Merge pull request #210 from cindykrafft/fix/issue-192-codon-fu #419
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| name: Build | |
| on: | |
| push: | |
| branches: ["*"] | |
| pull_request: | |
| branches: ["master"] | |
| # If a Second Commit is Pushed After, and Build is Not Complete, Cancel | |
| # Extremely Important with the High Computation Time and Power Required of Arm Linux Builds | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build-linux-x86-64: | |
| name: Linux x86-64 | |
| runs-on: ubuntu-22.04 | |
| env: | |
| # Disable glibc tcache to make peak RSS deterministic across runs. | |
| GLIBC_TUNABLES: glibc.malloc.tcache_count=0 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - clang-version: 22 | |
| cmake-version: latest | |
| upload: true | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: "recursive" | |
| - name: Add LLVM apt repository | |
| if: matrix.clang-version >= 16 | |
| run: | | |
| wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | sudo gpg --dearmor -o /usr/share/keyrings/llvm.gpg | |
| echo "deb [signed-by=/usr/share/keyrings/llvm.gpg] http://apt.llvm.org/jammy/ llvm-toolchain-jammy-${{ matrix.clang-version }} main" | sudo tee /etc/apt/sources.list.d/llvm.list | |
| sudo apt-get update -q -y | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update -q -y | |
| sudo apt-get install -q -y clang-${{ matrix.clang-version }} lld-${{ matrix.clang-version }} libomp-${{ matrix.clang-version }}-dev libeigen3-dev libboost-dev | |
| sudo ln -sf $(which ld.lld-${{ matrix.clang-version }}) /usr/local/bin/ld.lld | |
| # Install Rust | |
| - name: Install Rust | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| profile: minimal | |
| - name: Setup cmake | |
| uses: jwlawson/actions-setup-cmake@v2 | |
| with: | |
| cmake-version: ${{ matrix.cmake-version }} | |
| - name: Build | |
| run: | | |
| mkdir build | |
| cd build | |
| cmake .. -DUSE_MUTSEL=ON -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DIQTREE_FLAGS=static -DCMAKE_C_COMPILER=$(which clang-${{ matrix.clang-version }}) -DCMAKE_CXX_COMPILER=$(which clang++-${{ matrix.clang-version }}) | |
| make -j | |
| make package | |
| file iqtree3 | grep x86-64 | |
| file iqtree*.tar.gz | grep gzip | |
| - name: Upload Built Binary | |
| # Only upload for one of the gcc & cmake tests | |
| if: ${{ matrix.upload }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Linux x86-64 | |
| path: build/iqtree*.tar.gz | |
| if-no-files-found: error | |
| - name: Run benchmarks with IQ-TREE 2 (baseline) | |
| run: | | |
| chmod +x test_scripts/test_iqtree.sh | |
| ./test_scripts/test_iqtree.sh test_scripts/iqtree2/Linux-intel/iqtree2 time_log_iqtree2.tsv test_scripts/test_data/iqtree2_out | |
| - name: Run benchmarks with IQ-TREE 3 | |
| run: | | |
| ./test_scripts/test_iqtree.sh build/iqtree3 time_log_iqtree3.tsv | |
| - name: Run verify_results.sh | |
| run: | | |
| chmod +x test_scripts/verify_results.sh | |
| ./test_scripts/verify_results.sh | |
| - name: Run verify_runtimes.sh | |
| run: | | |
| chmod +x test_scripts/verify_runtime.sh | |
| ./test_scripts/verify_runtime.sh time_log_iqtree2.tsv time_log_iqtree3.tsv Linux-x86-64 | |
| - name: Run verify_memory.sh | |
| run: | | |
| chmod +x test_scripts/verify_memory.sh | |
| ./test_scripts/verify_memory.sh time_log_iqtree2.tsv time_log_iqtree3.tsv Linux-x86-64 | |
| build-linux-aarch64: | |
| name: Linux aarch64 | |
