Workflow file for this run
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| name: MODFLOW 6 continuous integration | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| - ci-diagnose* | |
| - netcdf-ci | |
| paths-ignore: | |
| - '**.md' | |
| - 'doc/**' | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| paths-ignore: | |
| - '**.md' | |
| - 'doc/**' | |
| jobs: | |
| netcdf_test_win: | |
| name: netcdf4 testing | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ windows-2022 ] | |
| #hdf5: [ 1.12.2 ] | |
| #netcdf: [ v4.7.4, v4.8.1, v4.9.0, main ] | |
| #netcdf: [ v4.9.0, main ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| GCC_V: 12 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v3 | |
| with: | |
| path: modflow6 | |
| - name: Setup MSYS2 | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: | | |
| git | |
| make | |
| mingw-w64-x86_64-gcc | |
| mingw-w64-x86_64-python | |
| mingw-w64-x86_64-python-pip | |
| mingw-w64-x86_64-python-pytest | |
| - name: Setup GNU Fortran ${{ env.GCC_V }} | |
| uses: awvwgk/setup-fortran@main | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC_V }} | |
| - name: Install System dependencies | |
| shell: msys2 {0} | |
| run: | | |
| pacman -Syu | |
| #pacman -Sy --noconfirm --needed automake autoconf libxml2 libtool git wget curl bzip2 m4 flex bison cmake tar base-devel | |
| pacman -S --noconfirm --needed base-devel unzip mingw-w64-x86_64-toolchain mingw-w64-x86_64-libtool mingw-w64-x86_64-cmake | |
| - name: Install hdf5 | |
| shell: msys2 {0} | |
| run: | | |
| pacman -U --noconfirm https://repo.msys2.org/mingw/mingw64/mingw-w64-x86_64-hdf5-1.12.2-2-any.pkg.tar.zst | |
| - name: Make netcdf-c | |
| shell: msys2 {0} | |
| run: | | |
| #cd $HOME | |
| mkdir ncc | |
| cd ncc | |
| wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.0.zip | |
| unzip v4.9.0.zip | |
| #cd $HOME/netcdf-c-4.9.0 | |
| cd netcdf-c-4.9.0 | |
| #./configure --enable-static --disable-shared --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets | |
| #LDFLAGS=-no-undefined ./configure --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets --disable-static --enable-shared --prefix=${HOME}/environments/netcdf-c | |
| #LDFLAGS=-no-undefined ./configure --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets --disable-static --enable-shared | |
| #echo "LDFLAGS=-no-undefined" >> $GITHUB_ENV | |
| ./configure --enable-static --disable-shared --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets --prefix=${HOME}/environments/netcdf-c | |
| make install | |
| which nc-config | |
| nc-config --all | |
| - name: Make netcdf-f | |
| shell: msys2 {0} | |
| run: | | |
| #cd $HOME | |
| mkdir ncf | |
| cd ncf | |
| wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.zip | |
| unzip v4.6.0.zip | |
| #cd $HOME/netcdf-fortran-4.6.0 | |
| cd netcdf-fortran-4.6.0 | |
| #LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared | |
| LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared --prefix=${HOME}/environments/netcdf-f | |
| #LIBS="$(nc-config --libs)" ./configure --disable-static --enable-shared | |
| make install | |
| which nf-config | |
| nf-config --all | |
| #echo "PATH=/mingw64/bin:${PATH}" >> $GITHUB_ENV | |
| #echo "PATH=${PATH}:/mingw64/bin" >> $GITHUB_ENV | |
| echo "/mingw64/bin" >> $GITHUB_PATH | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| #find /D/ | grep -i netcdf | |
| #find /C/ | grep -i netcdf | |
| pwd | |
| ls /mingw64/lib/pkgconfig | |
| find .. | grep pc$ | |
| find .. | grep nf-config | |
| find .. | grep nc-config | |
| which nf-config | |
| which nc-config | |
| #/D/a/_temp/msys64/home/runneradmin/netcdf-fortran-4.6.0/nf-config --all | |
| #/D/a/_temp/msys64/home/runneradmin/netcdf-c-4.9.0/nc-config --all | |
| nf-config --all | |
| nc-config --all | |
| nc-config --libdir | |
| #export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:"$(nc-config --libdir)" | |
| echo "0:" | |
| echo $GITHUB_WORKSPACE | |
| echo "1:" | |
| #ls -l $GITHUB_WORKSPACE\mingw64\lib | |
| #ls -l $GITHUB_WORKSPACE\mingw64\lib\pkgconfig | |
| echo "2:" | |
| #ls -l /D/a/_temp/msys64/mingw64/lib/pkgconfig/netcdf-fortran.pc | |
| #cat /D/a/_temp/msys64/mingw64/lib/pkgconfig/netcdf-fortran.pc | |
| echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE\modflow6\ncf\netcdf-fortran-4.6.0\pkgconfig" >> $GITHUB_ENV | |
| #echo "PKG_CONFIG_PATH=/D/a/_temp/msys64/mingw64/lib/pkgconfig" >> $GITHUB_ENV | |
| #echo "PKG_CONFIG_PATH=D:\a\_temp\msys64\mingw64\lib\pkgconfig" >> $GITHUB_ENV | |
