[jvm-packages] update version of 1.1.0 branch (#6435)

* [CI] Throttle Jenkins CI

* Don't use Jenkins master instance

.travis.yml

@@ -6,7 +6,7 @@ os:
   - linux
   - osx
 
-osx_image: xcode10.3
+osx_image: xcode10.1
 dist: bionic
 
 # Use Build Matrix to do lint and build seperately
@@ -21,6 +21,10 @@ env:
     # cmake test
     - TASK=cmake_test
 
+  global:
+    - secure: "PR16i9F8QtNwn99C5NDp8nptAS+97xwDtXEJJfEiEVhxPaaRkOp0MPWhogCaK0Eclxk1TqkgWbdXFknwGycX620AzZWa/A1K3gAs+GrpzqhnPMuoBJ0Z9qxXTbSJvCyvMbYwVrjaxc/zWqdMU8waWz8A7iqKGKs/SqbQ3rO6v7c="
+    - secure: "dAGAjBokqm/0nVoLMofQni/fWIBcYSmdq4XvCBX1ZAMDsWnuOfz/4XCY6h2lEI1rVHZQ+UdZkc9PioOHGPZh5BnvE49/xVVWr9c4/61lrDOlkD01ZjSAeoV0fAZq+93V/wPl4QV+MM+Sem9hNNzFSbN5VsQLAiWCSapWsLdKzqA="
+
 matrix:
   exclude:
     - os: linux

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.13)
-project(xgboost LANGUAGES CXX C VERSION 1.1.0)
+project(xgboost LANGUAGES CXX C VERSION 1.1.1)
 include(cmake/Utils.cmake)
 list(APPEND CMAKE_MODULE_PATH "${xgboost_SOURCE_DIR}/cmake/modules")
 cmake_policy(SET CMP0022 NEW)
@@ -57,6 +57,7 @@ address, leak, undefined and thread.")
 ## Plugins
 option(PLUGIN_LZ4 "Build lz4 plugin" OFF)
 option(PLUGIN_DENSE_PARSER "Build dense parser plugin" OFF)
+option(ADD_PKGCONFIG "Add xgboost.pc into system." ON)
 
 #-- Checks for building XGBoost
 if (USE_DEBUG_OUTPUT AND (NOT (CMAKE_BUILD_TYPE MATCHES Debug)))
@@ -274,3 +275,12 @@ endif (GOOGLE_TEST)
 # replace /MD with /MT. See https://github.com/dmlc/xgboost/issues/4462
 # for issues caused by mixing of /MD and /MT flags
 msvc_use_static_runtime()
+
+# Add xgboost.pc
+if (ADD_PKGCONFIG)
+  configure_file(${xgboost_SOURCE_DIR}/cmake/xgboost.pc.in ${xgboost_BINARY_DIR}/xgboost.pc @ONLY)
+
+  install(
+    FILES ${xgboost_BINARY_DIR}/xgboost.pc
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+endif (ADD_PKGCONFIG)

Jenkinsfile

@@ -31,13 +31,14 @@ pipeline {
 
   // Build stages
   stages {
-    stage('Jenkins Linux: Get sources') {
+    stage('Jenkins Linux: Initialize') {
-      agent { label 'linux && cpu' }
+      agent { label 'job_initializer' }
       steps {
         script {
           checkoutSrcs()
           commit_id = "${GIT_COMMIT}"
         }
+        sh 'python3 tests/jenkins_get_approval.py'
         stash name: 'srcs'
         milestone ordinal: 1
       }
@@ -48,7 +49,6 @@ pipeline {
         script {
           parallel ([
             'clang-tidy': { ClangTidy() },
-            'lint': { Lint() },
             'sphinx-doc': { SphinxDoc() },
             'doxygen': { Doxygen() }
           ])
@@ -64,7 +64,6 @@ pipeline {
             'build-cpu': { BuildCPU() },
             'build-cpu-rabit-mock': { BuildCPUMock() },
             'build-cpu-non-omp': { BuildCPUNonOmp() },
-            'build-gpu-cuda9.0': { BuildCUDA(cuda_version: '9.0') },
             'build-gpu-cuda10.0': { BuildCUDA(cuda_version: '10.0') },
             'build-gpu-cuda10.1': { BuildCUDA(cuda_version: '10.1') },
             'build-jvm-packages': { BuildJVMPackages(spark_version: '2.4.3') },
@@ -251,10 +250,10 @@ def BuildCUDA(args) {
     ${dockerRun} ${container_type} ${docker_binary} ${docker_args} bash -c "cd python-package && rm -rf dist/* && python setup.py bdist_wheel --universal"
     ${dockerRun} ${container_type} ${docker_binary} ${docker_args} python3 tests/ci_build/rename_whl.py python-package/dist/*.whl ${commit_id} manylinux2010_x86_64
     """
-    // Stash wheel for CUDA 9.0 target
+    // Stash wheel for CUDA 10.0 target
-    if (args.cuda_version == '9.0') {
+    if (args.cuda_version == '10.0') {
       echo 'Stashing Python wheel...'
-      stash name: 'xgboost_whl_cuda9', includes: 'python-package/dist/*.whl'
+      stash name: 'xgboost_whl_cuda10', includes: 'python-package/dist/*.whl'
       path = ("${BRANCH_NAME}" == 'master') ? '' : "${BRANCH_NAME}/"
       s3Upload bucket: 'xgboost-nightly-builds', path: path, acl: 'PublicRead', workingDir: 'python-package/dist', includePathPattern:'**/*.whl'
       echo 'Stashing C++ test executable (testxgboost)...'
@@ -298,7 +297,7 @@ def BuildJVMDoc() {
 
 def TestPythonCPU() {
   node('linux && cpu') {
-    unstash name: 'xgboost_whl_cuda9'
+    unstash name: 'xgboost_whl_cuda10'
     unstash name: 'srcs'
     unstash name: 'xgboost_cli'
     echo "Test Python CPU"
@@ -315,7 +314,7 @@ def TestPythonCPU() {
 def TestPythonGPU(args) {
   nodeReq = (args.multi_gpu) ? 'linux && mgpu' : 'linux && gpu'
   node(nodeReq) {
-    unstash name: 'xgboost_whl_cuda9'
+    unstash name: 'xgboost_whl_cuda10'
     unstash name: 'srcs'
     echo "Test Python GPU: CUDA ${args.cuda_version}"
     def container_type = "gpu"
@@ -326,25 +325,12 @@ def TestPythonGPU(args) {
       sh """
       ${dockerRun} ${container_type} ${docker_binary} ${docker_args} tests/ci_build/test_python.sh mgpu
       """
-      if (args.cuda_version != '9.0') {
-        echo "Running tests with cuDF..."
-        sh """
-        ${dockerRun} cudf ${docker_binary} ${docker_args} tests/ci_build/test_python.sh mgpu-cudf
-        """
-      }
     } else {
       echo "Using a single GPU"
       sh """
       ${dockerRun} ${container_type} ${docker_binary} ${docker_args} tests/ci_build/test_python.sh gpu
       """
-      if (args.cuda_version != '9.0') {
-        echo "Running tests with cuDF..."
-        sh """
-        ${dockerRun} cudf ${docker_binary} ${docker_args} tests/ci_build/test_python.sh cudf
-        """
     }
-    }
-    // For CUDA 10.0 target, run cuDF tests too
     deleteDir()
   }
 }

