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: | |
lint: | |
name: Check format | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- name: Checkout modflow6 | |
uses: actions/checkout@v3 | |
- name: Setup Micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: environment.yml | |
cache-environment: true | |
cache-downloads: true | |
- name: Check Fortran source formatting | |
run: python .github/common/fortran_format_check.py | |
build: | |
name: Build | |
runs-on: ubuntu-22.04 | |
defaults: | |
run: | |
shell: bash -l {0} | |
env: | |
FC: gfortran | |
GCC_V: 13 | |
steps: | |
- name: Checkout modflow6 | |
uses: actions/checkout@v3 | |
- name: Setup gfortran ${{ env.GCC_V }} | |
uses: awvwgk/setup-fortran@main | |
with: | |
compiler: gcc | |
version: ${{ env.GCC_V }} | |
- name: Setup Micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: environment.yml | |
cache-environment: true | |
cache-downloads: true | |
- name: Meson setup | |
run: meson setup builddir -Ddebug=false -Dwerror=true | |
- name: Meson compile | |
run: meson compile -C builddir | |
- name: Show build log | |
if: failure() | |
run: cat builddir/meson-logs/meson-log.txt | |
- name: Meson test | |
run: meson test --verbose --no-rebuild -C builddir | |
smoke_test: | |
name: Smoke test | |
runs-on: ubuntu-22.04 | |
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 GNU Fortran ${{ env.GCC_V }} | |
uses: awvwgk/setup-fortran@main | |
with: | |
compiler: gcc | |
version: ${{ env.GCC_V }} | |
- name: Setup Micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: modflow6/environment.yml | |
cache-environment: true | |
cache-downloads: true | |
- name: Build modflow6 | |
working-directory: modflow6 | |
run: | | |
meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
meson install -C builddir | |
- name: Show build log | |
if: failure() | |
working-directory: modflow6 | |
run: cat builddir/meson-logs/meson-log.txt | |
- name: Unit test programs | |
working-directory: modflow6 | |
run: meson test --verbose --no-rebuild -C builddir | |
- name: Update flopy | |
working-directory: modflow6/autotest | |
run: python update_flopy.py | |
- name: Get executables | |
working-directory: modflow6/autotest | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: pytest -v --durations 0 get_exes.py | |
- name: Test programs | |
working-directory: modflow6/autotest | |
run: | | |
if [ "${{ github.ref_name }}" == "master" ]; then | |
pytest -v -n auto --durations 0 -m "not slow and not regression and not developmode" | |
else | |
pytest -v -n auto --durations 0 -S | |
fi | |
netcdf_test: | |
name: netcdf4 testing | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ ubuntu-22.04 ] | |
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 GNU Fortran ${{ env.GCC_V }} | |
uses: awvwgk/setup-fortran@main | |
with: | |
compiler: gcc | |
version: ${{ env.GCC_V }} | |
# - name: Configure environment | |
# if: runner.os == 'Linux' | |
# run: | | |
# echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/linux-gnu/lib/pkgconfig" >> $GITHUB_ENV | |
# echo "$GITHUB_WORKSPACE/petsc/linux-gnu/bin" >> $GITHUB_PATH | |
# - name: Configure PETSc | |
# if: runner.os == 'Linux' | |
# working-directory: petsc | |
# run: | | |
# sudo ./configure PETSC_ARCH=linux-gnu --download-fblaslapack --download-openmpi | |
# sudo make all | |
- name: Install System dependencies | |
shell: bash -l {0} | |
run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev libzstd-dev gfortran | |
# run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev gfortran | |
### | |
# Set Environmental Variables | |
### | |
- name: Install System dependencies | |
shell: bash -l {0} | |
run: | | |
echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
### | |
# Installing libhdf4 and libhdf5 | |
### | |
- name: Cache libhdf5-${{ 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: | | |
#pushd $HOME | |
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 | |
#pushd hdf5-${{ matrix.hdf5 }} | |
cd hdf5-${{ matrix.hdf5 }} | |
./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --enable-hl --with-szlib | |
make -j | |
make install -j | |
#popd | |
- name: Build step 2 libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
if: steps.cache-hdf5.outputs.cache-hit != 'true' | |
run: | | |
if [[ ${{ matrix.netcdf }} != "main" ]]; then | |
