Sync fixes for CI and presets (#3855)

* Sync fixes for CI and presets * Sync the Fortran build changes * Update fortran test file * Sync hl/fortran files * Merge the nvidia compiler flag changes * Update link * Update links to doxygen refs for 1.14
HDFGroup · Nov 15, 2023 · af8c1d1 · af8c1d1
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diff --git a/.github/workflows/hdfeos5.yml b/.github/workflows/hdfeos5.yml
@@ -16,7 +16,7 @@ on:
 
 # Using concurrency to cancel any in-progress job or run
 concurrency:
-  group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
   cancel-in-progress: true
 
 permissions:

diff --git a/.github/workflows/intel-cmake.yml b/.github/workflows/intel-cmake.yml
@@ -13,69 +13,111 @@ permissions:
   contents: read
 
 jobs:
-  Intel_build_and_test:
-    name: "Intel ${{ inputs.build_mode }}"
+  # Linux (Ubuntu) w/ gcc + CMake
+  #
+  Intel_oneapi_linux:
+    name: "ubuntu-oneapi ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - name: add oneAPI to apt
-        shell: bash
-        run: |
-          cd /tmp
-          wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-          sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-          rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-          sudo add-apt-repository -y "deb https://apt.repos.intel.com/oneapi all main"
-
+      # Only CMake need ninja-build, but we just install it unilaterally
+      # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-          sudo apt update
-          sudo apt-get install ninja-build doxygen graphviz
-          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+           sudo apt update
+           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
 
-      - name: install oneAPI dpcpp and fortran compiler
-        shell: bash
-        run: |
-          sudo apt update
-          sudo apt install -y intel-oneapi-compiler-dpcpp-cpp
-          sudo apt install -y intel-oneapi-compiler-fortran
-
-      - name: install oneAPI MKL library
-        shell: bash
-        run: |
-          sudo apt install -y intel-oneapi-mkl-devel
+      - name: add oneAPI to env
+        uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: intel
+          version: '2023.2'
 
-      - name: CMake Configure with icx
+      - name: CMake Configure with oneapi
         shell: bash
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
         run: |
-          source /opt/intel/oneapi/setvars.sh
-          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
-          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake -G Ninja \
+          cmake -C ${{ github.workspace }}/config/cmake/cacheinit.cmake -G Ninja \
           -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
-          -DCMAKE_TOOLCHAIN_FILE=config/toolchain/intel.cmake \
-          -DMKL_ROOT="/opt/intel/oneapi/mkl/latest" \
-          -DTBB_ROOT="/opt/intel/oneapi/tbb/latest" \
           -DLIBAEC_USE_LOCALCONTENT=OFF \
           -DZLIB_USE_LOCALCONTENT=OFF \
-          -DHDF5_BUILD_FORTRAN=OFF \
           $GITHUB_WORKSPACE
 
       # BUILD
       - name: CMake Build
         shell: bash
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
         run: |
-          source /opt/intel/oneapi/setvars.sh
           cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
         working-directory: ${{ runner.workspace }}/build
 
       # RUN TESTS
       - name: CMake Run Tests
         shell: bash
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
         run: |
-          source /opt/intel/oneapi/setvars.sh
-          export SYCL_DEVICE_FILTER=opencl.cpu
           ctest . --parallel 2 -C ${{ inputs.build_mode }} -V
         working-directory: ${{ runner.workspace }}/build
+
+  Intel_oneapi_windows:
+    name: "windows-oneapi ${{ inputs.build_mode }}"
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Dependencies (Windows)
+        run: choco install ninja
+
+      - name: add oneAPI to env
+        uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: intel
+          version: '2023.2'
+
+      - name: CMake Configure with oneapi
+        shell: pwsh
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          Set-Location -Path "${{ runner.workspace }}\\build"
+          cmake -C ${{ github.workspace }}/config/cmake/cacheinit.cmake -G Ninja -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} -DHDF5_BUILD_FORTRAN=ON -DLIBAEC_USE_LOCALCONTENT=OFF -DZLIB_USE_LOCALCONTENT=OFF ${{ github.workspace }}
+
+      # BUILD
+      - name: CMake Build
+        shell: pwsh
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
+        run: |
+          cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
+        working-directory: ${{ runner.workspace }}/build
+
+      # RUN TESTS
+      - name: CMake Run Tests
+        shell: pwsh
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
+        run: |
+          ctest . --parallel 2 -C ${{ inputs.build_mode }} -V -E tfloatsattrs
+        working-directory: ${{ runner.workspace }}/build
diff --git a/.github/workflows/linux-auto-aocc-ompi.yml b/.github/workflows/linux-auto-aocc-ompi.yml
@@ -1,4 +1,4 @@
-name: linux autotools aocc ompi
+name: hdf5 1.14 autotools aocc ompi
 
 on:
   push:
@@ -16,7 +16,7 @@ on:
 
 # Using concurrency to cancel any in-progress job or run
 concurrency:
-  group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
   cancel-in-progress: true
 
 permissions:

diff --git a/.github/workflows/netcdf.yml b/.github/workflows/netcdf.yml
@@ -19,7 +19,7 @@ permissions:
 
