Commit Graph

23509 Commits

Author SHA1 Message Date
H. Joe Lee
ff7f5861cb
Fix Figure 9. table format in HDF5 Groups User Guide (#4295) 2024-04-01 12:02:14 -05:00
Allen Byrne
a7a4fc2445
Synch workflows and require apt-get update (#4294) 2024-04-01 11:04:55 -05:00
Neil Fortner
589f5238fe
Fix problems with background buffers and array datatypes (#4218)
* Fix bug in array conversion with strided background buffer. Convert some
memmove calls to non-overlapping buffers to memcpy.

* Revert inappropriate use of mempy to memmove in H5T__conv_array

* Add testing

* Add RELEASE.txt note and overwrite test case.
2024-03-31 22:49:45 -05:00
H. Joe Lee
23b78f6721
Use AOCC 4.2 and OpenMPI 4.1.6 (#4290) 2024-03-31 22:47:56 -05:00
bmribler
f24e8113a3
Add documentation (H5FD) (#4269) 2024-03-31 22:47:14 -05:00
jhendersonHDF
dc69e39f65
Add configure options for disabling extension features (#4277)
Add configure option to enable or disable extension features in general

Add configure option to enable or disable _Float16 support

Add new config options to various settings files
2024-03-31 22:45:50 -05:00
jhendersonHDF
ce53bc020d
Fixes for file format security issues (#4283) 2024-03-31 22:44:18 -05:00
Allen Byrne
875fb3e70a
Add missing foreach for VFD and Pasthrough runs (#4292) 2024-03-31 22:43:36 -05:00
Dana Robinson
80fc8558b0
Fix off_t straggers (#4291)
Convert off_t to HDoff_t (mainly for Windows):

* h5jam
* h5unjam
* chunk_info test
2024-03-31 12:12:26 -07:00
Allen Byrne
203a95abb5
Add autotools ExpressTest=0 (#4289) 2024-03-30 22:33:19 -07:00
Allen Byrne
530effbbc1
Fix example ref files path (#4285) 2024-03-30 06:45:57 -05:00
Scot Breitenfeld
54a42fc9d9
changed to if string contains instead (#4286) 2024-03-29 15:40:56 -07:00
H. Joe Lee
2d970ecba4
chore: improve error message (#4287)
close #192
2024-03-29 15:39:33 -07:00
Allen Byrne
6596c3edc3
Add TestExpress=0 workflow (#4281)
* Add TestExpress=0 CI
2024-03-29 14:19:58 -05:00
Dana Robinson
855b95b34b
Relaxed behavior of H5Pset_page_buffer_size() when opening files (#4280)
This API call sets the size of a file's page buffer cache. This call
was extremely strict about matching its parameters to the file strategy
and page size used to create the file, requiring a separate open of the
file to obtain these parameters.

These requirements have been relaxed when using the fapl to open
a previously-created file:

* When opening a file that does not use the H5F_FSPACE_STRATEGY_PAGE
  strategy, the setting is ignored and the file will be opened, but
  without a page buffer cache. This was previously an error.

* When opening a file that has a page size larger than the desired
  page buffer cache size, the page buffer cache size will be increased
  to the file's page size. This was previously an error.

The behavior when creating a file using H5Pset_page_buffer_size() is
unchanged.

Fixes GitHub issue #3382
2024-03-29 11:46:31 -07:00
Larry Knox
64f86353d1
Remove CRLF from NEWSLETTER.txt. (#4282) 2024-03-29 09:34:46 -07:00
jhendersonHDF
50d30bd4f0
Fix potential buffer read overflows in H5PB_read (#4279)
H5PB_read previously did not account for the fact that the size of the
read it's performing could overflow the page buffer pointer, depending
on the calculated offset for the read. This has been fixed by adjusting
the size of the read if it's determined that it would overflow the page.
2024-03-29 07:43:59 -05:00
jhendersonHDF
98c19af7c8
Fix range check in H5_addr_overlap (#4278)
When the H5_addr_overlap macro was updated to use H5_RANGE_OVERLAP,
it failed to take into account that H5_RANGE_OVERLAP expects the
range to be inclusive. This lead to an assertion failure in
H5MM_memcpy due to a memcpy operation on overlapping memory.
This has been fixed by subtracting 1 from the calculated high
bound values passed to H5_RANGE_OVERLAP
2024-03-29 07:41:42 -05:00
Allen Byrne
16ba713e31
Merge julia workflows into standard ci format (#4273) 2024-03-28 15:29:22 -07:00
Scot Breitenfeld
f6ae241032
Addresses configuration fortran testing flags (#4276)
* turn warnings to errors in fortran configure test

* Intel fortran test fix
2024-03-28 16:55:32 -05:00
H. Joe Lee
6c54122042
Update Cygwin installation guide (#4265) 2024-03-28 14:40:28 -05:00
Dana Robinson
e908accadf
Add release note for CVE-2017-17507 (#4275) 2024-03-28 12:08:05 -07:00
Dana Robinson
c3d1c7c0ab
CHECK --> CHECK_PTR in tmisc.c (#4274) 2024-03-28 12:07:52 -07:00
jhendersonHDF
03b6575b1b
Minor fixes after merge of file format security fixes (#4263)
* Update H5_IS_BUFFER_OVERFLOW to account for 'size' of 0

