Fixes from AmberTools 2025 Integration #272
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| name: 'Build and Test QUICK Serial Version' | |
| defaults: | |
| run: | |
| shell: bash | |
| on: | |
| push: | |
| paths-ignore: | |
| - '**.md' | |
| pull_request: | |
| paths-ignore: | |
| - '**.md' | |
| jobs: | |
| build-and-test-serial-legacy-configure-make: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: 'ubuntu-22.04' | |
| compiler-type: 'gnu' | |
| compiler-version: '10' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-10 g++-10 gfortran-10' | |
| - os: 'ubuntu-22.04' | |
| compiler-type: 'gnu' | |
| compiler-version: '11' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-11 g++-11 gfortran-11' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'gnu' | |
| compiler-version: '12' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-12 g++-12 gfortran-12' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'gnu' | |
| compiler-version: '13' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-13 g++-13 gfortran-13' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'gnu' | |
| compiler-version: '14' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-14 g++-14 gfortran-14' | |
| - os: 'ubuntu-24.04-arm' | |
| compiler-type: 'gnu' | |
| compiler-version: '14' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-14 g++-14 gfortran-14' | |
| runs-on: ${{ matrix.os }} | |
| name: ${{ matrix.os }} - Serial - Legacy - ${{ matrix.compiler-type }} - ${{ matrix.compiler-version }} | |
| steps: | |
| - name: 'Checkout Repository' | |
| uses: actions/checkout@v4 | |
| - name: 'Linux: Install Dependencies for Serial Version' | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install ${{ matrix.compiler-install }} parallel | |
| if [[ ${{ matrix.compiler-type }} == 'gnu' || ${{ matrix.compiler-type }} == 'clang' ]]; then | |
| sudo rm /usr/bin/${{ matrix.c-compiler }} | |
| sudo ln -s -T ${{ matrix.c-compiler }}-${{ matrix.compiler-version }} /usr/bin/${{ matrix.c-compiler }} | |
| sudo rm /usr/bin/${{ matrix.cxx-compiler }} | |
| sudo ln -s -T ${{ matrix.cxx-compiler }}-${{ matrix.compiler-version }} /usr/bin/${{ matrix.cxx-compiler }} | |
| if [[ ${{ matrix.compiler-type }} == 'gnu' ]]; then | |
| sudo rm /usr/bin/${{ matrix.fortran-compiler }} | |
| sudo ln -s -T ${{ matrix.fortran-compiler }}-${{ matrix.compiler-version }} /usr/bin/${{ matrix.fortran-compiler }} | |
| fi | |
| fi | |
| - name: 'Linux: Log Softare Environment Configuration' | |
| if: runner.os == 'Linux' | |
| run: | | |
| echo "OS version:" | |
| cat /etc/os-release | |
| echo | |
| echo "Kernel version:" | |
| uname -a | |
| echo | |
| ldd --version | |
| echo | |
| echo "Fortran compiler version:" | |
| ${{ matrix.fortran-compiler }} --version | |
| echo | |
| echo "GNU Parallel version:" | |
| parallel --version | |
| - name: 'Setup Environment Variables for Building and Running Tests' | |
| run: | | |
| echo "QUICK_BASIS=$PWD/install/basis" >> "$GITHUB_ENV" | |
| echo "PATH=$PWD/install/bin:$PATH" >> "$GITHUB_ENV" | |
| echo "LIBRARY_PATH=$PWD/install/lib/serial:$LIBRARY_PATH" >> "$GITHUB_ENV" | |
| echo "LD_LIBRARY_PATH=$PWD/install/lib/serial:$LD_LIBRARY_PATH" >> "$GITHUB_ENV" | |
