[CI] Stop vendoring libomp.dylib in MacOS Python wheels (#10440)

.github/workflows/python_wheels.yml

@@ -28,6 +28,10 @@ jobs:
     - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
       with:
         submodules: 'true'
+    - name: Set up homebrew
+      uses: Homebrew/actions/setup-homebrew@68fa6aeb1ccb0596d311f2b34ec74ec21ee68e54
+    - name: Install libomp
+      run: brew install libomp
     - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca  # v3.0.4
       with:
         miniforge-variant: Mambaforge

CMakeLists.txt

@@ -234,27 +234,16 @@ endif()
 
 find_package(Threads REQUIRED)
 
+# -- OpenMP
+include(cmake/FindOpenMPMacOS.cmake)
 if(USE_OPENMP)
   if(APPLE)
-    find_package(OpenMP)
+    find_openmp_macos()
-    if(NOT OpenMP_FOUND)
-      # Try again with extra path info; required for libomp 15+ from Homebrew
-      execute_process(COMMAND brew --prefix libomp
-                      OUTPUT_VARIABLE HOMEBREW_LIBOMP_PREFIX
-                      OUTPUT_STRIP_TRAILING_WHITESPACE)
-      set(OpenMP_C_FLAGS
-        "-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include")
-      set(OpenMP_CXX_FLAGS
-        "-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include")
-      set(OpenMP_C_LIB_NAMES omp)
-      set(OpenMP_CXX_LIB_NAMES omp)
-      set(OpenMP_omp_LIBRARY ${HOMEBREW_LIBOMP_PREFIX}/lib/libomp.dylib)
-      find_package(OpenMP REQUIRED)
-    endif()
   else()
     find_package(OpenMP REQUIRED)
   endif()
 endif()
+
 # Add for IBM i
 if(${CMAKE_SYSTEM_NAME} MATCHES "OS400")
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
@@ -380,6 +369,10 @@ if(JVM_BINDINGS)
   xgboost_target_defs(xgboost4j)
 endif()
 
+if(USE_OPENMP AND APPLE)
+  patch_openmp_path_macos(xgboost libxgboost)
+endif()
+
 if(KEEP_BUILD_ARTIFACTS_IN_BINARY_DIR)
   set_output_directory(xgboost ${xgboost_BINARY_DIR}/lib)
 else()

