Merge branch 'master' into gtest_32bit

.github/dependabot.yml

@@ -12,7 +12,7 @@ updates:
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j"
     schedule:
-      interval: "daily"
+      interval: "monthly"
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j-gpu"
     schedule:
@@ -24,7 +24,7 @@ updates:
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j-spark"
     schedule:
-      interval: "daily"
+      interval: "monthly"
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j-spark-gpu"
     schedule:

.github/workflows/freebsd.yml

@@ -0,0 +1,33 @@
+name: FreeBSD
+
+on: [push, pull_request]
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    name: A job to run test in FreeBSD
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: 'true'
+    - name: Test in FreeBSD
+      id: test
+      uses: vmactions/freebsd-vm@v1
+      with:
+        usesh: true
+        prepare: |
+          pkg install -y cmake git ninja googletest
+
+        run: |
+          mkdir build
+          cd build
+          cmake .. -GNinja -DGOOGLE_TEST=ON
+          ninja -v
+          ./testxgboost

.github/workflows/i386.yml

@@ -23,11 +23,11 @@ jobs:
       with:
         submodules: 'true'
     - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v3
+      uses: docker/setup-buildx-action@v3.6.1
       with:
         driver-opts: network=host
     - name: Build and push container
-      uses: docker/build-push-action@v5
+      uses: docker/build-push-action@v6
       with:
         context: .
         file: tests/ci_build/Dockerfile.i386

.github/workflows/jvm_tests.yml

@@ -12,6 +12,7 @@ concurrency:
 jobs:
   test-with-jvm:
     name: Test JVM on OS ${{ matrix.os }}
+    timeout-minutes: 30
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -23,7 +24,7 @@ jobs:
       with:
         submodules: 'true'
 
-    - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9  # v4.2.1
+    - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018  # v4.2.2
       with:
         distribution: 'temurin'
         java-version: '8'

.github/workflows/main.yml

@@ -74,7 +74,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8"]
+        python-version: ["3.10"]
     steps:
     - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
       with:
@@ -95,7 +95,7 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake .. -DGOOGLE_TEST=ON -DUSE_DMLC_GTEST=ON -DPLUGIN_SYCL=ON -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
+        cmake .. -DGOOGLE_TEST=ON -DUSE_DMLC_GTEST=ON -DPLUGIN_SYCL=ON -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
         make -j$(nproc)
     - name: Run gtest binary for SYCL
       run: |
@@ -116,7 +116,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.8"]
+        python-version: ["3.10"]
     steps:
     - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
       with:
@@ -180,9 +180,9 @@ jobs:
     - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
       with:
         submodules: 'true'
-    - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
       with:
-        python-version: "3.8"
+        python-version: "3.10"
         architecture: 'x64'
     - name: Install Python packages
       run: |

.github/workflows/python_tests.yml

@@ -84,7 +84,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-13, windows-latest]
-        python-version: ["3.8"]
+        python-version: ["3.10"]
     steps:
     - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
       with:
@@ -174,7 +174,7 @@ jobs:
     strategy:
       matrix:
         config:
-          - {os: windows-latest, python-version: '3.8'}
+          - {os: windows-latest, python-version: '3.10'}
 
     steps:
     - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
@@ -218,7 +218,7 @@ jobs:
     strategy:
       matrix:
         config:
-          - {os: ubuntu-latest, python-version: "3.8"}
+          - {os: ubuntu-latest, python-version: "3.10"}
 
     steps:
     - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
@@ -271,7 +271,7 @@ jobs:
     strategy:
       matrix:
         config:
-          - {os: ubuntu-latest, python-version: "3.8"}
+          - {os: ubuntu-latest, python-version: "3.10"}
 
     steps:
     - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
@@ -294,7 +294,7 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake .. -DPLUGIN_SYCL=ON -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
+        cmake .. -DPLUGIN_SYCL=ON -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
         make -j$(nproc)
     - name: Install Python package
       run: |
@@ -318,10 +318,10 @@ jobs:
         with:
           submodules: 'true'
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
+      - name: Set up Python 3.10
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
-          python-version: 3.8
+          python-version: "3.10"
 
       - name: Install ninja
         run: |

.github/workflows/python_wheels.yml

@@ -28,11 +28,15 @@ 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
         miniforge-version: latest
-        python-version: 3.9
+        python-version: "3.10"
         use-mamba: true
     - name: Build wheels
       run: bash tests/ci_build/build_python_wheels.sh ${{ matrix.platform_id }} ${{ github.sha }}

.github/workflows/r_tests.yml

@@ -84,9 +84,9 @@ jobs:
         key: ${{ runner.os }}-r-${{ matrix.config.r }}-7-${{ hashFiles('R-package/DESCRIPTION') }}
         restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-7-${{ hashFiles('R-package/DESCRIPTION') }}
 
-    - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
       with:
-        python-version: "3.8"
+        python-version: "3.10"
         architecture: 'x64'
 
     - uses: r-lib/actions/setup-tinytex@v2

.github/workflows/scorecards.yml

@@ -27,7 +27,7 @@ jobs:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@dc50aa9510b46c811795eb24b2f1ba02a914e534 # v2.3.3
+        uses: ossf/scorecard-action@62b2cac7ed8198b15735ed49ab1e5cf35480ba46 # v2.4.0
         with:
           results_file: results.sarif
           results_format: sarif
@@ -41,7 +41,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
         with:
           name: SARIF file
           path: results.sarif

