BLD: Set rpath for libomp on MacOS to fix compatibility with latest XGBoost version

.github/workflows/nonvendored_wheels.yml

@@ -49,10 +49,13 @@ jobs:
         python-version: "3.10"
 
     - name: Install cibuildwheel
-      run: python -m pip install cibuildwheel==2.18.0
+      run: python -m pip install cibuildwheel==2.21.3
 
     - name: Build wheels
       run: python -m cibuildwheel --output-dir wheelhouse
+      env:
+        CIBW_REPAIR_WHEEL_COMMAND_MACOS: "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}"
+        CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=12.0 CMAKE_ARGS="-DSDTN_ENABLE_ARCH_FLAGS=OFF -DSDTN_DISABLE_OPENMP=ON"
 
     - name: Verify clean directory
       run: git diff --exit-code

.github/workflows/wheels.yml

@@ -59,7 +59,7 @@ jobs:
     - name: Clone OpenMP repo
       if: matrix.os == 'macos-latest' && steps.clone-openmp.outputs.cache-hit != 'true'
       run: |
-        git clone --depth 1 --branch llvmorg-17.0.6 https://github.com/llvm/llvm-project
+        git clone --depth 1 --branch llvmorg-19.1.1 https://github.com/llvm/llvm-project
 
 
     - name: Build OpenMP
@@ -81,7 +81,7 @@ jobs:
         cmake --build openmp_build --target install --config Release
 
     - name: Install cibuildwheel
-      run: python -m pip install cibuildwheel==2.21.2
+      run: python -m pip install cibuildwheel==2.21.3
 
     - name: Build wheels
       run: python -m cibuildwheel --output-dir wheelhouse
@@ -90,7 +90,7 @@ jobs:
         CIBW_TEST_COMMAND: pytest {project}/tests && python -c "from sparse_dot_topn import _has_openmp_support;assert _has_openmp_support"
         # only build for arm; x86_64 wheels are build seperately
         CIBW_ARCHS_MACOS: "arm64"
-        CIBW_ENVIRONMENT_MACOS: PATH="$HOME/.local/:$PATH" MACOSX_DEPLOYMENT_TARGET="12.0" DYLD_LIBRARY_PATH="$HOME/.local/libomp/lib" CMAKE_ARGS="-DSDTN_ENABLE_ARCH_FLAGS=OFF -DSDTN_ENABLE_OPENMP=ON -DSDTN_DISABLE_OPENMP=OFF -DOpenMP_ROOT=$HOME/.local/libomp"
+        CIBW_ENVIRONMENT_MACOS: PATH="$HOME/.local/:$PATH" MACOSX_DEPLOYMENT_TARGET=12.0 DYLD_LIBRARY_PATH="$HOME/.local/libomp/lib" CMAKE_ARGS="-DSDTN_ENABLE_ARCH_FLAGS=OFF -DSDTN_VENDOR_OPENMP=ON -DSDTN_ENABLE_OPENMP=ON -DSDTN_DISABLE_OPENMP=OFF -DOpenMP_ROOT=$HOME/.local/libomp"
 
     - name: Verify clean directory
       run: git diff --exit-code
@@ -123,7 +123,7 @@ jobs:
     - name: Clone OpenMP repo
       if: steps.clone-openmp.outputs.cache-hit != 'true'
       run: |
-        git clone --depth 1 --branch llvmorg-17.0.6 https://github.com/llvm/llvm-project
+        git clone --depth 1 --branch llvmorg-19.1.1 https://github.com/llvm/llvm-project
 
     - name: Build OpenMP
       shell: bash
@@ -141,11 +141,11 @@ jobs:
             -DCMAKE_INSTALL_PREFIX="/usr/local"
         cmake --build openmp_build --target install --config Release
 
-    - uses: pypa/cibuildwheel@v2.21.2
+    - uses: pypa/cibuildwheel@v2.21.3
       env:
         # only build for x86_64, arm wheels are build seperately
         CIBW_ARCHS: "x86_64"
-        CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET="12.0" CMAKE_ARGS="-DSDTN_ENABLE_ARCH_FLAGS=OFF -DSDTN_ENABLE_OPENMP=ON -DSDTN_DISABLE_OPENMP=OFF -DOpenMP_ROOT=/usr/local"
+        CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=12.0 CMAKE_ARGS="-DSDTN_ENABLE_ARCH_FLAGS=OFF -DSDTN_VENDOR_OPENMP=ON -DSDTN_ENABLE_OPENMP=ON -DSDTN_DISABLE_OPENMP=OFF -DOpenMP_ROOT=/usr/local"
 
