Orca interface cleanup (#181) #1088
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: GFortran CI | |
| # WARNING: When updating the OS version of the Github Actions runner, | |
| # e.g. from Ubuntu 20.04 to 22.04, you need to manually update the cache keys! | |
| # This is because there's no easy way to get the OS version from within this workflow file. | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| env: | |
| # FFLAGS for building ABIN, applicable for most jobs | |
| ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized | |
| ABIN_LDLIBS: --coverage | |
| OPTIMIZED_FFLAGS: -O3 -fopenmp -fimplicit-none -Wall -Wno-integer-division | |
| # NOTE: It would be safer to only pass the secret token to the codecov-upload action, | |
| # but the impact of this token leaking is small anyway. | |
| # NOTE: It appears that even with this token there are issues, | |
| # so for now we let the CI succeed even if the upload fails. | |
| # Reported by many people also at: | |
| # https://github.com/codecov/codecov-action/issues/926 | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| FORCE_COLOR: 1 | |
| jobs: | |
| format: | |
| name: Code format check | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Set up uv | |
| # Install a specific uv version using the installer | |
| run: curl -LsSf https://astral.sh/uv/0.3.0/install.sh | sh | |
| - name: Run formatter (using uv) | |
| # uv ensures automatically that python dependencies are installed | |
| run: | | |
| uv run autoformat.py | |
| f=`git ls-files -m`; if [[ -n $f ]]; then echo -e "ERROR: Detected unformatted files:\n$f"; exit 1; fi | |
| basic_build: | |
| name: Basic build | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| gcc_v: [7, 9, 10] | |
| env: | |
| FC: gfortran | |
| GCC_V: ${{ matrix.gcc_v}} | |
| CODECOV_NAME: ${{format('{0} GCC-{1}', github.job, matrix.gcc_v)}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Install GCC-7 | |
| if: matrix.gcc_v == 7 | |
| run: | | |
| sudo apt install gcc-7 gfortran-7 g++-7 | |
| echo "ABIN_FFLAGS=${ABIN_FFLAGS/-fprofile-abs-path/}" >> $GITHUB_ENV | |
| - name: Set GFortran version | |
| run: | | |
| sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \ | |
| --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V} \ | |
| --slave /usr/bin/gcov gcov /usr/bin/gcov-${GCC_V} | |
| # pFUnit library is used to build and run unit tests | |
| - name: pFUnit build Cache | |
| id: pfunit-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/pfunit/build/installed | |
| # To force a pFUnit rebuild (bust the cache), make a change to install_pfunit.sh | |
| key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }} | |
| - name: Download and build pFUnit | |
| if: steps.pfunit-cache.outputs.cache-hit != 'true' | |
| run: ./dev_scripts/install_pfunit.sh ${HOME}/pfunit | |
| - name: Build ABIN | |
| run: ./configure --pfunit ${HOME}/pfunit/build/installed/ && make | |
| env: | |
| FFLAGS: ${{ env.ABIN_FFLAGS }} | |
| LDLIBS: ${{ env.ABIN_LDLIBS }} | |
| - name: Run Unit tests | |
| run: make unittest | |
| - name: Codecov upload unit tests | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{env.CODECOV_NAME}} | |
| flags: unittests | |
| fail_ci_if_error: false | |
| - name: Run End-to-End tests | |
| run: make e2etest | |
| - name: Codecov upload | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{env.CODECOV_NAME}} | |
| fail_ci_if_error: true | |
| debug_build: | |
| name: Debug build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: fortran-lang/setup-fortran@v1 | |
| id: setup-fortran | |
| with: | |
| compiler: gcc | |
| version: '13' | |
| - name: Build ABIN | |
| run: ./configure && make | |
| env: | |
| FFLAGS: ${{ env.ABIN_FFLAGS }} -fcheck=all -fsanitize=address,undefined,leak | |
| LDLIBS: ${{ env.ABIN_LDLIBS }} -fsanitize=address,undefined,leak | |
| - name: Run End-to-End tests | |
| run: make e2etest | |
| intel_build: | |
| name: Intel build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: fortran-lang/setup-fortran@v1 | |
| id: setup-fortran | |
| with: | |
| compiler: intel # ifx | |
| version: '2024.1' | |
| - name: Build ABIN | |
| run: ./configure && make | |
| env: | |
| FFLAGS: -O0 -qopenmp -warn all,noextern | |
| - name: Run End-to-End tests | |
| run: make e2etest | |
| tcpb_build: | |
| name: TCPB build | |
| runs-on: ubuntu-20.04 | |
| needs: basic_build | |
| env: | |
| FC: gfortran | |
