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| name: Sanitizers, static binaries and artifacts | |
| on: | |
| push: | |
| branches: [ "master", "dev" ] | |
| pull_request: | |
| branches: [ "master", "dev" ] | |
| jobs: | |
| sanitizer: | |
| strategy: | |
| matrix: | |
| compiler: [gcc, clang] | |
| type: [ASan, UBSan, TSan] | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Configure CMake | |
| run: | | |
| if [ "$CC" = "clang" ]; then | |
| CLANG_MAJOR=$(echo | clang -dM -E - | grep __clang_major__ | awk '{ print $3; }') | |
| sudo apt-get install libc++-${CLANG_MAJOR}-dev libc++abi-${CLANG_MAJOR}-dev libomp-${CLANG_MAJOR}-dev | |
| fi | |
| cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{matrix.type}} -DHAVE_SANITIZER=1 | |
| env: | |
| CC: ${{matrix.compiler}} | |
| CXX: ${{ fromJSON(matrix.compiler == 'gcc' && '"g++"' || '"clang++"') }} | |
| CXXFLAGS: ${{ fromJSON(matrix.compiler == 'clang' && '"-stdlib=libc++"' || '""') }} | |
| LDFLAGS: ${{ fromJSON(matrix.compiler == 'clang' && '"-lc++abi"' || '""') }} | |
| - name: Build | |
| run: cmake --build ${{github.workspace}}/build --config ${{matrix.type}} --parallel $(nproc --all) | |
| - name: ASan | |
| working-directory: ${{github.workspace}}/build | |
| run: | | |
| ./foldcomp compress ../test/test.pdb | |
| ./foldcomp decompress ../test/test.fcz ../test/test_fcz.pdb | |
| ./foldcomp compress ../test/test.cif.gz | |
| ./foldcomp decompress -a ../test/test.cif.fcz ../test/test.cif_fcz.pdb | |
| RMSD1=$(./foldcomp rmsd ../test/test.pdb ../test/test_fcz.pdb | cut -f6) | |
| awk -v check=$RMSD1 -v target=0.0826751 'BEGIN { diff = check - target; if (diff < 0) diff = -diff; if (diff > 0.001) { print check"!="target; exit 1 } }' | |
| RMSD2=$(./foldcomp rmsd ../test/test.cif.gz ../test/test.cif_fcz.pdb | cut -f6) | |
| awk -v check=$RMSD2 -v target=0.130284 'BEGIN { diff = check - target; if (diff < 0) diff = -diff; if (diff > 0.001) { print check"!="target; exit 1 } }' | |
| echo "All good!" | |
| compile: | |
| strategy: | |
| matrix: | |
| arch: [ {name: 'arm64', prefix: 'aarch64-linux-gnu-'}, {name: 'x86_64', prefix: ''} ] | |
| fail-fast: false | |
| needs: sanitizer | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Apt dependencies | |
| run: | | |
| sudo apt install -y cmake build-essential zlib1g-dev libc6-dev gcc-10 g++-10 | |
| sudo rm -rf /home/linuxbrew /usr/local/lib/android | |
| - name: "Install foreign arch dependencies" | |
| if: matrix.arch.name != 'x86_64' | |
| run: | | |
| sudo apt update | |
| sudo apt install -y crossbuild-essential-${{ matrix.arch.name }} gcc-10-aarch64-linux-gnu g++-10-aarch64-linux-gnu | |
| DIST=$(lsb_release -cs) | |
| cat << HEREDOC | sudo tee /etc/apt/sources.list | |
| deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ focal main universe multiverse | |
| deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ focal-updates main universe multiverse | |
| deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ focal-backports main universe multiverse | |
| deb [arch=amd64,i386] http://security.ubuntu.com/ubuntu/ focal-security main universe multiverse | |
| deb [arch=${{ matrix.arch.name }}] http://ports.ubuntu.com/ubuntu-ports/ focal main universe multiverse | |
| deb [arch=${{ matrix.arch.name }}] http://ports.ubuntu.com/ubuntu-ports/ focal-updates main universe multiverse | |
| deb [arch=${{ matrix.arch.name }}] http://ports.ubuntu.com/ubuntu-ports/ focal-backports main universe multiverse | |
| deb [arch=${{ matrix.arch.name }}] http://ports.ubuntu.com/ubuntu-ports/ focal-security main universe multiverse | |
| HEREDOC | |
| sudo rm -rf /etc/apt/sources.list.d/* | |
| sudo dpkg --add-architecture ${{ matrix.arch.name }} | |
| sudo apt update | |
| sudo apt install -y zlib1g-dev:${{ matrix.arch.name }} zlib1g:${{ matrix.arch.name }} | |
| - name: Build ${{ matrix.arch.name }} | |
| run: | | |
| export CC=${{ matrix.arch.prefix }}gcc-10 | |
| export CXX=${{ matrix.arch.prefix }}g++-10 | |
| cmake -B ${{github.workspace}}/build \ | |
| -DBUILD_SHARED_LIBS=OFF \ | |
| -DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc -static-libstdc++" \ | |
| -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \ | |
| -DZLIB_USE_STATIC_LIBS=ON | |
| cmake --build ${{github.workspace}}/build --config Release --parallel $(nproc --all) | |
