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| name: MODFLOW 6 continuous integration | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| - ci-diagnose* | |
| - ncci | |
| 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 -S --noconfirm --needed base-devel unzip mingw-w64-x86_64-toolchain mingw-w64-x86_64-libtool mingw-w64-x86_64-cmake | |
| which cygpath | |
| - name: Prepare netcdf build | |
| run: | | |
| mkdir ncc | |
| mkdir ncf | |
| - name: Install hdf5 and netcdf-c | |
| shell: msys2 {0} | |
| working-directory: ncc | |
| run: | | |
| pacman -U --noconfirm https://repo.msys2.org/mingw/mingw64/mingw-w64-x86_64-hdf5-1.12.2-2-any.pkg.tar.zst | |
| #pacman -S --noconfirm --needed mingw-w64-x86_64-netcdf | |
| echo "PWD:" | |
| pwd | |
| echo "LD_LIBRARY_PATH:" | |
| echo $LD_LIBRARY_PATH | |
| echo "PATH:" | |
| echo $PATH | |
| echo "LIBS:" | |
| echo $LIBS | |
| #wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.0.zip | |
| wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.zip | |
| #wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.8.1.zip | |
| unzip v4.9.2.zip | |
| cd netcdf-c-4.9.2 | |
| #LDFLAGS="-Wl,-no-undefined" ./configure --enable-shared --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets | |
| LDFLAGS="-Wl,-no-undefined,--export-all-symbols" ./configure --enable-shared --disable-dap --disable-testsets --disable-examples --disable-libxml2 | |
| #LDFLAGS="-Wl,-no-undefined" ./configure --enable-shared --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets | |
| echo "LD_LIBRARY_PATH=/d/a/_temp/msys64/mingw64/lib" >> $GITHUB_ENV | |
| echo "PATH=/d/a/_temp/msys64/mingw64/usr/bin:/d/a/_temp/msys64/mingw64/bin:/d/a/modflow6/modflow6/ncc/include:/d/a/modflow6/modflow6/ncf/netcdf-fortran-4.6.1/fortran/.libs:/d/a/modflow6/modflow6/modflow6/bin" >> $GITHUB_ENV | |
| which cygpath | |
| sed -i.bak -e "s/\(allow_undefined=\)yes/\1no/" libtool | |
| echo "grep:" | |
| grep -nrIl nc_inq_libvers . | |
| echo "ls -al:" | |
| ls -la | |
| echo "find:" | |
| find . | grep netcdf | |
| echo "find derror:" | |
| find . | grep -i derror | |
| echo "find ncdispatch.h:" | |
| find . | grep -i ncdispatch.h | |
| make install | |
| which ldd | |
| ls /mingw64/bin | grep netcdf | |
| ldd /mingw64/bin/libnetcdf-19.dll | |
| nc-config --all | |
| - name: Make netcdf-f | |
| shell: msys2 {0} | |
| working-directory: ncf | |
| run: | | |
| #echo "LD_LIBRARY_PATH=/d/a/_temp/msys64/mingw64/lib" >> $GITHUB_ENV | |
| #echo "PATH=/d/a/_temp/msys64/mingw64/bin:/d/a/modflow6/modflow6/modflow6/bin:/d/a/modflow6/modflow6/ncf/netcdf-fortran-4.6.0/fortran/.libs" >> $GITHUB_ENV | |
| #wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.zip | |
| wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.1.zip | |
| unzip v4.6.1.zip | |
| cd netcdf-fortran-4.6.1 | |
| #LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared --prefix=/mingw64 | |
| #LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared | |
| LDFLAGS="-Wl,-no-undefined" LIBS="$(nc-config --libs)" ./configure --enable-shared | |
| sed -i.bak -e "s/\(allow_undefined=\)yes/\1no/" libtool | |
| make install | |
| #ldconfig | |
| ls fortran/.libs | |
| ls -l | |
| find . | grep -i libnetcdff | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| create-args: >- | |
| pkg-config | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| log-level: 'trace' | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| #echo "LD_LIBRARY_PATH=/d/a/_temp/msys64/mingw64/lib" >> $GITHUB_ENV | |