| runs-on: ubuntu-22.04-arm | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: "recursive" | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update -q -y | |
| sudo apt-get install -q -y gcc g++ libeigen3-dev libboost-dev | |
| # Install Rust | |
| - name: Install Rust | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| profile: minimal | |
| - name: Build | |
| run: | | |
| mkdir build | |
| cd build | |
| cmake .. -DIQTREE_FLAGS=static -DUSE_MUTSEL=ON | |
| make -j | |
| make package | |
| file iqtree3 | grep aarch64 | |
| - name: Upload Built Binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Linux AArch64 | |
| path: build/iqtree*.tar.gz | |
| if-no-files-found: error | |
| - name: Run benchmarks with IQ-TREE 2 (baseline) | |
| run: | | |
| chmod +x test_scripts/test_iqtree.sh | |
| ./test_scripts/test_iqtree.sh test_scripts/iqtree2/Linux-arm/iqtree2 time_log_iqtree2.tsv test_scripts/test_data/iqtree2_out | |
| - name: Run benchmarks with IQ-TREE 3 | |
| run: | | |
| ./test_scripts/test_iqtree.sh build/iqtree3 time_log_iqtree3.tsv | |
| - name: Run verify_results.sh | |
| run: | | |
| chmod +x test_scripts/verify_results.sh | |
| ./test_scripts/verify_results.sh | |
| - name: Run verify_runtimes.sh | |
| run: | | |
| chmod +x test_scripts/verify_runtime.sh | |
| ./test_scripts/verify_runtime.sh time_log_iqtree2.tsv time_log_iqtree3.tsv Linux-aarch64 | |
| - name: Run verify_memory.sh | |
| run: | | |
| chmod +x test_scripts/verify_memory.sh | |
| ./test_scripts/verify_memory.sh time_log_iqtree2.tsv time_log_iqtree3.tsv Linux-aarch64 | |
| compile-linux-universal: | |
| name: Linux Universal | |
| runs-on: ubuntu-latest | |
| needs: | |
| - build-linux-x86-64 | |
| - build-linux-aarch64 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Download Linux x86-64 Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: Linux x86-64 | |
| path: x86 | |
| - name: Download Linux Arm Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: Linux AArch64 | |
| path: arm | |
| - name: Combine Artifacts | |
| run: | | |
| chmod +x test_scripts/make_linux_universal.sh | |
| file1=$(ls x86/iqtree*.tar.gz) | |
| file2=$(ls arm/iqtree*.tar.gz) | |
| test_scripts/make_linux_universal.sh "$file1" "$file2" | |
| - name: Upload Built Binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Linux Universal | |
| path: iqtree*.tar.gz | |
| if-no-files-found: error | |
| build-macos-x86_64: | |
| name: Mac OS x86-64 | |
| runs-on: macos-15-intel # replaces deprecated macos-13 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: "recursive" | |
| - name: Install dependencies | |
| run: brew install make eigen boost libomp | |
| # Install Rust | |
| - name: Install Rust | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| profile: minimal | |
| - name: Build | |
| run: | | |
| set -x | |
| mkdir build | |
| cd build | |
| export CPPFLAGS="-I/usr/local/opt/libomp/include" | |
| export CXXFLAGS="-I/usr/local/opt/libomp/include" | |
| cmake .. -DUSE_MUTSEL=ON -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DEIGEN3_INCLUDE_DIR=$(brew --prefix eigen)/include/eigen3 | |
| make -j | |
| make package | |
| file iqtree3 | grep x86_64 | |
| file iqtree*.zip | grep Zip | |
| - name: Upload Built Binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Mac x86-64 | |
| path: build/iqtree*.zip | |
| if-no-files-found: error | |
| - name: Run benchmarks with IQ-TREE 2 (baseline) | |
| run: | | |