| CODECOV_NAME: ${{format('{0}', github.job)}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Install protocol buffers library | |
| run: sudo apt install protobuf-compiler | |
| - name: TCBP build cache | |
| id: tcpb-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/tcpb-cpp/lib | |
| # To force a rebuild (bust the cache), make a change to install_tcpb.sh | |
| key: ${{ runner.os }}-ubuntu20.04-tcpb-gfortran-default-${{ hashFiles('dev_scripts/install_tcpb.sh') }} | |
| - name: Download and build tcpb_cpp | |
| if: steps.tcpb-cache.outputs.cache-hit != 'true' | |
| run: ./dev_scripts/install_tcpb.sh ${HOME}/tcpb-cpp | |
| - name: Build ABIN | |
| run: ./configure --tcpb ${HOME}/tcpb-cpp/lib && make | |
| env: | |
| FFLAGS: ${{ env.ABIN_FFLAGS }} | |
| LDLIBS: ${{ env.ABIN_LDLIBS }} | |
| - name: Run End-to-End tests | |
| run: make e2etest | |
| - name: Codecov upload | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: tcpb | |
| fail_ci_if_error: true | |
| optimized_build: | |
| name: Optimized build | |
| runs-on: ubuntu-22.04 | |
| needs: basic_build | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| gcc_v: [9, 12] | |
| env: | |
| FC: gfortran | |
| GCC_V: ${{ matrix.gcc_v}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Set GFortran version | |
| run: | | |
| sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \ | |
| --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V} | |
| - name: pFUnit build Cache | |
| id: pfunit-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/pfunit/build/installed | |
| key: ${{ runner.os }}-ubuntu22.04-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }} | |
| - name: Download and build pFUnit | |
| if: steps.pfunit-cache.outputs.cache-hit != 'true' | |
| run: ./dev_scripts/install_pfunit.sh ${HOME}/pfunit | |
| - name: build ABIN | |
| run: ./configure --pfunit ${HOME}/pfunit/build/installed/ && make | |
| env: | |
| FFLAGS: ${{ env.OPTIMIZED_FFLAGS }} | |
| - name: Run Unit tests | |
| run: make unittest | |
| - name: Run End-to-End tests | |
| run: make e2etest | |
| # Here we just take the defaults everywhere, except installing libfftw via apt | |
| # To use FFTW with other Gfortran versions, we would need to build it. | |
| fftw_build: | |
| runs-on: ubuntu-22.04 | |
| name: FFTW build | |
| needs: basic_build | |
| env: | |
| CODECOV_NAME: ${{format('{0}', github.job)}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Install FFTW libraries | |
| run: sudo apt-get install libfftw3-dev | |
| - name: pFUnit build Cache | |
| id: pfunit-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/pfunit/build/installed | |
| key: ${{ runner.os }}-ubuntu22.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} | |
| - name: Download and build pFUnit | |
| if: steps.pfunit-cache.outputs.cache-hit != 'true' | |
| run: ./dev_scripts/install_pfunit.sh ${HOME}/pfunit | |
| - name: Build ABIN | |
| run: ./configure --pfunit ${HOME}/pfunit/build/installed/ --fftw && make | |
| env: | |
| FFLAGS: ${{ env.ABIN_FFLAGS }} | |
| LDLIBS: ${{ env.ABIN_LDLIBS }} | |
| - name: Run Unit tests | |
| run: make unittest | |
| - name: Codecov upload unit tests | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{env.CODECOV_NAME}} | |
| flags: unittests | |
| - name: Run End-to-End tests | |
| run: make e2etest | |
| - name: Codecov upload | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{env.CODECOV_NAME}} | |
| fail_ci_if_error: true | |
| mpich_build: | |
| name: MPICH build | |
| runs-on: ubuntu-20.04 | |
| timeout-minutes: 25 | |
| needs: basic_build | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| gcc_v: [7, 10] | |
| mpich_v: ["3.4.3", "4.0.2"] | |
| env: | |
| # To speed-up MPICH build | |
| CFLAGS: -O0 | |
| GCC_V: ${{ matrix.gcc_v}} | |
| MPICH_V: ${{matrix.mpich_v}} | |
| CODECOV_NAME: ${{format('{0} GCC-{1} MPICH-{2}', github.job, matrix.gcc_v, matrix.mpich_v)}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Install GCC-7 | |
| if: matrix.gcc_v == 7 | |
| run: | | |
| sudo apt install gcc-7 gfortran-7 g++-7 | |
| echo "ABIN_FFLAGS=${ABIN_FFLAGS/-fprofile-abs-path/}" >> $GITHUB_ENV | |
| - name: Set GFortran version | |
| run: | | |
| sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \ | |
| --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V} \ | |
| --slave /usr/bin/gcov gcov /usr/bin/gcov-${GCC_V} | |
| - name: MPICH build Cache | |
