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linux.yml
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name: ParFlow CI Test
on: [push, pull_request]
jobs:
style-check:
runs-on: ubuntu-22.04
name: Check Style
steps:
- name: Checkout commit
uses: actions/checkout@v4
- name: Package Install
uses: awalsh128/cache-apt-pkgs-action@latest
with:
packages: curl cmake build-essential tcl-dev tk-dev
version: 1.0
execute_install_scripts: true
- name: Cache dependencies
uses: actions/cache@v4
id: cache-parflow-style-dependencies
env:
cache-name: cache-parflow-style-dependencies
cache-parflow-style-hit: ${{steps.cache-parflow-style-dependencies.outputs.cache-hit}}
with:
path: "~/depend"
key: cache-check-style-${{ secrets.CACHE_VERSION }}
- name: Directory Setup
run: |
mkdir -p $HOME/install
# Set necessary vars
PARFLOW_DIR="$HOME/install"
PARFLOW_DEP_DIR="$HOME/depend"
LD_LIBRARY_PATH=${PARFLOW_DEP_DIR}/lib64:${PARFLOW_DEP_DIR}/lib
# Create folders
mkdir -p ${PARFLOW_DIR} ${PARFLOW_DEP_DIR}/{include,lib}
# Verify if paths were correctly set
echo "PARFLOW_DIR=${PARFLOW_DIR}"
echo "PARFLOW_DEP_DIR=${PARFLOW_DEP_DIR}"
echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}"
# Vars pushed to GITHUB_ENV take effect only on the next CI steps.
echo "PARFLOW_DIR=${PARFLOW_DIR}" >> $GITHUB_ENV
echo "PARFLOW_DEP_DIR=${PARFLOW_DEP_DIR}" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" >> $GITHUB_ENV
echo "$HOME/depend/bin" >> $GITHUB_PATH
echo "$PARFLOW_DIR/bin" >> $GITHUB_PATH
- name: Build Uncrustify
env:
CACHE_HIT: ${{steps.cache-parflow-style-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
echo "cache-check-style-${{ secrets.CACHE_VERSION }}" > $HOME/depend/cache-key
curl -L -o uncrustify-0.79.0.tar.gz https://github.com/uncrustify/uncrustify/archive/uncrustify-0.79.0.tar.gz
tar -xf uncrustify-0.79.0.tar.gz
cd uncrustify-uncrustify-0.79.0
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..
make
sudo make -j 2 install
cd ../..
rm -fr uncrustify-uncrustify-0.79.0 uncrustify-0.79.0.tar.gz
fi
- name: CMake Install
env:
CACHE_HIT: ${{steps.cache-parflow-style-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
echo "Installing"
mkdir -p $HOME/depend/{include,lib}
cd $HOME/depend
echo "cache-${{ matrix.config.os }}-${{ matrix.config.backend }}-${{ secrets.CACHE_VERSION }}" > $HOME/depend/cache-key
wget -nv --no-check-certificate https://github.com/Kitware/CMake/releases/download/v3.25.1/cmake-3.25.1-linux-x86_64.tar.gz
tar -xf cmake-3.25.1-linux-x86_64.tar.gz
$HOME/depend/cmake-3.25.1-linux-x86_64/bin/cmake --version
echo "$HOME/depend/cmake-3.25.1-linux-x86_64/bin" >> $GITHUB_PATH
fi
- name: ParFlow CMake Configure
run: |
cmake -Bbuild -DPARFLOW_ENABLE_PYTHON=ON -DCMAKE_INSTALL_PREFIX=$PARFLOW_DIR
- name: ParFlow CMake Build
run: (cd build; make -j 2 install)
- name: Run Uncrustify
run: |
./bin/pfformat --check
build:
name: ${{ matrix.config.name }}
runs-on: ${{ matrix.config.os }}
strategy:
# fail-fast: true
matrix:
config:
- {
name: "Ubuntu 24.04 GCC",
os: ubuntu-24.04,
