Use smart pointers to manage metadynamics grid data #2222
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| name: "Library" | |
| on: | |
| push: | |
| jobs: | |
| basicchecks: | |
| name: Basic checks | |
| runs-on: ubuntu-latest | |
| outputs: | |
| hassecrets: ${{ steps.checksecrets.outputs.hassecrets }} | |
| env: | |
| CCACHE: ccache | |
| CCACHE_DIR: ${{ github.workspace }}/ccache | |
| steps: | |
| - name: Checkout Colvars | |
| uses: actions/checkout@v4 | |
| - name: Load compiler cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ github.workspace }}/ccache | |
| key: ${{ runner.os }}-build-basic-${{ github.sha }} | |
| restore-keys: ${{ runner.os }}-build-basic- | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Install build dependencies for library | |
| run: | | |
| sudo apt -y install ccache tcl8.6-dev clang | |
| - name: Test build recipes | |
| run: bash devel-tools/check_build_recipes | |
| - name: Convert BibTeX references to code | |
| shell: bash | |
| working-directory: doc | |
| run: | | |
| make update-code-refs | |
| if [ -n "$(git status --porcelain ../src/colvarmodule_refs.h)" ] ; then | |
| echo "Code citations out of date; please run make update-code-refs in the doc folder" >& 2 | |
| exit 1 | |
| fi | |
| - name: Build and test library (GCC) | |
| run: cmake -P devel-tools/build_test_library.cmake | |
| - name: Check documentation of command-line scripting interface | |
| shell: bash | |
| working-directory: doc | |
| run: | | |
| make update-cvscript-cmdline-doc | |
| if [ -n "$(git status --porcelain cvscript-tcl.tex)" ] ; then | |
| echo "Command-line scripting doc out of date; please run make update-cvscript-cmdline-doc and commit changes" >& 2 | |
| exit 1 | |
| fi | |
| - name: Build and test library (Clang) | |
| env: | |
| CMAKE_BUILD_DIR: build-clang | |
| CXX: clang++ | |
| CC: clang | |
| run: cmake -P devel-tools/build_test_library.cmake | |
| - name: Build library with debug code enabled (GCC) | |
| run: cmake -D COLVARS_DEBUG=ON -P devel-tools/build_test_library.cmake | |
| - name: Check whether secrets are available | |
| id: checksecrets | |
| env: | |
| PULL_ORACLE_DEVELOPER_STUDIO: ${{ secrets.PULL_ORACLE_DEVELOPER_STUDIO }} | |
| run: | | |
| echo "hassecrets=${{ env.PULL_ORACLE_DEVELOPER_STUDIO != '' }}" >> $GITHUB_OUTPUT | |
| - name: Print ccache stats | |
| run: ccache -s -v | |
| - name: Keep only one cache besides the one from this job | |
| shell: bash | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| bash ${{ github.workspace }}/devel-tools/cleanup-gh-cache.sh ${{ runner.os }}-build-basic- | |
| build-doc: | |
| name: Build documentation | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Apptainer | |
| shell: bash | |
| run: | | |
| sudo add-apt-repository -y ppa:apptainer/ppa | |
| sudo apt update | |
| sudo apt install -y apptainer-suid | |
| - name: Get container image | |
| shell: bash | |
| working-directory: devel-tools | |
| run: | | |
| apptainer pull texlive.sif oras://ghcr.io/colvars/devel-containers:texlive | |
| - name: Checkout website repository | |
| uses: actions/checkout@v4 | |
| with: | |
| ssh-key: ${{ secrets.PULL_PUSH_COLVARS_GITHUB_IO }} | |
| repository: 'Colvars/colvars.github.io' | |
| path: 'website' | |
| - name: Build doc for current branch | |
| working-directory: doc | |
| run: | | |
| make clean-all | |
| apptainer exec ${{ github.workspace }}/devel-tools/texlive.sif make | |
| - name: Install SSH key for access to website repository | |
| if: contains(github.event.head_commit.message, '[update-doc]') | |
| env: | |
| WEBSITE_SSH_KEY: ${{ secrets.PULL_PUSH_COLVARS_GITHUB_IO }} | |
| run: | | |
| mkdir -p -m 700 ~/.ssh | |
| echo "${WEBSITE_SSH_KEY}" > ~/.ssh/website | |
| chmod 600 ~/.ssh/website | |
| - name: Push updated doc to website repository | |
| working-directory: doc | |
| if: contains(github.event.head_commit.message, '[update-doc]') | |
| env: | |
| COLVARS_WEBSITE_TREE: ${{ github.workspace }}/website | |
| run: | | |
| apptainer exec ${{ github.workspace }}/devel-tools/texlive.sif make install | |