| pkg-config --list-all | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| - name: Show Meson logs | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test programs | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| branch="${{ github.ref_name }}" | |
| marker="not large" | |
| markers=$([ "$branch" == "master" ] && echo "$marker and not developmode" || echo "$marker") | |
| pytest -v -n auto --durations 0 -m "$markers" | |
| netcdf_test_mac: | |
| name: netcdf4 testing | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ macos-12 ] | |
| hdf5: [ 1.12.2 ] | |
| #netcdf: [ v4.9.0 ] | |
| netcdf: [ main ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| GCC_V: 13 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v3 | |
| with: | |
| path: modflow6 | |
| - name: Setup gfortran ${{ env.GCC_V }} | |
| uses: awvwgk/setup-fortran@main | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC_V }} | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "FCFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "FFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "CPPFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "DYLD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/bin:${PATH}" >> $GITHUB_ENV | |
| - run: brew install automake libaec | |
| ### | |
| # Installing libhdf4 and libhdf5 | |
| ### | |
| - name: Cache libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| id: cache-hdf5 | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| - name: Build libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| #if: steps.cache-hdf5.outputs.cache-hit != 'true' | |
| run: | | |
| cd $HOME | |
| wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(echo ${{ matrix.hdf5 }} | cut -d. -f 1,2)/hdf5-${{ matrix.hdf5 }}/src/hdf5-${{ matrix.hdf5 }}.tar.bz2 | |
| tar -jxf hdf5-${{ matrix.hdf5 }}.tar.bz2 | |
| cd hdf5-${{ matrix.hdf5 }} | |
| ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --enable-hl --with-szlib | |
| make -j | |
| make install -j | |
| - name: Build 2 libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| #if: steps.cache-hdf5.outputs.cache-hit != 'true' | |
| run: | | |
| cd $HOME | |
| git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
| cd netcdf-c | |
| autoreconf -if | |
| CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| make -j | |
| make install -j | |
| - run: echo "FCFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "FFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf}}" >> $GITHUB_ENV | |
| - run: brew install automake | |
| # - name: Fetch HDF Cache | |
| # id: cache-hdf5 | |
| # uses: actions/cache@v2 | |
| # with: | |
| # path: ~/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| # key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| # - name: Check Cache | |
| # shell: bash -l {0} | |
| # run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} && ls ${HOME}/environments/${{ matrix.hdf5 }}-${{matrix.netcdf}}/lib | |
| - name: Perform out-of-directory build | |
| shell: bash -l {0} | |
| run: | | |
| #mkdir build | |
| #cd build | |
| #LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} | |
| #- name: "Create build directory and run CMake" | |
| cd $HOME | |
| pwd | |
| #find . | grep -i CMakeLists.txt | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake -S netcdf-c -B build -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} | |
| #- name: "Build Project" | |
| #LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake --build build --target all --config Release -- -j4 | |
| # - name: Print Summary | |
| # shell: bash -l {0} | |
| # run: | | |
| # #cd build | |
| # #cat libnetcdff.settings | |
| # find . | grep -i libnetcdff.settings | |
| - name: Build All | |
| shell: bash -l {0} | |
| run: | | |
| cd $HOME | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j 12 | |
| if: ${{ success() }} | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: | | |
| cd $HOME | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest -j 1 . | |
| if: ${{ success() }} | |
| - name: Look at LastTest.log if error | |
| shell: bash -l {0} | |
| run: | | |
| cat /home/runner/work/netcdf-fortran/netcdf-fortran/build/Testing/Temporary/LastTest.log | |
| cd build | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest --rerun-failed --output-on-failure | |
| if: ${{ failure() }} | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| #find / | grep netcdf | |
| #/System/Volumes/Data/Users/runner/netcdf-c/nc-config --all | |
| nf-config --all | |
| nc-config --all | |
| nc-config --libdir | |
| #export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:"$(nc-config --libdir)" | |
