Commit Graph

23034 Commits

Author SHA1 Message Date
mattjala
68c48159e7
Support CMake VOL builds with FetchContent from local directory (#3455)
* Update VOL CMake for REST VOL

* Prevent linking static libs to VOLs

* index on fetch_local: 5c5c3f1505 Prevent linking static libs to VOLs

* index on (no branch): 9a36d3e7b1 On fetch_local: WIP:add source dir fetch option for vols

* Allow building of VOL from local source

* Move LOCAL_DIR option to HDF5_VOL_ALLOW_EXTERNAL
2023-09-01 14:01:37 -07:00
Allen Byrne
80fe48f2d3
Correct java test dimension (#3482) 2023-09-01 10:52:24 -07:00
jhendersonHDF
0b24f40b0f
Fix Subfiling VFD IOC assignment bug (#3456) 2023-09-01 09:59:28 -07:00
Scot Breitenfeld
896270cc6b
Removed all the ranks printing out testing information (#3457) 2023-08-31 21:34:57 -07:00
Dana Robinson
b0333a0f54
Add an h5py badge to README.md (#3477) 2023-08-31 19:02:40 -07:00
mattjala
627fba0ebc
Update VOL CMake for REST VOL (#3450)
* Update VOL CMake for REST VOL

* Prevent linking static libs to VOLs
2023-08-30 22:23:59 -05:00
H. Joe Lee
a993bb8f12
Disable SZIP for Intel oneAPI Action (#3449)
* Disable SZIP for Intel oneAPI Action

* Disable Fortran and parallel
2023-08-30 22:21:08 -05:00
Dana Robinson
54d19b0bcb
Add a CVE regression test action (#3445)
*
2023-08-30 07:38:24 -05:00
Dana Robinson
5bd65f7ebf
Add Intel oneAPI badges (#3433) 2023-08-28 11:36:49 -07:00
jhendersonHDF
df6f5d37d8
Output stderr file in CMake testing on failure (#3431) 2023-08-25 22:42:19 -07:00
Dana Robinson
ee0737f4e8
Add 1.14.4 to the release schedule (#3434) 2023-08-25 17:23:25 -07:00
Dana Robinson
627f7c5e02
Convert some H5MM calls to standard C equivalents (#2382)
* H5MM_calloc and malloc are now mapped to stdlib C calls
* H5MM_memcpy now maps directly to memcpy in release builds
* H5MM_memcpy is still implemented as a separate function that
   checks for buffer overlap when H5MM_DEBUG is defined
   (default w/ debug builds)
* Switches many library memcpy calls to use H5MM_memcpy
* Fixes a possible zero allocation in H5Olayout.c
2023-08-25 13:56:50 -07:00
Dana Robinson
3dd60d914e
Put H5T_CONV_ab macros in do..while loops (#3432)
Ever since a recent round of macro cleanup, bin/trace and clang-format
have been bickering over what H5Tconv.c should look like and neither
produces readable code.

This change puts the top-level H5T_CONV_ab macros in do..while loops,
adds appropriate semicolons, and adds the missing H5_CLANG_DIAG_ON|OFF
and H5_GCC_CLANG_DIAG_ON|OFF macros to the list of statement macros
clang-format recognizes. H5Tconv.c is now readable and both bin/trace
and clang-format are happy.
2023-08-25 11:24:42 -07:00
Allen Byrne
6e0e53039a
Fix the Fortran extension used in example links (#3430) 2023-08-25 09:16:27 -05:00
H. Joe Lee
df161ac293
chore: match function call and VRFY() output (#3428) 2023-08-25 08:13:32 -05:00
vchoi-hdfgroup
e7bb05a886
Fix for CVE-2018-15671. h5stat -S $POC will result in a crash with segmenetation fault. (#3427)
It is because the object in the testfile points back to the root group.
When the tool tries to traverse the object, it goes back to the root group and then back again.
2023-08-25 08:13:04 -05:00
H. Joe Lee
f6df114fa2
Remove intel oneapi warning (#3426) 2023-08-25 08:11:49 -05:00
jhendersonHDF
077898d738
Revise file close assertion failure fix (#3418) 2023-08-25 08:10:23 -05:00
Neil Fortner
1d79445a1d
Remove extraneous "33" in RELEASE.txt (#3425) 2023-08-24 10:43:36 -07:00
jhendersonHDF
b80eaf8631
Fix use of uninitialized value in testpar/t_dset.c test (#3423) 2023-08-24 12:30:06 -05:00
Allen Byrne
1e75fafe1f
Add parallel examples in doxygen (#3413) 2023-08-24 12:29:05 -05:00
jhendersonHDF
8ef463e9bd
Fix an issue with use of uninitialized memory in trefer_deprec.c test (#3422) 2023-08-24 08:55:35 -07:00
jhendersonHDF
216d2191c7
Skip atomicity tests for OpenMPI major versions < 5 (#3421) 2023-08-24 08:54:13 -07:00
jhendersonHDF
14645ae83e
Avoid H5Ocopy in h5repack for variable-length string types (#3419) 2023-08-24 08:53:05 -07:00
Allen Byrne
67246efd6a
Add other types and full type to enum/str/vlen dataformat for structblock[begin/end] (#3353) 2023-08-24 08:45:38 -07:00
H. Joe Lee
f346c74dc0
chore: remove gubbins comment (#3420) 2023-08-24 08:10:27 -05:00
Neil Fortner
b155ec5b10
Add RELEASE.txt entry for compound performance regression fix (#3376) (#3416) 2023-08-23 16:49:51 -05:00
H. Joe Lee
755dd4ea37
Add Intel oneAPI actions (#2949) (#2977)
* ci: add Intel oneAPI actions (#2949)

* ci: fix CMake installation

* ci: use absolute paths for libtool installation

* ci(oneAPI): update compiler versions and use cron
2023-08-23 14:45:34 -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
jhendersonHDF
f61522ec4d
Fix ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 (#3407) 2023-08-22 09:03:04 -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
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