| export GIT_SSH="ssh -i ~/.ssh/website" | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "CI runner" | |
| bash update_website.sh ${{ github.workspace }}/website | |
| codeql: | |
| name: CodeQL analysis | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| if: ${{ ! github.event.repository.private }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install build dependencies for library | |
| run: | | |
| sudo apt-get -y install tcl8.6-dev | |
| - name: Checkout OpenMM (for Lepton library) | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'openmm/openmm' | |
| ref: 'master' | |
| path: 'openmm-source' | |
| - name: Initialize CodeQL | |
| uses: github/codeql-action/init@v2 | |
| with: | |
| languages: cpp | |
| - name: Build Colvars library with CMake | |
| run: cmake -P devel-tools/build_test_library.cmake | |
| - name: Perform CodeQL Analysis | |
| uses: github/codeql-action/analyze@v2 | |
| static-analyser: | |
| name: Clang 14 Static Analyser | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install build dependencies for library | |
| run: | | |
| sudo apt -y install tcl8.6-dev clang-14 clang-tools-14 | |
| - name: Checkout OpenMM (for Lepton library) | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'openmm/openmm' | |
| ref: 'master' | |
| path: 'openmm-source' | |
| - name: Perform Clang Static Analyser | |
| env: | |
| CXX: clang++-14 | |
| CC: clang-14 | |
| run: | | |
| scan-build-14 --use-cc=clang-14 --use-c++=clang++-14 cmake -P devel-tools/build_test_library.cmake 2>&1 | tee build_analyser.log | |
| grep "CMake Error" build_analyser.log > build_errors.log || true | |
| if [ -s build_errors.log ] ; then | |
| echo "Found compiler errors during build" | |
| cat build_analyser.log | |
| exit 1 | |
| fi | |
| - name: Analyze logs | |
| run: | # Retrieve warnings generated but not the ones of OpenMM | |
| awk '/colvars\/colvars\/[^openmm].*warning:/,/warning.*generated|^$/' build_analyser.log | tee warnings_analyser.log || true | |
| if [ -s warnings_analyser.log ] ; then | |
| echo "Found compiler warning during build" | |
| exit 1 | |
| fi | |
| - name: Archive warnings artifacts | |
| uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: warnings_clang_static_analyser | |
| path: warnings_analyser.log | |
| address-sanitizer: | |
| name: Clang 16 address sanitizer | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| env: | |
| CCACHE: ccache | |
| CCACHE_DIR: ${{ github.workspace }}/ccache | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Load compiler ccache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ github.workspace }}/ccache | |
| key: ${{ runner.os }}-build-asan-${{ github.sha }} | |
| restore-keys: ${{ runner.os }}-build-asan- | |
| - name: Checkout OpenMM (for Lepton library) | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'openmm/openmm' | |
| ref: 'master' | |
| path: 'openmm-source' | |
| - name: Install Apptainer | |
| shell: bash | |
| run: | | |
| sudo add-apt-repository -y ppa:apptainer/ppa | |
| sudo apt update | |
| sudo apt install -y apptainer-suid | |
| - name: Get container images for build dependencies | |
| shell: bash | |
| working-directory: devel-tools | |
| run: | | |
| apptainer pull CentOS9-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel | |
| - name: Build with Clang 16 and address sanitizer | |
| env: | |
| CXX: clang++ | |
| CC: clang | |
| CMAKE_ADDRESS_SANITIZER: ON | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -P devel-tools/build_test_library.cmake | |
| - name: Archive warnings artifacts | |
| uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: Clang_address_sanitizer_output | |
| path: ${{github.workspace}}/build/Testing/Temporary/LastTest.log | |
| - name: Keep only one cache besides the one from this job | |
| shell: bash | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| bash ${{ github.workspace }}/devel-tools/cleanup-gh-cache.sh ${{ runner.os }}-build-asan- | |
| build-linux-x86_64-many: | |