| echo "PKG_CONFIG_PATH=$(nc-config --libdir)" >> $GITHUB_ENV | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| - name: Show Meson logs | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test programs | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| branch="${{ github.ref_name }}" | |
| marker="not large" | |
| markers=$([ "$branch" == "master" ] && echo "$marker and not developmode" || echo "$marker") | |
| pytest -v -n auto --durations 0 -m "$markers" | |
| parallel_test: | |
| name: Parallel testing | |
| #needs: | |
| #- lint | |
| #- build | |
| #- smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-12 ] #, windows-2022 ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| GCC_V: 12 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Setup MSYS2 | |
| if: runner.os == 'Windows' | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: | | |
| git | |
| make | |
| mingw-w64-x86_64-gcc | |
| mingw-w64-x86_64-python | |
| mingw-w64-x86_64-python-pip | |
| mingw-w64-x86_64-python-pytest | |
| - name: Setup MPI | |
| if: runner.os == 'Windows' | |
| uses: mpi4py/setup-mpi@v1 | |
| with: | |
| mpi: msmpi | |
| - name: Setup GNU Fortran ${{ env.GCC_V }} | |
| uses: awvwgk/setup-fortran@main | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC_V }} | |
| - name: Cache PETSc | |
| id: cache-petsc | |
| uses: actions/cache@v3 | |
| with: | |
| path: petsc | |
| key: ${{ runner.os }}-petsc | |
| - name: Clone PETSc | |
| if: runner.os != 'Windows' && steps.cache-petsc.outputs.cache-hit != 'true' | |
| run: git clone -b release https://gitlab.com/petsc/petsc.git petsc | |
| - name: Download PETSc | |
| if: runner.os == 'Windows' | |
| run: | | |
| curl https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.18.4.tar.gz -O -J | |
| mkdir petsc | |
| tar -xzf petsc-3.18.4.tar.gz -C petsc --strip-components=1 | |
| - name: Configure environment | |
| if: runner.os == 'Linux' | |
| run: | | |
| echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/linux-gnu/lib/pkgconfig" >> $GITHUB_ENV | |
| echo "$GITHUB_WORKSPACE/petsc/linux-gnu/bin" >> $GITHUB_PATH | |
| - name: Configure environment | |
| if: runner.os == 'macOS' | |
| run: | | |
| echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/lib/pkgconfig" >> $GITHUB_ENV | |
| echo "$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/bin" >> $GITHUB_PATH | |
| - name: Configure PETSc | |
| if: runner.os == 'Linux' | |
| working-directory: petsc | |
| run: | | |
| sudo ./configure PETSC_ARCH=linux-gnu --download-fblaslapack --download-openmpi | |
| sudo make all | |
| - name: Configure PETSc | |
| if: runner.os == 'macOS' | |
| working-directory: petsc | |
| run: | | |
| sudo ./configure PETSC_DIR="$GITHUB_WORKSPACE/petsc" PETSC_ARCH=arch-darwin-gcc-debug --download-fblaslapack --download-openmpi | |
| sudo make all | |
| - name: Configure PETSc | |
| if: runner.os == 'Windows' | |
| shell: msys2 {0} | |
| working-directory: petsc | |
| run: | | |
| pacman -Syu | |
| pacman -Sy --noconfirm autoconf automake-wrapper bison bsdcpio make git \ | |
| mingw-w64-x86_64-toolchain patch python flex \ | |
| pkg-config pkgfile tar unzip mingw-w64-x86_64-cmake \ | |
| mingw-w64-x86_64-msmpi mingw-w64-x86_64-openblas mingw-w64-x86_64-jq | |
| /usr/bin/python ./configure --with-mpiexec='/C/Program\ Files/Microsoft\ MPI/Bin/mpiexec' --with-shared-libraries=0 | |
| make all | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| create-args: >- | |
| netcdf-fortran | |
| #extra-specs: | | |
| # netcdf-fortran | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Edit netcdf-fortran.pc | |
| if: runner.os == 'Linux' | |
| working-directory: modflow6 | |
| run: sed -i "s|libdir=/home/runner/micromamba/envs/modflow6//home/runner/micromamba/envs/modflow6/lib|libdir=/home/runner/micromamba/envs/modflow6/lib|g" /home/runner/micromamba/envs/modflow6/lib/pkgconfig/netcdf-fortran.pc | |
| - name: Edit netcdf-fortran.pc | |
| if: runner.os == 'macOS' | |
| working-directory: modflow6 | |
| run: sed -i '' -e "s|libdir=/Users/runner/micromamba/envs/modflow6//Users/runner/micromamba/envs/modflow6/lib|libdir=/Users/runner/micromamba/envs/modflow6/lib|g" /Users/runner/micromamba/envs/modflow6/lib/pkgconfig/netcdf-fortran.pc | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false -Dparallel=true --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Show Meson logs | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test programs (parallel) | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| branch="${{ github.ref_name }}" | |
| marker="not large" | |
| markers=$([ "$branch" == "master" ] && echo "$marker and not developmode" || echo "$marker") | |
| pytest -v -n auto --parallel --durations 0 -m "$markers" | |