| echo "PARALLEL_TEST_COUNT=2" >> "$GITHUB_ENV" | |
| echo "CC=${{ matrix.c-compiler }}" >> "$GITHUB_ENV" | |
| echo "CXX=${{ matrix.cxx-compiler }}" >> "$GITHUB_ENV" | |
| echo "FC=${{ matrix.fortran-compiler }}" >> "$GITHUB_ENV" | |
| - name: 'Configure Serial Version' | |
| run: | | |
| ./configure --serial --enablef --shared --verbose --prefix $PWD/install \ | |
| ${{ matrix.compiler-type }} | |
| - name: 'Build and Install Serial Version Using 2 Jobs' | |
| run: | | |
| make -j2 all install | |
| - name: 'Run Tests for Serial Version (Make)' | |
| run: | | |
| make fulltest | |
| - name: 'Upload Test Artifacts for Serial Version' | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: serial-legacy-configure-make-tests-${{ matrix.os }}-${{ matrix.compiler-type }}-${{ matrix.compiler-version }} | |
| path: ${{ github.workspace }}/install/test/runs/serial | |
| retention-days: 3 | |
| compression-level: 6 | |
| - name: 'Download Test Artifacts for Serial Version' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: serial-legacy-configure-make-tests-${{ matrix.os }}-${{ matrix.compiler-type }}-${{ matrix.compiler-version }} | |
| - name: 'Display Artifacts' | |
| run: | | |
| ls -R | |
| build-and-test-serial-cmake: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: 'ubuntu-22.04' | |
| compiler-type: 'GNU' | |
| compiler-version: '10' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-10 g++-10 gfortran-10' | |
| - os: 'ubuntu-22.04' | |
| compiler-type: 'GNU' | |
| compiler-version: '11' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-11 g++-11 gfortran-11' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'GNU' | |
| compiler-version: '12' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-12 g++-12 gfortran-12' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'GNU' | |
| compiler-version: '13' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-13 g++-13 gfortran-13' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'GNU' | |
| compiler-version: '14' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-14 g++-14 gfortran-14' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'CLANG' | |
| compiler-version: '17' | |
| c-compiler: 'clang' | |
| cxx-compiler: 'clang++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'clang-17 gfortran' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'CLANG' | |
| compiler-version: '18' | |
| c-compiler: 'clang' | |
| cxx-compiler: 'clang++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'clang-18 gfortran' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'INTELLLVM' | |
| compiler-version: '2024.2.1' | |
| c-compiler: 'icx' | |
| cxx-compiler: 'icpx' | |
| fortran-compiler: 'ifx' | |
| compiler-install: 'intel-oneapi-compiler-dpcpp-cpp-2024.2 intel-oneapi-compiler-fortran-2024.2 intel-oneapi-mkl-2024.2 intel-oneapi-mkl-devel-2024.2' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'INTELLLVM' | |
| compiler-version: '2025.0.1' | |
| c-compiler: 'icx' | |
| cxx-compiler: 'icpx' | |
| fortran-compiler: 'ifx' | |
| compiler-install: 'intel-oneapi-compiler-dpcpp-cpp-2025.0 intel-oneapi-compiler-fortran-2025.0 intel-oneapi-mkl-2025.0 intel-oneapi-mkl-devel-2025.0' | |