cudaos: 'ubuntu2404',
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "false",
backend: "none",
amps_layer: mpi1,
netcdf: "true",
memory_manager: "none"
}
- {
name: "Ubuntu 24.04 LLVM",
os: ubuntu-24.04,
cudaos: 'ubuntu2404',
cc: "clang-18", cxx: "clang++-18", fc: "gfortran",
python: "false",
backend: "none",
amps_layer: mpi1,
netcdf: "true",
memory_manager: "none"
}
- {
name: "Ubuntu 22.04 GCC Python",
os: ubuntu-22.04,
cudaos: 'ubuntu2204',
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "true",
backend: "none",
amps_layer: mpi1,
netcdf: "true",
memory_manager: "none"
}
- {
name: "Ubuntu 20.04 GCC Python",
os: ubuntu-20.04,
cudaos: 'ubuntu2004',
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "true",
backend: "none",
amps_layer: mpi1,
netcdf: "false",
memory_manager: "none"
}
- {
name: "Ubuntu 22.04 GCC OMP",
os: ubuntu-22.04,
cudaos: 'ubuntu2204',
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "false",
backend: "omp",
amps_layer: mpi1,
netcdf: "false",
memory_manager: "none"
}
- {
name: "Ubuntu 24.04 LLVM OASIS3-MCT Build",
os: ubuntu-24.04,
cudaos: 'ubuntu2204',
cc: "clang-18", cxx: "clang++-18", fc: "gfortran",
python: "false",
backend: "omp",
amps_layer: oas3,
netcdf: "true",
memory_manager: "none"
}
- {
name: "Ubuntu 22.04 GCC CUDA/RMM Build",
os: ubuntu-22.04,
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "false",
backend: "cuda",
cudaos: 'ubuntu2204',
amps_layer: mpi1,
netcdf: "false",
memory_manager: "rmm"
}
- {
name: "Ubuntu 22.04 GCC CUDA/Umpire Build",
os: ubuntu-22.04,
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "false",
backend: "cuda",
cudaos: 'ubuntu2204',
amps_layer: mpi1,
netcdf: "false",
memory_manager: "umpire"
}
- {
name: "Ubuntu 22.04 GCC Kokkos/RMM Build",
os: ubuntu-22.04,
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "false",
backend: "kokkos",
cudaos: 'ubuntu2204',
amps_layer: mpi1,
netcdf: "false",
memory_manager: "rmm"
}
- {
name: "Ubuntu 22.04 GCC Kokkos/Umpire Build",
os: ubuntu-22.04,
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "false",
backend: "kokkos",
cudaos: 'ubuntu2204',
amps_layer: mpi1,
netcdf: "false",
memory_manager: "umpire"
}
steps:
- uses: actions/checkout@v4
- name: Package Install
uses: awalsh128/cache-apt-pkgs-action@latest
with:
packages: gfortran hdf5-helpers tcl-dev tk-dev libcurl4 libcurl4-gnutls-dev
version: 1.0
execute_install_scripts: true
- name: HDF5 and OpenMPI Install on Ubuntu 22.04
if: matrix.config.os == 'ubuntu-20.04' || matrix.config.os == 'ubuntu-22.04'
run: |
sudo apt-get -qq update
sudo apt -qq install libhdf5-openmpi-103 libhdf5-openmpi-dev
# libhdf5-openmpi-103 has been renamed in Ubuntu 24.04.
- name: HDF5 and OpenMPI Install on Ubuntu 24.04
if: matrix.config.os == 'ubuntu-24.04'
run: |
sudo apt-get -qq update
sudo apt -qq install libhdf5-openmpi-103-1t64 libhdf5-openmpi-dev
- name: LLVM 18.X Install
if: matrix.config.cc == 'clang-18'
run: |
sudo apt -qq install clang-18 libomp-18-dev
- name: Python Package Install
if: matrix.config.python == 'true'