 # Using concurrency to cancel any in-progress job or run
 concurrency:
-  group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
   cancel-in-progress: true
 
 jobs:

diff --git a/.github/workflows/nvhpc-auto.yml b/.github/workflows/nvhpc-auto.yml
@@ -31,21 +31,21 @@ jobs:
           curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg
           echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list
           sudo apt-get update -y
-          sudo apt-get install -y nvhpc-23-7          
-          echo "CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin/mpicc" >> $GITHUB_ENV
-          echo "FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin/mpifort" >> $GITHUB_ENV
+          sudo apt-get install -y nvhpc-23-9
+          echo "CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpicc" >> $GITHUB_ENV
+          echo "FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpifort" >> $GITHUB_ENV
           echo "NVHPCSDK=/opt/nvidia/hpc_sdk" >> $GITHUB_ENV
-          echo "OMPI_CXX=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin/nvc++" >> $GITHUB_ENV
-          echo "OMPI_CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin/nvc" >> $GITHUB_ENV
-          echo "OMPI_FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin/nvfortran" >> $GITHUB_ENV
-          echo "LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/lib" >> $GITHUB_ENV
+          echo "OMPI_CXX=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvc++" >> $GITHUB_ENV
+          echo "OMPI_CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvc" >> $GITHUB_ENV
+          echo "OMPI_FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvfortran" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/lib" >> $GITHUB_ENV
           echo "DESTDIR=/tmp" >> $GITHUB_ENV
 
       - name: Autotools Configure
         shell: bash
         run: |
           export RUNPARALLEL="mpiexec -np 2"
-          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin:$PATH
+          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
           sh ./autogen.sh
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
@@ -61,27 +61,27 @@ jobs:
       - name: Autotools Build
         shell: bash
         run: |
-          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin:$PATH
+          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
           make -j3
         working-directory: ${{ runner.workspace }}/build
 
       # RUN TESTS
       # NORMAL
       - name: Autotools Run Tests
         run: |
-          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin:$PATH
+          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
           make check -j
         working-directory: ${{ runner.workspace }}/build
 
       # INSTALL (note that this runs even when we don't run the tests)
       - name: Autotools Install
         run: |
-          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin:$PATH
+          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
           make install
         working-directory: ${{ runner.workspace }}/build
 
 #      - name: Autotools Verify Install
 #        run: |
-#          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin:$PATH
+#          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
 #          make check-install
 #        working-directory: ${{ runner.workspace }}/build
diff --git a/.github/workflows/nvhpc-cmake.yml b/.github/workflows/nvhpc-cmake.yml
@@ -32,20 +32,20 @@ jobs:
           curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg
           echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list
           sudo apt-get update -y
-          sudo apt-get install -y nvhpc-23-7          
+          sudo apt-get install -y nvhpc-23-9
           echo "CC=nvc" >> $GITHUB_ENV
           echo "FC=nvfortran" >> $GITHUB_ENV
           echo "NVHPCSDK=/opt/nvidia/hpc_sdk" >> $GITHUB_ENV
-          echo "OMPI_CXX=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin/nvc++" >> $GITHUB_ENV
-          echo "OMPI_CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin/nvc" >> $GITHUB_ENV
-          echo "OMPI_FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin/nvfortran" >> $GITHUB_ENV
-          echo "LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/cuda/12.2/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/lib" >> $GITHUB_ENV
+          echo "OMPI_CXX=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvc++" >> $GITHUB_ENV
+          echo "OMPI_CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvc" >> $GITHUB_ENV
+          echo "OMPI_FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvfortran" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/cuda/12.2/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/lib" >> $GITHUB_ENV
           echo "DESTDIR=/tmp" >> $GITHUB_ENV
 
       - name: CMake Configure with nvc
         shell: bash
         run: |
-          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin:$PATH
+          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
           cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake -G Ninja \
@@ -56,7 +56,7 @@ jobs:
           -DLIBAEC_USE_LOCALCONTENT=OFF \
           -DZLIB_USE_LOCALCONTENT=OFF \
           -DHDF5_BUILD_FORTRAN:BOOL=ON \
-          -DHDF5_ENABLE_ASSERTS:BOOL=ON \
+          -DHDF5_BUILD_JAVA:BOOL=OFF \
           -DMPIEXEC_MAX_NUMPROCS:STRING="2" \
           $GITHUB_WORKSPACE
           cat src/libhdf5.settings
@@ -69,8 +69,8 @@ jobs:
         working-directory: ${{ runner.workspace }}/build
 
       # RUN TESTS
-#      - name: CMake Run Tests
-#        shell: bash
-#        run: |
-#          ctest . --parallel 2 -C ${{ inputs.build_mode }} -V
-#        working-directory: ${{ runner.workspace }}/build
+      - name: CMake Run Tests
+        shell: bash
+        run: |
+          ctest . --parallel 2 -C ${{ inputs.build_mode }} -V
+        working-directory: ${{ runner.workspace }}/build
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -125,7 +125,7 @@ Please make sure that you check the items applicable to your pull request:
   * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros)
 * Documentation
   * [ ] Was the change described in the release_docs/RELEASE.txt file?
-  * [ ] Was the new function documented in the corresponding public header file using [Doxygen](https://docs.hdfgroup.org/hdf5/develop/_r_m_t.html)?
+  * [ ] Was the new function documented in the corresponding public header file using [Doxygen](https://hdfgroup.github.io/hdf5/v1_14/_r_m_t.html)?
   * [ ] Was new functionality documented for the HDF5 community (the level of documentation depends on the feature; ask us what would be appropriate)
 * Testing
   * [ ] Does the pull request have tests?