| - os: 'ubuntu-24.04' | |
| compiler-type: 'PGI' | |
| compiler-version: '25.1' | |
| c-compiler: 'pgcc' | |
| cxx-compiler: 'pgcc++' | |
| fortran-compiler: 'pgf90' | |
| compiler-install: 'nvhpc-25-1 gfortran' | |
| - os: 'ubuntu-24.04-arm' | |
| compiler-type: 'GNU' | |
| compiler-version: '14' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc-14 g++-14 gfortran-14' | |
| - os: 'ubuntu-24.04-arm' | |
| compiler-type: 'CLANG' | |
| compiler-version: '18' | |
| c-compiler: 'clang' | |
| cxx-compiler: 'clang++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'clang-18 gfortran' | |
| - os: 'macos-13' | |
| compiler-type: 'GNU' | |
| compiler-version: '14' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc@14' | |
| - os: 'macos-13' | |
| compiler-type: 'CLANG' | |
| compiler-version: '15' | |
| fortran-compiler-version: '14' | |
| c-compiler: 'clang' | |
| cxx-compiler: 'clang++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'llvm@15 gcc@14' | |
| - os: 'macos-14' | |
| compiler-type: 'GNU' | |
| compiler-version: '14' | |
| c-compiler: 'gcc' | |
| cxx-compiler: 'g++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'gcc@14' | |
| - os: 'macos-14' | |
| compiler-type: 'CLANG' | |
| compiler-version: '15' | |
| fortran-compiler-version: '14' | |
| c-compiler: 'clang' | |
| cxx-compiler: 'clang++' | |
| fortran-compiler: 'gfortran' | |
| compiler-install: 'llvm@15 gcc@14' | |
| runs-on: ${{ matrix.os }} | |
| name: ${{ matrix.os }} - Serial - CMake - ${{ matrix.compiler-type }} - ${{ matrix.compiler-version }} | |
| steps: | |
| - name: 'Checkout Repository' | |
| uses: actions/checkout@v4 | |
| - name: 'Linux: Setup Environment Variables for Building and Running Tests' | |
| if: runner.os == 'Linux' | |
| run: | | |
| echo "QUICK_BASIS=$PWD/install/basis" >> "$GITHUB_ENV" | |
| echo "PATH=$PWD/install/bin:$PATH" >> "$GITHUB_ENV" | |
| echo "LIBRARY_PATH=$PWD/install/lib:$LIBRARY_PATH" >> "$GITHUB_ENV" | |
| echo "LD_LIBRARY_PATH=$PWD/install/lib:$LD_LIBRARY_PATH" >> "$GITHUB_ENV" | |
| echo "PARALLEL_TEST_COUNT=2" >> "$GITHUB_ENV" | |
| echo "CC=${{ matrix.c-compiler }}" >> "$GITHUB_ENV" | |
| echo "CXX=${{ matrix.cxx-compiler }}" >> "$GITHUB_ENV" | |
| echo "FC=${{ matrix.fortran-compiler }}" >> "$GITHUB_ENV" | |
| if [ ${{ matrix.compiler-type }} == 'PGI' ]; then | |
| echo PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/${{ matrix.compiler-version }}/compilers/bin:$PATH >> "$GITHUB_ENV" | |
| echo INCLUDE_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/${{ matrix.compiler-version }}/compilers/include:$INCLUDE_PATH >> "$GITHUB_ENV" | |
| echo LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/${{ matrix.compiler-version }}/compilers/lib:$LIBRARY_PATH >> "$GITHUB_ENV" | |
| echo LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/${{ matrix.compiler-version }}/compilers/lib:$LD_LIBRARY_PATH >> "$GITHUB_ENV" | |
| echo CMAKE_PREFIX_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/${{ matrix.compiler-version }}/compilers/:$CMAKE_PREFIX_PATH >> "$GITHUB_ENV" | |
| echo "NVHPC=/opt/nvidia/hpc_sdk" >> "$GITHUB_ENV" | |
| echo NVHPC_ROOT=/opt/nvidia/hpc_sdk/Linux_x86_64/${{ matrix.compiler-version }} >> "$GITHUB_ENV" | |
| fi | |