Jenkinsfile-win64

@@ -12,13 +12,14 @@ pipeline {
   agent none
   // Build stages
   stages {
-    stage('Jenkins Win64: Get sources') {
+    stage('Jenkins Win64: Initialize') {
-      agent { label 'win64 && build' }
+      agent { label 'job_initializer' }
       steps {
         script {
           checkoutSrcs()
           commit_id = "${GIT_COMMIT}"
         }
+        sh 'python3 tests/jenkins_get_approval.py'
         stash name: 'srcs'
         milestone ordinal: 1
       }
@@ -28,7 +29,7 @@ pipeline {
       steps {
         script {
           parallel ([
-            'build-win64-cuda9.0': { BuildWin64() }
+            'build-win64-cuda10.0': { BuildWin64() }
           ])
         }
         milestone ordinal: 2
@@ -40,8 +41,6 @@ pipeline {
         script {
           parallel ([
             'test-win64-cpu': { TestWin64CPU() },
-            'test-win64-gpu-cuda9.0': { TestWin64GPU(cuda_target: 'cuda9') },
-            'test-win64-gpu-cuda10.0': { TestWin64GPU(cuda_target: 'cuda10_0') },
             'test-win64-gpu-cuda10.1': { TestWin64GPU(cuda_target: 'cuda10_1') }
           ])
         }
@@ -67,7 +66,7 @@ def checkoutSrcs() {
 }
 
 def BuildWin64() {
-  node('win64 && build') {
+  node('win64 && build && cuda10') {
     unstash name: 'srcs'
     echo "Building XGBoost for Windows AMD64 target..."
     bat "nvcc --version"
@@ -139,7 +138,7 @@ def TestWin64GPU(args) {
     """
     echo "Installing Python dependencies..."
     bat """
-     conda activate && conda upgrade scikit-learn pandas numpy
+     conda activate && conda upgrade scikit-learn pandas numpy && python -m pip uninstall -y cupy-cuda100 cupy-cuda101 cupy-cuda102
     """
     echo "Running Python tests..."
     bat """

R-package/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: xgboost
 Type: Package
 Title: Extreme Gradient Boosting
-Version: 1.1.0.1
+Version: 1.1.1.1
 Date: 2020-02-21
 Authors@R: c(
   person("Tianqi", "Chen", role = c("aut"),

R-package/configure

@@ -2698,7 +2698,7 @@ fi
 if test `uname -s` = "Darwin"
 then
   OPENMP_CXXFLAGS='-Xclang -fopenmp'
-  OPENMP_LIB='/usr/local/lib/libomp.dylib'
+  OPENMP_LIB='-lomp'
   ac_pkg_openmp=no
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether OpenMP will work in a package" >&5
 $as_echo_n "checking whether OpenMP will work in a package... " >&6; }

R-package/configure.ac

@@ -29,7 +29,7 @@ fi
 if test `uname -s` = "Darwin"
 then
   OPENMP_CXXFLAGS='-Xclang -fopenmp'
-  OPENMP_LIB='/usr/local/lib/libomp.dylib'
+  OPENMP_LIB='-lomp'
   ac_pkg_openmp=no
   AC_MSG_CHECKING([whether OpenMP will work in a package])
   AC_LANG_CONFTEST([AC_LANG_PROGRAM([[#include <omp.h>]], [[ return (omp_get_max_threads() <= 1); ]])])