git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
#pushd netcdf-c | |
cd netcdf-c | |
autoreconf -if | |
CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
make -j install | |
#popd | |
fi | |
#popd | |
- name: Install System dependencies | |
shell: bash -l {0} | |
run: | | |
echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf}}" >> $GITHUB_ENV | |
echo "HDF5_PLUGIN_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
echo "HDF5_PLUGIN_DIR=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
### | |
# Fetch Cache | |
### | |
# - name: Fetch HDF Cache | |
# id: cache-hdf5 | |
# uses: actions/cache@v2 | |
# with: | |
# path: ~/environments/${{ 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 | |
### | |
# Configure and build | |
### | |
- name: Build netcdf-c if main | |
run: | | |
#pushd $HOME | |
cd $HOME | |
git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
#pushd netcdf-c | |
cd netcdf-c | |
autoreconf -if | |
CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --with-plugin-dir=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib | |
make -j install | |
#popd | |
#popd | |
if: ${{ matrix.netcdf }} == "main" | |
- name: Perform out-of-directory build | |
shell: bash -l {0} | |
run: | | |
#ls -l | |
#ls -l ${CMAKE_PREFIX_PATH} | |
#mkdir build | |
#cd build | |
#LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake $(pwd)/../ -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} | |
#- name: "Create build directory and run CMake" | |
LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake -S . -B build -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} | |
#- name: "Build Project" | |
#LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake --build build --target all --config Release -- -j4 | |
- name: Print Summary | |
shell: bash -l {0} | |
run: | | |
cd build | |
cat libnetcdff.settings | |
- name: Build All | |
shell: bash -l {0} | |
run: | | |
cd build | |
LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j 12 | |
if: ${{ success() }} | |
- name: Setup Micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: modflow6/environment.yml | |
init-shell: >- | |
bash | |
powershell | |
cache-environment: true | |
cache-downloads: true | |
- name: Build modflow6 | |
working-directory: modflow6 | |
run: | | |
meson setup builddir -Ddebug=false --prefix=$(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_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 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: ${{ env.GCC_V }} | |
# - name: Configure PETSc | |
# if: runner.os == 'Windows' | |
# shell: msys2 {0} | |
# working-directory: petsc | |
# run: | | |
# pacman -Syu | |
# pacman -Sy --noconfirm autoconf automake-wrapper bison bsdcpio make git \ | |
# mingw-w64-x86_64-toolchain patch python flex \ | |
# pkg-config pkgfile tar unzip mingw-w64-x86_64-cmake \ | |
# mingw-w64-x86_64-msmpi mingw-w64-x86_64-openblas mingw-w64-x86_64-jq | |
# /usr/bin/python ./configure --with-mpiexec='/C/Program\ Files/Microsoft\ MPI/Bin/mpiexec' --with-shared-libraries=0 | |
# make all | |
- name: Install System dependencies | |
shell: msys2 {0} | |
run: | | |
pacman -Syu | |
#pacman -Sy --noconfirm libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev libzstd-dev | |
pacman -Sy --noconfirm --needed automake autoconf wget curl bzip2 m4 flex bison cmake tar base-devel | |
#pacman -Sy --noconfirm --needed base-devel automake autoconf m4 flex bison cmake base-devel | |
### | |
# Installing libhdf4 and libhdf5 | |
### | |
- name: Cache libhdf5-${{ 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: | | |
#pushd $HOME | |
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 | |
#pushd hdf5-${{ matrix.hdf5 }} | |
cd hdf5-${{ matrix.hdf5 }} | |
./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --enable-hl --with-szlib | |
make -j | |
make install -j | |
#popd | |
- name: Build 2 libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
if: steps.cache-hdf5.outputs.cache-hit != 'true' | |
run: | | |
if [[ ${{ matrix.netcdf }} != "main" ]]; then | |
git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
#pushd netcdf-c | |
cd netcdf-c | |
autoreconf -if | |
CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
make -j install | |
#popd | |
fi | |
#popd | |
