* commit '1f8cb03e11a46f853881f45dac18eff2dd68401e':
Fix errors in Makefile.am files that cause "make check" to repeat test, even when there are no changes to source files. (Also add a ggenerated script to the list of files cleaned up on 'make distclean')
Further minor cleanups
Checkpoint normalization against incoming hyperslab / selection / dataspace improvements.
them H5D calls.
* Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*.
* Moved the hl/test/test_dset_opt test to test/ and renamed to
direct_chunk.
* Moved the hl/test/dectris_hl_perf test to tools/test/perform
and renamed to direct_write_perf.
* Updated autotools and CMake files.
* commit '3211e907f4f9349ba7510d70cfbcc6ee36d99c58':
Remove vestiges of H5_DEBUG_BUILD macro, switching it to the more standard H5CX_DEBUG form.
Minor warning cleanup while working on VOL issues.
* commit '048ae59d2970dd21810577c999f756c028b6faaf':
Correct errors with non-"instrumented library" builds (production & parallel, generally speaking).
Update java error stack tests
Revert using H5MF_sect_small_can_shrink and H5MF_sect_small_shrink for the file's free space manager (and add a comment about them).
Add comment for the file flush when the file low / high bounds are changed after a file is open.
Expanded comments abuot H5CX_t fields.
Add an assert to verify that we don't write when between MPI_Barrier() calls during a flush.
Add comments for internal structs.
Remove redundant 'is_collective' parameter from H5CX_set_loc.
Correct typo in comment.
Revert some tangential code cleanups.
Add API context source files to CMake configuration file.
Corrections for parallel I/O & tests.
Update handling of reporting for breaking collective I/O when the default DXPL is used.
Update encoded DXPLs to reflect changes in properties.
Correct typo for error checking malloc return value.
Refactor H5CX code to reduce duplication.
Cleanup API context function usage.
Add API context interface and use it throughout the library.
* commit '9247388c3d14510341ea3f07847ce2cbb6e44a8e':
Rework new tests into one macro
Added a "won't fix" RELEASE.txt entry for HDFFV-10356.
Fix CMake test names
Fixed typo
Add release note for HDFFFV-10397.
Added a fix for HDFFV-10358.
Fixed documentation Description: - Updated the description of copy constructor for clarification. - Removed unnecessary comments. Platforms tested: Linux/64 (jelly)
Enhancement to the tool h5clear (HDFFV-10360)
Fix for HDFFV-10209 VDS SWMR test failure Free the object header when there are chksum retries.
* commit 'f08b8fa10e7bac5ae26e3b06f938d38ebb3f28e1':
Enhancement to the tool h5clear (HDFFV-10360)
Fix for HDFFV-10209 VDS SWMR test failure Free the object header when there are chksum retries.
Notes for gen_bounds.c
* commit '8155dba8d7cb8dbe2532c17c7ea5a27f52e3095b':
Improve code Description: Added notes and changed argument to H5Fcreate to clarify the latest situation Platforms tested: Linux/64 (jelly)
tests for version bounds.
* commit 'f05f9d4cffab5e008c67e19034c1b248e1b01b3c':
Miscellaneous test fixes Description: - dtypes.c: added the use of highest version of nested datatypes to verify the datatype's version. - miscellaneous typos Platforms tested: Linux/64 (jelly) Darwin (osx1010test)
Added h5repack tests Description: Added tests SUPERBLOCK and INVALIDBOUNDS, composed by ADB. Platforms tested: Linux/64 (jelly) - cmake
Added bounds_latest_latest.h5
Misc improvement Description: - Added test file for h5repack test VERIFY_INVALIDBOUNDS - Updated MANIFEST - Removed unnecessary header file in test - Update h5repack script to copy the new file to the test location Platforms tested: Linux/64 (jelly) Darwin (osx1010test)
Improving tests Description: - Added test for version bounds with nested datatypes - Added script for additional version bound test in h5repack - Cleaned up tests for consistency - Removed extra included header files Platforms tested: Linux/64 (jelly) Linux/64 (moohan) Darwin (osx1010test)
Description:
- dtypes.c: added the use of highest version of nested datatypes to
verify the datatype's version.
- miscellaneous typos
Platforms tested:
Linux/64 (jelly)
Darwin (osx1010test)
Description:
- Added test file for h5repack test VERIFY_INVALIDBOUNDS
- Updated MANIFEST
- Removed unnecessary header file in test
- Update h5repack script to copy the new file to the test location
Platforms tested:
Linux/64 (jelly)
Darwin (osx1010test)
The failure occurs when HDF5TestExpress is set to 0.
The check for file size check fails due to persisting free-space when creating the file.
The fix is to set libver bounds (v18, latest) when creating the test file.