R-package/vignettes/xgboostPresentation.Rmd

@@ -410,7 +410,7 @@ In some very specific cases, like when you want to pilot **XGBoost** from `caret
 
 ```{r saveLoadRBinVectorModel, message=F, warning=F}
 # save model to R's raw vector
-rawVec <- xgb.save.raw(bst)
+rawVec <- xgb.serialize(bst)
 
 # print class
 print(class(rawVec))

cmake/Python_version.in

@@ -1 +1 @@
-@xgboost_VERSION_MAJOR@.@xgboost_VERSION_MINOR@.@xgboost_VERSION_PATCH@-SNAPSHOT
+@xgboost_VERSION_MAJOR@.@xgboost_VERSION_MINOR@.@xgboost_VERSION_PATCH@

cmake/xgboost.pc.in

@@ -0,0 +1,12 @@
+prefix=@CMAKE_INSTALL_PREFIX@
+version=@xgboost_VERSION@
+exec_prefix=${prefix}/bin
+libdir=${prefix}/lib
+includedir=${prefix}/include
+
+Name: xgboost
+Description: XGBoost - Scalable and Flexible Gradient Boosting.
+Version: ${version}
+
+Cflags: -I${includedir}
+Libs: -L${libdir} -lxgboost

doc/dump.schema

@@ -0,0 +1,55 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "definitions": {
+        "split_node": {
+            "type": "object",
+            "properties": {
+                "nodeid": {
+                    "type": "number",
+                    "minimum": 0
+                },
+                "depth": {
+                    "type": "number",
+                    "minimum": 0
+                },
+                "yes": {
+                    "type": "number",
+                    "minimum": 0
+                },
+                "no": {
+                    "type": "number",
+                    "minimum": 0
+                },
+                "split": {
+                    "type": "string"
+                },
+                "children": {
+                    "type": "array",
+                    "items": {
+                        "oneOf": [
+                            {"$ref": "#/definitions/split_node"},
+                            {"$ref": "#/definitions/leaf_node"}
+                        ]
+                    },
+                    "maxItems": 2
+                }
+            },
+            "required": ["nodeid", "depth", "yes", "no", "split", "children"]
+        },
+        "leaf_node": {
+            "type": "object",
+            "properties": {
+                "nodeid": {
+                    "type": "number",
+                    "minimum": 0
+                },
+                "leaf": {
+                    "type": "number"
+                }
+            },
+            "required": ["nodeid", "leaf"]
+        }
+    },
+    "type": "object",
+    "$ref": "#/definitions/split_node"
+}

doc/tutorials/aft_survival_analysis.rst

@@ -35,7 +35,7 @@ There are four kinds of censoring:
 
 * **Uncensored**: the label is not censored and given as a single number.
 * **Right-censored**: the label is of form :math:`[a, +\infty)`, where :math:`a` is the lower bound.
-* **Left-censored**: the label is of form :math:`(-\infty, b]`, where :math:`b` is the upper bound.
+* **Left-censored**: the label is of form :math:`[0, b]`, where :math:`b` is the upper bound.
 * **Interval-censored**: the label is of form :math:`[a, b]`, where :math:`a` and :math:`b` are the lower and upper bounds, respectively.
 
 Right-censoring is the most commonly used.
@@ -83,7 +83,7 @@ Censoring type    Interval form        Lower bound finite? Upper bound finite?
 ================= ==================== =================== ===================
 Uncensored        :math:`[a, a]`       |tick|              |tick|
 Right-censored    :math:`[a, +\infty)` |tick|              |cross|
-Left-censored     :math:`(-\infty, b]` |cross|             |tick|
+Left-censored     :math:`[0, b]`       |tick|              |tick|
 Interval-censored :math:`[a, b]`       |tick|              |tick|
 ================= ==================== =================== ===================
 
@@ -102,7 +102,7 @@ Collect the lower bound numbers in one array (let's call it ``y_lower_bound``) a
   # Associate ranged labels with the data matrix.
   # This example shows each kind of censored labels.
   #                         uncensored    right     left  interval
-  y_lower_bound = np.array([      2.0,     3.0, -np.inf,     4.0])
+  y_lower_bound = np.array([      2.0,     3.0,     0.0,     4.0])
   y_upper_bound = np.array([      2.0, +np.inf,     4.0,     5.0])
   dtrain.set_float_info('label_lower_bound', y_lower_bound)
   dtrain.set_float_info('label_upper_bound', y_upper_bound)
@@ -120,7 +120,7 @@ Collect the lower bound numbers in one array (let's call it ``y_lower_bound``) a
   # Associate ranged labels with the data matrix.
   # This example shows each kind of censored labels.
   #                   uncensored  right  left  interval
-  y_lower_bound <- c(        2.,    3., -Inf,       4.)
+  y_lower_bound <- c(        2.,    3.,   0.,       4.)
   y_upper_bound <- c(        2.,  +Inf,   4.,       5.)
   setinfo(dtrain, 'label_lower_bound', y_lower_bound)
   setinfo(dtrain, 'label_upper_bound', y_upper_bound)
@@ -136,7 +136,7 @@ Now we are ready to invoke the training API:
             'aft_loss_distribution_scale': 1.20,
             'tree_method': 'hist', 'learning_rate': 0.05, 'max_depth': 2}
   bst = xgb.train(params, dtrain, num_boost_round=5,
-                  evals=[(dtrain, 'train'), (dvalid, 'valid')])
+                  evals=[(dtrain, 'train')])
 
 .. code-block:: r
   :caption: R

include/xgboost/c_api.h

@@ -418,7 +418,14 @@ XGB_DLL int XGBoosterEvalOneIter(BoosterHandle handle,
  *          4:output feature contributions to individual predictions
  * \param ntree_limit limit number of trees used for prediction, this is only valid for boosted trees
  *    when the parameter is set to 0, we will use all the trees
- * \param training Whether the prediction value is used for training.
+ * \param training Whether the prediction function is used as part of a training loop.
+ *    Prediction can be run in 2 scenarios:
+ *    1. Given data matrix X, obtain prediction y_pred from the model.
+ *    2. Obtain the prediction for computing gradients. For example, DART booster performs dropout
+ *       during training, and the prediction result will be different from the one obtained by normal
+ *       inference step due to dropped trees.
+ *    Set training=false for the first scenario. Set training=true for the second scenario.
+ *    The second scenario applies when you are defining a custom objective function.
  * \param out_len used to store length of returning result
  * \param out_result used to set a pointer to array
  * \return 0 when success, -1 when failure happens

include/xgboost/data.h

@@ -9,6 +9,7 @@
 
 #include <dmlc/base.h>
 #include <dmlc/data.h>
+#include <dmlc/serializer.h>
 #include <rabit/rabit.h>
 #include <xgboost/base.h>
 #include <xgboost/span.h>
@@ -102,7 +103,7 @@ class MetaInfo {
   /*!
    * \brief Validate all metainfo.
    */
-  void Validate() const;
+  void Validate(int32_t device) const;
 
   MetaInfo Slice(common::Span<int32_t const> ridxs) const;
   /*!
@@ -554,5 +555,21 @@ inline BatchSet<EllpackPage> DMatrix::GetBatches(const BatchParam& param) {
 
 namespace dmlc {
 DMLC_DECLARE_TRAITS(is_pod, xgboost::Entry, true);
-}
+
+namespace serializer {
+
+template <>
+struct Handler<xgboost::Entry> {
+  inline static void Write(Stream* strm, const xgboost::Entry& data) {
+    strm->Write(data.index);
+    strm->Write(data.fvalue);
+  }
+
+  inline static bool Read(Stream* strm, xgboost::Entry* data) {
+    return strm->Read(&data->index) && strm->Read(&data->fvalue);
+  }
+};
+
+}  // namespace serializer
+}  // namespace dmlc
 #endif  // XGBOOST_DATA_H_

include/xgboost/span.h

@@ -30,6 +30,7 @@
 #define XGBOOST_SPAN_H_
 
 #include <xgboost/base.h>
+#include <xgboost/logging.h>
 
 #include <cinttypes>          // size_t
 #include <limits>             // numeric_limits
@@ -85,9 +86,11 @@ namespace common {
     }                                                                          \
   } while (0);
 
-#ifdef __CUDA_ARCH__
+#if defined(__CUDA_ARCH__)
 #define SPAN_CHECK KERNEL_CHECK
-#else
+#elif defined(XGBOOST_STRICT_R_MODE) && XGBOOST_STRICT_R_MODE == 1  // R package
+#define SPAN_CHECK CHECK  // check from dmlc
+#else  // not CUDA, not R