| - name: 'MacOS: Setup Environment Variables for Building and Running Tests' | |
| if: runner.os == 'macOS' | |
| run: | | |
| echo "QUICK_BASIS=$PWD/install/basis" >> "$GITHUB_ENV" | |
| echo "PATH=$PWD/install/bin:$PATH" >> "$GITHUB_ENV" | |
| echo "LIBRARY_PATH=$PWD/install/lib:$LIBRARY_PATH" >> "$GITHUB_ENV" | |
| echo "LD_LIBRARY_PATH=$PWD/install/lib:$LD_LIBRARY_PATH" >> "$GITHUB_ENV" | |
| echo "PARALLEL_TEST_COUNT=2" >> "$GITHUB_ENV" | |
| echo "CC=${{ matrix.c-compiler }}" >> "$GITHUB_ENV" | |
| echo "CXX=${{ matrix.cxx-compiler }}" >> "$GITHUB_ENV" | |
| echo "FC=${{ matrix.fortran-compiler }}" >> "$GITHUB_ENV" | |
| if [[ ${{ matrix.os }} == 'macos-13' ]]; then | |
| echo "BREW_COMPILER_PREFIX=/usr/local/bin" >> "$GITHUB_ENV" | |
| echo "PATH=/usr/local/bin:$PATH" >> "$GITHUB_ENV" | |
| elif [[ ${{ matrix.os }} == 'macos-14' ]]; then | |
| echo "BREW_COMPILER_PREFIX=/opt/homebrew/bin" >> "$GITHUB_ENV" | |
| echo "PATH=/opt/homebrew/bin:$PATH" >> "$GITHUB_ENV" | |
| fi | |
| - name: 'Linux: Install Dependencies for Serial Version' | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| if [ ${{ matrix.compiler-type }} == 'INTELLLVM' ]; then | |
| sudo apt install -y gpg-agent wget | |
| wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \ | |
| | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null | |
| echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" \ | |
| | sudo tee /etc/apt/sources.list.d/oneAPI.list | |
| sudo apt update | |
| elif [ ${{ matrix.compiler-type }} == 'PGI' ]; then | |
| sudo apt install -y gpg-agent wget | |
| wget -O- https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK \ | |
| | gpg --dearmor | sudo tee /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg > /dev/null | |
| 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 update | |
| fi | |
| sudo apt-get -y install ${{ matrix.compiler-install }} cmake parallel | |
| if [[ ${{ matrix.compiler-type }} == 'GNU' || ${{ matrix.compiler-type }} == 'CLANG' ]]; then | |
| sudo rm /usr/bin/${{ matrix.c-compiler }} | |
| sudo ln -s -T ${{ matrix.c-compiler }}-${{ matrix.compiler-version }} /usr/bin/${{ matrix.c-compiler }} | |
| sudo rm /usr/bin/${{ matrix.cxx-compiler }} | |
| sudo ln -s -T ${{ matrix.cxx-compiler }}-${{ matrix.compiler-version }} /usr/bin/${{ matrix.cxx-compiler }} | |
| if [[ ${{ matrix.compiler-type }} == 'GNU' ]]; then | |
| sudo rm /usr/bin/${{ matrix.fortran-compiler }} | |
| sudo ln -s -T ${{ matrix.fortran-compiler }}-${{ matrix.compiler-version }} /usr/bin/${{ matrix.fortran-compiler }} | |
| fi | |
| fi | |
| - name: 'MacOS: Install Dependencies for Serial Version' | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install --formula --quiet ${{ matrix.compiler-install }} cmake parallel | |
| if [[ ${{ matrix.compiler-type }} == 'GNU' || ${{ matrix.compiler-type }} == 'CLANG' ]]; then | |
| sudo ln -Fs $BREW_COMPILER_PREFIX/${{ matrix.c-compiler }}-${{ matrix.compiler-version }} \ | |
| $BREW_COMPILER_PREFIX/${{ matrix.c-compiler }} | |
| sudo ln -Fs $BREW_COMPILER_PREFIX/${{ matrix.cxx-compiler }}-${{ matrix.compiler-version }} \ | |
| $BREW_COMPILER_PREFIX/${{ matrix.cxx-compiler }} | |
| if [[ ${{ matrix.compiler-type }} == 'GNU' ]]; then | |
