Correcting NaI conversion units for NAC #1095
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| 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 |