fix(gwfuzf): fix array assignment to prevent stack overflow (#1221) #44
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name: MODFLOW 6 continuous integration | |
on: | |
push: | |
branches: | |
- master | |
- develop | |
- ci-diagnose* | |
paths-ignore: | |
- '**.md' | |
- 'doc/**' | |
pull_request: | |
branches: | |
- master | |
- develop | |
paths-ignore: | |
- '**.md' | |
- 'doc/**' | |
jobs: | |
lint: | |
name: Lint (fprettify) | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- name: Checkout modflow6 | |
uses: actions/checkout@v3 | |
- name: Setup Micromamba | |
uses: mamba-org/provision-with-micromamba@main | |
with: | |
cache-downloads: true | |
cache-env: true | |
- name: Check Fortran source formatting | |
run: python .github/common/fortran_format_check.py | |
build: | |
name: Build (gfortran 12) | |
runs-on: ubuntu-22.04 | |
defaults: | |
run: | |
shell: bash -l {0} | |
env: | |
FC: gfortran | |
GCC_V: 12 | |
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/provision-with-micromamba@main | |
with: | |
cache-downloads: true | |
cache-env: true | |
- name: Meson setup | |
run: meson setup builddir -Ddebug=false -Dwerror=true | |
- name: Meson compile | |
run: meson compile -C builddir | |
- name: Meson test | |
run: meson test --verbose --no-rebuild -C builddir | |
smoke_test: | |
name: Smoke test (gfortran 12) | |
runs-on: ubuntu-22.04 | |
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: ${{ env.GCC_V }} | |
- name: Setup Micromamba | |
uses: mamba-org/provision-with-micromamba@main | |
with: | |
environment-file: modflow6/environment.yml | |
cache-downloads: true | |
cache-env: true | |
- name: Build modflow6 | |
working-directory: modflow6 | |
run: | | |
meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
meson install -C builddir | |
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 | |
test_gfortran_latest: | |
name: Test (gfortran 12) | |
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@v3 | |
with: | |
path: modflow6 | |
- name: Checkout modflow6-testmodels | |
uses: actions/checkout@v3 | |
with: | |
repository: MODFLOW-USGS/modflow6-testmodels | |
path: modflow6-testmodels | |
- name: Setup GNU Fortran ${{ env.GCC_V }} | |
uses: awvwgk/setup-fortran@main | |
with: | |
compiler: gcc | |
version: ${{ env.GCC_V }} | |
- name: Setup Micromamba | |
uses: mamba-org/provision-with-micromamba@main | |
with: | |
environment-file: modflow6/environment.yml | |
cache-downloads: true | |
cache-env: true | |
- name: Build modflow6 | |
working-directory: modflow6 | |
run: | | |
meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
meson install -C builddir | |
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 | |
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 | |
working-directory: modflow6/distribution | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: pytest -v --durations 0 | |
test_gfortran_previous: | |
name: Test gfortran (${{ matrix.GCC_V }}, ${{ matrix.os }}) | |
needs: | |
- lint | |
- build | |
- smoke_test | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ ubuntu-20.04 ] | |
GCC_V: [ 7, 8, 9, 10, 11 ] | |
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: Setup GNU Fortran ${{ matrix.GCC_V }} | |
uses: awvwgk/setup-fortran@main | |
with: | |
compiler: gcc | |
version: ${{ matrix.GCC_V }} | |
- name: Setup Micromamba | |
uses: mamba-org/provision-with-micromamba@main | |
with: | |
environment-file: modflow6/environment.yml | |
cache-downloads: true | |
cache-env: true | |
- name: Update flopy | |
working-directory: modflow6/autotest | |
run: python update_flopy.py | |
- name: Build modflow6 | |
working-directory: modflow6 | |
run: | | |
meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
meson install -C builddir | |
meson test --verbose --no-rebuild -C builddir | |
- name: Get executables | |
working-directory: modflow6/autotest | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: pytest -v --durations 0 get_exes.py | |
- name: Test modflow6 | |
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 | |
test_ifort: | |
name: Test (ifort) | |
needs: | |
- lint | |
- build | |
- smoke_test | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ ubuntu-latest, macos-latest, windows-latest ] | |
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/provision-with-micromamba@main | |
with: | |
environment-file: modflow6/environment.yml | |
cache-downloads: true | |
cache-env: true | |
- name: Setup Intel Fortran | |
uses: modflowpy/install-intelfortran-action@v1 | |
- name: Fix Micromamba path (Windows) | |
if: runner.os == 'Windows' | |
shell: pwsh | |
run: | | |
# https://github.com/modflowpy/install-intelfortran-action#conda-scripts | |
$mamba_bin = "C:\Users\runneradmin\micromamba-root\envs\modflow6\Scripts" | |
echo $mamba_bin | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append | |
- name: Update version files | |
working-directory: modflow6/distribution | |
run: python update_version.py | |
- name: Build modflow6 | |
if: runner.os != 'Windows' | |
working-directory: modflow6 | |
run: | | |
meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
meson install -C builddir | |
meson test --verbose --no-rebuild -C builddir | |
- name: Build modflow6 (Windows) | |
if: runner.os == 'Windows' | |
working-directory: modflow6 | |
shell: pwsh | |
run: | | |
meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
meson install -C builddir | |
meson test --verbose --no-rebuild -C builddir | |
- name: Update flopy | |
working-directory: modflow6/autotest | |
run: python update_flopy.py | |
- name: Get executables | |
if: runner.os != 'Windows' | |
working-directory: modflow6/autotest | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: pytest -v --durations 0 get_exes.py | |
- name: Get executables (Windows) | |
if: runner.os == 'Windows' | |
working-directory: modflow6/autotest | |
shell: pwsh | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: pytest -v --durations 0 get_exes.py | |
- name: Test programs | |
if: runner.os != 'Windows' | |
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 programs (Windows) | |
if: runner.os == 'Windows' | |
working-directory: modflow6/autotest | |
shell: pwsh | |
env: | |
REPOS_PATH: ${{ github.workspace }} | |
run: | | |
if ( "${{ github.ref_name }}" -eq "master" ) { | |
pytest -v -n auto --durations 0 -m "not large and not developmode" | |
} else { | |
pytest -v -n auto --durations 0 -m "not large" | |
} | |
- name: Test scripts | |
if: runner.os != 'Windows' | |
working-directory: modflow6/distribution | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: pytest -v --durations 0 | |
- name: Test scripts (Windows) | |
if: runner.os == 'Windows' | |
working-directory: modflow6/distribution | |
shell: pwsh | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |
run: pytest -v --durations 0 | |
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@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/provision-with-micromamba@main | |
with: | |
environment-file: modflow6/environment.yml | |
cache-downloads: true | |
cache-env: 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: ${{ github.workspace }} | |
run: | | |
if [ "${{ github.ref_name }}" == "master" ]; then | |
pytest -v -n auto --parallel --durations 0 -m "not large and not developmode" | |
else | |
pytest -v -n auto --parallel --durations 0 -m "not large" | |
fi | |