Workflow file for this run
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: 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 | |
| - name: Prepare netcdf build | |
| run: | | |
| mkdir ncc | |
| mkdir ncf | |
| #cd ncf | |
| #wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.zip | |
| #unzip v4.6.0.zip | |
| - 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 | |
| unzip v4.9.0.zip | |
| cd netcdf-c-4.9.0 | |
| #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-static --disable-dap --disable-testsets --disable-examples --disable-utilities | |
| #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/bin:/d/a/modflow6/modflow6/ncc/include:/d/a/modflow6/modflow6/ncf/netcdf-fortran-4.6.0/fortran/.libs:/d/a/modflow6/modflow6/modflow6/bin" >> $GITHUB_ENV | |
| 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.dll | |
| nc-config --all | |
| - name: Download netcdf-f | |
| run: | | |
| mkdir ncf | |
| #cd ncf | |
| #wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.zip | |
| #unzip v4.6.0.zip | |
| - 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" >> $GITHUB_ENV | |
| wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.zip | |
| unzip v4.6.0.zip | |
| cd netcdf-fortran-4.6.0 | |
| #LIBS="$(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 | |
| - 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-4.6.0/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" | |