     - name: Verify clean directory
       run: git diff --exit-code

.gitignore

@@ -18,3 +18,4 @@ mprofile_*.dat
 .python-version
 .pymon
 .cache
+*.dylib

CHANGES.md

@@ -1,5 +1,11 @@
 # Release history:
 
+## v1.1.5
+
+### Changes
+
+BLD: Set rpath for libomp on MacOS to fix compatibility with latest XGBoost version
+
 ## v1.1.4
 
 ### Changes

CMakeLists.txt

@@ -36,6 +36,10 @@ if (NOT SKBUILD)
   after editing C++ files.")
 endif()
 
+if(SDTN_MBUILD)
+  set(CMAKE_INSTALL_PREFIX "${PROJECT_SOURCE_DIR}/src")
+endif()
+
 set(SDTN_INCLUDE_DIR "${PROJECT_SOURCE_DIR}/src/sparse_dot_topn_core/include")
 set(SDTN_SRC_PREF "${PROJECT_SOURCE_DIR}/src/sparse_dot_topn_core/src/")
 set(SDTN_SRC_FILES
@@ -49,6 +53,7 @@ include(FindDependencies)
 include(ConfigureBuildType)
 # -- target
 nanobind_add_module(_sparse_dot_topn_core STABLE_ABI NB_STATIC LTO NOMINSIZE ${SDTN_SRC_FILES})
+
 include(ConfigureTarget)
-include(InstallTarget)
+install(TARGETS _sparse_dot_topn_core LIBRARY DESTINATION "${PROJECT_NAME}/lib")
 include(CleanUp)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "sparse_dot_topn"
-version = "1.1.4"
+version = "1.1.5"
 description = "This package boosts a sparse matrix multiplication followed by selecting the top-n multiplication"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -57,7 +57,7 @@ SDTN_ENABLE_ARCH_FLAGS = true
 [tool.cibuildwheel]
 archs = ["auto64"]
 skip = ["*-win32", "*-manylinux_i686", "*-musllinux_x86_64"]
-build = ["cp38-*", "cp39-*", "cp310-*", "cp311-*", "cp312-*"]
+build = ["cp38-*", "cp39-*", "cp310-*", "cp311-*", "cp312-*", "cp313-*"]
 
 # make sure to build generic wheels
 environment = {CMAKE_ARGS="-DSDTN_ENABLE_ARCH_FLAGS=OFF -DSDTN_DISABLE_OPENMP=ON"}
@@ -77,8 +77,7 @@ repair-wheel-command = "auditwheel repair -w {dest_dir} {wheel}"
 [tool.cibuildwheel.macos]
 archs = ["x86_64", "arm64"]
 # Needed for full C++17 support
-environment = { MACOSX_DEPLOYMENT_TARGET = "12.0", CMAKE_ARGS="-DSDTN_ENABLE_ARCH_FLAGS=OFF -DSDTN_DISABLE_OPENMP=ON" }
-repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}"
+repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel} --exclude libomp.dylib"
 
 [tool.cibuildwheel.windows]
 before-build = "pip install delvewheel"