| sudo ln -Fs $BREW_COMPILER_PREFIX/${{ matrix.fortran-compiler }}-${{ matrix.compiler-version }} \ | |
| $BREW_COMPILER_PREFIX/${{ matrix.fortran-compiler }} | |
| elif [[ ${{ matrix.compiler-type }} == 'CLANG' ]]; then | |
| sudo ln -Fs $BREW_COMPILER_PREFIX/${{ matrix.fortran-compiler }}-${{ matrix.fortran-compiler-version }} \ | |
| $BREW_COMPILER_PREFIX/${{ matrix.fortran-compiler }} | |
| fi | |
| fi | |
| - name: 'Linux: Log Softare Environment Configuration' | |
| if: runner.os == 'Linux' | |
| run: | | |
| if [ ${{ matrix.compiler-type }} == 'INTELLLVM' ]; then | |
| source /opt/intel/oneapi/setvars.sh | |
| fi | |
| echo "OS version:" | |
| cat /etc/os-release | |
| echo | |
| echo "Kernel version:" | |
| uname -a | |
| echo | |
| ldd --version | |
| echo | |
| echo "Fortran compiler version:" | |
| ${{ matrix.fortran-compiler }} --version | |
| echo | |
| if [ ${{ matrix.compiler-type }} == 'INTELLLVM' ]; then | |
| echo "MKL install directory:" | |
| echo "${MKLROOT}" | |
| echo | |
| fi | |
| echo "CMake version:" | |
| cmake --version | |
| echo | |
| echo "GNU Parallel version:" | |
| parallel --version | |
| - name: 'MacOS: Log Softare Environment Configuration' | |
| if: runner.os == 'macOS' | |
| run: | | |
| echo "OS version:" | |
| cat /System/Library/CoreServices/SystemVersion.plist | |
| echo | |
| echo "Kernel version:" | |
| uname -a | |
| echo | |
| echo "Fortran compiler version:" | |
| ${{ matrix.fortran-compiler }} --version | |
| echo | |
| echo "CMake version:" | |
| cmake --version | |
| echo | |
| echo "GNU Parallel version:" | |
| parallel --version | |
| - name: 'Configure Serial Version' | |
| run: | | |
| mkdir build | |
| cd build | |
| if [ ${{ matrix.compiler-type }} == 'INTELLLVM' ]; then | |
| source /opt/intel/oneapi/setvars.sh | |
| cmake .. -DCOMPILER=${{ matrix.compiler-type }} \ | |
| -DENABLEF=TRUE -DCMAKE_INSTALL_PREFIX=$PWD/../install \ | |
| -DMKL_HOME=$MKLROOT -DMKL_MULTI_THREADED=FALSE -DTRUST_SYSTEM_LIBS=TRUE | |
| else | |
| cmake .. -DCOMPILER=${{ matrix.compiler-type }} \ | |
| -DENABLEF=TRUE -DCMAKE_INSTALL_PREFIX=$PWD/../install | |
| fi | |
| - name: 'Build and Install Serial Version Using 2 Jobs' | |
| run: | | |
| if [ ${{ matrix.compiler-type }} == 'INTELLLVM' ]; then | |
| source /opt/intel/oneapi/setvars.sh | |
| fi | |
| cd build | |
| cmake --build . --parallel 2 --verbose | |
| cmake --install . | |
| - name: 'Run Tests for Serial Version' | |
| run: | | |
| if [ ${{ matrix.compiler-type }} == 'INTELLLVM' ]; then | |
| source /opt/intel/oneapi/setvars.sh | |
| fi | |
| cd install | |
| ./runtest --serial --full | |
| - name: 'Upload Test Artifacts for Serial Version' | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: serial-cmake-tests-${{ matrix.os }}-${{ matrix.compiler-type }}-${{ matrix.compiler-version }} | |
| path: ${{ github.workspace }}/install/test/runs/serial | |
| retention-days: 3 | |
| compression-level: 6 | |
| - name: 'Download Test Artifacts for Serial Version' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: serial-cmake-tests-${{ matrix.os }}-${{ matrix.compiler-type }}-${{ matrix.compiler-version }} | |
| - name: 'Display Artifacts' | |
| run: ls -R |