cmake/FindOpenMPMacOS.cmake

@@ -0,0 +1,124 @@
+# Find OpenMP library on MacOS
+# Automatically handle locating libomp from the Homebrew package manager
+
+# lint_cmake: -package/consistency
+
+macro(find_openmp_macos)
+  if(NOT APPLE)
+    message(FATAL_ERROR "${CMAKE_CURRENT_FUNCTION}() must only be used on MacOS")
+  endif()
+  find_package(OpenMP)
+  if(NOT OpenMP_FOUND)
+    # Try again with extra path info. This step is required for libomp 15+ from Homebrew,
+    # as libomp 15.0+ from brew is keg-only
+    # See https://github.com/Homebrew/homebrew-core/issues/112107#issuecomment-1278042927.
+    execute_process(COMMAND brew --prefix libomp
+                    OUTPUT_VARIABLE HOMEBREW_LIBOMP_PREFIX
+                    OUTPUT_STRIP_TRAILING_WHITESPACE)
+    set(OpenMP_C_FLAGS
+      "-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include")
+    set(OpenMP_CXX_FLAGS
+      "-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include")
+    set(OpenMP_C_LIB_NAMES omp)
+    set(OpenMP_CXX_LIB_NAMES omp)
+    set(OpenMP_omp_LIBRARY ${HOMEBREW_LIBOMP_PREFIX}/lib/libomp.dylib)
+    find_package(OpenMP REQUIRED)
+  endif()
+endmacro()
+
+# Patch libxgboost.dylib so that it depends on @rpath/libomp.dylib instead of
+# /opt/homebrew/opt/libomp/lib/libomp.dylib or other hard-coded paths.
+# Doing so enables XGBoost to interoperate with multiple kinds of OpenMP
+# libraries. See https://github.com/microsoft/LightGBM/pull/6391 for detailed
+# explanation. Adapted from https://github.com/microsoft/LightGBM/pull/6391
+# by James Lamb.
+# MacOS only.
+function(patch_openmp_path_macos target target_default_output_name)
+  if(NOT APPLE)
+    message(FATAL_ERROR "${CMAKE_CURRENT_FUNCTION}() must only be used on MacOS")
+  endif()
+  # Get path to libomp found at build time
+  get_target_property(
+    __OpenMP_LIBRARY_LOCATION
+    OpenMP::OpenMP_CXX
+    INTERFACE_LINK_LIBRARIES
+  )
+  # Get the base name of the OpenMP lib
+  # Usually: libomp.dylib, libgomp.dylib, or libiomp.dylib
+  get_filename_component(
+    __OpenMP_LIBRARY_NAME
+    ${__OpenMP_LIBRARY_LOCATION}
+    NAME
+  )
+  # Get the directory containing the OpenMP lib
+  get_filename_component(
+    __OpenMP_LIBRARY_DIR
+    ${__OpenMP_LIBRARY_LOCATION}
+    DIRECTORY
+  )
+  # Get the name of the XGBoost lib, e.g. libxgboost
+  get_target_property(
+    __LIBXGBOOST_OUTPUT_NAME
+    ${target}
+    OUTPUT_NAME
+  )
+  if(NOT __LIBXGBOOST_OUTPUT_NAME)
+    set(__LIBXGBOOST_OUTPUT_NAME "${target_default_output_name}")
+  endif()
+
+  # Get the file name of the XGBoost lib, e.g. libxgboost.dylib
+  if(CMAKE_SHARED_LIBRARY_SUFFIX_CXX)
+    set(
+      __LIBXGBOOST_FILENAME_${target} "${__LIBXGBOOST_OUTPUT_NAME}${CMAKE_SHARED_LIBRARY_SUFFIX_CXX}"
+      CACHE INTERNAL "Shared library filename ${target}"
+    )
+  else()
+    set(
+      __LIBXGBOOST_FILENAME_${target} "${__LIBXGBOOST_OUTPUT_NAME}.dylib"
+      CACHE INTERNAL "Shared library filename ${target}"
+    )
+  endif()
+
+  message(STATUS "Creating shared lib for target ${target}: ${__LIBXGBOOST_FILENAME_${target}}")
+
+  # Override the absolute path to OpenMP with a relative one using @rpath.
+  #
+  # This also ensures that if a libomp.dylib has already been loaded, it'll just use that.
+  if(KEEP_BUILD_ARTIFACTS_IN_BINARY_DIR)
+    set(__LIB_DIR ${xgboost_BINARY_DIR}/lib)
+  else()
+    set(__LIB_DIR ${xgboost_SOURCE_DIR}/lib)
+  endif()
+  add_custom_command(
+    TARGET ${target}
+    POST_BUILD
+      COMMAND
+        install_name_tool
+        -change
+        ${__OpenMP_LIBRARY_LOCATION}
+        "@rpath/${__OpenMP_LIBRARY_NAME}"
+        "${__LIBXGBOOST_FILENAME_${target}}"
+      WORKING_DIRECTORY ${__LIB_DIR}
+  )
+  message(STATUS
+    "${__LIBXGBOOST_FILENAME_${target}}: "
+    "Replacing hard-coded OpenMP install_name with '@rpath/${__OpenMP_LIBRARY_NAME}'..."
+  )
+  # Add RPATH entries to ensure the loader looks in the following, in the following order:
+  #
+  #   - /opt/homebrew/opt/libomp/lib  (where 'brew install' / 'brew link' puts libomp.dylib)
+  #   - ${__OpenMP_LIBRARY_DIR}       (wherever find_package(OpenMP) found OpenMP at build time)
+  #
+  # Note: This list will only be used if libomp.dylib isn't already loaded into memory.
+  #       So Conda users will likely use ${CONDA_PREFIX}/libomp.dylib
+  execute_process(COMMAND brew --prefix libomp
+                  OUTPUT_VARIABLE HOMEBREW_LIBOMP_PREFIX
+                  OUTPUT_STRIP_TRAILING_WHITESPACE)
+  set_target_properties(
+    ${target}
+    PROPERTIES
+      BUILD_WITH_INSTALL_RPATH TRUE
+      INSTALL_RPATH "${HOMEBREW_LIBOMP_PREFIX}/lib;${__OpenMP_LIBRARY_DIR}"
+      INSTALL_RPATH_USE_LINK_PATH FALSE
+  )
+endfunction()

jvm-packages/CMakeLists.txt

@@ -24,3 +24,8 @@ target_include_directories(xgboost4j
   ${PROJECT_SOURCE_DIR}/dmlc-core/include)
 