 #define SPAN_CHECK(cond)                                                       \
   do {                                                                         \
     if (XGBOOST_EXPECT(!(cond), false)) {                                      \

include/xgboost/version_config.h

@@ -6,6 +6,6 @@
 
 #define XGBOOST_VER_MAJOR 1
 #define XGBOOST_VER_MINOR 1
-#define XGBOOST_VER_PATCH 0
+#define XGBOOST_VER_PATCH 1
 
 #endif  // XGBOOST_VERSION_CONFIG_H_

jvm-packages/pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>ml.dmlc</groupId>
     <artifactId>xgboost-jvm_2.12</artifactId>
-    <version>1.1.0-SNAPSHOT</version>
+    <version>1.1.2</version>
     <packaging>pom</packaging>
     <name>XGBoost JVM Package</name>
     <description>JVM Package for XGBoost</description>

jvm-packages/xgboost4j-example/pom.xml

@@ -6,10 +6,10 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm_2.12</artifactId>
-        <version>1.1.0-SNAPSHOT</version>
+        <version>1.1.2</version>
     </parent>
     <artifactId>xgboost4j-example_2.12</artifactId>
-    <version>1.1.0-SNAPSHOT</version>
+    <version>1.1.2</version>
     <packaging>jar</packaging>
     <build>
         <plugins>
@@ -26,7 +26,7 @@
         <dependency>
             <groupId>ml.dmlc</groupId>
             <artifactId>xgboost4j-spark_${scala.binary.version}</artifactId>
-            <version>1.1.0-SNAPSHOT</version>
+            <version>1.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.apache.spark</groupId>
@@ -37,7 +37,7 @@
         <dependency>
             <groupId>ml.dmlc</groupId>
             <artifactId>xgboost4j-flink_${scala.binary.version}</artifactId>
-            <version>1.1.0-SNAPSHOT</version>
+            <version>1.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>

jvm-packages/xgboost4j-flink/pom.xml

@@ -6,10 +6,10 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm_2.12</artifactId>
-        <version>1.1.0-SNAPSHOT</version>
+        <version>1.1.2</version>
     </parent>
     <artifactId>xgboost4j-flink_2.12</artifactId>
-    <version>1.1.0-SNAPSHOT</version>
+    <version>1.1.2</version>
     <build>
         <plugins>
             <plugin>
@@ -26,7 +26,7 @@
         <dependency>
             <groupId>ml.dmlc</groupId>
             <artifactId>xgboost4j_${scala.binary.version}</artifactId>
-            <version>1.1.0-SNAPSHOT</version>
+            <version>1.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>

jvm-packages/xgboost4j-spark/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm_2.12</artifactId>
-        <version>1.1.0-SNAPSHOT</version>
+        <version>1.1.2</version>
     </parent>
     <artifactId>xgboost4j-spark_2.12</artifactId>
     <build>
@@ -24,7 +24,7 @@
         <dependency>
             <groupId>ml.dmlc</groupId>
             <artifactId>xgboost4j_${scala.binary.version}</artifactId>
-            <version>1.1.0-SNAPSHOT</version>
+            <version>1.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.apache.spark</groupId>

jvm-packages/xgboost4j/pom.xml

@@ -6,10 +6,10 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm_2.12</artifactId>
-        <version>1.1.0-SNAPSHOT</version>
+        <version>1.1.2</version>
     </parent>
     <artifactId>xgboost4j_2.12</artifactId>
-    <version>1.1.0-SNAPSHOT</version>
+    <version>1.1.2</version>
     <packaging>jar</packaging>
 
     <dependencies>

python-package/xgboost/VERSION

@@ -1 +1 @@
-1.1.0-SNAPSHOT
+1.1.1

python-package/xgboost/core.py

@@ -159,8 +159,9 @@ def _load_lib():
             'XGBoost Library ({}) could not be loaded.\n'.format(libname) +
             'Likely causes:\n' +
             '  * OpenMP runtime is not installed ' +
-            '(vcomp140.dll or libgomp-1.dll for Windows, ' +
+            '(vcomp140.dll or libgomp-1.dll for Windows, libomp.dylib for Mac OSX, ' +
-            'libgomp.so for UNIX-like OSes)\n' +
+            'libgomp.so for Linux and other UNIX-like OSes). Mac OSX users: Run ' +
+            '`brew install libomp` to install OpenMP runtime.\n' +
             '  * You are running 32-bit Python on a 64-bit OS\n' +
             'Error message(s): {}\n'.format(os_error_list))
     lib.XGBGetLastError.restype = ctypes.c_char_p
@@ -1466,6 +1467,7 @@ class Booster(object):
         self._validate_features(data)
         return self.eval_set([(data, name)], iteration)
 
+    # pylint: disable=too-many-function-args
     def predict(self,
                 data,
                 output_margin=False,
@@ -1587,7 +1589,7 @@ class Booster(object):
                 ngroup = int(chunk_size / ((data.num_col() + 1) *
                                            (data.num_col() + 1)))
                 if ngroup == 1:
-                    preds = preds.reshape(nrow,
+                    preds = preds.reshape(nrow,  # pylint: disable=too-many-function-args
                                           data.num_col() + 1,
                                           data.num_col() + 1)
                 else:

src/c_api/c_api.cc

@@ -181,7 +181,7 @@ XGB_DLL int XGDMatrixSliceDMatrixEx(DMatrixHandle handle,
         << "slice does not support group structure";
   }
   DMatrix* dmat = static_cast<std::shared_ptr<DMatrix>*>(handle)->get();
-  *out = new std::shared_ptr<DMatrix>(dmat->Slice({idxset, len}));
+  *out = new std::shared_ptr<DMatrix>(dmat->Slice({idxset, static_cast<std::size_t>(len)}));
   API_END();
 }
 
@@ -426,7 +426,7 @@ XGB_DLL int XGBoosterPredict(BoosterHandle handle,
                              DMatrixHandle dmat,
                              int option_mask,
                              unsigned ntree_limit,
-                             int32_t training,
+                             int training,
                              xgboost::bst_ulong *len,
                              const bst_float **out_result) {
   API_BEGIN();

src/common/column_matrix.h

@@ -82,14 +82,16 @@ template <typename BinIdxType>
 class DenseColumn: public Column<BinIdxType> {
  public:
   DenseColumn(ColumnType type, common::Span<const BinIdxType> index,
-              uint32_t index_base,
+              uint32_t index_base, const std::vector<bool>& missing_flags,
-              const std::vector<bool>::const_iterator missing_flags)
+              size_t feature_offset)
       : Column<BinIdxType>(type, index, index_base),
-        missing_flags_(missing_flags) {}
+        missing_flags_(missing_flags),
-  bool IsMissing(size_t idx) const { return missing_flags_[idx]; }
+        feature_offset_(feature_offset) {}
+  bool IsMissing(size_t idx) const { return missing_flags_[feature_offset_ + idx]; }
  private:
   /* flags for missing values in dense columns */
-  std::vector<bool>::const_iterator missing_flags_;
+  const std::vector<bool>& missing_flags_;
+  size_t feature_offset_;
 };
 
 /*! \brief a collection of columns, with support for construction from
@@ -208,10 +210,8 @@ class ColumnMatrix {
                                                  column_size };
     std::unique_ptr<const Column<BinIdxType> > res;
     if (type_[fid] == ColumnType::kDenseColumn) {
-      std::vector<bool>::const_iterator column_iterator = missing_flags_.begin();
-      advance(column_iterator, feature_offset);  // increment iterator to right position
       res.reset(new DenseColumn<BinIdxType>(type_[fid], bin_index, index_base_[fid],
-                                            column_iterator));
+                                             missing_flags_, feature_offset));
     } else {
       res.reset(new SparseColumn<BinIdxType>(type_[fid], bin_index, index_base_[fid],
                                        {&row_ind_[feature_offset], column_size}));

src/data/data.cc

@@ -37,7 +37,7 @@ template <typename T>
 void SaveScalarField(dmlc::Stream *strm, const std::string &name,
                      xgboost::DataType type, const T &field) {
   strm->Write(name);
-  strm->Write(type);
+  strm->Write(static_cast<uint8_t>(type));
   strm->Write(true);  // is_scalar=True
   strm->Write(field);
 }
@@ -47,7 +47,7 @@ void SaveVectorField(dmlc::Stream *strm, const std::string &name,
                      xgboost::DataType type, std::pair<uint64_t, uint64_t> shape,
