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ci2.yml
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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:
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 -Sy --noconfirm --needed automake autoconf libxml2 libtool git wget curl bzip2 m4 flex bison cmake tar base-devel
pacman -S --noconfirm --needed base-devel unzip mingw-w64-x86_64-toolchain mingw-w64-x86_64-libtool mingw-w64-x86_64-cmake
- name: Install hdf5
shell: msys2 {0}
run: |
pacman -U --noconfirm https://repo.msys2.org/mingw/mingw64/mingw-w64-x86_64-hdf5-1.12.2-2-any.pkg.tar.zst
- name: Make netcdf-c
shell: msys2 {0}
run: |
#cd $HOME
mkdir ncc
cd ncc
wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.0.zip
unzip v4.9.0.zip
#cd $HOME/netcdf-c-4.9.0
cd netcdf-c-4.9.0
#./configure --enable-static --disable-shared --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets
#LDFLAGS=-no-undefined ./configure --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets --disable-static --enable-shared --prefix=${HOME}/environments/netcdf-c
#LDFLAGS=-no-undefined ./configure --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets --disable-static --enable-shared
#echo "LDFLAGS=-no-undefined" >> $GITHUB_ENV
#./configure --enable-static --disable-shared --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets --prefix=${HOME}/environments/netcdf-c
#./configure --enable-static --disable-shared --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets --prefix=/mingw64
./configure --enable-static --disable-shared --disable-dap --disable-examples --disable-v2 --disable-utilities --disable-testsets --prefix=/c/Users/runneradmin/micromamba/envs/modflow6/Library/mingw-w64
make install
#echo "PATH=${HOME}/environments/netcdf-c/bin:${PATH}" >> $GITHUB_ENV
#echo "LD_LIBRARY_PATH=${HOME}/environments/netcdf-c/lib:${LD_LIBRARY_PATH}" >> $GITHUB_ENV
#echo "PKG_CONFIG_PATH=D:${HOME}/environments/netcdf-c/lib:${PKG_CONFIG_PATH}" >> $GITHUB_ENV
echo "PATH=/c/Users/runneradmin/micromamba/envs/modflow6/Library/mingw-w64/bin:${PATH}" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=/c/Users/runneradmin/micromamba/envs/modflow6/Library/mingw-w64/lib" >> $GITHUB_ENV
echo "PKG_CONFIG_PATH=/c/Users/runneradmin/micromamba/envs/modflow6/Library/mingw-w64/lib" >> $GITHUB_ENV
echo "CPPFLAGS=-I$(pwd)/include" >> $GITHUB_ENV
echo "CFLAGS=-I$(pwd)/include" >> $GITHUB_ENV
echo "LDFLAGS=-L$(pwd)/lib" >> $GITHUB_ENV
#ls ${HOME}/environments/netcdf-c/lib
#ls ${HOME}/environments/netcdf-c/lib/pkgconfig
#ls ${HOME}/environments/netcdf-c/bin
ls /c/Users/runneradmin/micromamba/envs/modflow6/Library/mingw-w64
ls /c/Users/runneradmin/micromamba/envs/modflow6/Library/mingw-w64/bin
ls /c/Users/runneradmin/micromamba/envs/modflow6/Library/mingw-w64/lib
#which nc-config
#nc-config --all
#${HOME}/environments/netcdf-c/bin/nc-config --all
#echo $PATH
#echo $LD_LIBRARY_PATH
#echo $PKG_CONFIG_PATH
- name: Make netcdf-f
shell: msys2 {0}
run: |
#cd $HOME
mkdir ncf
cd ncf
wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.zip
unzip v4.6.0.zip
#cd $HOME/netcdf-fortran-4.6.0
cd netcdf-fortran-4.6.0
#LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared
#LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared --prefix=${HOME}/environments/netcdf-f
#LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared --prefix=/mingw64
LIBS="$(nc-config --libs)" ./configure --enable-static --disable-shared --prefix=/c/Users/runneradmin/micromamba/envs/modflow6/Library/mingw-w64
#LIBS="$(nc-config --libs)" ./configure --disable-static --enable-shared
make install
#echo "PATH=${HOME}/environments/netcdf-f/bin:${PATH}" >> $GITHUB_ENV
#echo "LD_LIBRARY_PATH=${HOME}/environments/netcdf-f/lib:${LD_LIBRARY_PATH}" >> $GITHUB_ENV
#echo "PKG_CONFIG_PATH=D:${HOME}/environments/netcdf-f/lib:${PKG_CONFIG_PATH}" >> $GITHUB_ENV
#ls ${HOME}/environments/netcdf-f/lib
#ls ${HOME}/environments/netcdf-f/lib/pkgconfig
#ls ${HOME}/environments/netcdf-f/bin
#which nc-config
#${HOME}/environments/netcdf-f/bin/nf-config --all
which nf-config