| #echo "PATH=/d/a/_temp/msys64/mingw64/bin" >> $GITHUB_ENV | |
| #echo "PATH=/d/a/_temp/msys64/mingw64/bin:/d/a/modflow6/modflow6/modflow6/bin:/d/a/modflow6/modflow6/ncf/netcdf-fortran-4.6.0/fortran/.libs" >> $GITHUB_ENV | |
| echo "PWD:" | |
| pwd | |
| echo "ls cmake/netCDF:" | |
| ls -l /d/a/_temp/msys64/mingw64/lib/cmake/netCDF | |
| echo "find netcdf:" | |
| find /d/a/_temp/msys64/mingw64 | grep -i netcdf | |
| echo "find netcdf2:" | |
| find ../ncf/netcdf-fortran-4.6.1/fortran/.libs | grep -i netcdf | |
| which nf-config | |
| which nc-config | |
| #nf-config --all | |
| #nc-config --all | |
| #nc-config --libdir | |
| echo "0:" | |
| echo $GITHUB_WORKSPACE | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| #echo "PATH=/d/a/modflow6/modflow6/modflow6/bin" >> $GITHUB_ENV | |
| #ln -sf /d/a/_temp/msys64/mingw64/bin/libnetcdf.dll bin/libnetcdf.dll | |
| - name: Show Meson logs | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Check exe | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| which dumpbin | |
| which dumpbin.exe | |
| echo "LD_LIBRARY_PATH:" | |
| echo $LD_LIBRARY_PATH | |
| echo "PATH:" | |
| echo $PATH | |
| ls -l /d/a/modflow6/modflow6/modflow6/bin | |
| echo "FILE:" | |
| file /d/a/modflow6/modflow6/modflow6/bin/mf6.exe | |
| echo "LDD1:" | |
| ldd /d/a/modflow6/modflow6/modflow6/bin/mf6.exe | |
| #echo "LDD hdf:" | |
| #ldd /d/a/_temp/msys64/mingw64/bin | |
| echo "LDD nc:" | |
| ldd /d/a/_temp/msys64/mingw64/bin/libnetcdf.dll | |
| echo "LDD ncf:" | |
| ldd /d/a/_temp/msys64/mingw64/bin/libnetcdff-7.dll | |
| #/d/a/modflow6/modflow6/modflow6/bin/mf6.exe --version | |
| which mf6.exe | |
| #mf6.exe | |
| mf6.exe --version | |
| - 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 nc4 program | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| pytest -v test_gwf_chd01.py -s --keep temp | |
| cat temp/test_mf6model[chd01]0/mfsim.lst | grep -i netcdf | |
| - 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 | |
| pkg-config | |
| 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: Check exe | |
| if: runner.os == 'Linux' | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| echo "LD_LIBRARY_PATH:" | |
| echo $LD_LIBRARY_PATH | |
| echo "PATH:" | |
| echo $PATH | |
| ls -l /home/runner/work/modflow6/modflow6/modflow6/bin | |
| echo "FILE:" | |
| file /home/runner/work/modflow6/modflow6/modflow6/bin/mf6 | |
| echo "LDD1:" | |
| ldd /home/runner/work/modflow6/modflow6/modflow6/bin/mf6 | |
| #/d/a/modflow6/modflow6/modflow6/bin/mf6 --version | |
| #which mf6 | |
| #mf6 | |
| /home/runner/work/modflow6/modflow6/modflow6/bin/mf6 --version | |
| - name: Check exe | |
| if: runner.os == 'macOS' | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| echo "LD_LIBRARY_PATH:" | |
| echo $LD_LIBRARY_PATH | |
| echo "PATH:" | |
| echo $PATH | |
| ls -l /Users/runner/work/modflow6/modflow6/modflow6/bin | |
| echo "FILE:" | |
| file /Users/runner/work/modflow6/modflow6/modflow6/bin/mf6 | |
| echo "LDD1:" | |
| ldd /Users/runner/work/modflow6/modflow6/modflow6/bin/mf6 | |
| #/d/a/modflow6/modflow6/modflow6/bin/mf6 --version | |
| #which mf6 | |
| #mf6 | |
| /Users/runner/work/modflow6/modflow6/modflow6/bin/mf6 --version | |
| - 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 nc4 program | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| pytest -v test_gwf_chd01.py -s --keep temp | |
| ls -l temp | |
| ls -l temp/test_mf6model[chd01]0 | |
| cat temp/test_mf6model[chd01]0/mfsim.lst | grep -i netcdf | |
| #ls -l /tmp | |
| - 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" | |