22438 Commits

Author SHA1 Message Date
jhendersonHDF
d67d709a3a
Remove duplicated H5_IS_BUFFER_OVERFLOW macro (#2700) 2023-04-12 12:56:51 -07:00
Allen Byrne
e94071fe53
Change name of test file to avoid conflict (#2701) 2023-04-12 12:50:46 -07:00
Dana Robinson
7b46484292
Revert "Added tables of CVE issues (#2685)" (#2696)
This reverts commit b749a4ef09a6fa2bdb02cf49eddda364dcb9a0cc.
2023-04-11 21:23:52 -07:00
bmribler
b749a4ef09
Added tables of CVE issues (#2685) 2023-04-11 23:08:27 -05:00
vchoi-hdfgroup
67d4b5eaf8
Fix for github issue #2599: (#2665)
* 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.
2023-04-11 23:06:29 -05:00
Dana Robinson
d1727fe8f3
Use additional CPUs in GitHub actions (#2695)
* Build: 3 CPUs
* Tests: 2 CPUs

For both Autotools and CMake
2023-04-11 20:58:39 -07:00
Quincey Koziol
82b7221208
Cache tidy (#2693)
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.

* Committing clang-format changes

* Allow spaces (and tabs) in VOL connector info string from environment variable.

* Parse connector name from HDF5_PLUGIN_PATH environment variable better

* Correct H5VLquery_optional to use H5VL routine instead of H5I.  Also add an
error message to the failure return value from not finding a plugin.

* Play nice with existing plugin paths

* Use API routine to determine if native connector is terminal.

* Committing clang-format changes

* Make string size larger, to allow for connectors with longer names.

* Be more flexible about testing external pass through connectors, especially if
they have registered new optional operations.

* Bring style closer to library's agreed coding style

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
2023-04-11 20:57:47 -07:00
glennsong09
367e4a3933
Clean up memory allocated when reading messages in H5Dlayout on error (#2602) (#2687) 2023-04-11 16:09:05 -05:00
mattjala
2eedc8e8f7
Fix invalid memory access in H5O__ginfo_decode (#2663) 2023-04-11 15:22:11 -05:00
jhendersonHDF
bc8fa3a477
Add buffer overrun checks to H5O__layout_decode and H5O__sdspace_decode (#2679)
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2023-04-11 14:47:51 -05:00
Scot Breitenfeld
2e7d8f7ed5
Perlmutter was fixed (#2677) 2023-04-11 14:41:06 -05:00
jhendersonHDF
b77cb393b8
Fix improper include of build directory (#2422, #2621) (#2667) 2023-04-11 14:31:25 -05:00
Julien Schueller
70d9616672
CMake: Let runtime checks through stdout only (#2666)
This avoids mixing emulators errors on stderr to configure results
while cross-compiling with wine.
2023-04-11 14:28:32 -05:00
H. Joe Lee
3bca79c7aa
ci: add HDF-EOS5 test action (#2415) (#2625) 2023-04-11 14:20:10 -05:00
jhendersonHDF
027ee7c633
Fix a heap buffer overflow during H5D__compact_readvv (GitHub #2606) (#2664) 2023-04-11 14:08:46 -05:00
Allen Byrne
281071907b
Remove -Wunused-but-set-variable warnings in tests (#2661) 2023-04-11 14:07:14 -05:00
Dana Robinson
92177ef21e
Update release schedule (#2692) 2023-04-11 11:01:54 -07:00
Quincey Koziol
3290889de3
Dead code removal (#2690)
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.

* Committing clang-format changes

* Allow spaces (and tabs) in VOL connector info string from environment variable.

* Parse connector name from HDF5_PLUGIN_PATH environment variable better

* Correct H5VLquery_optional to use H5VL routine instead of H5I.  Also add an
error message to the failure return value from not finding a plugin.

* Play nice with existing plugin paths

* Use API routine to determine if native connector is terminal.

* Committing clang-format changes

* Make string size larger, to allow for connectors with longer names.

* Be more flexible about testing external pass through connectors, especially if
they have registered new optional operations.