Description:
- Added test for version bounds with nested datatypes
- Added script for additional version bound test in h5repack
- Cleaned up tests for consistency
- Removed extra included header files
Platforms tested:
Linux/64 (jelly)
Linux/64 (moohan)
Darwin (osx1010test)
Description:
- Revised and add more variety to version bound tests per review
- Revised gen_bounds.c per review
Platforms tested:
Linux/64 (jelly)
Linux/32 (jam)
Darwin (osx1010test)
* commit '758b9667b3e07a7562107f19f7dabee027e5bd53': (41 commits)
HDFFV-10223 Shared libraries fail test on OSX with fortran enabled with cmake
removed duplicate exports of DS subroutines
removed duplicate exports of DS subroutines
Normalization with VOL integration branch.
clean-up
moved dll export to Module
Fixed typo.
removed parameters
added missing parameter
added missing parameter
removed duplicate exports of DS subroutines
removed fortran comments
Various code cleanup Description: - Replaced H5Location::exists with H5Location::nameExists and marked H5Location::exists as deprecated. - Miscellaneous test cleanup for consistency. Platforms tested: Linux/32 2.6 (jam) Linux/64 (jelly) Darwin (osx1010test)
exported global variables for windows
export var.
initialized integer constants
Update macros
Changed casts to const void *
Casted pointers to void to quiet warnings on Linux.
Added CHECK_PTR_EQ macro to testhdf5 to quiet cast warnings on Windows.
...
Added gen_bounds.c to generate data files for version bounds testing in 1.8 and 1.6.
* commit 'daa0eb801561dc1831065e4c8c06d6cd68330200':
Further improvement
Fixed comment.
Adding data file generator Description: Added gen_bounds.c to generate the following files: - bounds_earliest_latest.h5 - bounds_earliest_v18.h5 - bounds_latest_latest.h5 - bounds_v18_latest.h5 - bounds_v18_v18.h5 for testing the version bounds fix in 1.8 and 1.6.
Description:
Added gen_bounds.c to generate the following files:
- bounds_earliest_latest.h5
- bounds_earliest_v18.h5
- bounds_latest_latest.h5
- bounds_v18_latest.h5
- bounds_v18_v18.h5
for testing the version bounds fix in 1.8 and 1.6.
(2) Add two new options to h5repack for low and high bounds as in H5Pset_libver_bounds.
(3) Modify message pre_copy callbacks so that H5Ocopy can handle version bounds check.
(4) Add version bounds check for cache image feature.
an object header chunk, where the total amount deleted was greater than
64K, an error would occur due to an off by one error in the code that
handled that case. Fixed this and added a test case.
* commit 'bca20b40b4966552a844051c3d912d6aec50592f':
Initialize hid_t variables in test_Attr_bug9.
Fix HDFFV-10274. When deleting all (or almost all) of the messages in an object header chunk, where the total amount deleted was greater than 64K, an error would occur due to an off by one error in the code that handled that case. Fixed this and added a test case.
* commit '3e4f6138b60d8363c377e453d63f875775ec907a':
Removed asserts from H5MM calls that conflict with stated behavior and added a test to ensure that this doesn't happen in the future.
an object header chunk, where the total amount deleted was greater than
64K, an error would occur due to an off by one error in the code that
handled that case. Fixed this and added a test case.
allows them to be successfully linked but not installed. The change was
added for the HDF5 1.8.20 release, but is also needed for all other HDF5
branches.
a) multi/split drivers and
b) persisting free-space or using paged aggregation strategy
because the library will fail file creation (temporary) for the above conditions.
over.
Brings coding standards in line with the rest of the library,
enforces better software engineering principles, and makes
everything more maintainable.
The function H5VM_power2up() returns the next power of 2 for n.
When n exceeds 2^63, it overflows and becomes 0 causing the infinite looping.
The fix ensures that the function checks for n >= 2^63 and returns 0.
* commit '191147ec90d72619632a24242c003ecb3bccfffd':
* Yanked the smoke check that was recently introduced to test the unused H5I_REFERENCE ID type in test_misc19(). This fails when running testhdf5 and skipping the reference test since the H5R package won't be initialized. H5I_REFERENCE will be going away soon and the ID type is unused so there's really no point to doing anything to test it. * Cleaned up test_misc13(), which is a basic test of userblock functionality, to not emit warnings due to the large global array.
the unused H5I_REFERENCE ID type in test_misc19(). This fails
when running testhdf5 and skipping the reference test since
the H5R package won't be initialized. H5I_REFERENCE will
be going away soon and the ID type is unused so there's really
no point to doing anything to test it.
* Cleaned up test_misc13(), which is a basic test of userblock
functionality, to not emit warnings due to the large global
array.
