introduce msacontainer object, overhaul main alignment routine #65
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| name: Build & upload binaries | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - '**/README.md' | |
| workflow_dispatch: | |
| env: | |
| regression: 1 | |
| jobs: | |
| build_macos: | |
| name: macOS | |
| runs-on: macos-12 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Install Rust Toolchain | |
| run: | | |
| rustup update | |
| rustup target install x86_64-apple-darwin | |
| rustup target install aarch64-apple-darwin | |
| - name: Build | |
| run: | | |
| cd ${{ github.workspace }} | |
| ./util/build_osx.sh . build | |
| - name: Run Regression Suite | |
| if: ${{ env.regression == 1 }} | |
| run: | | |
| ${{ github.workspace }}/regression/run_regression.sh ${{ github.workspace }}/build/foldmason ${{ github.workspace }}/scratch | |
| - name: Upload MacOS Universal | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: foldmason-darwin-universal | |
| path: ${{ github.workspace }}/build/foldmason | |
| build_ubuntu: | |
| name: Build Ubuntu | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 120 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - SIMD: AVX2 | |
| STATIC: 1 | |
| MPI: 0 | |
| BUILD_TYPE: RelWithDebInfo | |
| - SIMD: SSE4_1 | |
| STATIC: 1 | |
| MPI: 0 | |
| BUILD_TYPE: RelWithDebInfo | |
| - SIMD: SSE2 | |
| STATIC: 1 | |
| MPI: 0 | |
| BUILD_TYPE: RelWithDebInfo | |
| - SIMD: AVX2_MPI | |
| STATIC: 0 | |
| MPI: 1 | |
| BUILD_TYPE: RelWithDebInfo | |
| - SIMD: AVX2 | |
| STATIC: 0 | |
| MPI: 0 | |
| BUILD_TYPE: ASan | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Install G++ | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y g++-12 rustc cargo | |
| - name: Install Dependencies | |
| if: matrix.MPI == 1 | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install mpi-default-dev mpi-default-bin | |
| - name: Build Foldmason | |
| run: | | |
| mkdir build | |
| cd build | |
| export CC=gcc-12 | |
| export CXX=g++-12 | |
| if [ "${{ matrix.STATIC }}" -eq "1" ]; then | |
| cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} -DHAVE_TESTS=1 \ | |
| -DBUILD_SHARED_LIBS=OFF \ | |
| -DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc \ | |
| -static-libstdc++" -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \ | |
| -DENABLE_WERROR=1 -DHAVE_${{ matrix.SIMD }}=1 -DHAVE_MPI=${{ matrix.MPI }} .. | |
| else | |
| cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} -DHAVE_TESTS=1 \ | |
| -DENABLE_WERROR=1 -DHAVE_${{ matrix.SIMD }}=1 -DHAVE_MPI=${{ matrix.MPI }} .. | |
| fi | |
| make -j $(nproc --all) | |
| - name: Run Regression Suite | |
| if: ${{ env.regression == 1 }} | |
| run: | | |
| export TTY=0 | |
| ${{ github.workspace }}/regression/run_regression.sh ${{ github.workspace }}/build/src/foldmason ${{ github.workspace }}/regression | |
| - name: Upload Linux | |
| if: matrix.STATIC == 1 | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: foldmason-linux-${{ matrix.SIMD }} | |
| path: build/src/foldmason | |
| build_ubuntu_cross: | |
| name: Ubuntu Cross-Compile | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 120 | |
| strategy: | |
| matrix: | |
| include: | |
| - SIMD: ARM8 | |
| ARCH: arm64 | |
| CPREF: aarch64 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Install Toolchain | |
| run: | | |
| sudo dpkg --add-architecture ${{ matrix.ARCH }} | |
| cat << HEREDOC | sudo tee /etc/apt/sources.list | |
| deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ jammy main universe multiverse | |
| deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ jammy-updates main universe multiverse | |
| deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ jammy-backports main universe multiverse | |
| deb [arch=amd64,i386] http://security.ubuntu.com/ubuntu/ jammy-security main universe multiverse | |
| deb [arch=${{ matrix.ARCH }}] http://ports.ubuntu.com/ubuntu-ports/ jammy main universe multiverse | |
| deb [arch=${{ matrix.ARCH }}] http://ports.ubuntu.com/ubuntu-ports/ jammy-updates main universe multiverse | |
| deb [arch=${{ matrix.ARCH }}] http://ports.ubuntu.com/ubuntu-ports/ jammy-backports main universe multiverse | |