run: |
sudo apt-get -qq update
sudo apt -qq install python3 python3-venv
# Cache dependencies so don't have to rebuild on each test.
# Can flush caches by resetting the CACHE_VERSION secret on GitHub
# settings for the project (using date-timestamp for secret).
- name: Cache dependencies
uses: actions/cache@v4
id: cache-parflow-dependencies
env:
cache-name: cache-parflow-dependencies
cache-parflow-hit: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
with:
path: "~/depend"
key: cache-${{ matrix.config.os }}-${{ matrix.config.backend }}-${{ matrix.config.memory_manager }}-${{ secrets.CACHE_VERSION }}
- name: Directory Setup
run: |
mkdir -p $HOME/install
# Set necessary vars
PARFLOW_DIR="$HOME/install"
PARFLOW_DEP_DIR="$HOME/depend"
LD_LIBRARY_PATH=${PARFLOW_DEP_DIR}/lib64:${PARFLOW_DEP_DIR}/lib
# Create folders
mkdir -p ${PARFLOW_DIR} ${PARFLOW_DEP_DIR}/{include,lib}
# Verify if paths were correctly set
echo "PARFLOW_DIR=${PARFLOW_DIR}"
echo "PARFLOW_DEP_DIR=${PARFLOW_DEP_DIR}"
echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}"
# Vars pushed to GITHUB_ENV take effect only on the next CI steps.
echo "PARFLOW_DIR=${PARFLOW_DIR}" >> $GITHUB_ENV
echo "PARFLOW_DEP_DIR=${PARFLOW_DEP_DIR}" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" >> $GITHUB_ENV
echo "$HOME/depend/bin" >> $GITHUB_PATH
echo "$PARFLOW_DIR/bin" >> $GITHUB_PATH
- name: Configure OpenMPI backend compiler
run: |
export OMPI_CC=${{ matrix.config.cc }}
export OMPI_CXX=${{ matrix.config.cxx }}
export OMPI_FC=${{ matrix.config.fc }}
echo "OMPI_CC=${{ matrix.config.cc }}" >> $GITHUB_ENV
echo "OMPI_CXX=${{ matrix.config.cxx }}" >> $GITHUB_ENV
echo "OMPI_FC=${{ matrix.config.fc }}" >> $GITHUB_ENV
echo " mpicc: $(mpicc --version | head -n 1)"
echo " mpicxx: $(mpicxx --version | head -n 1)"
echo "mpifort: $(mpifort --version | head -n 1)"
- name: CMake Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
echo "Installing CMake v3.25.1"
cd $HOME/depend
echo "cache-${{ matrix.config.os }}-${{ matrix.config.backend }}-${{ secrets.CACHE_VERSION }}" > $HOME/depend/cache-key
wget -nv --no-check-certificate https://github.com/Kitware/CMake/releases/download/v3.25.1/cmake-3.25.1-linux-x86_64.tar.gz
tar -xf cmake-3.25.1-linux-x86_64.tar.gz
$HOME/depend/cmake-3.25.1-linux-x86_64/bin/cmake --version
fi
echo "$HOME/depend/cmake-3.25.1-linux-x86_64/bin" >> $GITHUB_PATH
- name: NVidia Driver Install
if: matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos'
run: |
sudo add-apt-repository -y ppa:graphics-drivers
sudo apt-get update -qq
sudo apt-get install -y nvidia-driver-440
- name: CUDA Install
if: matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos'
run: |
export CUDA_VERSION_MAJOR_MINOR=11.8.0
export CUDA_SHORT=11.8
export CUDA_OS=${{ matrix.config.cudaos }}
./bin/install-cuda.sh
export CUDA_HOME=/usr/local/cuda-${CUDA_SHORT}
echo "CUDA_HOME=${CUDA_HOME}" >> $GITHUB_ENV
export LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${LD_LIBRARY_PATH}
echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" >> $GITHUB_ENV
export LIBRARY_PATH=${CUDA_HOME}/lib64/stubs
echo "LIBRARY_PATH=${LIBRARY_PATH}" >> $GITHUB_ENV
echo "${CUDA_HOME}/bin" >> $GITHUB_PATH