Temporary skip this test for split/multi driver.
Further investigation to resolve the failure is needed.
Please enter the commit message for your changes. Lines starting
Changes made so that raw data for dataset objects are copied from cached info when possible instead of flushing objects to file and read them back in again.
* Changed return type of H5FD_driver_query() to herr_t.
* Updated swmr.c to use H5FDdriver_query() instead of the private call.
* Added some flags tests to vfd.c.
* Moved H5FD_driver_query() to H5FDint.c.
* Minor typo fixes in H5I.c.
* Updated swmr.c to check the VFD feature flags and skip the
retries test when the VFD is not compatible with H5P_DEFAULT.
(1) Repeated open/close of a compact dataset fails due to the
increment of ndims in the dataset structure for every open.
--This is done only for chunked dataset via H5D__chunk_set_sizes().
(2) layout "dirty" flag for a compact dataset is not reset
properly after flushing the data at dataset close.
--Reset the "dirty" flag before flushing the message to the object header
via H5O_msg_write().
Tested on moohan, kituo, platypus, ostrich, osx1010test, quail, emu.
the same for hdf5_1_10 and hdf5_1_10_1 because the hooks don't reliably
work. In the develop branch they are causing make install failures
because the autotools' install commands sometimes attempt to chmod these
files when they no longer exist.
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* commit '7bd516f2ead21e8470cc25c0b664ad6b56c723a0':
Our best effort to build dynamic plugin tests and not install them with "make install". It seems the install-exec-hook doesn't remove the last to be installed.
Add targets for plugin test libraries to avoid linking to external libs.
Modified test/cache.c to skip the smoke checks with paged aggregation
for all express test levels other than 0
Change to src/H5PL.c seems to be the result of autogen.sh. As it
seems to be correct, I am checking it in.
Tested serial and parallel (debug only) on jelly.
Skip the two tests for page buffering in test/fheap.c because this feature is disabled in parallel.
Activate full testing when this feature is re-enabled in the future for parallel build.
1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0
2) Minor fixes to test/fheap.c that somehow were missed from last check in. See pull request #396 review comments.
Modify test/fheap.c to run with different combinations of file space strategies and page buffering
only when ExpressMode is 0 (HDF5TestExpress is 0).
Tested on ostrich, platypus, mayll, emu, osx1010test, quail, kite, kituo.
* commit '60bb3fd1108e2006a79b008d031a0f68a1e6b393':
Re-enabled fixed array index testing in the test_random_rank4_vl() test in test/set_extent. This was fixed some time ago, but the test was never re-enabled for that index type.
* commit '2412158ed8326a3f3d62fbd947e470667d0b5951':
Add new file COPYING_LBNL_HDF5.
Revert "Clear hdf5 1.10 entries from RELEASE.txt in the develop branch. Entries"
Add LBNL license file and modify COPYING file accordingly.
Omnibus checkin for several relatively minor modifications:
Clear hdf5 1.10 entries from RELEASE.txt in the develop branch. Entries in this branch version of RELEASE.txt should be intended for the future 1.12.0 release.
Fix HDFFV-8089 Description: Some code within an "ifdef H5D_CHUNK_DEBUG" block was using outdated data structure but not caught because the case of H5D_CHUNK_DEBUG being defined was never tested. It was commented out. I defined H5D_CHUNK_DEBUG, tested, and commented out again. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
1) Added code test/page_buffer.c to verify that page buffering is
disabled in parallel builds.
2) Added code to test/cache_image.c to verify correct interaction
between evict on close and cache image -- in particular management
of a file containing a cache image containing dirty metadata that
has been opened R/O. Also fix for the bug exposed.
3) Added code to testpar/t_cache_image.c to verify expected procedure
for reading cache images, and also supporting stats collection code
needed for the test.
4) Repair of an overactive sanity check in H5C__reconstruct_cache_contents().
5) Other minor tidies in passing.
Tested serial and parallel, debug and production on Jelly.
Comment added to address HDFFV-8270. The sample ontput in the
file's comments are not up-to-date with the scripts in the file
that remove output unique to certain systems when running test
scripts. This output doesn't match expected output files for
the tests, causing them to fail. Ther output_filter.sh file
removes such output. Currently we don't have access to these
systems to update the comments.
testflushrefresh.sh.in:
flushrefresh and other SWMR tests have been failing
occasionally but regularly since bringing them to the develop
branch. The logs and debugging point to unexpected deletion of
signal files as the point of failure, and John Mainzer suggests
that two such tests running simultaneously in the same directory
may lead to the operating system deleting the other test's
signal file. Running the flushrefresh test in its own directory
seems to solve the problem.
