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Sync develop changes August 21 - 27 to hdf5_1_14 (#4774)
* Use gfortran 14 for cmake-ctest.yml on mac (#4739) * Use gfortran 14 for cmake-test on mac * Remove notarization step * Address @byrnHDF review * Fix enum type mismatch warning (#4741) * Fix macro redefined warnings (#4744) Removes a duplicated HDopen macro from the performance testing programs * Update nvhpc CI version to 24.7 (#4740) * Return basic HTTP range GET logging to ROS3 (#4738) * Add minimal amount of S3 request logging to ROS3 * Fix ROS3 logging ifdef conditions * Replace non-VOL calls with VOL calls - part 1 (#4745) This PR is part of the incremental switching H5I_object() and H5I_object_verify() to their VOL counterpart, H5VL_object() and H5VL_vol_object_verify(), a newly addedinternal function. Fixes GH-4730 partially. * Fix inconsistent documentation of get_name functions (#4715) - Verified that the listed functions do not include null terminator in the returned length - Improved some of the tests - Corrected documentation Fixes GH-4704 * Casted a positive int to size_t * Remove HDF-EOS5 CI action (#4750) The code can't be downloaded due to changes that put it behind an EarthData login. We'll disable this while we figure out a work-around. * Replace non-VOL calls with VOL calls - part 2 (#4748) This PR switches H5I_object_verify() to H5VL_vol_object_verify() in the H5F API and fixes documentation of H5Fmount and H5Funmount. * More on H5F API * Restore rand_r in a few parallel tests (#4749) The t_pmulti_dset and t_select_io_dset tests rely on the behavior of the previous private rand_r-like implementation to get the correct sequence of random numbers to pass. This has been restored using a fully private rand_r-like implementation that doesn't rely on rand_r and will work on Windows and other platforms where rand_r doesn't exist. * Don't run AOCC parallel tests with -j2 (#4752) Don't run parallel tests in both Autotools and CMake with multiple processes. ph5diff still runs with -j2 w/ Autotools since the test script is in the tools/test/h5diff directory. * Split off AOCC CMake parallel tests * Remove unnecessary NPROCS env vars * Put NPROCS back in serial tests We run ph5diff tests there * Replace non-VOL calls with VOL calls - part 3 (#4756) This PR switches H5I_object_verify() to H5VL_vol_object_verify() in the H5G API and removes unnecessary casts. * Turn on parallel CI tests in Autotools & CMake (#4573) * Fix typo in H5Centry.c (#4762) * Set/Unset VOL wrapping context in H5VL_attr_close (#4759) * Add missing C++ and Fortran to Intel oneAPI CI (#4761) * Add Fortran and C++ to Autotools * Add Fortran and C++ to Linux CMake * Add C++ to Windows CMake * Fix bad GitHub workspace variable * Remove early test exit (#4757) * Don't skip file tests * Remove test with invalid flag for H5Fopen * Verify that create/open of unseekable file fails * Remove failure verification * Restore Julia CI (#4763) Fixes #4539 * Capitalize f in (#4766) * Add testing to NVHPC CI actions (CMake & Autotools) (#4760) Turns on testing, both serial and parallel, but skips: * dt_arith and dtransform in CMake * All main library tests in the Autotools Due to dt_arith and dtransform segfaults when handling long doubles. * Fix typo in H5T_order_t enum (#4773) 'bit endian' --> 'big endian' * Correct julia workflows name for hdf5_1_14 branch. --------- Co-authored-by: H. Joe Lee <[email protected]> Co-authored-by: Aleksandar Jelenak <[email protected]> Co-authored-by: bmribler <[email protected]> Co-authored-by: Dana Robinson <[email protected]> Co-authored-by: jhendersonHDF <[email protected]> Co-authored-by: mattjala <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| name: hdf5 1.14 autotools julia | ||
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| on: | ||
| workflow_call: | ||
| inputs: | ||
| build_mode: | ||
| description: "release vs. debug build" | ||
| required: true | ||
| type: string | ||
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| permissions: | ||
| contents: read | ||
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| jobs: | ||
| julia_build_and_test: | ||
| name: "julia ${{ inputs.build_mode }}" | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Get Sources | ||
| uses: actions/[email protected] | ||
|
|
||
| - name: Install Dependencies | ||
| shell: bash | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install autoconf automake libtool libtool-bin libaec-dev | ||
| sudo apt-get install doxygen graphviz | ||
| sudo apt install -y zlib1g-dev libcurl4-openssl-dev libjpeg-dev wget curl bzip2 | ||
| sudo apt install -y m4 flex bison cmake libzip-dev openssl build-essential | ||
| - name: Autotools Configure | ||
| shell: bash | ||
| run: | | ||
| sh ./autogen.sh | ||
| mkdir "${{ runner.workspace }}/build" | ||
| cd "${{ runner.workspace }}/build" | ||
| $GITHUB_WORKSPACE/configure \ | ||
| --enable-build-mode=${{ inputs.build_mode }} \ | ||
| --disable-fortran \ | ||
| --enable-shared \ | ||
| --disable-parallel \ | ||
| --prefix=/tmp | ||
| - name: Autotools Build | ||
| shell: bash | ||
| run: | | ||
| make -j3 | ||
| working-directory: ${{ runner.workspace }}/build | ||
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||
| - name: Install HDF5 | ||
| shell: bash | ||
| run: | | ||