- name: UCX
if: matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos'
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
sudo apt install -qq -y autoconf automake libtool
URL=https://github.com/openucx/ucx/releases/download/v1.13.1/ucx-1.13.1.tar.gz
mkdir ucx
cd ucx
curl -L $URL | tar --strip-components=1 -xz
./contrib/configure-release --with-cuda=$CUDA_HOME --with-java=no --with-go=no --disable-numa --prefix=$PARFLOW_DEP_DIR
make -j 2 install
fi
- name: RMM Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: (matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos') && matrix.config.memory_manager == 'rmm'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
git clone -b branch-0.10 --single-branch --recurse-submodules https://github.com/rapidsai/rmm.git
cd rmm
cmake . -DCMAKE_CXX_FLAGS="-DTHRUST_IGNORE_DEPRECATED_CPP_DIALECT" -DCMAKE_INSTALL_PREFIX=$PARFLOW_DEP_DIR
make -j 2 install
fi
echo "RMM_FLAGS=-DRMM_ROOT=$PARFLOW_DEP_DIR" >> $GITHUB_ENV
- name: Umpire Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: (matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos') && matrix.config.memory_manager == 'umpire'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
git clone --recursive https://github.com/LLNL/Umpire.git
cd Umpire
mkdir build
cd build
cmake ../ -DCMAKE_INSTALL_PREFIX=$PARFLOW_DEP_DIR/Umpire -DENABLE_CUDA=On
make
make install
fi
echo "UMPIRE_FLAGS=-Dumpire_ROOT=$PARFLOW_DEP_DIR/Umpire" >> $GITHUB_ENV
- name: Kokkos Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: matrix.config.backend == 'kokkos'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
URL=https://github.com/kokkos/kokkos/archive/refs/tags/4.2.01.tar.gz
mkdir kokkos
cd kokkos
curl -L $URL | tar --strip-components=1 -xz
mkdir build
cd build
cmake .. -DCMAKE_CXX_COMPILER=$(pwd)/../bin/nvcc_wrapper -DCMAKE_INSTALL_PREFIX=$PARFLOW_DEP_DIR -DKokkos_ENABLE_CUDA=On -DKokkos_ENABLE_CUDA_LAMBDA=On -DKokkos_ENABLE_CUDA_UVM=On -DKokkos_ARCH_VOLTA70=On
make -j 2 install
fi
echo "KOKKOS_FLAGS=-DKOKKOS_ROOT=$PARFLOW_DEP_DIR" >> $GITHUB_ENV
- name: OpenMPI Install for CUDA
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
URL=https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz
mkdir openmpi
cd openmpi
curl -L $URL | tar --strip-components=1 -xz
./configure --with-cuda=$CUDA_HOME --with-ucx=$PARFLOW_DEP_DIR --prefix=$PARFLOW_DEP_DIR
sudo make -j 2 install
cd ..
fi
sudo ldconfig
# Package netcdf is missing features needed by the ParFlow writers, build from source
# netcdf is True when we want to build the PF NetCDF writer. OASIS is using the Fortran interface
# which is currently not built here. This is currently incompatible with the OASIS build which uses the NetCDF packages.
- name: NetCDF Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: matrix.config.netcdf == 'true'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
URL=https://github.com/Unidata/netcdf-c/archive/v4.9.0.tar.gz
mkdir netcdf-c
cd netcdf-c
curl -L $URL | tar --strip-components=1 -xz
CC=mpicc CPPFLAGS=-I/usr/include/hdf5/openmpi LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi ./configure --prefix=$PARFLOW_DEP_DIR
make
make install
cd ..
