae202d3d62
Add buffer overrun checks to H5O__layout_decode and H5O__sdspace_decode (#2679) (#2728) 2023-04-14 17:28:02 -07:00
Dana Robinson
69c720bffa
Merge "Use additional CPUs" and related fixes (#2742)
* 2720 Fix java depends and pdb lib install
* 2695 Use additional CPUs in GitHub actions
2023-04-14 15:14:38 -07:00
Dana Robinson
69dcba9b6b
Remove 1.14 release schedule (#2743)
There is no need to maintain the release schedule in each branch, so
it's being removed from all branches aside from develop.

Also removes the badges that don't pertain to 1.14
2023-04-14 15:14:21 -07:00
Dana Robinson
cc3b550bf0
Add Elena to CODEOWNERS for Fortran 2023-04-14 12:30:38 -07:00
jhendersonHDF
537c910823
Fix a heap buffer overflow during H5D__compact_readvv (GitHub #2606) (#2664) (#2725) 2023-04-14 05:50:32 -07:00
vchoi-hdfgroup
a66bff93b2
Fix for github issue #2599: (#2665) (#2706)
* Fix for github issue #2599:
As indicated in the description, memory leak is detected when running "./h5dump pov".

The problem is: when calling H5O__add_cont_msg() from H5O__chunk_deserialize(),
memory is allocated for cont_msg_info->msgs.  Eventually, when the library tries to load
the continuation message via H5AC_protect() in H5O_protect(), error is
encountered due to illegal info in the continuation message.
Due to the error, H5O_protect() exits but the memory allocated for cont_msg_info->msgs is not freed.

When we figure out how to handle fuzzed files that we didn't generate,
a test needs to be added to run h5dump with the provided "pov" file.

* Add message to release notes for the fix to github issue #2599.
2023-04-13 14:36:24 -07:00
Allen Byrne
2319d4a092
Change name of test file to avoid conflict (#2703) 2023-04-13 11:05:32 -07:00
jhendersonHDF
9fff85d7e6
CMake - Match Autotools behavior for library instrumentation (#2648) (#2674)
Enable library instrumentation by default for parallel debug builds
2023-04-13 09:17:27 -07:00
jhendersonHDF
5b4df7b2cd
Minor fixes for Subfiling VFD tests (#2633) (#2671) 2023-04-13 09:16:06 -07:00
jhendersonHDF
8d9e964b64
Avoid suppressing error output for non-tentative file opens (#2632) (#2670)
* Avoid suppressing error output for non-tentative file opens

* Update comment about tentative file opens
2023-04-13 09:14:00 -07:00
Allen Byrne
e9604656eb
Fix #2598 sanitize leak (#2675) 2023-04-13 09:12:27 -07:00
jhendersonHDF
02c6873974
Fix improper include of build directory (#2422, #2621) (#2667) (#2713) 2023-04-13 09:06:26 -07:00
Dana Robinson
66b28fe395
Fix memory leaks and aborts in H5O EFL decode (#2656) (#2707)
* Convert asserts to error handling in efl decode

The function that decodes external data files object header messages
would call assert() when parsing malformed files, causing applications
to crash when linked against the debug library.

This change converts these assert() calls to HDF5 error checks, so
the messages are sanity checked in both release and debug mode and
debug mode no longer crashes applications.

Also cleaned up some error handling usage and debug checks.

* Free memory on H5O efl decode errors

* Add buffer size checks to efl msg decode

* Add parentheses to math expressions

Fixes GitHub #2605
2023-04-12 22:18:28 -07:00
Larry Knox
37a8e3024e
Minor cherry-pick merges to 1.14 (#2582)
* Enclose MESG in do...while loop (#2576)

Enclose MSG macro in a do...while loop

* Add a clang-format comment about permissions (#2577)

* Remove an obsolete comment from the MDS test (#2578)

The seed is now broadcast from rank 0, so the warning about multiple
machines having different seeds is unnecessary.