                      const std::vector<T>& field) {
   strm->Write(name);
-  strm->Write(type);
+  strm->Write(static_cast<uint8_t>(type));
   strm->Write(false);  // is_scalar=False
   strm->Write(shape.first);
   strm->Write(shape.second);
@@ -71,7 +71,9 @@ void LoadScalarField(dmlc::Stream* strm, const std::string& expected_name,
   CHECK(strm->Read(&name)) << invalid;
   CHECK_EQ(name, expected_name)
       << invalid << " Expected field: " << expected_name << ", got: " << name;
-  CHECK(strm->Read(&type)) << invalid;
+  uint8_t type_val;
+  CHECK(strm->Read(&type_val)) << invalid;
+  type = static_cast<xgboost::DataType>(type_val);
   CHECK(type == expected_type)
       << invalid << "Expected field of type: " << static_cast<int>(expected_type) << ", "
       << "got field type: " << static_cast<int>(type);
@@ -91,7 +93,9 @@ void LoadVectorField(dmlc::Stream* strm, const std::string& expected_name,
   CHECK(strm->Read(&name)) << invalid;
   CHECK_EQ(name, expected_name)
     << invalid << " Expected field: " << expected_name << ", got: " << name;
-  CHECK(strm->Read(&type)) << invalid;
+  uint8_t type_val;
+  CHECK(strm->Read(&type_val)) << invalid;
+  type = static_cast<xgboost::DataType>(type_val);
   CHECK(type == expected_type)
     << invalid << "Expected field of type: " << static_cast<int>(expected_type) << ", "
     << "got field type: " << static_cast<int>(type);
@@ -338,7 +342,7 @@ void MetaInfo::SetInfo(const char* key, const void* dptr, DataType dtype, size_t
   }
 }
 
-void MetaInfo::Validate() const {
+void MetaInfo::Validate(int32_t device) const {
   if (group_ptr_.size() != 0 && weights_.Size() != 0) {
     CHECK_EQ(group_ptr_.size(), weights_.Size() + 1)
         << "Size of weights must equal to number of groups when ranking "
@@ -350,30 +354,44 @@ void MetaInfo::Validate() const {
         << "Invalid group structure.  Number of rows obtained from groups "
            "doesn't equal to actual number of rows given by data.";
   }
+  auto check_device = [device](HostDeviceVector<float> const &v) {
+    CHECK(v.DeviceIdx() == GenericParameter::kCpuId ||
+          device  == GenericParameter::kCpuId ||
+          v.DeviceIdx() == device)
+        << "Data is resided on a different device than `gpu_id`. "
+        << "Device that data is on: " << v.DeviceIdx() << ", "
+        << "`gpu_id` for XGBoost: " << device;
+  };
+
   if (weights_.Size() != 0) {
     CHECK_EQ(weights_.Size(), num_row_)
         << "Size of weights must equal to number of rows.";
+    check_device(weights_);
     return;
   }
   if (labels_.Size() != 0) {
     CHECK_EQ(labels_.Size(), num_row_)
         << "Size of labels must equal to number of rows.";
+    check_device(labels_);
     return;
   }
   if (labels_lower_bound_.Size() != 0) {
     CHECK_EQ(labels_lower_bound_.Size(), num_row_)
         << "Size of label_lower_bound must equal to number of rows.";
+    check_device(labels_lower_bound_);
     return;
   }
   if (labels_upper_bound_.Size() != 0) {
     CHECK_EQ(labels_upper_bound_.Size(), num_row_)
         << "Size of label_upper_bound must equal to number of rows.";
+    check_device(labels_upper_bound_);
     return;
   }
   CHECK_LE(num_nonzero_, num_col_ * num_row_);
   if (base_margin_.Size() != 0) {
     CHECK_EQ(base_margin_.Size() % num_row_, 0)
         << "Size of base margin must be a multiple of number of rows.";
+    check_device(base_margin_);
   }
 }
 

src/data/device_dmatrix.cu

@@ -201,6 +201,7 @@ template <typename AdapterT>
 DeviceDMatrix::DeviceDMatrix(AdapterT* adapter, float missing, int nthread, int max_bin) {
   common::HistogramCuts cuts =
       common::AdapterDeviceSketch(adapter, max_bin, missing);
+  dh::safe_cuda(cudaSetDevice(adapter->DeviceIdx()));
   auto& batch = adapter->Value();
   // Work out how many valid entries we have in each row
   dh::caching_device_vector<size_t> row_counts(adapter->NumRows() + 1, 0);

src/data/simple_dmatrix.cu

@@ -99,6 +99,7 @@ void CopyDataRowMajor(AdapterT* adapter, common::Span<Entry> data,
 // be supported in future. Does not currently support inferring row/column size
 template <typename AdapterT>
 SimpleDMatrix::SimpleDMatrix(AdapterT* adapter, float missing, int nthread) {
+  dh::safe_cuda(cudaSetDevice(adapter->DeviceIdx()));
   CHECK(adapter->NumRows() != kAdapterUnknownSize);
   CHECK(adapter->NumColumns() != kAdapterUnknownSize);
 

src/learner.cc

@@ -689,15 +689,23 @@ class LearnerIO : public LearnerConfiguration {
       warn_old_model = false;
     }
 
-    if (mparam_.major_version >= 1) {
+    if (mparam_.major_version < 1) {
-      learner_model_param_ = LearnerModelParam(mparam_,
-                                               obj_->ProbToMargin(mparam_.base_score));
-    } else {
       // Before 1.0.0, base_score is saved as a transformed value, and there's no version
-      // attribute in the saved model.
+      // attribute (saved a 0) in the saved model.
-      learner_model_param_ = LearnerModelParam(mparam_, mparam_.base_score);
+      std::string multi{"multi:"};
+      if (!std::equal(multi.cbegin(), multi.cend(), tparam_.objective.cbegin())) {
+        HostDeviceVector<float> t;
+        t.HostVector().resize(1);
+        t.HostVector().at(0) = mparam_.base_score;
+        this->obj_->PredTransform(&t);
+        auto base_score = t.HostVector().at(0);
+        mparam_.base_score = base_score;
+      }
       warn_old_model = true;
     }
+
+    learner_model_param_ =
+        LearnerModelParam(mparam_, obj_->ProbToMargin(mparam_.base_score));
     if (attributes_.find("objective") != attributes_.cend()) {
       auto obj_str = attributes_.at("objective");
       auto j_obj = Json::Load({obj_str.c_str(), obj_str.size()});
@@ -1052,7 +1060,7 @@ class LearnerImpl : public LearnerIO {
 
   void ValidateDMatrix(DMatrix* p_fmat) const {
     MetaInfo const& info = p_fmat->Info();
-    info.Validate();
+    info.Validate(generic_parameters_.gpu_id);
 
     auto const row_based_split = [this]() {
       return tparam_.dsplit == DataSplitMode::kRow ||

src/metric/survival_metric.cc

@@ -70,8 +70,7 @@ struct EvalAFT : public Metric {
 
     double nloglik_sum = 0.0;
     double weight_sum = 0.0;
-    #pragma omp parallel for default(none) \
+    #pragma omp parallel for \
-     firstprivate(nsize, is_null_weight, aft_loss_distribution_scale) \
      shared(weights, y_lower, y_upper, yhat) reduction(+:nloglik_sum, weight_sum)
     for (omp_ulong i = 0; i < nsize; ++i) {
       // If weights are empty, data is unweighted so we use 1.0 everywhere

src/objective/aft_obj.cc

@@ -56,8 +56,7 @@ class AFTObj : public ObjFunction {
     const omp_ulong nsize = static_cast<omp_ulong>(yhat.size());
     const float aft_loss_distribution_scale = param_.aft_loss_distribution_scale;
 
-    #pragma omp parallel for default(none) \
+    #pragma omp parallel for \
-      firstprivate(nsize, is_null_weight, aft_loss_distribution_scale) \
       shared(weights, y_lower, y_upper, yhat, gpair)
     for (omp_ulong i = 0; i < nsize; ++i) {
       // If weights are empty, data is unweighted so we use 1.0 everywhere
@@ -74,7 +73,7 @@ class AFTObj : public ObjFunction {
     // Trees give us a prediction in log scale, so exponentiate
     std::vector<bst_float> &preds = io_preds->HostVector();
     const long ndata = static_cast<long>(preds.size()); // NOLINT(*)
-    #pragma omp parallel for default(none) firstprivate(ndata) shared(preds)
+    #pragma omp parallel for shared(preds)
     for (long j = 0; j < ndata; ++j) {  // NOLINT(*)
       preds[j] = std::exp(preds[j]);
     }

src/objective/regression_obj.cu

@@ -41,10 +41,11 @@ struct RegLossParam : public XGBoostParameter<RegLossParam> {
 template<typename Loss>
 class RegLossObj : public ObjFunction {
  protected:
-  HostDeviceVector<int> label_correct_;
+  HostDeviceVector<float> additional_input_;
 
  public:
-  RegLossObj() = default;
+  // 0 - label_correct flag, 1 - scale_pos_weight, 2 - is_null_weight
+  RegLossObj(): additional_input_(3) {}
 
   void Configure(const std::vector<std::pair<std::string, std::string> >& args) override {
     param_.UpdateAllowUnknown(args);