# - name: Install System dependencies | |
# shell: bash -l {0} | |
# run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev libzstd-dev | |
### | |
# Set Environmental Variables | |
### | |
### | |
# Fetch Cache | |
### | |
# - name: Fetch HDF Cache | |
# id: cache-hdf5 | |
# uses: actions/cache@v2 | |
# with: | |
# path: ~/environments/${{ 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 | |
### | |
# Configure and build | |
### | |
- name: Build netcdf-c if main | |
run: | | |
#pushd $HOME | |
cd $HOME | |
git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
#pushd netcdf-c | |
cd netcdf-c | |
autoreconf -if | |
CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --with-plugin-dir=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib | |
make -j install | |
#popd | |
#popd | |
if: ${{ matrix.netcdf }} == "main" | |
- name: Perform out-of-directory build | |
shell: bash -l {0} | |
run: | | |
#ls -l | |
#ls -l ${CMAKE_PREFIX_PATH} | |
#mkdir build | |
#cd build | |
#LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake $(pwd)/../ -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} | |
#- name: "Create build directory and run CMake" | |
LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake -S . -B build -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} | |
#- name: "Build Project" | |
#LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake --build build --target all --config Release -- -j4 | |
- name: Print Summary | |
shell: bash -l {0} | |
run: | | |
cd build | |
cat libnetcdff.settings | |
- name: Build All | |
shell: bash -l {0} | |
run: | | |
cd build | |
LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j 12 | |
if: ${{ success() }} | |
- name: Setup Micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: modflow6/environment.yml | |
init-shell: >- | |
bash | |
powershell | |
cache-environment: true | |
cache-downloads: true | |
- name: Build modflow6 | |
working-directory: modflow6 | |
run: | | |
meson setup builddir -Ddebug=false --prefix=$(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: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ macos-12 ] | |
hdf5: [ 1.12.2 ] | |
#netcdf: [ v4.7.4, v4.8.1, v4.9.0, main ] | |
netcdf: [ v4.9.0, main ] | |
defaults: | |
run: | |
shell: bash -l {0} | |
env: | |
FC: gfortran | |
GCC_V: 12 | |
steps: | |
- name: Checkout modflow6 | |
uses: actions/checkout@v3 | |
with: | |
path: modflow6 | |
### | |
# Set Environmental Variables | |
### | |
- run: echo "FCFLAGS=-I${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: | | |
#pushd $HOME | |
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 | |
#pushd hdf5-${{ matrix.hdf5 }} | |
cd hdf5-${{ matrix.hdf5 }} | |
./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --enable-hl --with-szlib | |
make -j | |
make install -j | |
#popd | |
- name: Build 2 libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
if: steps.cache-hdf5.outputs.cache-hit != 'true' | |
run: | | |
git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
#pushd netcdf-c | |
cd netcdf-c | |
autoreconf -if | |
CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
make -j | |
make install -j | |
#popd | |
#popd | |
### | |
# Set Environmental Variables | |
### | |
- run: echo "FCFLAGS=-I${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" >> $GITHUB_ENV | |
- run: echo "LDFLAGS=-L${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}}" >> $GITHUB_ENV | |
- run: brew install automake | |
### | |
# Fetch Cache | |
### | |
# - name: Fetch HDF Cache | |
# id: cache-hdf5 | |
# uses: actions/cache@v2 | |
# with: | |
# path: ~/environments/${{ 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 }}-${{matrix.netcdf}}/lib | |
### | |
# Configure and build | |
### | |
- name: Perform out-of-directory build | |
shell: bash -l {0} | |
run: | | |
#mkdir build | |
#cd build | |
#LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} | |
#- name: "Create build directory and run CMake" | |
LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake -S . -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 | |
- name: Build All | |
shell: bash -l {0} | |
run: | | |
cd build | |
LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j 12 | |
if: ${{ success() }} | |
- name: Run Tests | |
shell: bash -l {0} | |
run: | | |
cd build | |
LD_LIBRARY_PATH=${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() }} | |