| id: mpich-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/mpich/${{ env.MPICH_V }}/install | |
| key: ${{runner.os}}-ubuntu20.04-mpich${{ env.MPICH_V }}-gfortran${{ env.GCC_V }}-${{hashFiles('dev_scripts/install_mpich.sh')}} | |
| - name: Build and Install MPICH | |
| if: steps.mpich-cache.outputs.cache-hit != 'true' | |
| # Without the extra "-fallow-argument-mismatch" FFLAG, configure with GFortran-10 fails with: | |
| # "The Fortran compiler gfortran does not accept programs | |
| # that call the same routine with arguments of different types" | |
| # Unfortunately, previous GCC versions do not have this flag | |
| # so we need to set it conditionally. | |
| # MPICH 4.0 also needs FCFLAGS set. | |
| # We also need to set it for ABIN compilation below. | |
| run: | | |
| if [ $GCC_V -ge 10 ];then export FFLAGS="-fallow-argument-mismatch";export FCFLAGS="-fallow-argument-mismatch";fi && \ | |
| ./dev_scripts/install_mpich.sh ${HOME}/mpich ${MPICH_V} | |
| - name: build ABIN | |
| run: | | |
| if [ $GCC_V -ge 10 ];then export FFLAGS="-fallow-argument-mismatch $FFLAGS";fi && \ | |
| ./configure --mpi ${HOME}/mpich/${MPICH_V}/install && make | |
| env: | |
| FFLAGS: ${{ env.ABIN_FFLAGS }} -g | |
| LDLIBS: ${{ env.ABIN_LDLIBS }} | |
| - name: test ABIN | |
| run: make test | |
| - name: Codecov upload | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{env.CODECOV_NAME}} | |
| fail_ci_if_error: true | |
| openmpi_build: | |
| name: OpenMPI build | |
| runs-on: ubuntu-20.04 | |
| timeout-minutes: 25 | |
| needs: basic_build | |
| strategy: | |
| fail-fast: false | |
| env: | |
| # To speed-up OpenMPI build | |
| CFLAGS: -O0 | |
| CODECOV_NAME: ${{format('{0} OpenMPI-4.0', github.job)}} | |
| OPENMPI_V: "4.1" | |
| OPENMPI_PATCH: "2" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: OpenMPI build cache | |
| id: openmpi-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/openmpi/${{ env.OPENMPI_V }}/install | |
| key: ${{runner.os}}-ubuntu20.04-openmpi${{ env.OPENMPI_V }}-gfortran-default-${{hashFiles('dev_scripts/install_openmpi.sh')}} | |
| - name: Build and Install OpenMPI | |
| if: steps.openmpi-cache.outputs.cache-hit != 'true' | |
| run: ./dev_scripts/install_openmpi.sh ${HOME}/openmpi ${OPENMPI_V} ${OPENMPI_PATCH} | |
| - name: build ABIN | |
| run: ./configure --mpi "${HOME}/openmpi/${OPENMPI_V}/install" && make | |
| env: | |
| FFLAGS: ${{ env.ABIN_FFLAGS }} | |
| LDLIBS: ${{ env.ABIN_LDLIBS }} | |
| - name: test ABIN | |
| run: make test | |
| - name: Codecov upload | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{env.CODECOV_NAME}} | |
| fail_ci_if_error: true | |
| plumed_build: | |
| name: PLUMED build | |
| runs-on: ubuntu-20.04 | |
| needs: basic_build | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| plumed_v: [2.7.6, 2.8.2] | |
| env: | |
| PLUMED_V: ${{ matrix.plumed_v}} | |
| # Speeding up the Plumed build | |
| CFLAGS: -O0 | |
| CXXLAGS: -O0 | |
| CODECOV_NAME: ${{format('{0} PLUMED-{1}', github.job, matrix.plumed_v)}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Plumed build cache | |
| id: plumed-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/plumed/${{ env.PLUMED_V }}/install | |
| key: ${{runner.os}}-ubuntu20.04-plumed${{env.PLUMED_V}}-gcc-default-${{hashFiles('dev_scripts/install_plumed.sh')}} | |
| - name: Build and Install PLUMED | |
| if: steps.plumed-cache.outputs.cache-hit != 'true' | |
| run: ./dev_scripts/install_plumed.sh ${HOME}/plumed ${PLUMED_V} | |
| - name: pFUnit build Cache | |
| id: pfunit-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/pfunit/build/installed | |
| key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} | |
| - name: Download and build pFUnit | |
| if: steps.pfunit-cache.outputs.cache-hit != 'true' | |
| run: ./dev_scripts/install_pfunit.sh ${HOME}/pfunit | |
| - name: build ABIN | |
| run: | | |
| ./configure --plumed "${HOME}/plumed/${PLUMED_V}/install"\ | |
| --pfunit ~/pfunit/build/installed/ &&\ | |
| make | |
| env: | |
| FFLAGS: ${{ env.ABIN_FFLAGS }} | |
| LDLIBS: ${{ env.ABIN_LDLIBS }} | |
| - name: Run Unit tests | |
| run: make unittest | |
| - name: Codecov upload unit tests | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{env.CODECOV_NAME}} | |
| flags: unittests | |
| - name: Run End-to-End tests | |
| run: make e2etest | |
| - name: Codecov upload | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| name: ${{env.CODECOV_NAME}} | |
| fail_ci_if_error: true |