nf-config --all
#echo "PATH=/mingw64/bin:${PATH}" >> $GITHUB_ENV
#echo "PATH=${PATH}:/mingw64/bin" >> $GITHUB_ENV
#echo "/mingw64/bin" >> $GITHUB_PATH
#echo $PATH
#echo $LD_LIBRARY_PATH
#echo $PKG_CONFIG_PATH
- 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: |
#find /D/ | grep -i netcdf
#find /C/ | grep -i netcdf
pwd
echo "C"
ls -l /c/
ls -l /c/mingw64
ls -l /c/mingw64/bin
ls -l /c/mingw64/lib
echo "D"
ls -l /d/
ls -l /d/mingw64
ls -l /d/mingw64/bin
ls -l /d/mingw64/lib
echo "GHWRK"
echo $GITHUB_WORKSPACE
ls $GITHUB_WORKSPACE
which nf-config
which nc-config
#/D/a/_temp/msys64/home/runneradmin/netcdf-fortran-4.6.0/nf-config --all
#/D/a/_temp/msys64/home/runneradmin/netcdf-c-4.9.0/nc-config --all
nf-config --all
nc-config --all
nc-config --libdir
#export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:"$(nc-config --libdir)"
echo "0:"
echo $GITHUB_WORKSPACE
echo "1:"
#ls -l $GITHUB_WORKSPACE\mingw64\lib
#ls -l $GITHUB_WORKSPACE\mingw64\lib\pkgconfig
echo "2:"
#ls -l /D/a/_temp/msys64/mingw64/lib/pkgconfig/netcdf-fortran.pc
#cat /D/a/_temp/msys64/mingw64/lib/pkgconfig/netcdf-fortran.pc
#echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE\modflow6\ncf\netcdf-fortran-4.6.0\pkgconfig" >> $GITHUB_ENV
#echo "PKG_CONFIG_PATH=/D/a/_temp/msys64/mingw64/lib/pkgconfig" >> $GITHUB_ENV
#echo "PKG_CONFIG_PATH=D:\a\_temp\msys64\mingw64\lib\pkgconfig" >> $GITHUB_ENV
pkg-config --list-all
meson setup builddir -Ddebug=false --prefix=$(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: [ v4.9.0 ]
netcdf: [ main ]
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 gfortran ${{ env.GCC_V }}
uses: awvwgk/setup-fortran@main
with:
compiler: gcc
version: ${{ env.GCC_V }}
###
# Set Environmental Variables
###
- run: echo "FCFLAGS=-I${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: |
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
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
- name: Build 2 libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }}
#if: steps.cache-hdf5.outputs.cache-hit != 'true'
run: |
cd $HOME
git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c
cd netcdf-c
autoreconf -if
CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}
make -j
make install -j
- run: echo "FCFLAGS=-I${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}}" >> $GITHUB_ENV
- run: brew install automake
# - name: Fetch HDF Cache
# id: cache-hdf5
# uses: actions/cache@v2
# with:
# path: ~/environments/${{ 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 }}-${{matrix.netcdf}}/lib
- name: Perform out-of-directory build
shell: bash -l {0}
run: |
#mkdir build
#cd build
#LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH}
#- name: "Create build directory and run CMake"
cd $HOME
pwd
#find . | grep -i CMakeLists.txt
LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake -S netcdf-c -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
# find . | grep -i libnetcdff.settings
- name: Build All
shell: bash -l {0}
run: |
cd $HOME
cd build
LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j 12
if: ${{ success() }}
- name: Run Tests
shell: bash -l {0}
run: |
cd $HOME
cd build
LD_LIBRARY_PATH=${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: ${{ failure() }}
- name: Setup Micromamba
uses: mamba-org/setup-micromamba@v1
with:
environment-file: modflow6/environment.yml
init-shell: >-
bash
powershell
cache-environment: true
cache-downloads: true
- name: Build modflow6
working-directory: modflow6
run: |
#find / | grep netcdf
#/System/Volumes/Data/Users/runner/netcdf-c/nc-config --all
nf-config --all
nc-config --all
nc-config --libdir
#export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:"$(nc-config --libdir)"
echo "PKG_CONFIG_PATH=$(nc-config --libdir)" >> $GITHUB_ENV
meson setup builddir -Ddebug=false --prefix=$(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"
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
#extra-specs: |
# netcdf-fortran
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: 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"