* Subfiling VFD - fix issues with I/O concentrator selection strategies (#2571)

Fix multiple bugs with the SELECT_IOC_EVERY_NTH_RANK and
SELECT_IOC_TOTAL I/O concentrator selection strategies and add a
regression test for them

* Check for overflow when calculating on-disk attribute data size (#2459)

* Remove duplicate code

Signed-off-by: Egbert Eich <eich@suse.com>

* Add test case for CVE-2021-37501

Bogus sizes in this test case causes the on-disk data size
calculation in H5O__attr_decode() to overflow so that the
calculated size becomes 0. This causes the read to overflow
and h5dump to segfault.
This test case was crafted, the test file was not directly
generated by HDF5.
Test case from:
https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.md

---------

Co-authored-by: glennsong09 <43005495+glennsong09@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Egbert Eich <eich@suse.com>
2023-04-04 12:36:27 -05:00
jhendersonHDF
101210c16e
Subfiling VFD - fix issues with I/O concentrator selection strategies (#2571) (#2618)
Fix multiple bugs with the SELECT_IOC_EVERY_NTH_RANK and
SELECT_IOC_TOTAL I/O concentrator selection strategies and add a
regression test for them
2023-04-04 12:35:52 -05:00
Allen Byrne
f13f8705b1
Make sure that ONLY_SHARED_LIBS option is correctly set (#2545) 2023-04-04 11:36:23 -05:00
jhendersonHDF
ec0d4d6486
Fix a memory corruption issue in H5S__point_project_simple (#2626) (#2631) 2023-04-04 11:35:49 -05:00
Allen Byrne
097f65e7a6
Update java logger version (#2644) 2023-04-04 11:35:23 -05:00
Larry Knox
a1fb8d70e1
Cherry-pick merges from develop to hdf5_1_14 (#2572)
Co-authored-by: Mark (he/his) C. Miller <miller86@llnl.gov>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
2023-03-16 06:23:26 -05:00
Larry Knox
b2da35ea74
1.14 Fix H5Dchunk_iter doxygen example, cherry-pick of 04682f2 (#2519) (#2548)
* Fix H5Dchunk_iter doxygen example, cherry-pick of ef3bed6 (#2519)

Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
2023-03-15 20:06:41 -05:00
jhendersonHDF
32755b3fb2
Subfiling VFD - add option to specify config file prefix (#2495) (#2570) 2023-03-15 18:16:08 -05:00
Larry Knox
6df5f12527
Update ReferenceManual.dox (#2517) (#2569)
Co-authored-by: mattjala <124107509+mattjala@users.noreply.github.com>
2023-03-15 18:15:43 -05:00
Larry Knox
fcd3b5a880
docs: in -> out (#2514) (#2516) (#2568)
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
2023-03-15 18:15:20 -05:00
Larry Knox
f24debb1a2
Remove redundant and flawed documentation of H5D_chunk_iter_op_t from H5D.c (#2512) (#2566)
Forward port of 9f252f1 from #2329

Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
2023-03-15 18:14:48 -05:00
Allen Byrne
0491aba7d2
Update cross compile checks and files #2497 (#2564) 2023-03-15 18:14:00 -05:00
Allen Byrne
d018e6f88c
Change libaec URL to actively maintained repo GH#2552 (#2560) 2023-03-15 18:12:45 -05:00
Allen Byrne
7a5f4f60c6
GH issue #2538, print must have verbose on first (#2541) 2023-03-15 18:10:21 -05:00
Larry Knox
8e7ad56526
Add concurrency option to cancel in-progress jobs (#2539) (#2558)
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
2023-03-15 09:08:32 -05:00
Larry Knox
06bf32bf4a
Fix new codespell issues (#2521) (#2533)
* Fix new codespell issues

* Have codespell ignore ./config/sanitizer/sanitizers.cmake

Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
2023-03-10 14:28:02 -06:00
Allen Byrne
d51c97e7f5
1.14 Merge doxygen plist tables changes #2470 from develop (#2503)
* Merge doxygen plist tables changes from develop

* Doxy corrections
2023-02-28 17:08:02 -08:00