Commit Graph

22357 Commits

Author SHA1 Message Date
Dana Robinson
423ee69c1e
Updates README.md (#2387)
* Updates release schedule for 2023

* Fixes broken build badge

* Another build badge tweak

* Even more badge tweaking

* More branch tweaking

* More badge tweaking

* More badge tweaks

* Even more badge tweaking

* Adds badges for other branches
2023-01-04 12:44:51 -08:00
Quincey Koziol
c2e3c732f0
Correct VOL connector env string parsing issue (#2350)
* 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.

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>
2023-01-04 13:04:07 -06:00
Dana Robinson
83f81a6422
Adds -Warray-temporaries to the developer warnings (#2385)
These generate a LOT of noise that we are not going to address anytime
soon.
2023-01-03 06:18:48 -08:00
Dana Robinson
d326f6fae8
Adds 'make install' and 'make check-install' to the CI (Autotools only) (#2381) 2023-01-03 06:17:56 -08:00
Dana Robinson
c0b3646193
Adds RELEASE.txt notes and updates Doxygen (#2377) (#2379) 2022-12-29 12:58:54 -08:00
Dana Robinson
3da2551adb
Adds Doxygen markup for H5FDdriver_query() (#2376) 2022-12-28 13:07:39 -08:00
Larry Knox
d261272ffa
Restore line 264 of main.yml: "thread_safety:" (#2374) 2022-12-28 10:30:57 -08:00
Dana Robinson
23ccd7ee3b
Purged references to HDF5 1.13.x from the Doxygen documentation (#2365) 2022-12-27 12:33:14 -08:00
Dana Robinson
298c7efe76
Adds missing Doxygen for H5ESpublic.h (#2364)
* Adds missing Doxygen for H5ESpublic.h

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-27 11:42:31 -08:00
Dana Robinson
1cf9ecccf5
Fix for Autotools --disable-deprecated-symbols (#2363)
* Fix for Autotools --disable-deprecated-symbols

When we added v116 as a valid option, we left the default as v114 so
using --disable-deprecated-symbols leads configure to complain that you
can't set a default API that was deprecated.

The GitHub action didn't catch this because it explicitly specifies v116

This only affects develop w/ the Autotools when
--disable-deprecated-symbols is requested.

* Added v116 & default to the --with-default-api-version help string

The Autotools --with-default-api-version help string was missing v116.
This has been added, as well as a "default" target so the CI can catch
version problems when we forget to update the defaults upon creating
a new major version.

The GitHub CI also now uses "default" as the target for the deprecated
symbols build.

* Fixes the 1.14 API GitHub CI threadsafe/build_mode

This action still had the bug we fixed where we set the build mode
and threadsafety using an array of size one instead of an object.
2022-12-24 11:36:38 -08:00
Dana Robinson
cfd5059e77
HL GIF tools changes (#2360)
* Fixes the broken Autotools option
* Removes the "build HL tools" option
2022-12-23 16:05:31 -08:00
Larry Knox
9a694db450
Update testh5cc.sh.in for new major version 1.14. (#2349)
* Update testh5cc.sh.in for new major version 1.14.

* iFix sha256sum commands in release script.
2022-12-22 13:38:51 -06:00
Dana Robinson
ab0a778593
Adds Doxygen VOL flag markup (#2340)
* Initial doxygen markup

* Committing clang-format changes

* Adds Doxygen comments to VOL flags

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-21 13:44:50 -08:00
Dana Robinson
57af2ff798
Onion VFD header cleanup (#2337)
* Partial work towards cleaning up the onion VFD code

* Committing clang-format changes

* A few minor tweaks to the onion VFD public header

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-21 10:46:05 -08:00
Allen Byrne
9f5cf0a457
H5F_LIBVER_LATEST changes for move to 1.15 (#2288)
* H5F_LIBVER_LATEST changes for move to 1.15

* Add new default api check

* Format fixes

* Fix default configure

* fix lib version tests

* Fix another version variable

* Add 1.14 doc link
2022-12-21 10:07:25 -08:00
vchoi-hdfgroup
976e8c9750
Fix up the H5Pencode2 test for virtual layout. (#2325)
* Fix up the H5Pencode2 test for virtual layout.

* Committing clang-format changes

* Remove VERIFY and use TEST_ERROR.