src/sparse_dot_topn_core/cmake/ConfigureTarget.cmake

@@ -1,14 +1,86 @@
 target_include_directories(_sparse_dot_topn_core PUBLIC ${SDTN_INCLUDE_DIR})
 if(OpenMP_CXX_FOUND)
-    target_link_libraries(_sparse_dot_topn_core PUBLIC OpenMP::OpenMP_CXX)
-    target_compile_definitions(_sparse_dot_topn_core PRIVATE SDTN_OMP_ENABLED=TRUE)
+  target_link_libraries(_sparse_dot_topn_core PUBLIC OpenMP::OpenMP_CXX)
+  target_compile_definitions(_sparse_dot_topn_core PRIVATE SDTN_OMP_ENABLED=TRUE)
+  if(APPLE)
+    # Modified implementation from LightGBM written by JamesLamb
+    # see https://github.com/microsoft/LightGBM/pull/6391
+    # store path to libomp found at build time in a variable
+    get_target_property(
+        OpenMP_LIBRARY_LOCATION
+        OpenMP::OpenMP_CXX
+        INTERFACE_LINK_LIBRARIES
+      )
+    # get just the filename of that path
+    # (to deal with the possibility that it might be 'libomp.dylib' or 'libgomp.dylib' or 'libiomp.dylib')
+    get_filename_component(
+        OpenMP_LIBRARY_NAME
+        ${OpenMP_LIBRARY_LOCATION}
+        NAME
+      )
+    # get directory of that path
+    get_filename_component(
+        OpenMP_LIBRARY_DIR
+        ${OpenMP_LIBRARY_LOCATION}
+        DIRECTORY
+      )
+
+    # 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.
+    add_custom_command(
+        TARGET _sparse_dot_topn_core
+        POST_BUILD
+          COMMAND
+            install_name_tool
+            -change
+            ${OpenMP_LIBRARY_LOCATION}
+            "@rpath/${OpenMP_LIBRARY_NAME}"
+            $<TARGET_FILE:_sparse_dot_topn_core>
+          WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+          COMMENT "Replacing hard-coded OpenMP install_name with '@rpath/${OpenMP_LIBRARY_NAME}'..."
+      )
+    if (SDTN_VENDOR_OPENMP)
+      set(OpenMP_target_location ${CMAKE_INSTALL_PREFIX}/${PROJECT_NAME}/.dylibs/${OpenMP_LIBRARY_NAME})
+
+      message(STATUS "Copying ${OpenMP_LIBRARY_NAME} to ${OpenMP_target_location}")
+      add_custom_command(
+          TARGET _sparse_dot_topn_core
+          POST_BUILD
+          COMMAND ${CMAKE_COMMAND} -E copy
+          ${OpenMP_LIBRARY_LOCATION}
+          ${OpenMP_target_location}
+      )
+      # add RPATH entries to ensure the loader looks in the following, in the following order:
+      #   - @loader_path/../.dylibs/     the dylib we're shipping alongside
+      set_target_properties(
+          _sparse_dot_topn_core
+          PROPERTIES
+            BUILD_WITH_INSTALL_RPATH TRUE
+            INSTALL_RPATH "@loader_path/../.dylibs/"
+            INSTALL_RPATH_USE_LINK_PATH FALSE
+        )
+    else()
+      # add RPATH entries to ensure the loader looks in the following, in the following order:
+      #   - ${OpenMP_LIBRARY_DIR}        (wherever find_package(OpenMP) found OpenMP at build time)
+      #   - /opt/homebrew/opt/libomp/lib (where 'brew install' / 'brew link' puts libomp.dylib)
+      set_target_properties(
+          _sparse_dot_topn_core
+          PROPERTIES
+            BUILD_WITH_INSTALL_RPATH TRUE
+            INSTALL_RPATH "${OpenMP_LIBRARY_DIR};/opt/homebrew/opt/libomp/lib"
+            INSTALL_RPATH_USE_LINK_PATH FALSE
+        )
+
+    endif()
+  endif()
 endif()
 
 target_compile_definitions(_sparse_dot_topn_core PRIVATE VERSION_INFO=${SKBUILD_PROJECT_VERSION})
 
 # -- Optional
 if(SDTN_ENABLE_DEVMODE)
-    target_compile_options(_sparse_dot_topn_core PRIVATE ${SDTN_DEVMODE_OPTIONS})
+  target_compile_options(_sparse_dot_topn_core PRIVATE ${SDTN_DEVMODE_OPTIONS})
 endif()
 
 # -- Options & Properties
@@ -19,41 +91,41 @@ set_property(TARGET _sparse_dot_topn_core PROPERTY POSITION_INDEPENDENT_CODE ON)
 include(CheckCXXCompilerFlag)
 
 function(check_cxx_support FLAG DEST)
-    string(SUBSTRING ${FLAG} 1 -1 STRIPPED_FLAG)
-    string(REGEX REPLACE "=" "_" STRIPPED_FLAG ${STRIPPED_FLAG})
-    string(TOUPPER ${STRIPPED_FLAG} STRIPPED_FLAG)
-    set(RES_VAR "${STRIPPED_FLAG}_SUPPORTED")
-    check_cxx_compiler_flag("${FLAG}" ${RES_VAR})
-    if(${RES_VAR})
-        set(${DEST} "${${DEST}} ${FLAG}" PARENT_SCOPE)
-    endif()
+  string(SUBSTRING ${FLAG} 1 -1 STRIPPED_FLAG)
+  string(REGEX REPLACE "=" "_" STRIPPED_FLAG ${STRIPPED_FLAG})
+  string(TOUPPER ${STRIPPED_FLAG} STRIPPED_FLAG)
+  set(RES_VAR "${STRIPPED_FLAG}_SUPPORTED")
+  check_cxx_compiler_flag("${FLAG}" ${RES_VAR})
+  if(${RES_VAR})
+    set(${DEST} "${${DEST}} ${FLAG}" PARENT_SCOPE)
+  endif()
 endfunction()
 