@@ -64,8 +65,7 @@ class RegLossObj : public ObjFunction {
     size_t const ndata = preds.Size();
     out_gpair->Resize(ndata);
     auto device = tparam_->gpu_id;
-    label_correct_.Resize(1);
+    additional_input_.HostVector().begin()[0] = 1;  // Fill the label_correct flag
-    label_correct_.Fill(1);
 
     bool is_null_weight = info.weights_.Size() == 0;
     if (!is_null_weight) {
@@ -73,37 +73,39 @@ class RegLossObj : public ObjFunction {
           << "Number of weights should be equal to number of data points.";
     }
     auto scale_pos_weight = param_.scale_pos_weight;
-    common::Transform<>::Init(
+    additional_input_.HostVector().begin()[1] = scale_pos_weight;
-        [=] XGBOOST_DEVICE(size_t _idx,
+    additional_input_.HostVector().begin()[2] = is_null_weight;
-                           common::Span<int> _label_correct,
+
+    common::Transform<>::Init([] XGBOOST_DEVICE(size_t _idx,
+                           common::Span<float> _additional_input,
                            common::Span<GradientPair> _out_gpair,
                            common::Span<const bst_float> _preds,
                            common::Span<const bst_float> _labels,
                            common::Span<const bst_float> _weights) {
+          const float _scale_pos_weight = _additional_input[1];
+          const bool _is_null_weight = _additional_input[2];
+
           bst_float p = Loss::PredTransform(_preds[_idx]);
-          bst_float w = is_null_weight ? 1.0f : _weights[_idx];
+          bst_float w = _is_null_weight ? 1.0f : _weights[_idx];
           bst_float label = _labels[_idx];
           if (label == 1.0f) {
-            w *= scale_pos_weight;
+            w *= _scale_pos_weight;
           }
           if (!Loss::CheckLabel(label)) {
             // If there is an incorrect label, the host code will know.
-            _label_correct[0] = 0;
+            _additional_input[0] = 0;
           }
           _out_gpair[_idx] = GradientPair(Loss::FirstOrderGradient(p, label) * w,
                                           Loss::SecondOrderGradient(p, label) * w);
         },
         common::Range{0, static_cast<int64_t>(ndata)}, device).Eval(
-            &label_correct_, out_gpair, &preds, &info.labels_, &info.weights_);
+            &additional_input_, out_gpair, &preds, &info.labels_, &info.weights_);
 
-    // copy "label correct" flags back to host
+    auto const flag = additional_input_.HostVector().begin()[0];
-    std::vector<int>& label_correct_h = label_correct_.HostVector();
-    for (auto const flag : label_correct_h) {
     if (flag == 0) {
       LOG(FATAL) << Loss::LabelErrorMsg();
     }
   }
-  }
 
  public:
   const char* DefaultEvalMetric() const override {

src/tree/tree_model.cc

@@ -68,20 +68,20 @@ class TreeGenerator {
     return result;
   }
 
-  virtual std::string Indicator(RegTree const& tree, int32_t nid, uint32_t depth) {
+  virtual std::string Indicator(RegTree const& tree, int32_t nid, uint32_t depth) const {
     return "";
   }
-  virtual std::string Integer(RegTree const& tree, int32_t nid, uint32_t depth) {
+  virtual std::string Integer(RegTree const& tree, int32_t nid, uint32_t depth) const {
     return "";
   }
-  virtual std::string Quantitive(RegTree const& tree, int32_t nid, uint32_t depth) {
+  virtual std::string Quantitive(RegTree const& tree, int32_t nid, uint32_t depth) const {
     return "";
   }
-  virtual std::string NodeStat(RegTree const& tree, int32_t nid) {
+  virtual std::string NodeStat(RegTree const& tree, int32_t nid) const {
     return "";
   }
 
-  virtual std::string PlainNode(RegTree const& tree, int32_t nid, uint32_t depth) = 0;
+  virtual std::string PlainNode(RegTree const& tree, int32_t nid, uint32_t depth) const = 0;
 
   virtual std::string SplitNode(RegTree const& tree, int32_t nid, uint32_t depth) {
     auto const split_index = tree[nid].SplitIndex();
@@ -110,7 +110,7 @@ class TreeGenerator {
     return result;
   }
 
-  virtual std::string LeafNode(RegTree const& tree, int32_t nid, uint32_t depth) = 0;
+  virtual std::string LeafNode(RegTree const& tree, int32_t nid, uint32_t depth) const = 0;
   virtual std::string BuildTree(RegTree const& tree, int32_t nid, uint32_t depth) = 0;
 
  public:
@@ -181,7 +181,7 @@ class TextGenerator : public TreeGenerator {
   TextGenerator(FeatureMap const& fmap, std::string const& attrs, bool with_stats) :
       TreeGenerator(fmap, with_stats) {}
 
-  std::string LeafNode(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string LeafNode(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     static std::string kLeafTemplate = "{tabs}{nid}:leaf={leaf}{stats}";
     static std::string kStatTemplate = ",cover={cover}";
     std::string result = SuperT::Match(
@@ -195,7 +195,7 @@ class TextGenerator : public TreeGenerator {
     return result;
   }
 
-  std::string Indicator(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string Indicator(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     static std::string const kIndicatorTemplate = "{nid}:[{fname}] yes={yes},no={no}";
     int32_t nyes = tree[nid].DefaultLeft() ?
                    tree[nid].RightChild() : tree[nid].LeftChild();
@@ -211,7 +211,7 @@ class TextGenerator : public TreeGenerator {
 
   std::string SplitNodeImpl(
       RegTree const& tree, int32_t nid, std::string const& template_str,
-      std::string cond, uint32_t depth) {
+      std::string cond, uint32_t depth) const {
     auto split_index = tree[nid].SplitIndex();
     std::string const result = SuperT::Match(
         template_str,
@@ -226,7 +226,7 @@ class TextGenerator : public TreeGenerator {
     return result;
   }
 
-  std::string Integer(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string Integer(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     static std::string const kIntegerTemplate =
         "{tabs}{nid}:[{fname}<{cond}] yes={left},no={right},missing={missing}";
     auto cond = tree[nid].SplitCond();
@@ -238,21 +238,21 @@ class TextGenerator : public TreeGenerator {
                          std::to_string(integer_threshold), depth);
   }
 
-  std::string Quantitive(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string Quantitive(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     static std::string const kQuantitiveTemplate =
         "{tabs}{nid}:[{fname}<{cond}] yes={left},no={right},missing={missing}";
     auto cond = tree[nid].SplitCond();
     return SplitNodeImpl(tree, nid, kQuantitiveTemplate, SuperT::ToStr(cond), depth);
   }
 
-  std::string PlainNode(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string PlainNode(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     auto cond = tree[nid].SplitCond();
     static std::string const kNodeTemplate =
         "{tabs}{nid}:[f{fname}<{cond}] yes={left},no={right},missing={missing}";
     return SplitNodeImpl(tree, nid, kNodeTemplate, SuperT::ToStr(cond), depth);
   }
 
-  std::string NodeStat(RegTree const& tree, int32_t nid) override {
+  std::string NodeStat(RegTree const& tree, int32_t nid) const override {
     static std::string const kStatTemplate = ",gain={loss_chg},cover={sum_hess}";
     std::string const result = SuperT::Match(
         kStatTemplate,
@@ -297,7 +297,7 @@ class JsonGenerator : public TreeGenerator {
   JsonGenerator(FeatureMap const& fmap, std::string attrs, bool with_stats) :
       TreeGenerator(fmap, with_stats) {}
 
-  std::string Indent(uint32_t depth) {
+  std::string Indent(uint32_t depth) const {
     std::string result;
     for (uint32_t i = 0; i < depth + 1; ++i) {
       result += "  ";
@@ -305,7 +305,7 @@ class JsonGenerator : public TreeGenerator {
     return result;
   }
 
-  std::string LeafNode(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string LeafNode(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     static std::string const kLeafTemplate =
         R"L({ "nodeid": {nid}, "leaf": {leaf} {stat}})L";
     static std::string const kStatTemplate =
@@ -321,11 +321,11 @@ class JsonGenerator : public TreeGenerator {
     return result;
   }
 