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-20 16:48:56 -08:00
Allen Byrne
c1e44d32e6
Fix doxygen warnings and remove javadocs (#2324)
* Fix doxygen warnings and remove javadocs

* fix typo
2022-12-20 16:59:40 -06:00
Mark Kittisopikul
b9244a85d9
Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074)
* Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info

* Modify chunk_info test to for unsigned / hsize_t types

* Fix types in test
2022-12-19 15:13:43 -08:00
Scot Breitenfeld
70cf2c390b
Removed idioms and misc. text clean-up (#2320)
* removed idioms and misc. text clean-up, Issue #2135

* removed idioms and misc. text clean-up, Issue #2135
2022-12-16 19:56:52 -08:00
Allen Byrne
149b8e9769
Disable hl tools by default (#2313)
* Disable hl tools by default

* identify the tools

* Only GIF tools are depecated

* Add new option

* Update autotools
2022-12-16 19:56:07 -08:00
Scot Breitenfeld
8102fa8c97
Only document Fortran functions (#2319)
* Only document Fortran functions

* Only document Fortran functions

* Only document Fortran functions

* Only document Fortran functions
2022-12-16 19:52:08 -08:00
Scot Breitenfeld
784061b15e
moved onion VFD to FAPL group (#2321) 2022-12-16 19:51:52 -08:00
vchoi-hdfgroup
6b6bcdead6
Hdffv 11052 (#2315)
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump.
When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the
closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value"
all the way till the end of the routine.  The user-provided corrupted file has an illegal
file size causing failure when reading the image during the closing process.
At the end of this routine it sets f->shared to NULL and then frees "f".
This is done whether there is error or not in "ret_value".
Due to the failure in reading the file earlier, the routine then returns error.
The error return from H5F__dest() causes the file object "f" not being removed from the
ID node table.  When the library finally exits, it will try to close the
file objects in the table.  This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f).
Fix:
a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine.
b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before.
c) h5debug.c main(): track error return from H5Fclose().

* Committing clang-format changes

* Add test and release note info for fix to HDFFV-11052 which is merged via PR#2291.

* Committing clang-format changes

* Add the test file to Cmake.

* Skip test_misc37() for drivers that is not default compatible as it is using a pre-generated file.

* Committing clang-format changes

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-16 13:47:29 -08:00
Dana Robinson
0e76abaf64
Removes duplicated build mode from -Werror GitHub actions (#2314) 2022-12-16 12:05:01 -08:00
Dana Robinson
4bbda3038a
Converts the YAML build mode arrays to objects in special runs (#2308)
* Converts the YAML build mode arrays to objects in special runs

* Adds a dump of the matrix context for each test

This would have made it a LOT easier to debug the build_mode issues...

* Disable the mirror VFD in the -Werror checks

We can re-enable this after we fix the warnings, but I don't want to
conflate code and GitHub changes, so this is a better way to get the
CI to pass for now.
2022-12-15 23:03:02 -08:00
Gerd Heber
138daa8846
Merge pull request #2304 from gheber/develop
Update hdf5_header.html
2022-12-15 13:25:18 -06:00
Gerd Heber
10c693a04f
Update hdf5_header.html
Use less awkward language.
2022-12-15 08:49:19 -06:00
vchoi-hdfgroup
0cb5808087
Hdffv 11052 (#2303)
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump.
When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the
closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value"
all the way till the end of the routine.  The user-provided corrupted file has an illegal
file size causing failure when reading the image during the closing process.
At the end of this routine it sets f->shared to NULL and then frees "f".
This is done whether there is error or not in "ret_value".
Due to the failure in reading the file earlier, the routine then returns error.
The error return from H5F__dest() causes the file object "f" not being removed from the
ID node table.  When the library finally exits, it will try to close the
file objects in the table.  This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f).
Fix:
a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine.
b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before.
c) h5debug.c main(): track error return from H5Fclose().

* Committing clang-format changes

* Add test and release note info for fix to HDFFV-11052 which is merged via PR#2291.

* Committing clang-format changes

* Add the test file to Cmake.

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-15 05:32:23 -08:00
Dana Robinson
1b06e868fd
Fixes broken CI matrix actions involving -Werror and API versions (#2302) 2022-12-14 18:05:15 -06:00
Dana Robinson
93938b3a8d
Adds 'unused' hints for MDS io_info parameters (#2301)
* Adds 'unused' hints for MDS io_info parameters

* Committing clang-format changes

* Fix issue with formatter

* Committing clang-format changes

* Final fix for formatter

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-14 14:54:51 -08:00
Scot Breitenfeld
a1c81eda20
added doc. warning for H5Literate_async return value (#2295) 2022-12-14 15:22:37 -06:00
Allen Byrne
b7511c19d0
Update windows worker compilers (#2286)
* Update windows worker compilers

* Update bin and test issues

* Update script and revert java test
2022-12-14 08:58:20 -06:00
Scot Breitenfeld
502b32b0f2
Updated H5ES documenation (#2293) 2022-12-13 10:56:48 -08:00
vchoi-hdfgroup
a9036005c3
Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump.
When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the
closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value"
all the way till the end of the routine.  The user-provided corrupted file has an illegal
file size causing failure when reading the image during the closing process.
At the end of this routine it sets f->shared to NULL and then frees "f".
This is done whether there is error or not in "ret_value".
Due to the failure in reading the file earlier, the routine then returns error.
The error return from H5F__dest() causes the file object "f" not being removed from the
ID node table.  When the library finally exits, it will try to close the
file objects in the table.  This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f).
Fix:
a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine.
b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before.
c) h5debug.c main(): track error return from H5Fclose().

