cde84cdc8f
* Fix MPI Fortran configuration for HDF5Examples (#6206) When building Fortran parallel examples without MPI wrappers, the compiler couldn't find mpi.mod because MPI_Fortran_INCLUDE_DIRS was not populated. This occurred because find_package(MPI) was only called for C, not Fortran. Added enable_language(Fortran) and find_package(MPI REQUIRED COMPONENTS Fortran) to properly configure MPI for Fortran examples, ensuring MPI include directories and libraries are correctly set. * Adds RFCs to the RFC table (#6190) * Added two RFCs to the RFC table "Adding support for digitally signed plugins to HDF5" " Write-Ahead log" * Updated to use the ACM link * Add HDF5 2.0.0 Library Migration Guide (#6183) * Add HDF5 2.0.0 Library Migration Guide * Revise HDF5 migration guide for version 2.0.0 Use 2.0.0 consistently. * Clarify API changes in HDF5 2.0.0 Migration Guide * Fixes the "multiple @param documentation sections" doxygen warnings (#6195) Addresses the "multiple @ param documentation sections" warnings are caused by the interaction of three things: 1. MACRO_EXPANSION = YES with EXPAND_ONLY_PREDEF = NO in Doxyfile.in 2. Versioned API macros in H5version.h like: \def documentation in APIVersions.dox like: 3. \def H5Tarray_create \api_vers_2{H5Tarray_create,H5Tarray_create1,H5Tarray_create2} Because Doxygen expands all macros, it sees H5Tarray_create as an alias for H5Tarray_create1. It then associates documentation from both the \def block (for the macro) and the function's own doc block (with \param entries) with the same function — resulting in "multiple @ param documentation sections." * Update Doxygen version from 1.16.0 to 1.16.1 Use Doxygen 1.16.1 for all platforms. This version includes the latest bug fixes and improvements while maintaining compatibility with our documentation format. * Fix Windows Doxygen installation for version 1.16.1 Handle different Windows binary naming conventions across Doxygen versions: - 1.16.1 uses: doxygen-VERSION.windows.x64.bin.zip - 1.16.0 uses: doxygen-VERSION.x64.bin.zip Try the newer naming convention first, then fall back to the older one if the download fails. This ensures compatibility across versions. * Use ssciwr/doxygen-install in setup-doxygen action Replace direct installation of official Doxygen binaries with ssciwr/doxygen-install action. This avoids Java documentation parsing errors that occur with official binaries but not with distribution builds. The setup-doxygen action now serves as a thin wrapper around ssciwr/doxygen-install@f13be16c83 (v1), using commit hash for security and reproducibility. * Remove redundant version specification from workflows The setup-doxygen action already has a default version (1.16.1), so explicit version specification in workflows is unnecessary. This follows DRY principles and makes version updates simpler. * Updates to #6205 (#6208) * Fix MPI Fortran configuration for HDF5Examples (#6205) When building Fortran parallel examples standalone without MPI wrappers, the compiler cannot find mpi.mod because MPI_Fortran_INCLUDE_DIRS is not populated. * Use MPI::MPI_Fortran imported target instead of raw MPI variables Replace manual MPI_Fortran_LIBRARIES, MPI_Fortran_LINK_FLAGS, and MPI_Fortran_INCLUDE_DIRS usage with the MPI::MPI_Fortran imported target, which transitively carries all include dirs, compile flags, and link flags. This eliminates the CMAKE_Fortran_EXE_LINKER_FLAGS hack and the manual target_include_directories in H5PAR. * Update nvhpc version to 26.1 with CUDA version 13.1. (#6213) # branches: [develop] * Inherit Debug C build flags in Developer build mode (#6182) * Bump the github-actions group across 1 directory with 11 updates (#6215) * Bump the github-actions group across 1 directory with 11 updates Bumps the github-actions group with 11 updates in the / directory: | Package | From | To | | --- | --- | --- | | [actions/cache](https://github.com/actions/cache) | `5.0.1` | `5.0.3` | | [lukka/get-cmake](https://github.com/lukka/get-cmake) | `4.2.1` | `4.2.3` | | [softwareforgood/check-artifact-v4-existence](https://github.com/softwareforgood/check-artifact-v4-existence) | `0.3.0` | `0.4.1` | | [github/codeql-action](https://github.com/github/codeql-action) | `3.31.9` | `4.32.2` | | [azure/trusted-signing-action](https://github.com/azure/trusted-signing-action) | `0.5.11` | `1.1.0` | | [cygwin/cygwin-install-action](https://github.com/cygwin/cygwin-install-action) | `7d2dc1e241644c3318bed9ec74115d1929baa681` | `2566376092c4e280f21131be027af3f5bb2420a4` | | [aws-actions/configure-aws-credentials](https://github.com/aws-actions/configure-aws-credentials) | `5.1.1` | `6.0.0` | | [vmactions/freebsd-vm](https://github.com/vmactions/freebsd-vm) | `1.3.4` | `1.4.2` | | [vmactions/openbsd-vm](https://github.com/vmactions/openbsd-vm) | `1.3.1` | `1.3.5` | | [mpi4py/setup-mpi](https://github.com/mpi4py/setup-mpi) | `1.4.1` | `1.4.2` | | [actions/setup-python](https://github.com/actions/setup-python) | `6.1.0` | `6.2.0` | vmactions/openbsd-vm@d6c29ce1b4 (`1.3.5`) failed to run ssh on the github runner. 271a1ba62300483cfc58345ff9f425f1349a2cab for v1.3.4 was used instead. * Fix issue with some Subfiling VFD test files not getting deleted (#6212) * CMake: Fix Fortran cross-compilation support Refactor the cross-compilation infrastructure to rely on the standard CMAKE_CROSSCOMPILING_EMULATOR variable instead of the custom CROSSCOMPILING_PATH environment hack. Key changes: - Removed `ENVIRONMENT "${CROSSCOMPILING_PATH}"` from all test definitions. - Updated custom commands (e.g., H5match_types, H5_gen) to invoke the emulator explicitly when cross-compiling. - Updated ConfigureChecks.cmake and HDF5UseFortran.cmake to enable `try_run` checks when an emulator is defined. - Added config/toolchain/mingw-w64-x86-64-wine.sh wrapper to automatically locate MinGW runtime libraries (like libgfortran) for Wine execution. - Cleaned up toolchain files to remove hardcoded emulator paths, deferring configuration to the build environment. * Add Doxygen setup that results in missing Doygen documentation. (#6217) * Added setup-doxygen action in ctest.yml Ubuntu gcc workflow. * Also added actions/checkout for setup-doxygen. * Fixes link checker failure (#6219) Removed https:// as a workaround to avoid error by the link checker. * Remove force-setting of ZLIB_USE_EXTERNAL / SZIP_USE_EXTERNAL (#6222) Removes the force-setting of ZLIB_USE_EXTERNAL and SZIP_USE_EXTERNAL to ON when HDF5_ALLOW_EXTERNAL_SUPPORT is GIT or TGZ so that zlib and szip can be independently built from the system or externally as desired * Truncate Subfiling VFD's stub file when truncating subfiles (#6210) Ensure that the Subfiling VFD's stub file gets truncated when subfiles are being truncated to avoid a potentially unreadable file when the EOF doesn't match the stored EOF value Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Add CMake function to extract pkg-config info from libraries (#6220) * Consistent extension for C++ (#6214) Except for this file, all use cpp instead of cxx. No obvious reason why the same file types should have different extensions. * Enable Windows ARM64 CTest CI for release binaries (#6177) * ci: add Windows ARM64 MSVC CTest job * ci: add MSYS2 clangarm64 build on Windows ARM64 * cmake: add MSVC ARM64 presets for Windows * zlib: fix MSVC static library flags for ARM64 builds * Renamed .hxx file to .h and updated the #include for it. * Committing clang-format changes --------- Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Julien Schueller <schueller@phimeca.com> Co-authored-by: Martin Diehl <mail@martin-diehl.net> Co-authored-by: Harish RS <harish.rajaselvan@multicorewareinc.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
HDF5 API Tests
This directory contains several test applications that exercise HDF5's public API and serve as regression tests for HDF5 VOL Connectors.