| name: Linux x86_64 (GCC, Clang) | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| env: | |
| CCACHE: ccache | |
| CMAKE_GENERATOR: Ninja | |
| CCACHE_DIR: ${{ github.workspace }}/ccache | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Load compiler ccache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ github.workspace }}/ccache | |
| key: ${{ runner.os }}-build-multiple-${{ github.sha }} | |
| restore-keys: ${{ runner.os }}-build-multiple- | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Install Apptainer | |
| shell: bash | |
| run: | | |
| sudo add-apt-repository -y ppa:apptainer/ppa | |
| sudo apt update | |
| sudo apt install -y apptainer-suid | |
| - name: Get container images for build dependencies | |
| shell: bash | |
| working-directory: devel-tools | |
| run: | | |
| apptainer pull CentOS7-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS7-devel | |
| apptainer pull CentOS9-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel | |
| - name: GCC 4.8, C++11 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 11 | |
| CXX: g++ | |
| CXX_VERSION: 4.8 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: Clang 3.4, C++11 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 11 | |
| CXX: clang++ | |
| CXX_VERSION: 11 | |
| CC: clang | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: Clang 7, C++17 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 17 | |
| CXX: clang++ | |
| CXX_VERSION: 7 | |
| CC: clang | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| scl enable llvm-toolset-${CXX_VERSION} -- \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 8, C++17 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 17 | |
| CXX: g++ | |
| CXX_VERSION: 8 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| scl enable devtoolset-${CXX_VERSION} -- \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 9, C++14 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 14 | |
| CXX: g++ | |
| CXX_VERSION: 9 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| scl enable devtoolset-${CXX_VERSION} -- \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 10, C++17 (CentOS 7) | |
| env: | |
| CXX_STANDARD: 17 | |
| CXX: g++ | |
| CXX_VERSION: 10 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| scl enable devtoolset-${CXX_VERSION} -- \ | |
| cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 11, C++11 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 11 | |
| CXX: g++ | |
| CXX_VERSION: 11 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 11, C++20 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 20 | |
| CXX: g++ | |
| CXX_VERSION: 11 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 12, C++20 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 20 | |
| CXX: g++ | |
| CXX_VERSION: 12 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| scl enable gcc-toolset-12 -- \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: GCC 13, C++20 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 20 | |
| CXX: g++ | |
| CXX_VERSION: 13 | |
| CC: gcc | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| scl enable gcc-toolset-13 -- \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: Clang 16, C++11 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 11 | |
| CXX: clang++ | |
| CXX_VERSION: 16 | |
| CC: clang | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: Clang 16, C++20 (CentOS 9) | |
| env: | |
| CXX_STANDARD: 20 | |
| CXX: clang++ | |
| CXX_VERSION: 16 | |
| CC: clang | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \ | |
| cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake | |
| - name: Keep only one cache besides the one from this job | |
| shell: bash | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| bash ${{ github.workspace }}/devel-tools/cleanup-gh-cache.sh Linux-build-multiple- | |
| build-linux-x86_64-sun: | |
| name: Linux x86_64 (Sun compiler) | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| if: needs.basicchecks.outputs.hassecrets == 'true' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Checkout Sun compiler (Oracle Developer Studio) | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'Colvars/oracle' | |
