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name: CD
on: [push, workflow_dispatch]
env:
REGISTRY: ghcr.io
IMAGE_NAME: ${{ github.repository }}
jobs:
build-and-push-image:
runs-on: ubuntu-latest
permissions:
contents: read
packages: write
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Log in to the Container registry
uses: docker/login-action@v3
with:
registry: ${{ env.REGISTRY }}
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Extract metadata (tags, labels) for Docker
id: meta
uses: docker/metadata-action@v5
with:
images: "${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}"
- name: Build and push Docker image
uses: docker/build-push-action@v5
with:
context: .
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
native-build:
name:
native-build-${{ matrix.platform }}
strategy:
fail-fast: false
matrix:
platform: [macos-13, windows-latest, ubuntu-latest, macos-14]
runs-on: ${{ matrix.platform }}
steps:
- name: checkout vcell-solvers repo
uses: actions/checkout@v4
- name: Install Intel MacOS dependencies
if: matrix.platform == 'macos-13'
shell: bash
run: |
brew install boost
brew install hdf5
brew install ninja
brew install llvm
echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
source /Users/runner/.bash_profile
ln -s $(which gfortran-14) /usr/local/bin/gfortran
gcc --version
gfortran --version
cmake --version
brew info boost
brew info hdf5
- name: Install ARM MacOS dependencies
if: matrix.platform == 'macos-14'
shell: bash
run: |
brew install boost
brew install hdf5
brew install ninja
brew install llvm
echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
ln -s /opt/homebrew/bin/gfortran-14 /usr/local/bin/gfortran
gcc --version
gfortran --version
cmake --version
brew info boost
brew info hdf5
- name: Build Macos ARM
if: matrix.platform == 'macos-14'
run: |
platform=macos
echo "working dir is $PWD"
mkdir build
cd build
export PATH="/opt/homebrew/opt/llvm/bin:$PATH"
cmake \
-G Ninja \
-DCMAKE_C_COMPILER=/opt/homebrew/opt/llvm/bin/clang \
-DCMAKE_CXX_COMPILER=/opt/homebrew/opt/llvm/bin/clang++ \
-DOPTION_MINGW=ON \
-DOPTION_TARGET_MESSAGING=OFF \
-DOPTION_TARGET_PARALLEL=OFF \
-DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
-DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
-DOPTION_TARGET_SMOLDYN_SOLVER=ON \
-DOPTION_TARGET_FV_SOLVER=ON \
-DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
-DOPTION_TARGET_NFSIM_SOLVER=ON \
-DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=ON \
-DOPTION_TARGET_SUNDIALS_SOLVER=ON \
-DOPTION_TARGET_HY3S_SOLVERS=OFF \
-B . -S ..
ninja
- name: Build Macos Intel
if: matrix.platform == 'macos-13'
run: |
platform=macos
echo "working dir is $PWD"
mkdir build
cd build
export PATH="/usr/local/opt/llvm/bin:$PATH"
cmake \
-G Ninja \
-DCMAKE_C_COMPILER=/usr/local/opt/llvm/bin/clang \
-DCMAKE_CXX_COMPILER=/usr/local/opt/llvm/bin/clang++ \
-DOPTION_MINGW=ON \
-DOPTION_TARGET_MESSAGING=OFF \
-DOPTION_TARGET_PARALLEL=OFF \
-DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
-DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
-DOPTION_TARGET_SMOLDYN_SOLVER=ON \
-DOPTION_TARGET_FV_SOLVER=ON \
-DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
-DOPTION_TARGET_NFSIM_SOLVER=ON \
-DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=ON \
-DOPTION_TARGET_SUNDIALS_SOLVER=ON \
-DOPTION_TARGET_HY3S_SOLVERS=OFF \
-B . -S ..