| chmod +x test_scripts/test_iqtree.sh test_scripts/iqtree2/macOS-intel/iqtree2 | |
| ./test_scripts/test_iqtree.sh test_scripts/iqtree2/macOS-intel/iqtree2 time_log_iqtree2.tsv test_scripts/test_data/iqtree2_out | |
| - name: Run benchmarks with IQ-TREE 3 | |
| run: | | |
| ./test_scripts/test_iqtree.sh build/iqtree3 time_log_iqtree3.tsv | |
| - name: Run verify_results.sh | |
| run: | | |
| chmod +x test_scripts/verify_results.sh | |
| ./test_scripts/verify_results.sh | |
| - name: Run verify_runtimes.sh | |
| run: | | |
| chmod +x test_scripts/verify_runtime.sh | |
| ./test_scripts/verify_runtime.sh time_log_iqtree2.tsv time_log_iqtree3.tsv mac-os-x86-64 | |
| - name: Run verify_memory.sh | |
| run: | | |
| chmod +x test_scripts/verify_memory.sh | |
| ./test_scripts/verify_memory.sh time_log_iqtree2.tsv time_log_iqtree3.tsv mac-os-x86-64 | |
| build-macos-arm: | |
| name: Mac OS ARM64 | |
| runs-on: macos-14 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: "recursive" | |
| - name: Install dependencies | |
| run: brew install make eigen boost libomp | |
| # Install Rust | |
| - name: Install Rust | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| profile: minimal | |
| - name: Build | |
| run: | | |
| set -x | |
| mkdir build | |
| cd build | |
| export CPPFLAGS="-I/opt/homebrew/opt/libomp/include" | |
| export CXXFLAGS="-I/opt/homebrew/opt/libomp/include" | |
| cmake .. -DUSE_MUTSEL=ON -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DEIGEN3_INCLUDE_DIR=$(brew --prefix eigen)/include/eigen3 | |
| make -j | |
| make package | |
| file iqtree3 | grep arm64 | |
| file iqtree*.zip | grep Zip | |
| - name: Upload Built Binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Mac Arm | |
| path: build/iqtree*.zip | |
| if-no-files-found: error | |
| - name: Run benchmarks with IQ-TREE 2 (baseline) | |
| run: | | |
| chmod +x test_scripts/test_iqtree.sh test_scripts/iqtree2/macOS-arm/iqtree2 | |
| ./test_scripts/test_iqtree.sh test_scripts/iqtree2/macOS-arm/iqtree2 time_log_iqtree2.tsv test_scripts/test_data/iqtree2_out | |
| - name: Run benchmarks with IQ-TREE 3 | |
| run: | | |
| ./test_scripts/test_iqtree.sh build/iqtree3 time_log_iqtree3.tsv | |
| - name: Run verify_results.sh | |
| run: | | |
| chmod +x test_scripts/verify_results.sh | |
| ./test_scripts/verify_results.sh | |
| - name: Run verify_runtimes.sh | |
| run: | | |
| chmod +x test_scripts/verify_runtime.sh | |
| ./test_scripts/verify_runtime.sh time_log_iqtree2.tsv time_log_iqtree3.tsv mac-os-arm64 | |
| - name: Run verify_memory.sh | |
| run: | | |
| chmod +x test_scripts/verify_memory.sh | |
| ./test_scripts/verify_memory.sh time_log_iqtree2.tsv time_log_iqtree3.tsv mac-os-arm64 | |
| compile-mac-universal: | |
| name: Mac OS Universal | |
| runs-on: macos-14 | |
| needs: | |
| - build-macos-x86_64 | |
| - build-macos-arm | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Download Mac x86-64 Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: Mac x86-64 | |
| path: x86 | |
| - name: Download Mac Arm Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: Mac Arm | |
| path: arm | |
| - name: Combine Artifacts | |
| run: | | |
| chmod +x test_scripts/make_universal.sh | |
| file1=$(ls x86/iqtree*.zip) | |
| file2=$(ls arm/iqtree*.zip) | |
| test_scripts/make_universal.sh "$file1" "$file2" | |
| - name: Upload Built Binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Mac Universal | |