-  std::string Indicator(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string Indicator(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     int32_t nyes = tree[nid].DefaultLeft() ?
                    tree[nid].RightChild() : tree[nid].LeftChild();
     static std::string const kIndicatorTemplate =
-        R"ID( "nodeid": {nid}, "depth": {depth}, "split": "{fname}", "yes": {yes}, "no": {no}})ID";
+        R"ID( "nodeid": {nid}, "depth": {depth}, "split": "{fname}", "yes": {yes}, "no": {no})ID";
     auto split_index = tree[nid].SplitIndex();
     auto result = SuperT::Match(
         kIndicatorTemplate,
@@ -337,8 +337,9 @@ class JsonGenerator : public TreeGenerator {
     return result;
   }
 
-  std::string SplitNodeImpl(RegTree const& tree, int32_t nid,
+  std::string SplitNodeImpl(RegTree const &tree, int32_t nid,
-                            std::string const& template_str, std::string cond, uint32_t depth) {
+                            std::string const &template_str, std::string cond,
+                            uint32_t depth) const {
     auto split_index = tree[nid].SplitIndex();
     std::string const result = SuperT::Match(
         template_str,
@@ -353,7 +354,7 @@ class JsonGenerator : public TreeGenerator {
     return result;
   }
 
-  std::string Integer(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string Integer(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     auto cond = tree[nid].SplitCond();
     const bst_float floored = std::floor(cond);
     const int32_t integer_threshold
@@ -367,7 +368,7 @@ class JsonGenerator : public TreeGenerator {
                          std::to_string(integer_threshold), depth);
   }
 
-  std::string Quantitive(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string Quantitive(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     static std::string const kQuantitiveTemplate =
         R"I( "nodeid": {nid}, "depth": {depth}, "split": "{fname}", )I"
         R"I("split_condition": {cond}, "yes": {left}, "no": {right}, )I"
@@ -376,7 +377,7 @@ class JsonGenerator : public TreeGenerator {
     return SplitNodeImpl(tree, nid, kQuantitiveTemplate, SuperT::ToStr(cond), depth);
   }
 
-  std::string PlainNode(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string PlainNode(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     auto cond = tree[nid].SplitCond();
     static std::string const kNodeTemplate =
         R"I( "nodeid": {nid}, "depth": {depth}, "split": {fname}, )I"
@@ -385,7 +386,7 @@ class JsonGenerator : public TreeGenerator {
     return SplitNodeImpl(tree, nid, kNodeTemplate, SuperT::ToStr(cond), depth);
   }
 
-  std::string NodeStat(RegTree const& tree, int32_t nid) override {
+  std::string NodeStat(RegTree const& tree, int32_t nid) const override {
     static std::string kStatTemplate =
         R"S(, "gain": {loss_chg}, "cover": {sum_hess})S";
     auto result = SuperT::Match(
@@ -529,7 +530,7 @@ class GraphvizGenerator : public TreeGenerator {
  protected:
   // Only indicator is different, so we combine all different node types into this
   // function.
-  std::string PlainNode(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string PlainNode(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     auto split = tree[nid].SplitIndex();
     auto cond = tree[nid].SplitCond();
     static std::string const kNodeTemplate =
@@ -563,7 +564,7 @@ class GraphvizGenerator : public TreeGenerator {
     return result;
   };
 
-  std::string LeafNode(RegTree const& tree, int32_t nid, uint32_t depth) override {
+  std::string LeafNode(RegTree const& tree, int32_t nid, uint32_t depth) const override {
     static std::string const kLeafTemplate =
         "    {nid} [ label=\"leaf={leaf-value}\" {params}]\n";
     auto result = SuperT::Match(kLeafTemplate, {

tests/ci_build/Dockerfile.cudf

@@ -1,37 +0,0 @@
-ARG CUDA_VERSION
-FROM nvidia/cuda:$CUDA_VERSION-runtime-ubuntu16.04
-
-# Environment
-ENV DEBIAN_FRONTEND noninteractive
-SHELL ["/bin/bash", "-c"]   # Use Bash as shell
-
-# Install all basic requirements
-RUN \
-    apt-get update && \
-    apt-get install -y wget unzip bzip2 libgomp1 build-essential && \
-    # Python
-    wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3.sh -b -p /opt/python
-
-ENV PATH=/opt/python/bin:$PATH
-
-# Create new Conda environment with cuDF, Dask, and cuPy
-RUN \
-    conda create -n cudf_test -c rapidsai -c nvidia -c conda-forge -c defaults \
-        python=3.7 cudf cudatoolkit=$CUDA_VERSION dask dask-cuda dask-cudf cupy \
-        numpy pytest scipy scikit-learn pandas matplotlib wheel python-kubernetes urllib3 graphviz
-
-ENV GOSU_VERSION 1.10
-
-# Install lightweight sudo (not bound to TTY)
-RUN set -ex; \
-    wget -O /usr/local/bin/gosu "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-amd64" && \
-    chmod +x /usr/local/bin/gosu && \
-    gosu nobody true
-
-# Default entry-point to use if running locally
-# It will preserve attributes of created files
-COPY entrypoint.sh /scripts/
-
-WORKDIR /workspace
-ENTRYPOINT ["/scripts/entrypoint.sh"]

tests/ci_build/Dockerfile.gpu

@@ -3,6 +3,7 @@ FROM nvidia/cuda:$CUDA_VERSION-runtime-ubuntu16.04
 
 # Environment
 ENV DEBIAN_FRONTEND noninteractive
+SHELL ["/bin/bash", "-c"]   # Use Bash as shell
 
 # Install all basic requirements
 RUN \
@@ -14,11 +15,11 @@ RUN \
 
 ENV PATH=/opt/python/bin:$PATH
 
-# Install Python packages
+# Create new Conda environment with cuDF, Dask, and cuPy
 RUN \
     conda create -n gpu_test -c rapidsai -c nvidia -c conda-forge -c defaults \
-        python=3.7 dask dask-cuda numpy pytest scipy  scikit-learn pandas \
+        python=3.7 cudf=0.14 cudatoolkit=$CUDA_VERSION dask dask-cuda dask-cudf cupy \
-        matplotlib wheel python-kubernetes urllib3 graphviz
+        numpy pytest scipy scikit-learn pandas matplotlib wheel python-kubernetes urllib3 graphviz
 
 ENV GOSU_VERSION 1.10
 

tests/ci_build/rename_whl.py

@@ -21,8 +21,6 @@ whl_path = sys.argv[1]
 commit_id = sys.argv[2]
 platform_tag = sys.argv[3]
 
-assert platform_tag in ['manylinux1_x86_64', 'manylinux2010_x86_64', 'win_amd64']
-
 dirname, basename = os.path.dirname(whl_path), os.path.basename(whl_path)
 
 with cd(dirname):

tests/ci_build/test_python.sh

@@ -44,20 +44,6 @@ case "$suite" in
     cd -
     ;;
 
-  cudf)
-    source activate cudf_test
-    install_xgboost
-    pytest -v -s -rxXs --fulltrace -m "not mgpu" \
-           tests/python-gpu/test_from_cudf.py tests/python-gpu/test_from_cupy.py \
-	   tests/python-gpu/test_gpu_prediction.py
-    ;;
-
-  mgpu-cudf)
-    source activate cudf_test
-    install_xgboost
-    pytest -v -s -rxXs --fulltrace -m "mgpu" tests/python-gpu/test_gpu_with_dask.py
-    ;;
-
   cpu)
     install_xgboost
     pytest -v -s --fulltrace tests/python
@@ -72,7 +58,7 @@ case "$suite" in
     ;;
 
   *)
-    echo "Usage: $0 {gpu|mgpu|cudf|cpu|cpu-py35}"
+    echo "Usage: $0 {gpu|mgpu|cpu|cpu-py35}"
     exit 1
     ;;
 esac

tests/cpp/data/test_metainfo.cc

@@ -149,9 +149,17 @@ TEST(MetaInfo, Validate) {
   info.num_col_ = 3;
   std::vector<xgboost::bst_group_t> groups (11);
   info.SetInfo("group", groups.data(), xgboost::DataType::kUInt32, 11);
-  EXPECT_THROW(info.Validate(), dmlc::Error);
+  EXPECT_THROW(info.Validate(0), dmlc::Error);
 
   std::vector<float> labels(info.num_row_ + 1);
   info.SetInfo("label", labels.data(), xgboost::DataType::kFloat32, info.num_row_ + 1);
-  EXPECT_THROW(info.Validate(), dmlc::Error);
+  EXPECT_THROW(info.Validate(0), dmlc::Error);
+
+#if defined(XGBOOST_USE_CUDA)
+  info.group_ptr_.clear();
+  labels.resize(info.num_row_);
+  info.SetInfo("label", labels.data(), xgboost::DataType::kFloat32, info.num_row_);
+  info.labels_.SetDevice(0);
+  EXPECT_THROW(info.Validate(1), dmlc::Error);
+#endif  // defined(XGBOOST_USE_CUDA)
 }

tests/cpp/tree/test_tree_model.cc

@@ -151,6 +151,10 @@ TEST(Tree, DumpJson) {
 
   str = tree.DumpModel(fmap, false, "json");
   ASSERT_EQ(str.find("cover"), std::string::npos);
+
+
+  auto j_tree = Json::Load({str.c_str(), str.size()});
+  ASSERT_EQ(get<Array>(j_tree["children"]).size(), 2);
 }
 
 TEST(Tree, DumpText) {

tests/jenkins_get_approval.py