URL=https://github.com/Unidata/netcdf-fortran/archive/v4.5.4.tar.gz
mkdir netcdf-fortran
cd netcdf-fortran
curl -L $URL | tar --strip-components=1 -xz
CC=mpicc FC=mpifort CPPFLAGS=-I${PARFLOW_DEP_DIR}/include LDFLAGS=-L${PARFLOW_DEP_DIR}/lib ./configure --prefix=${PARFLOW_DEP_DIR}
make
make install
fi
echo "NETCDF_FLAGS=-DNETCDF_DIR=$PARFLOW_DEP_DIR -DNETCDF_Fortran_ROOT=$PARFLOW_DEP_DIR -DPARFLOW_ENABLE_HDF5=TRUE" >> $GITHUB_ENV
- name: OASIS3-MCT Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: matrix.config.amps_layer == 'oas3'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
git clone --depth 1 --branch OASIS3-MCT_5.1 https://gitlab.com/cerfacs/oasis3-mct.git
cd oasis3-mct
export OASIS_ROOT=$(pwd)
cd util/make_dir
echo 'include $(GITHUB_WORKSPACE)/misc/build_scripts/build.oasis3.ubuntu22.04' > make.inc
make realclean static-libs -f TopMakefileOasis3
mv -v ${OASIS_ROOT}/install/include/* ${PARFLOW_DEP_DIR}/include/
mv -v ${OASIS_ROOT}/install/lib/* ${PARFLOW_DEP_DIR}/lib/
fi
- name: SILO Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
URL=https://github.com/LLNL/Silo/archive/refs/tags/4.11.tar.gz
mkdir silo
cd silo
curl -L $URL | tar --strip-components=1 -xz
./configure --disable-silex --disable-hzip --disable-fpzip --prefix=$PARFLOW_DEP_DIR
make -j 2 install
fi
- name: HYPRE Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
URL=https://github.com/hypre-space/hypre/archive/v2.26.0.tar.gz
mkdir hypre
cd hypre
curl -L $URL | tar --strip-components=1 -xz
cd src
./configure --prefix=$PARFLOW_DEP_DIR
make -j 2 install
fi
- name: ParFlow CMake Configure
run: |
cat $HOME/depend/cache-key
export OMPI_MCA_rmaps_base_oversubscribe=1
export OMP_NUM_THREADS=1
${{ matrix.config.cc }} -v
mpicc -v
if [[ "${{ matrix.config.amps_layer }}" == "oas3" ]]; then HAVE_CLM="OFF"; else HAVE_CLM="ON"; fi
CFLAGS="-Wall -Werror -Wno-unused-result -Wno-unused-function -Wno-stringop-overread"
if [[ "${{ matrix.config.cc }}" == "gcc" ]]; then CFLAGS="${CFLAGS} -Wno-stringop-overread"; fi
export CC=mpicc CXX=mpicxx F77=mpif77 FC=mpif90
cmake -Bbuild \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_C_FLAGS=$CFLAGS \
-DPARFLOW_ENABLE_TIMING=TRUE \
-DPARFLOW_AMPS_LAYER=${{ matrix.config.amps_layer }} \
-DMPIEXEC_POSTFLAGS='--oversubscribe' \
-DPARFLOW_ACCELERATOR_BACKEND=${{ matrix.config.backend }} \
-DPARFLOW_AMPS_SEQUENTIAL_IO=true \
-DPARFLOW_HAVE_CLM=${HAVE_CLM} \
-DHYPRE_ROOT=$PARFLOW_DEP_DIR \
-DOAS3_ROOT=$PARFLOW_DEP_DIR \
-DSILO_ROOT=$PARFLOW_DEP_DIR \
-DPARFLOW_ENABLE_PYTHON=${{ matrix.config.python }} \
-DCMAKE_INSTALL_PREFIX=$PARFLOW_DIR \
$NETCDF_FLAGS $KOKKOS_FLAGS $RMM_FLAGS $UMPIRE_FLAGS
- name: ParFlow CMake Build
run: (cd build; make -j 2 install)
# Can't test with GPU since have no GPU hardware on testing nodes, GPU test is build only
- name: ParFlow CTest
if: matrix.config.backend != 'cuda' && matrix.config.backend != 'kokkos'
run: |
export OMPI_MCA_rmaps_base_oversubscribe=1
export OMP_NUM_THREADS=1
(cd build; ctest --output-on-failure)