 set_output_directory(xgboost4j ${PROJECT_SOURCE_DIR}/lib)
+
+# MacOS: Patch libxgboost4j.dylib to use @rpath/libomp.dylib
+if(USE_OPENMP AND APPLE)
+  patch_openmp_path_macos(xgboost4j libxgboost4j)
+endif()

tests/ci_build/build_python_wheels.sh

@@ -11,33 +11,19 @@ fi
 platform_id=$1
 commit_id=$2
 
-# Bundle libomp 11.1.0 when targeting MacOS.
-# This is a workaround in order to prevent segfaults when running inside a Conda environment.
-# See https://github.com/dmlc/xgboost/issues/7039#issuecomment-1025125003 for more context.
-# The workaround is also used by the scikit-learn project.
 if [[ "$platform_id" == macosx_* ]]; then
-    # Make sure to use a libomp version binary compatible with the oldest
-    # supported version of the macos SDK as libomp will be vendored into the
-    # XGBoost wheels for MacOS.
-
     if [[ "$platform_id" == macosx_arm64 ]]; then
         # MacOS, Apple Silicon
-        # arm64 builds must cross compile because CI is on x64
-        # cibuildwheel will take care of cross-compilation.
         wheel_tag=macosx_12_0_arm64
         cpython_ver=39
         cibw_archs=arm64
         export MACOSX_DEPLOYMENT_TARGET=12.0
-        #OPENMP_URL="https://anaconda.org/conda-forge/llvm-openmp/11.1.0/download/osx-arm64/llvm-openmp-11.1.0-hf3c4609_1.tar.bz2"
-        OPENMP_URL="https://xgboost-ci-jenkins-artifacts.s3.us-west-2.amazonaws.com/llvm-openmp-11.1.0-hf3c4609_1-osx-arm64.tar.bz2"
     elif [[ "$platform_id" == macosx_x86_64 ]]; then
         # MacOS, Intel
         wheel_tag=macosx_10_15_x86_64.macosx_11_0_x86_64.macosx_12_0_x86_64
         cpython_ver=39
         cibw_archs=x86_64
         export MACOSX_DEPLOYMENT_TARGET=10.15
-        #OPENMP_URL="https://anaconda.org/conda-forge/llvm-openmp/11.1.0/download/osx-64/llvm-openmp-11.1.0-hda6cdc1_1.tar.bz2"
-        OPENMP_URL="https://xgboost-ci-jenkins-artifacts.s3.us-west-2.amazonaws.com/llvm-openmp-11.1.0-hda6cdc1_1-osx-64.tar.bz2"
     else
         echo "Platform not supported: $platform_id"
         exit 3
@@ -48,26 +34,23 @@ if [[ "$platform_id" == macosx_* ]]; then
     export CIBW_ENVIRONMENT=${setup_env_var}
     export CIBW_TEST_SKIP='*-macosx_arm64'
     export CIBW_BUILD_VERBOSITY=3
-
-    mamba create -n build $OPENMP_URL
-    PREFIX="$HOME/miniconda3/envs/build"
-
-    # Set up build flags for cibuildwheel
-    # This is needed to bundle libomp lib we downloaded earlier
-    export CC=/usr/bin/clang
-    export CXX=/usr/bin/clang++
-    export CPPFLAGS="$CPPFLAGS -Xpreprocessor -fopenmp"
-    export CFLAGS="$CFLAGS -I$PREFIX/include"
-    export CXXFLAGS="$CXXFLAGS -I$PREFIX/include"
-    export LDFLAGS="$LDFLAGS -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lomp"
 else
     echo "Platform not supported: $platform_id"
     exit 2
 fi
 
+# Tell delocate-wheel to not vendor libomp.dylib into the wheel"
+export CIBW_REPAIR_WHEEL_COMMAND_MACOS="delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel} --exclude libomp.dylib"
+
 python -m pip install cibuildwheel
 python -m cibuildwheel python-package --output-dir wheelhouse
 python tests/ci_build/rename_whl.py  \
   --wheel-path wheelhouse/*.whl  \
   --commit-hash ${commit_id}  \
   --platform-tag ${wheel_tag}
+
+# List dependencies of libxgboost.dylib
+mkdir tmp
+unzip -j wheelhouse/xgboost-*.whl xgboost/lib/libxgboost.dylib -d tmp
+otool -L tmp/libxgboost.dylib
+rm -rf tmp