Build Process and options
These HDF5 API tests are enabled by default, but can be disabled by passing the
-DHDF5_TEST_API=OFF option to CMake. The following build options are available
to influence how the API tests get built:
CMake
To set an option, it should be prepended with -D when passed to the cmake command.
For example,
cmake -DHDF5_TEST_API=OFF ..
HDF5_TEST_API (Default: ON) - Determines whether the API tests will be built.
HDF5_TEST_API_INSTALL (Default: OFF) - Determines whether the API tests should be installed
on the system.
HDF5_TEST_API_ENABLE_ASYNC (Default: OFF) - Determines whether tests for HDF5's asynchronous
I/O capabilities should be enabled. Note that the "native" HDF5 VOL connector doesn't support
this functionality, so these tests are directed towards VOL connectors that do.
HDF5_TEST_ENABLE_DRIVER (Default: OFF) - Determines whether the API test driver program should
be built. This driver program is useful when a VOL connector relies upon a server executable
(as well as possible additional executables) in order to function. The driver program can be
supplied with a server executable and server/client arguments to use when running the API
tests.
HDF5_TEST_API_SERVER (Default: empty string) - If HDF5_TEST_ENABLE_DRIVER is set to ON, this
option should be edited to point to the server executable that the driver program should attempt
to launch before running the API tests.
Autotools
Currently unsupported
Usage
These API tests currently only support usage with the native HDF5 VOL connector and HDF5 VOL connectors that can be loaded dynamically as a plugin. For information on how to build a VOL connector in this manner, refer to section 2.3 of the HDF5 VOL Connector Author Guide.
If an HDF5 VOL connector has been built alongside the library, these API tests can be used for testing that VOL connector at the same time that HDF5 is test. For more information on how to build a VOL connector alongside the HDF5 library, refer to Building and testing HDF5 VOL connectors with CMake FetchContent.
These API tests can also be used to test an HDF5 VOL connector that is external to the library.
For convenience, the HDF5_TEST_API_INSTALL option can be used to install these tests on the
system where other HDF5 executables (such as h5dump) are installed. To run these tests manually
with your VOL connector, set the following two environment variables:
HDF5_VOL_CONNECTOR - This environment variable should be set to the name chosen for the VOL connector
to be used. For example, HDF5's DAOS VOL connector uses the name "daos"
and would therefore set:
HDF5_VOL_CONNECTOR=daos
HDF5_PLUGIN_PATH - This environment variable should be set to the directory that contains the built
library for the VOL connector to be used.
Once these are set, the HDF5 API tests will attempt to automatically load the specified VOL connector and use it when running tests. If HDF5 is unable to locate or load the VOL connector specified, it will fall back to running the tests with the native HDF5 VOL connector and an error similar to the following will appear in the test output:
HDF5-DIAG: Error detected in HDF5 (X.XX.X) MPI-process 0:
#000: /home/user/git/hdf5/src/H5.c line 1010 in H5open(): library initialization failed
major: Function entry/exit
minor: Unable to initialize object
#001: /home/user/git/hdf5/src/H5.c line 277 in H5_init_library(): unable to initialize vol interface
major: Function entry/exit
minor: Unable to initialize object
#002: /home/user/git/hdf5/src/H5VLint.c line 199 in H5VL_init_phase2(): unable to set default VOL connector
major: Virtual Object Layer
minor: Can't set value
#003: /home/user/git/hdf5/src/H5VLint.c line 429 in H5VL__set_def_conn(): can't register connector
major: Virtual Object Layer
minor: Unable to register new ID
#004: /home/user/git/hdf5/src/H5VLint.c line 1321 in H5VL__register_connector_by_name(): unable to load VOL connector
major: Virtual Object Layer
minor: Unable to initialize object
Help and Support
For help with building or using the HDF5 API tests, please contact the HDF Help Desk.