 # -- Compiler Flags
 if (SDTN_ENABLE_ARCH_FLAGS AND "${CMAKE_CXX_FLAGS}" STREQUAL "${CMAKE_CXX_FLAGS_DEFAULT}")
-    set(SDTN_ARCHITECTURE_FLAGS "")
-    if (APPLE AND (${CMAKE_SYSTEM_PROCESSOR} STREQUAL "arm64"))
-        # see https://github.com/google/highway/issues/745
-        check_cxx_support("-march=native" SDTN_ARCHITECTURE_FLAGS)
-    else()
-        include(FindSse)
-        include(FindAvx)
-        SDTN_CHECK_FOR_SSE()
-        add_definitions(${SSE_DEFINITIONS})
-        SDTN_CHECK_FOR_AVX()
-        string(APPEND SDTN_ARCHITECTURE_FLAGS "${SSE_FLAGS} ${AVX_FLAGS}")
-    endif()
+  set(SDTN_ARCHITECTURE_FLAGS "")
+  if (APPLE AND (${CMAKE_SYSTEM_PROCESSOR} STREQUAL "arm64"))
+    # see https://github.com/google/highway/issues/745
+    check_cxx_support("-march=native" SDTN_ARCHITECTURE_FLAGS)
+  else()
+    include(FindSse)
+    include(FindAvx)
+    SDTN_CHECK_FOR_SSE()
+    add_definitions(${SSE_DEFINITIONS})
+    SDTN_CHECK_FOR_AVX()
+    string(APPEND SDTN_ARCHITECTURE_FLAGS "${SSE_FLAGS} ${AVX_FLAGS}")
+  endif()
 
-    if (NOT ${SDTN_ARCHITECTURE_FLAGS} STREQUAL "")
-        string(STRIP ${SDTN_ARCHITECTURE_FLAGS} SDTN_ARCHITECTURE_FLAGS)
-        message(STATUS "sparse-dot-topn | Enabled arch flags: ${SDTN_ARCHITECTURE_FLAGS}")
-        if (MSVC)
-            separate_arguments(SDTN_ARCHITECTURE_FLAGS WINDOWS_COMMAND "${SDTN_ARCHITECTURE_FLAGS}")
-        else()
-            separate_arguments(SDTN_ARCHITECTURE_FLAGS UNIX_COMMAND "${SDTN_ARCHITECTURE_FLAGS}")
-        endif()
-        target_compile_options(_sparse_dot_topn_core PRIVATE $<$<CONFIG:RELEASE>:${SDTN_ARCHITECTURE_FLAGS}>)
+  if (NOT ${SDTN_ARCHITECTURE_FLAGS} STREQUAL "")
+    string(STRIP ${SDTN_ARCHITECTURE_FLAGS} SDTN_ARCHITECTURE_FLAGS)
+    message(STATUS "sparse-dot-topn | Enabled arch flags: ${SDTN_ARCHITECTURE_FLAGS}")
+    if (MSVC)
+      separate_arguments(SDTN_ARCHITECTURE_FLAGS WINDOWS_COMMAND "${SDTN_ARCHITECTURE_FLAGS}")
     else()
-        message(STATUS "sparse-dot-topn | Architecture flags enabled but no valid flags were found")
+      separate_arguments(SDTN_ARCHITECTURE_FLAGS UNIX_COMMAND "${SDTN_ARCHITECTURE_FLAGS}")
     endif()
+    target_compile_options(_sparse_dot_topn_core PRIVATE $<$<CONFIG:RELEASE>:${SDTN_ARCHITECTURE_FLAGS}>)
+  else()
+    message(STATUS "sparse-dot-topn | Architecture flags enabled but no valid flags were found")
+  endif()
 endif()

src/sparse_dot_topn_core/cmake/FindAvx.cmake

@@ -1,4 +1,4 @@
-###############################################################################
+# ##############################################################################
 # Check for the presence of AVX and figure out the flags to use for it.
 # This routine is a modified version of `PCL_CHECK_FOR_AVX`
 # Reference: https://github.com/PointCloudLibrary/pcl/blob/master/cmake/pcl_find_avx.cmake

src/sparse_dot_topn_core/cmake/FindSse.cmake

@@ -1,4 +1,4 @@
-###############################################################################
+# ##############################################################################
 # Check for the presence of SSE and figure out the flags to use for it.
 # This routine is a modified version of `PCL_CHECK_FOR_SSE`
 # https://github.com/PointCloudLibrary/pcl/blob/master/cmake/pcl_find_sse.cmake