* Committing clang-format changes

Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-13 09:40:59 -08:00
Scot Breitenfeld
b9f4c001ad
added doc. warning for H5Oflush in parallel (#2289) 2022-12-09 21:31:13 -06:00
Scot Breitenfeld
4a8be219e0
fixed unclosed objects in test (#2290) 2022-12-09 21:30:42 -06:00
Neil Fortner
ef4f1f2bd4
Check for size==0 for all datatypes read from disk, not just compound (#2287)
members
2022-12-08 10:30:29 -06:00
Egbert Eich
0b4e9cf976
Compound datatypes may not have members of size 0 (#2243)
* Compound datatypes may not have members of size 0

A member size of 0 may lead to an FPE later on as reported in
CVE-2021-46244. To avoid this, check for this as soon as the
member is decoded.
This should probably be done in H5O_dtype_decode_helper() already,
however it is not clear whether all sizes are expected to be != 0.

This fixes CVE-2021-46244 / Bug #2242.

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

* Rework error recovery code in H5O__dtype_decode_helper() and
H5O__dtype_decode().

* Format changes for src/H5Odtype.c.

Signed-off-by: Egbert Eich <eich@suse.com>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2022-12-07 16:14:40 -06:00
Allen Byrne
dcccc35526
Correct requires setting for pkgconfig files (#2280)
* Correct requires setting for pkgconfig files

* Add issue number
2022-12-07 16:05:51 -06:00
Dana Robinson
64514392fb
Fixes warnings in H5Opline.c error messages (#2281)
* Fixes warnings in H5Opline.c error messages

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-12-06 11:32:39 -08:00
Allen Byrne
0a2006d9c6
Add text about release notes (#2246) 2022-12-06 06:02:21 -08:00
Allen Byrne
2376723d4a
Develop jni trans (#2266)
* Add compound and refactor out atomic types

* Add Array String tests back

* Convert Attribute version of compound example

* Update transfer atom8ic read to return object
2022-12-05 22:29:42 -06:00
V. Armando Solé
281984b3e3
H5E_ERR_CLS_g symbol missing when compiling C++ plugins (#2269)
C++ HDF5 filter plugin SZ3 fails to build under windows with failure at linking time unless that extern "C" block is added.
2022-12-05 19:19:53 -06:00
Scot Breitenfeld
c1c131260a
return error message related to calling API (#2276) 2022-12-02 14:24:43 -06:00
Egbert Eich
24700e8f06
CVE 2021 46242 develop (#2255)
* When evicting driver info block, NULL the corresponding entry

Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the  flag
H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing the
pointer in  f->shared->drvinfo will prevent use-after-free  when it is used in other
functions (like  H5F__dest()) - as other places will check whether the pointer is
initialized before using its value.

This fixes CVE-2021-46242 / Bug #2254

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

* When evicting the superblock, NULL the corresponding entry

The call to H5AC_expunge_entry() will free the corresonding structure,
to avoid a use-after-free, the corrsponding pointer entry will be NULLed.

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

Signed-off-by: Egbert Eich <eich@suse.com>
2022-12-02 14:24:14 -06:00
Allen Byrne
88b24c258b
Output should only be printed if verbose. (#2273)
* Output should only be printed if verbose.

* Add note
2022-12-02 09:39:49 -08:00
Egbert Eich
4e0277c35a
Report error if dimensions of chunked storage in data layout < 2 (#2241)
For Data Layout Messages version 1 & 2 the specification state
that the value stored in the data field is 1 greater than the
number of dimensions in the dataspace. For version 3 this is
not explicitly stated but the implementation suggests it to be
the case.
Thus the set value needs to be at least 2. For dimensionality
< 2 an out-of-bounds access occurs as in CVE-2021-45833.

This fixes CVE-2021-45833 / Bug #2240.

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

Signed-off-by: Egbert Eich <eich@suse.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2022-12-01 23:04:42 -06:00
Allen Byrne
96a4e10102
Add aarch64 toolchain and change dump test to long opt (#2271) 2022-12-01 14:32:34 -08:00
Larry Knox
cf232a757f
Develop fix ubuntu 22.04 openmpi install on github (#2268)
* Update install openmpi-bin to also install mpi-default-dev instead of
libopenmpi-dev.  This according to
https://bugs.launchpad.net/ubuntu/+source/openmpi/+bug/1870780.
2022-11-28 13:20:24 -06:00
Egbert Eich
158dff6b50
Make sure testsuite can handle multiple dependent scripts (#2256)
Commit afc54d75a1 to the test suite to eliminate a separate
shell script did not take into account that there may be
multiple dependent test scripts which resulted in the
message:
`/bin/sh: line 7: [: too many arguments`.
when running the test suite.

Beware that this new version still makes use of non-posix GNU
extensions to `test`.

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

Signed-off-by: Egbert Eich <eich@suse.com>
2022-11-28 13:19:31 -06:00