.gitignore

@@ -33,6 +33,7 @@ ipch
 *.filters
 *.user
 *log
+rmm_log.txt
 Debug
 *suo
 .Rhistory
@@ -63,6 +64,7 @@ java/xgboost4j-demo/data/
 java/xgboost4j-demo/tmp/
 java/xgboost4j-demo/model/
 nb-configuration*
+
 # Eclipse
 .project
 .cproject
@@ -84,6 +86,7 @@ target
 *.gcov
 *.gcda
 *.gcno
+*.ubj
 build_tests
 /tests/cpp/xgboost_test
 
@@ -97,6 +100,7 @@ metastore_db
 
 # files from R-package source install
 **/config.status
+R-package/config.h
 R-package/src/Makevars
 *.lib
 
@@ -152,3 +156,6 @@ model*.json
 *.rds
 Rplots.pdf
 *.zip
+
+# nsys
+*.nsys-rep

CMakeLists.txt

@@ -1,8 +1,6 @@
 cmake_minimum_required(VERSION 3.18 FATAL_ERROR)
 
 if(PLUGIN_SYCL)
-  set(CMAKE_CXX_COMPILER  "g++")
-  set(CMAKE_C_COMPILER  "gcc")
   string(REPLACE " -isystem ${CONDA_PREFIX}/include" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
 endif()
 
@@ -73,7 +71,6 @@ option(HIDE_CXX_SYMBOLS "Build shared library and hide all C++ symbols" OFF)
 option(KEEP_BUILD_ARTIFACTS_IN_BINARY_DIR "Output build artifacts in CMake binary dir" OFF)
 ## CUDA
 option(USE_CUDA  "Build with GPU acceleration" OFF)
-option(USE_PER_THREAD_DEFAULT_STREAM "Build with per-thread default stream" ON)
 option(USE_NCCL  "Build with NCCL to enable distributed GPU support." OFF)
 # This is specifically designed for PyPI binary release and should be disabled for most of the cases.
 option(USE_DLOPEN_NCCL "Whether to load nccl dynamically." OFF)
@@ -221,9 +218,26 @@ if(USE_CUDA)
   if(DEFINED GPU_COMPUTE_VER)
     compute_cmake_cuda_archs("${GPU_COMPUTE_VER}")
   endif()
-  add_subdirectory(${PROJECT_SOURCE_DIR}/gputreeshap)
 
   find_package(CUDAToolkit REQUIRED)
+  find_package(CCCL CONFIG)
+  if(NOT CCCL_FOUND)
+    message(STATUS "Standalone CCCL not found. Attempting to use CCCL from CUDA Toolkit...")
+    find_package(CCCL CONFIG
+      HINTS ${CUDAToolkit_LIBRARY_DIR}/cmake)
+    if(NOT CCCL_FOUND)
+      message(STATUS "Could not locate CCCL from CUDA Toolkit. Using Thrust and CUB from CUDA Toolkit...")
+      find_package(libcudacxx CONFIG REQUIRED
+        HINTS ${CUDAToolkit_LIBRARY_DIR}/cmake)
+      find_package(CUB CONFIG REQUIRED
+        HINTS ${CUDAToolkit_LIBRARY_DIR}/cmake)
+      find_package(Thrust CONFIG REQUIRED
+        HINTS ${CUDAToolkit_LIBRARY_DIR}/cmake)
+      thrust_create_target(Thrust HOST CPP DEVICE CUDA)
+      add_library(CCCL::CCCL INTERFACE IMPORTED GLOBAL)
+      target_link_libraries(CCCL::CCCL INTERFACE libcudacxx::libcudacxx CUB::CUB Thrust)
+    endif()
+  endif()
 endif()
 
 if(FORCE_COLORED_OUTPUT AND (CMAKE_GENERATOR STREQUAL "Ninja") AND
@@ -234,28 +248,17 @@ endif()
 
 find_package(Threads REQUIRED)
 
+# -- OpenMP
+include(cmake/FindOpenMPMacOS.cmake)
 if(USE_OPENMP)
   if(APPLE)
-    find_package(OpenMP)
-    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 ${HOMEBREW_LIBOMP_PREFIX}/lib/libomp.dylib)
-      find_package(OpenMP REQUIRED)
-    endif()
+    find_openmp_macos()
   else()
     find_package(OpenMP REQUIRED)
   endif()
 endif()
-#Add for IBM i
+
+# Add for IBM i
 if(${CMAKE_SYSTEM_NAME} MATCHES "OS400")
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
   set(CMAKE_CXX_ARCHIVE_CREATE "<CMAKE_AR> -X64 qc <TARGET> <OBJECTS>")
@@ -380,6 +383,10 @@ 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()

NEWS.md

@@ -1,6 +1,8 @@
 XGBoost Change Log
 ==================
 
+**Starting from 2.1.0, release note is recorded in the documentation.**
+
 This file records the changes in xgboost library in reverse chronological order.
 
 ## 2.0.0 (2023 Aug 16)

R-package/DESCRIPTION

@@ -57,7 +57,8 @@ Suggests:
     igraph (>= 1.0.1),
     float,
     titanic,
-    RhpcBLASctl
+    RhpcBLASctl,
+    survival
 Depends:
     R (>= 4.3.0)
 Imports:
@@ -66,6 +67,6 @@ Imports:
     data.table (>= 1.9.6),
     jsonlite (>= 1.0)
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 SystemRequirements: GNU make, C++17

R-package/NAMESPACE

@@ -13,6 +13,7 @@ S3method(predict,xgb.Booster)
 S3method(print,xgb.Booster)
 S3method(print,xgb.DMatrix)
 S3method(print,xgb.cv.synchronous)
+S3method(print,xgboost)
 S3method(setinfo,xgb.Booster)
 S3method(setinfo,xgb.DMatrix)
 S3method(variable.names,xgb.Booster)