| ssh-key: ${{ secrets.PULL_ORACLE_DEVELOPER_STUDIO }} | |
| ref: 'master' | |
| path: ${{github.workspace}}/oracle | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Install Apptainer | |
| shell: bash | |
| run: | | |
| sudo add-apt-repository -y ppa:apptainer/ppa | |
| sudo apt update | |
| sudo apt install -y apptainer-suid | |
| - name: Get container images for build dependencies | |
| shell: bash | |
| working-directory: devel-tools | |
| run: | | |
| apptainer pull CentOS7-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS7-devel | |
| - name: Build library with Sun compiler (Oracle Developer Studio) | |
| shell: bash | |
| env: | |
| CC: ${{github.workspace}}/oracle/developerstudio12.6/bin/cc | |
| CXX: ${{github.workspace}}/oracle/developerstudio12.6/bin/CC | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \ | |
| cmake3 -D CMAKE_CXX_STANDARD=11 -P devel-tools/build_test_library.cmake | |
| build-linux-x86_64-intel: | |
| name: Linux x86_64 (Intel oneAPI) | |
| runs-on: ubuntu-latest | |
| needs: basicchecks | |
| env: | |
| CCACHE: ccache | |
| CMAKE_GENERATOR: Ninja | |
| CCACHE_DIR: ${{ github.workspace }}/ccache | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Load compiler ccache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ github.workspace }}/ccache | |
| key: ${{ runner.os }}-build-oneapi-${{ github.sha }} | |
| restore-keys: ${{ runner.os }}-build-oneapi- | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Install Apptainer | |
| shell: bash | |
| run: | | |
| sudo add-apt-repository -y ppa:apptainer/ppa | |
| sudo apt update | |
| sudo apt install -y apptainer-suid | |
| - name: Get container images for build dependencies | |
| shell: bash | |
| working-directory: devel-tools | |
| run: | | |
| apptainer pull CentOS9-devel-oneAPI.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel-oneAPI | |
| - name: Intel oneAPI 2024.2, C++11 | |
| shell: bash | |
| env: | |
| CC: icx | |
| CXX: icpx | |
| CXX_STANDARD: 11 | |
| BASH_ENV: "/etc/profile.d/oneapi.sh" | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \ | |
| bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake" | |
| - name: Intel oneAPI 2024.2, C++14 | |
| shell: bash | |
| env: | |
| CC: icx | |
| CXX: icpx | |
| CXX_STANDARD: 14 | |
| BASH_ENV: "/etc/profile.d/oneapi.sh" | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \ | |
| bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake" | |
| - name: Intel oneAPI 2024.2, C++17 | |
| shell: bash | |
| env: | |
| CC: icx | |
| CXX: icpx | |
| CXX_STANDARD: 17 | |
| BASH_ENV: "/etc/profile.d/oneapi.sh" | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \ | |
| bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake" | |
| - name: Intel oneAPI 2024.2, C++20 | |
| shell: bash | |
| env: | |
| CC: icx | |
| CXX: icpx | |
| CXX_STANDARD: 20 | |
| BASH_ENV: "/etc/profile.d/oneapi.sh" | |
| run: | | |
| apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \ | |
| bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake" | |
| build-windows-x86_64-msvc: | |
| name: Windows x86_64 (MSVC) | |
| runs-on: windows-latest | |
| needs: basicchecks | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Build and test library with CMake | |
| # We need to set CMAKE_SYSTEM_NAME manually in script mode | |
| run: cmake -D CMAKE_SYSTEM_NAME=Windows -P devel-tools/build_test_library.cmake | |
| build-macos-ARM64-clang: | |
| name: macOS ARM64 (AppleClang) | |
| runs-on: macos-latest | |
| needs: basicchecks | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Get small downloadable packages | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'Colvars/build-tools-packages' | |
| ref: 'master' | |
| path: 'devel-tools/packages' | |
| - name: Build and test library with CMake | |
| # We need to set CMAKE_SYSTEM_NAME manually in script mode | |
| run: cmake -D CMAKE_SYSTEM_NAME=Darwin -P devel-tools/build_test_library.cmake |