ninja
- name: Test Macos
if: matrix.platform == 'macos-13' || matrix.platform == 'macos-14'
run: |
platform=macos
echo "working dir is $PWD"
cd build
ctest -VV
echo "------ running FiniteVolume_x64 ------"
./bin/FiniteVolume_x64 || true
echo
echo "------ running NFsim_x64 ------"
./bin/NFsim_x64 || true
echo "------ running SundialsSolverStandalone_x64 ------"
./bin/SundialsSolverStandalone_x64 || true
echo "------ running VCellStoch_x64 ------"
./bin/VCellStoch_x64 || true
echo "------ running smoldyn_x64 ------"
./bin/smoldyn_x64 || true
echo "------ running testzip ------"
./bin/testzip || true
echo "------ running ziptool ------"
./bin/ziptool || true
# - name: Setup tmate session
# uses: mxschmitt/action-tmate@v3
# with:
# limit-access-to-actor: false
# - name: Install Windows Dependencies
# if: matrix.platform == 'windows-latest'
# uses: msys2/setup-msys2@v2
# with:
# msystem: CLANG64
# update: true
# install: >
# zip
# git
# mingw-w64-clang-x86_64-curl
# mingw-w64-clang-x86_64-toolchain
# mingw-w64-clang-x86_64-flang
# mingw-w64-clang-x86_64-cmake
# mingw-w64-clang-x86_64-boost
# mingw-w64-clang-x86_64-hdf5
# mingw-w64-clang-x86_64-libzip
# mingw-w64-clang-x86_64-netcdf
# mingw-w64-clang-x86_64-zlib
# mingw-w64-clang-x86_64-libaec
#
## - name: Setup tmate session
## uses: mxschmitt/action-tmate@v3
## with:
## limit-access-to-actor: false
#
# - name: Build Windows
# if: matrix.platform == 'windows-latest'
# shell: msys2 {0}
# run: |
# platform=windows
# echo "working dir is $PWD"
#
# mkdir build
# cd build
#
# export PATH="/c/Program\ Files/LLVM/bin:$PATH"
#
# cmake \
# -G Ninja \
# -DCMAKE_C_COMPILER="clang.exe" \
# -DCMAKE_CXX_COMPILER="clang++.exe" \
# -DOPTION_TARGET_MESSAGING=OFF \
# -DOPTION_TARGET_PARALLEL=OFF \
# -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
# -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
# -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
# -DOPTION_TARGET_FV_SOLVER=ON \
# -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
# -DOPTION_TARGET_NFSIM_SOLVER=ON \
# -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
# -DOPTION_TARGET_SUNDIALS_SOLVER=ON \
# -DOPTION_TARGET_HY3S_SOLVERS=OFF \
# -DOPTION_TARGET_DOCS=OFF \
# -B . -S ..
#
# ninja -j 1
#
# ctest -VV || true
#
# echo "------ running FiniteVolume_x64 ------"
# ./bin/FiniteVolume_x64 || true
# echo
# echo "------ running NFsim_x64 ------"
# ./bin/NFsim_x64 || true
# echo "------ running SundialsSolverStandalone_x64 ------"
# ./bin/SundialsSolverStandalone_x64 || true
# echo "------ running VCellStoch_x64 ------"
# ./bin/VCellStoch_x64 || true
# echo "------ running smoldyn_x64 ------"
# ./bin/smoldyn_x64 || true
# echo "------ running testzip ------"
# ./bin/testzip || true
# echo "------ running ziptool ------"
# ./bin/ziptool || true
#
#
# - name: Test Windows
# if: matrix.platform == 'windows-latest'
# shell: msys2 {0}
# run: |
# export platform=windows
# echo "working dir is $PWD"
#
# cd build
#
# export PATH="/c/Program\ Files/LLVM/bin:$PATH"
#
# ctest -VV
#
# echo "------ running FiniteVolume_x64 ------"
# ./bin/FiniteVolume_x64 || true
# echo
# echo "------ running NFsim_x64 ------"
# ./bin/NFsim_x64 || true
# echo "------ running SundialsSolverStandalone_x64 ------"
# ./bin/SundialsSolverStandalone_x64 || true
# echo "------ running VCellStoch_x64 ------"
# ./bin/VCellStoch_x64 || true
# echo "------ running smoldyn_x64 ------"
# ./bin/smoldyn_x64 || true
# echo "------ running testzip ------"
# ./bin/testzip || true
# echo "------ running ziptool ------"
# ./bin/ziptool || true
# - name: Setup Visual Studio build tools
# if: matrix.platform == 'windows-latest'
# uses: actions/vs-build-tools@v1
# with:
# installPath: C:\BuildTools
# version: 16
# components: Microsoft.VisualStudio.Component.VC.Tools.x86.x64
#
# - name: Add clang-cl to PATH
# if: matrix.platform == 'windows-latest'
# run: echo "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\Llvm\bin" >> $GITHUB_PATH
- name: Install Windows Dependencies
if: matrix.platform == 'windows-latest'
uses: msys2/setup-msys2@v2
with:
msystem: MINGW64
update: true
install: >
zip
git
cmake
ninja
- name: Build Windows
if: matrix.platform == 'windows-latest'
shell: msys2 {0}
run: |
echo "working dir is $PWD"
mkdir build
cd build
cmake \
-G Ninja \
-DCMAKE_C_COMPILER="/c/Program Files/LLVM/bin/clang-cl.exe" \
-DCMAKE_CXX_COMPILER="/c/Program Files/LLVM/bin/clang-cl.exe" \
-DOPTION_TARGET_MESSAGING=OFF \
-DOPTION_TARGET_PARALLEL=OFF \
-DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
-DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
-DOPTION_TARGET_SMOLDYN_SOLVER=ON \
-DOPTION_TARGET_FV_SOLVER=ON \
-DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
-DOPTION_TARGET_NFSIM_SOLVER=ON \
-DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
-DOPTION_TARGET_SUNDIALS_SOLVER=ON \
-DOPTION_TARGET_HY3S_SOLVERS=OFF \
-DOPTION_TARGET_DOCS=OFF \
-B . -S ..