| path: iqtree*.zip | |
| if-no-files-found: error | |
| build-windows-x86-64: | |
| name: Windows x86-64 | |
| runs-on: windows-2022 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: "recursive" | |
| - name: Install LLVM v14 | |
| shell: cmd | |
| run: | | |
| setlocal EnableDelayedExpansion | |
| set RETRIES=3 | |
| set WAIT_SECONDS=20 | |
| for /L %%i in (1,1,%RETRIES%) do ( | |
| echo Attempt %%i/%RETRIES%: installing LLVM 14.0.6 via Chocolatey | |
| choco install llvm --version=14.0.6 --allow-downgrade | |
| if !ERRORLEVEL! EQU 0 goto :success | |
| if %%i LSS %RETRIES% ( | |
| echo Install failed. Waiting %WAIT_SECONDS%s before retry... | |
| timeout /t %WAIT_SECONDS% /nobreak >nul | |
| ) | |
| ) | |
| echo LLVM installation failed after %RETRIES% attempts. | |
| exit /b 1 | |
| :success | |
| echo LLVM installed successfully. | |
| - name: Download and Extract Boost 1.84.0 | |
| shell: pwsh | |
| run: | | |
| curl -L -o boost.tar.gz https://github.com/MarkusJx/prebuilt-boost/releases/download/1.84.0/boost-1.84.0-windows-2022-mingw-static-x86.tar.gz | |
| tar -xzf boost.tar.gz | |
| mv boost C:/local/boost | |
| - name: Install Eigen3 | |
| shell: cmd | |
| run: choco install eigen | |
| # Install Rust | |
| - name: Install Rust | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| profile: minimal | |
| target: x86_64-pc-windows-gnu | |
| - name: Compile | |
| shell: cmd | |
| run: | | |
| if exist build rd /s /q build | |
| mkdir build | |
| cd build | |
| cmake -G "MinGW Makefiles" ^ | |
| -DUSE_MUTSEL=ON ^ | |
| -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ ^ | |
| -DCMAKE_C_FLAGS="--target=x86_64-pc-windows-gnu --sysroot=C:/mingw64 -B C:/mingw64/bin" ^ | |
| -DCMAKE_CXX_FLAGS="--target=x86_64-pc-windows-gnu --sysroot=C:/mingw64 -B C:/mingw64/bin" ^ | |
| -DCMAKE_MAKE_PROGRAM=mingw32-make ^ | |
| -DBoost_INCLUDE_DIR="C:/local/boost/include" ^ | |
| -DBoost_LIBRARY_DIRS="C:/local/boost/lib" ^ | |
| -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ^ | |
| -DIQTREE_FLAGS="static" .. | |
| type CMakeFiles\iqtree3.dir\link.txt | |
| type CMakeFiles\iqtree3.dir\linkLibs.rsp | |
| make -j | |
| make package | |
| env: | |
| BOOST_ROOT: "C:/local/boost" | |
| - name: Check File Arch | |
| shell: bash | |
| run: | | |
| cd build | |
| file iqtree3.exe | grep x86-64 | |
| file iqtree*.zip | |
| - name: Upload Built Binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Windows x86-64 | |
| path: build/iqtree*.zip | |
| if-no-files-found: error | |
| - name: Run benchmarks with IQ-TREE 2 (baseline) | |
| shell: pwsh | |
| run: | | |
| ./test_scripts/test_iqtree.ps1 -IQTreeBin test_scripts/iqtree2/Windows/iqtree2.exe -LogFile time_log_iqtree2.tsv -OutDir test_scripts/test_data/iqtree2_out | |
| - name: Run benchmarks with IQ-TREE 3 | |
| shell: pwsh | |
| run: | | |
| ./test_scripts/test_iqtree.ps1 -IQTreeBin "./build/iqtree3.exe" -LogFile time_log_iqtree3.tsv | |
| - name: Run verify_results.ps1 | |
| shell: pwsh | |
| run: | | |
| ./test_scripts/verify_results.ps1 | |
| - name: Run verify_runtimes.ps1 | |
| shell: pwsh | |
| run: | | |
| ./test_scripts/verify_runtime.ps1 -IQTree2Log time_log_iqtree2.tsv -IQTree3Log time_log_iqtree3.tsv -FallbackColumn windows-x86 | |
| - name: Run verify_memory.ps1 | |
| shell: pwsh | |
| run: | | |
| ./test_scripts/verify_memory.ps1 -IQTree2Log time_log_iqtree2.tsv -IQTree3Log time_log_iqtree3.tsv -FallbackColumn windows-x86 |