| deb [arch=${{ matrix.ARCH }}] http://ports.ubuntu.com/ubuntu-ports/ jammy-security main universe multiverse | |
| HEREDOC | |
| sudo apt-get update | |
| sudo apt-get -y install -o APT::Immediate-Configure=false crossbuild-essential-${{ matrix.ARCH }} zlib1g-dev:${{ matrix.ARCH }} libbz2-dev:${{ matrix.ARCH }} g++-12-${{ matrix.CPREF }}-linux-gnu | |
| rustup target add ${{ matrix.CPREF }}-unknown-linux-gnu | |
| - name: Build Cross | |
| run: | | |
| mkdir build && cd build | |
| CC=${{ matrix.CPREF }}-linux-gnu-gcc-12 CXX=${{ matrix.CPREF }}-linux-gnu-g++-12 \ | |
| cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -DHAVE_TESTS=1 \ | |
| -DBUILD_SHARED_LIBS=OFF \ | |
| -DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc -static-libstdc++" \ | |
| -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \ | |
| -DRust_CARGO_TARGET=${{ matrix.CPREF }}-unknown-linux-gnu \ | |
| -DENABLE_WERROR=1 -DHAVE_${{ matrix.SIMD }}=1 .. | |
| make -j $(nproc --all) | |
| - name: Upload Linux Artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: foldmason-linux-${{ matrix.SIMD }} | |
| path: build/src/foldmason | |
| upload_artifacts: | |
| name: Upload Artifacts | |
| runs-on: ubuntu-latest | |
| needs: [build_macos, build_ubuntu, build_ubuntu_cross] | |
| if: github.event_name != 'pull_request' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Prepare Artifacts Directory | |
| run: | | |
| mkdir foldmason | |
| cp -f README.md LICENSE.md foldmason | |
| mkdir foldmason/bin | |
| # MacOS | |
| - name: Download foldmason-darwin-universal Artifact | |
| uses: actions/[email protected] | |
| with: | |
| name: foldmason-darwin-universal | |
| path: foldmason/bin | |
| - name: Archive Mac Binary | |
| run: | | |
| chmod +x foldmason/bin/foldmason | |
| tar -czvf foldmason-osx-universal.tar.gz foldmason | |
| # Linux SSE41 | |
| - name: Download foldmason-linux-SSE4_1 Artifact | |
| uses: actions/[email protected] | |
| with: | |
| name: foldmason-linux-SSE4_1 | |
| path: foldmason/bin | |
| - name: Archive SSE4_1 Binary | |
| run: | | |
| chmod +x foldmason/bin/foldmason | |
| tar -czvf foldmason-linux-sse41.tar.gz foldmason | |
| # Linux SSE2 | |
| - name: Download foldmason-linux-SSE2 Artifact | |
| uses: actions/[email protected] | |
| with: | |
| name: foldmason-linux-SSE2 | |
| path: foldmason/bin | |
| - name: Archive SSE2 Binary | |
| run: | | |
| chmod +x foldmason/bin/foldmason | |
| tar -czvf foldmason-linux-sse2.tar.gz foldmason | |
| # Linux AVX2 | |
| - name: Download foldmason-linux-AVX2 Artifact | |
| uses: actions/[email protected] | |
| with: | |
| name: foldmason-linux-AVX2 | |
| path: foldmason/bin | |
| - name: Archive AVX2 Binary | |
| run: | | |
| chmod +x foldmason/bin/foldmason | |
| tar -czvf foldmason-linux-avx2.tar.gz foldmason | |
| # Linux ARM64 | |
| - name: Download foldmason-linux-ARM8 Artifact | |
| uses: actions/[email protected] | |
| with: | |
| name: foldmason-linux-ARM8 | |
| path: foldmason/bin | |
| - name: Archive ARM8 Binary | |
| run: | | |
| chmod +x foldmason/bin/foldmason | |
| tar -czvf foldmason-linux-arm64.tar.gz foldmason | |
| - name: Get Deployment Key | |
| run: | | |
| mkdir -p $HOME/.ssh | |
| echo "$PRIVATE_KEY" > $HOME/.ssh/id_rsa | |
| chmod 700 $HOME/.ssh && chmod 600 $HOME/.ssh/id_rsa | |
| ssh-keygen -f $HOME/.ssh/id_rsa -y > $HOME/.ssh/id_rsa.pub | |
| env: | |
| PRIVATE_KEY : ${{ secrets.PRIVATE_KEY }} | |
| - name: Sign and Upload Artifacts | |
| run: | | |
| ssh-keygen -Y sign -f $HOME/.ssh/id_rsa -n file foldmason-osx-universal.tar.gz foldmason-linux-sse2.tar.gz foldmason-linux-sse41.tar.gz foldmason-linux-avx2.tar.gz foldmason-linux-arm64.tar.gz | |
| curl --retry 5 --retry-all-errors -X POST \ | |
| -F file[][email protected] -F signature[][email protected] \ | |
| -F file[][email protected] -F signature[][email protected] \ | |
| -F file[][email protected] -F signature[][email protected] \ | |
| -F file[][email protected] -F signature[][email protected] \ | |
| -F file[][email protected] -F signature[][email protected] \ | |
| -F identifier="foldmason" -F directory="${{ github.sha }}" \ | |
| https://mmseqs.com/upload |