* Dead code removal

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
2023-04-11 09:30:02 -07:00
Quincey Koziol
49a71463a0
Comment cleanup (#2689)
* Clean up content and redundant logging in comments.
2023-04-11 09:41:32 -05:00
Dana Robinson
1ad030f669
Remove dead code hidden behind #ifdef LATER (#2686) 2023-04-10 11:39:46 -07:00
Allen Byrne
fc91e8856f
Fix #2598 sanitize leak (#2660) 2023-04-07 10:35:51 -07:00
Allen Byrne
526f0769a3
Minor fixes for CMake code and install docs (#2623) 2023-04-03 14:38:10 -07:00
Allen Byrne
fa388e6ba4
Update java logger version (#2643) 2023-04-03 14:36:23 -07:00
jhendersonHDF
b8c27cec17
Minor fixes for Subfiling VFD tests (#2633) 2023-04-03 13:09:08 -05:00
jhendersonHDF
f105dcc20a
Synchronize HDF5 tests with VOL tests (#2628) 2023-04-03 13:08:39 -05:00
Dana Robinson
1c1af33a12
Fix memory leaks and aborts in H5O EFL decode (#2656)
* 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
2023-04-03 11:06:36 -07:00
jhendersonHDF
7b426bf3ea
CMake - Match Autotools behavior for library instrumentation (#2648)
Enable library instrumentation by default for parallel debug builds
2023-03-31 22:38:15 -05:00
H. Joe Lee
879575f3fa
chore: make comment consistent (#2654)
Use a 3rd person verb to match "Does not" in the next sentence.
2023-03-31 22:37:12 -05:00
jhendersonHDF
d3d1a03f2c
Avoid suppressing error output for non-tentative file opens (#2632)
* Avoid suppressing error output for non-tentative file opens

* Update comment about tentative file opens
2023-03-31 22:36:28 -05:00
jhendersonHDF
31c26e72c5
Fix a memory corruption issue in H5S__point_project_simple (#2626) 2023-03-23 22:55:34 -05:00
Dana Robinson
7fd9a4435f
Fix minor things noted when doing 1.10 merges (#2610)
* Duplicated HDF_RESOURCES_DIR from cmake_ext_mod merge
* Typos in comments
2023-03-23 22:55:18 -05:00
Dana Robinson
af2666013f
Bring new release_docs scheme from 1.14 (#2614) 2023-03-22 18:41:00 -07:00
Dana Robinson
7b5e67b066
Fix test script names in cleanup code (#2590)
When the test scripts were renamed, DISTCLEANFILES in Makefile.am
was not updated.
2023-03-20 08:04:27 -07:00
jhendersonHDF
1392b9fc17
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
2023-03-17 15:45:07 -05:00
Dana Robinson
549fbcba86
Add a clang-format comment about permissions (#2577) 2023-03-17 12:56:14 -05:00
Dana Robinson
a89f1a4d75
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.
2023-03-17 12:55:32 -05:00
Mark Kittisopikul
f35a99e4e6
Fix 2nd argument of Java H5Fis_accessible (#2535) 2023-03-17 12:25:56 -05:00
glennsong09
dfa4d550de
Enclose MESG in do...while loop (#2576)
Enclose MSG macro in a do...while loop
2023-03-17 09:41:54 -07:00
Allen Byrne
2ca2a300ac
Change libaec URL to actively maintained repo GH#2552 (#2559) 2023-03-15 18:48:54 -05:00
Dana Robinson
469a93790e
Rename clang-format fix action (#2550)
The clang-format fix and check actions have the same name. This
also makes some small changes to the action's text fields.
2023-03-14 00:57:38 -07:00
Dana Robinson
19a9b12eea
Add Glenn Song to the CODEOWNERS file (#2551)
Also removes Ray Lu
2023-03-14 00:57:19 -07:00
Allen Byrne
cb679af19d
Make sure that ONLY_SHARED_LIBS option is correctly set (#2544) 2023-03-13 16:24:49 -05:00
Scot Breitenfeld
3d8dc012a4
Add concurrency option to cancel in-progress jobs (#2539) 2023-03-13 16:24:15 -05:00
Allen Byrne
42d1e89755
GH issue #1142, print must have verbose on first (#2540) 2023-03-13 16:23:33 -05:00
Scot Breitenfeld
d2345e9f0c
Addressed various Doxygen grammar issues. (#2524)
* reviewed H5A

* Addressed various grammar issues.

* remove double words, spelling fixes

* replace the use of rawdata with raw data
2023-03-13 11:53:08 -05:00
Mark (he/his) C. Miller
befbbd0b6d
Elaborate how cd_values get stored (#2522) 2023-03-08 16:46:10 -06:00
H. Joe Lee
d6f931d67b
docs: in -> out (#2514) (#2516) 2023-03-08 15:09:06 -06:00
mattjala
4b7bdfec69
Update ReferenceManual.dox (#2517) 2023-03-08 15:08:04 -06:00
Mark Kittisopikul
04682f2788
Fix H5Dchunk_iter doxygen example, cherry-pick of ef3bed6 (#2519) 2023-03-08 15:06:17 -06:00
Mark Kittisopikul
9884e189ac
Remove redundant and flawed documentation of H5D_chunk_iter_op_t from H5D.c (#2512)
Forward port of 9f252f1 from #2329
2023-03-08 14:46:47 -06:00