* Invert a few checks to avoid function call
2024-03-28 11:49:50 -07:00
jhendersonHDF
372381c530
Prevent stack overflows in H5E__push_stack (#4264) 2024-03-28 11:12:19 -07:00
Allen Byrne
1dfaef2586
replace deprecated CMAKE_COMPILER_IS_GNU** (#4272) 2024-03-28 09:20:57 -07:00
Dana Robinson
8787e7f325
Fix uninitialized memory issues in packet table (#4271) 2024-03-27 20:26:34 -07:00
Dana Robinson
82442ed983
Clean up test/cmpd_dtransform.c (#4270)
* Clean up test/cmpd_dtransform.c

* Fix uninitialized memory warning from sanitizers
* FAIL_STACK_ERROR --> TEST_ERROR
* Emit output
* Delete test file when done

* Fix typo

* H5Fdelete() --> remove()
2024-03-27 20:26:08 -07:00
Scot Breitenfeld
df9d2eafab
MPI type correction (#4268)
* corrected type for MPI_*_f2c APIs

* fixed return type of callback

* reset compilation flags of logical test program
2024-03-27 22:20:25 -05:00
bmribler
bdbe584d44
Add documentation (H5P) (#4262) 2024-03-27 21:06:43 -05:00
bmribler
44738f17a2
Add documentation (H5M) (#4259) 2024-03-27 20:14:23 -05:00
Dana Robinson
fe4f9fb38c
Improve the CMake clang -fsanitize=memory flags (#4267)
-fsanitize=memory is almost useless without
using -fsanitize-memory-track-origins=2 and we shoud probably add
-fno-optimize-sibling-calls as well.
2024-03-27 17:54:15 -07:00
H. Joe Lee
ce3784de25
Replace user-define with user-defined (#4261) 2024-03-27 13:55:44 -07:00
Allen Byrne
72fd150ccb
Add job timeout to cygwin workflow (#4260) 2024-03-27 13:55:19 -07:00
Dana Robinson
136739b37a
File format security issues (#4234) 2024-03-27 13:12:32 -07:00
Dana Robinson
74498cb211
Remove an error check regarding large cache objects (#4254)
* Remove an error check regarding large cache objects

In PR#4231 an assert() call was converted to a normal HDF5 error
check. It turns out that the original assert() was added by a
developer as a way of being alerted that large cache objects
existed instead of as a guard against incorrect behavior, making
it unnecessary in either debug or release builds.

The error check has been removed.

* Update RELEASE.txt
2024-03-27 10:55:28 -05:00
Allen Byrne
b687822541
Add tgz extensions on names (#4255) 2024-03-27 08:03:12 -07:00
jhendersonHDF
37df21707b
Rewrite H5T__path_find_real for clarity (#4225)
* Move conversion path free logic to helper function
2024-03-27 08:07:57 -05:00
Dana Robinson
fb62a68888
Re-revert to using autoreconf in autogen.sh (#4253)
We previously tried removing the per-tool invocation of the Autotools
and instead simply invoked autoreconf (PR #1906). This was reverted
when it turned out that the NAG Fortran compiler had trouble with an
undecorated -shared linker flag.

It turns out that this is due to a bug in libtool 2.4.2 and earlier.
Since this version of libtool is over a decade old, we're un-reverting
the change. We've added a release note for anyone who has to build
from source on elderly platforms.

Fixes #1343
2024-03-27 08:05:21 -05:00
H. Joe Lee
967db7f226
Add Julia GitHub Actions. (#4123) 2024-03-27 07:56:18 -05:00
H. Joe Lee
c4d2891bac
Match generators with real cmake -G output on Windows (#4252) 2024-03-26 15:08:12 -07:00
jhendersonHDF
9ea01546b6
Skip userblock test in chunk_info.c for multi-file VFDs (#4249) 2024-03-26 16:17:35 -05:00
Scot Breitenfeld
724eaaf618
Determine MPI LOGICAL during build, used in tests. (#4246) 2024-03-26 09:05:51 -07:00
Allen Byrne
42f9d2426f
Correct reference copy for 16 API (#4244) 2024-03-26 09:04:36 -07:00
Allen Byrne
eacb0157dc
Rework Fortran macros to use the proper code. (#4240) 2024-03-26 09:20:11 -05:00
jhendersonHDF
fb12776610
Update Windows CI to not install ninja (#4230) 2024-03-26 07:41:01 -05:00
jhendersonHDF
db8193def5
Turn on -Werror for Java in GitHub -Werror workflows (#4243) 2024-03-26 07:40:16 -05:00
jhendersonHDF
9a08e3f476
Fix a minor warning in h5test.c (#4242) 2024-03-25 21:56:34 -05:00
Dana Robinson
fc46c83614
Take user block into account when returning chunk addresses (#4236)
Both H5Dchunk_iter() and H5Dget_chunk_info(_by_coord)() did not take
the size of the user block into account when reporting addresses. Since
the #1 use of these functions is to root around in the file for the raw
data, this is kind of a problem.

Fixes GitHub issue #3003
2024-03-25 19:27:14 -07:00
H. Joe Lee
cb3169fc5a
Match minimum CMake version to 3.18 (#4215) 2024-03-25 09:51:01 -07:00