| make install | ||
| working-directory: ${{ runner.workspace }}/build | ||
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||
| - name: Install julia | ||
| uses: julia-actions/setup-julia@latest | ||
| with: | ||
| version: '1.6' | ||
| arch: 'x64' | ||
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||
| - name: Get julia hdf5 source | ||
| uses: actions/[email protected] | ||
| with: | ||
| repository: JuliaIO/HDF5.jl | ||
| path: . | ||
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||
| - name: Generate LocalPreferences | ||
| run: | | ||
| echo '[HDF5]' >> LocalPreferences.toml | ||
| echo 'libhdf5 = "/tmp/lib/libhdf5.so"' >> LocalPreferences.toml | ||
| echo 'libhdf5_hl = "/tmp/lib/libhdf5_hl.so"' >> LocalPreferences.toml | ||
| - uses: julia-actions/julia-buildpkg@latest | ||
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||
| - name: Julia Run Tests | ||
| uses: julia-actions/julia-runtest@latest | ||
| env: | ||
| JULIA_DEBUG: Main |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
| name: hdf5 1.14 CMake julia | ||
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| on: | ||
| workflow_call: | ||
| inputs: | ||
| build_mode: | ||
| description: "release vs. debug build" | ||
| required: true | ||
| type: string | ||
|
|
||
| permissions: | ||
| contents: read | ||
|
|
||
| jobs: | ||
| julia_build_and_test: | ||
| name: "julia ${{ inputs.build_mode }}" | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Get Sources | ||
| uses: actions/[email protected] | ||
|
|
||
| - name: Install Dependencies | ||
| shell: bash | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install ninja-build doxygen graphviz | ||
| sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev | ||
| sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential | ||
| - name: CMake Configure | ||
| shell: bash | ||
| run: | | ||
| mkdir "${{ runner.workspace }}/build" | ||
| cd "${{ runner.workspace }}/build" | ||
| cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake -G Ninja \ | ||
| -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \ | ||
| -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF \ | ||
| -DHDF5_ENABLE_PARALLEL:BOOL=OFF \ | ||
| -DHDF5_BUILD_CPP_LIB:BOOL=OFF \ | ||
| -DLIBAEC_USE_LOCALCONTENT=OFF \ | ||
| -DZLIB_USE_LOCALCONTENT=OFF \ | ||
| -DHDF5_BUILD_FORTRAN:BOOL=OFF \ | ||
| -DHDF5_BUILD_JAVA:BOOL=OFF \ | ||
| -DCMAKE_INSTALL_PREFIX=/tmp \ | ||
| $GITHUB_WORKSPACE | ||
| - name: CMake Build | ||
| shell: bash | ||
| run: | | ||
| cmake --build . --parallel 3 --config ${{ inputs.build_mode }} | ||
| working-directory: ${{ runner.workspace }}/build | ||
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| - name: Install HDF5 | ||
| shell: bash | ||
| run: | | ||
| cmake --install . | ||
| working-directory: ${{ runner.workspace }}/build | ||
|
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||
| - name: Install julia | ||
| uses: julia-actions/setup-julia@latest | ||
| with: | ||
| version: '1.6' | ||
| arch: 'x64' | ||
|
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||
| - name: Get julia hdf5 source | ||
| uses: actions/[email protected] | ||
| with: | ||
| repository: JuliaIO/HDF5.jl | ||
| path: . | ||
|
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||
| - name: Generate LocalPreferences | ||
| run: | | ||
| echo '[HDF5]' >> LocalPreferences.toml | ||
| echo 'libhdf5 = "/tmp/lib/libhdf5.so"' >> LocalPreferences.toml | ||
| echo 'libhdf5_hl = "/tmp/lib/libhdf5_hl.so"' >> LocalPreferences.toml | ||
| - uses: julia-actions/julia-buildpkg@latest | ||
|
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||
| - name: Julia Run Tests | ||
| uses: julia-actions/julia-runtest@latest | ||
| env: | ||
| JULIA_DEBUG: Main |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -50,8 +50,9 @@ jobs: | |
| - name: Get Sources | ||
| uses: actions/[email protected] | ||
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| # AUTOTOOLS CONFIGURE | ||
| - name: Autotools Configure | ||
| env: | ||
| NPROCS: 2 | ||
| run: | | ||
| sh ./autogen.sh | ||
| mkdir "${{ runner.workspace }}/build" | ||
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@@ -71,7 +72,28 @@ jobs: | |
| --with-szlib=yes | ||
| shell: bash | ||
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| # BUILD | ||
| - name: Autotools Build | ||
| run: make -j3 | ||
| working-directory: ${{ runner.workspace }}/build | ||
|
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| # ph5diff tests are in the tools/tests directory so they will get run | ||
| # here, so leave NPROCS set here as well | ||
| - name: Autotools Run Tests | ||
| env: | ||
| NPROCS: 2 | ||
| run: | | ||
| cd test && make check -j2 && cd .. | ||
| cd tools && make check -j2 && cd .. | ||
| cd hl && make check -j2 && cd .. | ||
| cd fortran/test && make check -j2 && cd ../.. | ||
| working-directory: ${{ runner.workspace }}/build | ||
| if: ${{ inputs.thread_safety == 'disable' }} | ||
|
|
||
| - name: Autotools Run Parallel Tests | ||
| env: | ||
| NPROCS: 2 | ||
| run: | | ||
| cd testpar && make check && cd .. | ||
| cd fortran/testpar && make check -j2 && cd ../.. | ||
| working-directory: ${{ runner.workspace }}/build | ||
| if: ${{ inputs.thread_safety == 'disable' }} | ||
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