test_gfortran: | |
name: Test (gfortran) | |
needs: | |
- lint | |
- build | |
- smoke_test | |
- netcdf_test | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
# compatible combinations from https://github.com/awvwgk/setup-fortran#runner-compatibility | |
include: | |
- {os: ubuntu-20.04, gcc_v: 7, test: false} | |
- {os: ubuntu-20.04, gcc_v: 8, test: false} | |
- {os: ubuntu-20.04, gcc_v: 9, test: false} | |
- {os: ubuntu-20.04, gcc_v: 10, test: false} | |
- {os: ubuntu-20.04, gcc_v: 11, test: false} | |
- {os: ubuntu-22.04, gcc_v: 12, test: false} | |
# only run autotests on latest version on each platform | |
- {os: ubuntu-22.04, gcc_v: 13, test: true} | |
- {os: macos-12, gcc_v: 7, test: false} | |
- {os: macos-12, gcc_v: 8, test: false} | |
- {os: macos-12, gcc_v: 9, test: false} | |
- {os: macos-12, gcc_v: 10, test: false} | |
- {os: macos-12, gcc_v: 11, test: false} | |
- {os: macos-12, gcc_v: 12, test: false} | |
- {os: macos-12, gcc_v: 13, test: true} | |
- {os: windows-2022, gcc_v: 9, test: false} | |
- {os: windows-2022, gcc_v: 10, test: false} | |
- {os: windows-2022, gcc_v: 11, test: false} | |
- {os: windows-2022, gcc_v: 12, test: true} | |
defaults: | |
run: | |
shell: bash -l {0} | |
env: | |
FC: gfortran | |
steps: | |
- name: Checkout modflow6 | |
uses: actions/checkout@v3 | |
with: | |
path: modflow6 | |
- name: Checkout modflow6-testmodels | |
uses: actions/checkout@v3 | |
with: | |
repository: MODFLOW-USGS/modflow6-testmodels | |
path: modflow6-testmodels | |
- name: Checkout modflow6-examples | |
uses: actions/checkout@v3 | |
with: | |
repository: MODFLOW-USGS/modflow6-examples | |
path: modflow6-examples | |
- name: Setup GNU Fortran ${{ matrix.gcc_v }} | |
uses: awvwgk/setup-fortran@main | |
with: | |
compiler: gcc | |
version: ${{ matrix.gcc_v }} | |
- name: Setup Micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: modflow6/environment.yml | |
init-shell: >- | |
bash | |
powershell | |
cache-environment: true | |
cache-downloads: true | |
- name: Build modflow6 | |
working-directory: modflow6 | |
run: | | |
meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
meson install -C builddir | |
- name: Show build log | |
if: failure() | |
working-directory: modflow6 | |
run: cat builddir/meson-logs/meson-log.txt | |
- name: Unit test programs | |
working-directory: modflow6 | |
run: meson test --verbose --no-rebuild -C builddir | |
- name: Update flopy | |
if: matrix.test | |
working-directory: modflow6/autotest | |
run: python update_flopy.py | |
- name: Get executables | |
if: matrix.test | |
working-directory: modflow6/autotest | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: | | |
pytest -v --durations 0 get_exes.py | |
- name: Test modflow6 | |
if: matrix.test | |
working-directory: modflow6/autotest | |
env: | |
REPOS_PATH: ${{ github.workspace }} | |
run: | | |
if [ "${{ github.ref_name }}" == "master" ]; then | |
pytest -v -n auto --durations 0 -m "not large and not developmode" | |
else | |
pytest -v -n auto --durations 0 -m "not large" | |
fi | |
- name: Checkout usgslatex | |
if: matrix.test && runner.os == 'Linux' | |
uses: actions/checkout@v3 | |
with: | |
repository: MODFLOW-USGS/usgslatex | |
path: usgslatex | |
- name: Install TeX Live | |
if: matrix.test && runner.os == 'Linux' | |
run: | | |
sudo apt-get update | |
sudo apt install texlive-science \ | |
texlive-latex-extra \ | |
texlive-font-utils \ | |
texlive-fonts-recommended \ | |
texlive-fonts-extra | |
- name: Install USGS LaTeX style files and Univers font | |
if: matrix.test && runner.os == 'Linux' | |
working-directory: usgslatex/usgsLaTeX | |
run: sudo ./install.sh --all-users | |
- name: Test distribution scripts | |
if: matrix.test | |
working-directory: modflow6/distribution | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: pytest -v --durations 0 | |
test_intel_fortran: | |
name: Test (Intel) | |
needs: | |
- lint | |
- build | |
- smoke_test | |
- netcdf_test | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
include: | |
### ifx | |
## 2022.2.x autotests disabled | |
# - mf5to6 test_evt: failure to converge | |
# - mf6 Keating_[disu_]dev: bad head comparison | |
- {os: ubuntu-22.04, compiler: intel, version: 2022.2.1, test: false} | |
- {os: ubuntu-22.04, compiler: intel, version: 2022.2, test: false} | |