| tar -czf foldcomp-linux-${{ matrix.arch.name }}.tar.gz -C ${{github.workspace}}/build foldcomp | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| path: foldcomp-linux-${{ matrix.arch.name }}.tar.gz | |
| compile_macos: | |
| needs: sanitizer | |
| runs-on: macos-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Homebrew dependencies | |
| run: | | |
| brew install cmake gnu-tar libomp jq | |
| brew uninstall zlib -f --ignore-dependencies | |
| - name: Download libomp.a for arm64 | |
| run: | | |
| mkdir ${{github.workspace}}/libomp_arm64 | |
| BOTTLE_URL=$(brew info libomp --json | jq -r '.[].bottle.stable.files.arm64_sonoma.url') | |
| curl -s -L -H "Authorization: Bearer QQ==" -o libomp_arm64_sonoma.tar.gz $BOTTLE_URL | |
| file libomp_arm64_sonoma.tar.gz | |
| gtar --strip-components=2 -xzf libomp_arm64_sonoma.tar.gz -C ${{github.workspace}}/libomp_arm64 | |
| - name: Build x86_64 x86_64h arm64 | |
| run: | | |
| for i in arm64 x86_64 x86_64h; do | |
| LIBOMP=$(brew --prefix libomp) | |
| if [ "$i" = "arm64" ]; then | |
| LIBOMP=${{github.workspace}}/libomp_arm64 | |
| fi | |
| cmake -B build_${i} -DCMAKE_OSX_ARCHITECTURES=${i} \ | |
| -DBUILD_SHARED_LIBS=OFF -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \ | |
| -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I${LIBOMP}/include" -DOpenMP_C_LIB_NAMES=omp \ | |
| -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I${LIBOMP}/include" -DOpenMP_CXX_LIB_NAMES=omp \ | |
| -DOpenMP_omp_LIBRARY=${LIBOMP}/lib/libomp.a -DZLIB_USE_STATIC_LIBS=OFF . | |
| cmake --build build_${i} --config Release --parallel $(sysctl -n hw.ncpu) | |
| done | |
| mkdir dist | |
| lipo -create \ | |
| -arch x86_64 ${{github.workspace}}/build_x86_64/foldcomp \ | |
| -arch x86_64h ${{github.workspace}}/build_x86_64h/foldcomp \ | |
| -arch arm64 ${{github.workspace}}/build_arm64/foldcomp \ | |
| -output "dist/foldcomp" | |
| tar -C dist -czf foldcomp-macos-universal.tar.gz foldcomp | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| path: foldcomp-macos-universal.tar.gz | |
| compile_windows: | |
| needs: sanitizer | |
| runs-on: windows-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build x64 | |
| shell: cmd | |
| run: | | |
| call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\Common7\Tools\VsDevCmd.bat" -arch=amd64 -no_logo | |
| vcpkg install zlib:x64-windows-static | |
| vcpkg integrate install | |
| set VCPKG_TOOLCHAIN=C:/vcpkg/scripts/buildsystems/vcpkg.cmake | |
| cmake -G Ninja -B build ^ | |
| "-DVCPKG_TARGET_TRIPLET=x64-windows-static" ^ | |
| "-DCMAKE_TOOLCHAIN_FILE=%VCPKG_TOOLCHAIN%" ^ | |
| "-DCMAKE_C_COMPILER:FILEPATH=%VCINSTALLDIR%\Tools\Llvm\x64\bin\clang.exe" ^ | |
| "-DCMAKE_CXX_COMPILER:FILEPATH=%VCINSTALLDIR%\Tools\Llvm\x64\bin\clang.exe" ^ | |
| "-DCMAKE_LINKER:FILEPATH=%VCINSTALLDIR%\Tools\Llvm\x64\bin\lld-link.exe" | |
| cmake --build build --config Release --parallel %NUMBER_OF_PROCESSORS% | |
| copy /Y "%VCINSTALLDIR%\Tools\Llvm\x64\bin\libomp.dll" build/libomp.dll | |
| tar.exe -C build -acvf foldcomp-windows-x64.zip foldcomp.exe libomp.dll | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| path: foldcomp-windows-x64.zip | |
| upload_all: | |
| needs: [compile, compile_macos, compile_windows] | |
| runs-on: ubuntu-latest | |
| if: github.ref == 'refs/heads/master' && github.event_name != 'pull_request' | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: artifact | |
| path: . | |
| - name: Create private key for upload | |
| run: | | |
| mkdir ~/.ssh | |
| chmod 700 ~/.ssh | |
| echo "$SSH_KEY" > ~/.ssh/id_rsa | |
| chmod 600 ~/.ssh/id_rsa | |
| ssh-keygen -f ~/.ssh/id_rsa -y > ~/.ssh/id_rsa.pub | |
| shell: bash | |
| env: | |
| SSH_KEY: ${{secrets.SSH_PRIVKEY}} | |
| - name: SCP to server | |
| run: | | |
| ssh-keygen -Y sign -f ~/.ssh/id_rsa -n file \ | |
| foldcomp-linux-x86_64.tar.gz \ | |
| foldcomp-linux-arm64.tar.gz \ | |
| foldcomp-macos-universal.tar.gz \ | |
| foldcomp-windows-x64.zip | |
| curl --retry 2 --retry-all-errors -X POST \ | |
| -F file[]=@foldcomp-linux-x86_64.tar.gz -F signature[]=@foldcomp-linux-x86_64.tar.gz.sig \ | |
| -F file[]=@foldcomp-linux-arm64.tar.gz -F signature[]=@foldcomp-linux-arm64.tar.gz.sig \ | |
| -F file[]=@foldcomp-macos-universal.tar.gz -F signature[]=@foldcomp-macos-universal.tar.gz.sig \ | |
| -F file[]=@foldcomp-windows-x64.zip -F signature[]=@foldcomp-windows-x64.zip.sig \ | |
| -F identifier="foldcomp" -F directory="${{github.sha}}" \ | |
| https://mmseqs.com/upload |