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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 | |
- 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 | |
wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.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-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" | |