@@ -0,0 +1,26 @@
+import boto3
+import json
+
+lambda_client = boto3.client('lambda', region_name='us-west-2')
+
+# Source code for the Lambda function is available at https://github.com/hcho3/xgboost-devops
+r = lambda_client.invoke(
+    FunctionName='XGBoostCICostWatcher',
+    InvocationType='RequestResponse',
+    Payload='{}'.encode('utf-8')
+)
+
+payload = r['Payload'].read().decode('utf-8')
+if 'FunctionError' in r:
+    msg = 'Error when invoking the Lambda function. Stack trace:\n'
+    error = json.loads(payload)
+    msg += f"    {error['errorType']}: {error['errorMessage']}\n"
+    for trace in error['stackTrace']:
+        for line in trace.split('\n'):
+            msg += f'    {line}\n'
+    raise RuntimeError(msg)
+response = json.loads(payload)
+if response['approved']:
+    print(f"Testing approved. Reason: {response['reason']}")
+else:
+    raise RuntimeError(f"Testing rejected. Reason: {response['reason']}")

tests/pytest.ini

@@ -1,3 +1,4 @@
 [pytest]
 markers =
     mgpu: Mark a test that requires multiple GPUs to run.
+    ci: Mark a test that runs only on CI.

tests/python-gpu/test_from_cupy.py

@@ -136,3 +136,14 @@ Arrow specification.'''
         n = 100
         X = cp.random.random((n, 2))
         xgb.DeviceQuantileDMatrix(X.toDlpack())
+
+    @pytest.mark.skipif(**tm.no_cupy())
+    @pytest.mark.mgpu
+    def test_specified_device(self):
+        import cupy as cp
+        cp.cuda.runtime.setDevice(0)
+        dtrain = dmatrix_from_cupy(
+            np.float32, xgb.DeviceQuantileDMatrix, np.nan)
+        with pytest.raises(xgb.core.XGBoostError):
+            xgb.train({'tree_method': 'gpu_hist', 'gpu_id': 1},
+                      dtrain, num_boost_round=10)

tests/python-gpu/test_gpu_basic_models.py

@@ -12,25 +12,15 @@ rng = np.random.RandomState(1994)
 class TestGPUBasicModels(unittest.TestCase):
     cputest = test_bm.TestModels()
 
-    def test_eta_decay_gpu_hist(self):
+    def run_cls(self, X, y, deterministic):
-        self.cputest.run_eta_decay('gpu_hist')
-
-    def test_deterministic_gpu_hist(self):
-        kRows = 1000
-        kCols = 64
-        kClasses = 4
-        # Create large values to force rounding.
-        X = np.random.randn(kRows, kCols) * 1e4
-        y = np.random.randint(0, kClasses, size=kRows)
-
         cls = xgb.XGBClassifier(tree_method='gpu_hist',
-                                deterministic_histogram=True,
+                                deterministic_histogram=deterministic,
                                 single_precision_histogram=True)
         cls.fit(X, y)
         cls.get_booster().save_model('test_deterministic_gpu_hist-0.json')
 
         cls = xgb.XGBClassifier(tree_method='gpu_hist',
-                                deterministic_histogram=True,
+                                deterministic_histogram=deterministic,
                                 single_precision_histogram=True)
         cls.fit(X, y)
         cls.get_booster().save_model('test_deterministic_gpu_hist-1.json')
@@ -40,7 +30,24 @@ class TestGPUBasicModels(unittest.TestCase):
         with open('test_deterministic_gpu_hist-1.json', 'r') as fd:
             model_1 = fd.read()
 
-        assert hash(model_0) == hash(model_1)
-
         os.remove('test_deterministic_gpu_hist-0.json')
         os.remove('test_deterministic_gpu_hist-1.json')
+
+        return hash(model_0), hash(model_1)
+
+    def test_eta_decay_gpu_hist(self):
+        self.cputest.run_eta_decay('gpu_hist')
+
+    def test_deterministic_gpu_hist(self):
+        kRows = 1000
+        kCols = 64
+        kClasses = 4
+        # Create large values to force rounding.
+        X = np.random.randn(kRows, kCols) * 1e4
+        y = np.random.randint(0, kClasses, size=kRows) * 1e4
+
+        model_0, model_1 = self.run_cls(X, y, True)
+        assert model_0 == model_1
+
+        model_0, model_1 = self.run_cls(X, y, False)
+        assert model_0 != model_1

tests/python-gpu/test_gpu_prediction.py

@@ -121,6 +121,7 @@ class TestGPUPredict(unittest.TestCase):
     @pytest.mark.skipif(**tm.no_cupy())
     def test_inplace_predict_cupy(self):
         import cupy as cp
+        cp.cuda.runtime.setDevice(0)
         rows = 1000
         cols = 10
         cp_rng = cp.random.RandomState(1994)

tests/python/test_basic_models.py

@@ -325,7 +325,7 @@ class TestModels(unittest.TestCase):
         assert locale.getpreferredencoding(False) == loc
 
     @pytest.mark.skipif(**tm.no_json_schema())
-    def test_json_schema(self):
+    def test_json_io_schema(self):
         import jsonschema
         model_path = 'test_json_schema.json'
         path = os.path.dirname(
@@ -342,3 +342,35 @@ class TestModels(unittest.TestCase):
         jsonschema.validate(instance=json_model(model_path, parameters),
                             schema=schema)
         os.remove(model_path)
+
+    @pytest.mark.skipif(**tm.no_json_schema())
+    def test_json_dump_schema(self):
+        import jsonschema
+
+        def validate_model(parameters):
+            X = np.random.random((100, 30))
+            y = np.random.randint(0, 4, size=(100,))
+
+            parameters['num_class'] = 4
+            m = xgb.DMatrix(X, y)
+
+            booster = xgb.train(parameters, m)
+            dump = booster.get_dump(dump_format='json')
+
+            for i in range(len(dump)):
+                jsonschema.validate(instance=json.loads(dump[i]),
+                                    schema=schema)
+
+        path = os.path.dirname(
+            os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+        doc = os.path.join(path, 'doc', 'dump.schema')
+        with open(doc, 'r') as fd:
+            schema = json.load(fd)
+
+        parameters = {'tree_method': 'hist', 'booster': 'gbtree',
+                      'objective': 'multi:softmax'}
+        validate_model(parameters)
+
+        parameters = {'tree_method': 'hist', 'booster': 'dart',
+                      'objective': 'multi:softmax'}
+        validate_model(parameters)

tests/python/test_model_compatibility.py

@@ -4,6 +4,7 @@ import generate_models as gm
 import json
 import zipfile
 import pytest
+import copy
 
 
 def run_model_param_check(config):
@@ -124,6 +125,9 @@ def test_model_compatibility():
         if name.startswith('xgboost-'):
             booster = xgboost.Booster(model_file=path)
             run_booster_check(booster, name)
+            # Do full serialization.
+            booster = copy.copy(booster)
+            run_booster_check(booster, name)
         elif name.startswith('xgboost_scikit'):
             run_scikit_model_check(name, path)
         else:

tests/travis/run_test.sh

@@ -23,18 +23,42 @@ if [ ${TASK} == "python_test" ]; then
     mkdir build && cd build
     cmake .. -DUSE_OPENMP=ON -DCMAKE_VERBOSE_MAKEFILE=ON
     make -j$(nproc)
-    cd ..
 
     echo "-------------------------------"
     conda activate python3
     conda --version
     python --version
 
+    # Build binary wheel
+    cd ../python-package
+    python setup.py bdist_wheel
+    TAG=macosx_10_13_x86_64.macosx_10_14_x86_64.macosx_10_15_x86_64
+    python ../tests/ci_build/rename_whl.py dist/*.whl ${TRAVIS_COMMIT} ${TAG}
+    python -m pip install ./dist/xgboost-*-py3-none-${TAG}.whl
+
+    # Run unit tests
+    cd ..
     python -m pip install graphviz pytest pytest-cov codecov
     python -m pip install datatable
     python -m pip install numpy scipy pandas matplotlib scikit-learn dask[complete]
     python -m pytest -v --fulltrace -s tests/python --cov=python-package/xgboost || exit -1
     codecov
+
+    # Deploy binary wheel to S3
+    python -m pip install awscli
+    if [ "${TRAVIS_PULL_REQUEST}" != "false" ]
+    then
+        S3_DEST="s3://xgboost-nightly-builds/PR-${TRAVIS_PULL_REQUEST}/"
+    else
+        if [ "${TRAVIS_BRANCH}" == "master" ]
+        then
+            S3_DEST="s3://xgboost-nightly-builds/"
+        elif [ -z "${TRAVIS_TAG}" ]
+        then
+            S3_DEST="s3://xgboost-nightly-builds/${TRAVIS_BRANCH}/"
+        fi
+    fi
+    python -m awscli s3 cp python-package/dist/*.whl "${S3_DEST}" --acl public-read || true
 fi
 
 if [ ${TASK} == "java_test" ]; then