ninja -j 1
- name: Test Windows
if: matrix.platform == 'windows-latest'
shell: msys2 {0}
run: |
echo "working dir is $PWD"
cd build
ctest -VV
echo "------ running FiniteVolume_x64 ------"
./bin/FiniteVolume_x64.exe || true
echo
echo "------ running NFsim_x64 ------"
./bin/NFsim_x64.exe || true
echo "------ running SundialsSolverStandalone_x64 ------"
./bin/SundialsSolverStandalone_x64.exe || true
echo "------ running VCellStoch_x64 ------"
./bin/VCellStoch_x64.exe || true
echo "------ running smoldyn_x64 ------"
./bin/smoldyn_x64.exe || true
echo "------ running testzip ------"
./bin/testzip.exe || true
echo "------ running ziptool ------"
./bin/ziptool.exe || true
- name: Install Linux Dependencies
if: matrix.platform == 'ubuntu-latest'
run: |
sudo apt-get update
sudo apt-get install -y libboost-all-dev
sudo apt-get install -y libhdf5-dev
sudo apt-get install -y ninja-build
gcc --version
gfortran --version
cmake --version
dpkg -s libboost-all-dev
dpkg -s libhdf5-dev
- name: Build Linux
if: matrix.platform == 'ubuntu-latest'
run: |
platform=linux
echo "working dir is $PWD"
mkdir build
cd build
cmake \
-G Ninja \
-DOPTION_TARGET_MESSAGING=OFF \
-DOPTION_TARGET_PARALLEL=OFF \
-DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
-DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
-DOPTION_TARGET_SMOLDYN_SOLVER=ON \
-DOPTION_TARGET_FV_SOLVER=ON \
-DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
-DOPTION_TARGET_NFSIM_SOLVER=ON \
-DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=ON \
-DOPTION_TARGET_SUNDIALS_SOLVER=ON \
-DOPTION_TARGET_HY3S_SOLVERS=OFF \
-B . -S ..
ninja
- name: Test Linux
if: matrix.platform == 'ubuntu-latest'
run: |
platform=linux
echo "working dir is $PWD"
cd build
ctest -VV
echo "------ running FiniteVolume_x64 ------"
./bin/FiniteVolume_x64 || true
echo
echo "------ running NFsim_x64 ------"
./bin/NFsim_x64 || true
echo "------ running SundialsSolverStandalone_x64 ------"
./bin/SundialsSolverStandalone_x64 || true
echo "------ running VCellStoch_x64 ------"
./bin/VCellStoch_x64 || true
echo "------ running smoldyn_x64 ------"
./bin/smoldyn_x64 || true
echo "------ running testzip ------"
./bin/testzip || true
echo "------ running ziptool ------"
./bin/ziptool || true
- name: fix Macos shared object paths
if: matrix.platform == 'macos-13' || matrix.platform == 'macos-14'
shell: bash
run: |
mkdir build/upload
cd build/bin
rm hello_test TestVCellStoch testzip ziptool || true
ls *_x64 | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true
ls *.dylib | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true
ls *.dylib | awk '{print $1}' | xargs -I '{}' otool -L '{}' | grep ")" | grep -v "build" | grep -v "System" | awk '{print $1}' | xargs -I '{}' cp -vn '{}' . || true
chmod u+w,+x *
tar czvf ../upload/mac64_bad_paths.tgz .
../../.github/scripts/install_name_tool_macos.sh
tar czvf ../upload/mac64.tgz --dereference .
- name: handle shared object paths for Windows native build
if: matrix.platform == 'windows-latest'
shell: msys2 {0}
run: |
mkdir build/upload
cd build/bin
rm hello_test TestVCellStoch testzip ziptool || true
ls *.exe | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
ls *.dll | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
ls *.dll | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep '=> /' | grep -v build | grep -iv windows | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
chmod u+w,+x *
zip ../upload/win64.zip ./*
cd ../..
# fi
- name: handle shared object paths for Linux native build
if: matrix.platform == 'ubuntu-latest'
shell: bash
run: |
mkdir build/upload
cd build/bin
rm hello_test TestVCellStoch testzip ziptool || true
ls *_x64 | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
ls *.so | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
ls *.so | awk '{print $1}' | xargs -I '{}' ldd '{}' | grep "=> /" | grep -v "build" | awk '{print $3}' | xargs -I '{}' cp -vn '{}' . || true
chmod u+w,+x *
tar czvf ../upload/linux64.tgz --dereference .
cd ../..
- name: Upload Intel Macos binaries
if: matrix.platform == 'macos-13'
uses: actions/upload-artifact@v4
with:
name: macos_x86_64.tgz
path: build/upload/mac64.tgz
- name: Upload ARM Macos binaries
if: matrix.platform == 'macos-14'
uses: actions/upload-artifact@v4
with:
name: macos_arm64.tgz
path: build/upload/mac64.tgz
- name: Upload Windows binaries
if: matrix.platform == 'windows-latest'
uses: actions/upload-artifact@v4
with:
name: win64.zip
path: build/upload/win64.zip
- name: Upload Linux binaries
if: matrix.platform == 'ubuntu-latest'
uses: actions/upload-artifact@v4
with:
name: linux64.tgz
path: build/upload/linux64.tgz
- name: Setup tmate session
if: ${{ failure() }}
uses: mxschmitt/action-tmate@v3
with:
limit-access-to-actor: false