## 2021.1 segfault in meson serial sim test | |
# - {os: ubuntu-22.04, compiler: intel, version: 2022.1, test: false} | |
## 2022.0 & 2021.[1,2,4] segfault at compile time | |
# - {os: ubuntu-22.04, compiler: intel, version: "2022.0", test: false} | |
# - {os: ubuntu-22.04, compiler: intel, version: 2021.4, test: false} | |
# - {os: ubuntu-22.04, compiler: intel, version: 2021.2, test: false} | |
# - {os: ubuntu-22.04, compiler: intel, version: 2021.1, test: false} | |
## ifx not yet supported on macOS | |
# - {os: macos-12, compiler: intel, version: 2023.2, test: true} | |
## 2023.[0,1] fail to compile | |
# - {os: windows-2022, compiler: intel, version: 2023.1, test: false} | |
# - {os: windows-2022, compiler: intel, version: "2023.0", test: false} | |
- {os: windows-2022, compiler: intel, version: 2022.2, test: false} | |
## 2022.1 fail to link | |
# - {os: windows-2022, compiler: intel, version: 2022.1, test: false} | |
### ifort | |
## only autotest latest on each platform | |
- {os: ubuntu-22.04, compiler: intel-classic, version: "2021.10", test: false} | |
- {os: ubuntu-22.04, compiler: intel-classic, version: 2021.9, test: false} | |
- {os: ubuntu-22.04, compiler: intel-classic, version: 2021.8, test: false} | |
- {os: ubuntu-22.04, compiler: intel-classic, version: 2021.7, test: true} | |
- {os: ubuntu-22.04, compiler: intel-classic, version: 2021.6, test: false} | |
- {os: macos-12, compiler: intel-classic, version: "2021.10", test: false} | |
- {os: macos-12, compiler: intel-classic, version: 2021.9, test: false} | |
- {os: macos-12, compiler: intel-classic, version: 2021.8, test: false} | |
- {os: macos-12, compiler: intel-classic, version: 2021.7, test: true} | |
- {os: macos-12, compiler: intel-classic, version: 2021.6, test: false} | |
- {os: windows-2022, compiler: intel-classic, version: "2021.10", test: false} | |
- {os: windows-2022, compiler: intel-classic, version: 2021.9, test: false} | |
- {os: windows-2022, compiler: intel-classic, version: 2021.8, test: false} | |
- {os: windows-2022, compiler: intel-classic, version: 2021.7, test: true} | |
- {os: windows-2022, compiler: intel-classic, version: 2021.6, test: false} | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- name: Checkout modflow6 | |
uses: actions/checkout@v3 | |
with: | |
path: modflow6 | |
- name: Checkout modflow6-testmodels | |
uses: actions/checkout@v3 | |
with: | |
repository: MODFLOW-USGS/modflow6-testmodels | |
path: modflow6-testmodels | |
- 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: Setup Intel Fortran | |
uses: awvwgk/setup-fortran@main | |
with: | |
compiler: ${{ matrix.compiler }} | |
version: ${{ matrix.version }} | |
- name: Update version files | |
working-directory: modflow6/distribution | |
run: python update_version.py | |
- name: Build modflow6 | |
working-directory: modflow6 | |
run: | | |
meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
meson install -C builddir | |
- name: Show build log | |
if: failure() | |
working-directory: modflow6 | |
run: cat builddir/meson-logs/meson-log.txt | |
- name: Unit test programs | |
working-directory: modflow6 | |
run: meson test --verbose --no-rebuild -C builddir | |
- name: Update flopy | |
if: matrix.test | |
working-directory: modflow6/autotest | |
run: python update_flopy.py | |
- name: Get executables | |
if: matrix.test | |
working-directory: modflow6/autotest | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: pytest -v --durations 0 get_exes.py | |
- name: Test programs | |
if: matrix.test | |
working-directory: modflow6/autotest | |
env: | |
REPOS_PATH: ${{ github.workspace }} | |
run: | | |
if [ "${{ github.ref_name }}" == "master" ]; then | |
pytest -v -n auto --durations 0 -m "not large and not developmode" | |
else | |
pytest -v -n auto --durations 0 -m "not large" | |
fi | |
- name: Test scripts | |
if: matrix.test | |
working-directory: modflow6/distribution | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: pytest -v --durations 0 | |
parallel_test: | |
name: Parallel testing | |
needs: | |
- lint | |
- build | |
- smoke_test | |
- netcdf_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@v3 | |
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 | |
init-shell: >- | |
bash | |
powershell | |
cache-environment: true | |
cache-downloads: true | |
- 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" | |