[dask] dask cudf inplace prediction.

Jenkinsfile

@@ -296,19 +296,25 @@ 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
- if (args.cuda_version == '10.0') {
- echo "Running tests with cuDF..."
- sh """
- ${dockerRun} cudf ${docker_binary} ${docker_args} tests/ci_build/test_python.sh cudf
- """
- }
  deleteDir()
  }
 }

python-package/xgboost/core.py

@@ -209,15 +209,32 @@ def ctypes2numpy(cptr, length, dtype):
 
 def ctypes2cupy(cptr, length, dtype):
  """Convert a ctypes pointer array to a cupy array."""
- import cupy # pylint: disable=import-error
- mem = cupy.zeros(length.value, dtype=dtype, order='C')
+ # pylint: disable=import-error
+ import cupy
+ from cupy.cuda.memory import MemoryPointer
+ from cupy.cuda.memory import UnownedMemory
+ CUPY_TO_CTYPES_MAPPING = {
+ cupy.float32: ctypes.c_float,
+ cupy.uint32: ctypes.c_uint
+ }
+ if dtype not in CUPY_TO_CTYPES_MAPPING.keys():
+ raise RuntimeError('Supported types: {}'.format(
+ CUPY_TO_CTYPES_MAPPING.keys()
+ ))
  addr = ctypes.cast(cptr, ctypes.c_void_p).value
  # pylint: disable=c-extension-no-member,no-member
- cupy.cuda.runtime.memcpy(
- mem.__cuda_array_interface__['data'][0], addr,
- length.value * ctypes.sizeof(ctypes.c_float),
- cupy.cuda.runtime.memcpyDeviceToDevice)
- return mem
+ device = cupy.cuda.runtime.pointerGetAttributes(addr).device
+ # The owner field is just used to keep the memory alive with ref count. As
+ # unowned's life time is scoped within this function we don't need that.
+ unownd = UnownedMemory(
+ addr, length.value * ctypes.sizeof(CUPY_TO_CTYPES_MAPPING[dtype]),
+ owner=None)
+ memptr = MemoryPointer(unownd, 0)
+ # pylint: disable=unexpected-keyword-arg
+ mem = cupy.ndarray((length.value, ), dtype=dtype, memptr=memptr)
+ assert mem.device.id == device
+ arr = cupy.array(mem, copy=True)
+ return arr
 
 
 def ctypes2buffer(cptr, length):

python-package/xgboost/dask.py

@@ -101,6 +101,11 @@ def concat(value): # pylint: disable=too-many-return-statements
  return CUDF_concat(value, axis=0)
  if lazy_isinstance(value[0], 'cupy.core.core', 'ndarray'):
  import cupy # pylint: disable=import-error
+ # pylint: disable=c-extension-no-member,no-member
+ d = cupy.cuda.runtime.getDevice()
+ for v in value:
+ d_v = v.device.id
+ assert d_v == d, 'Concatenating arrays on different devices.'
  return cupy.concatenate(value, axis=0)
  return dd.multi.concat(list(value), axis=0)
 
@@ -623,8 +628,6 @@ def mapped_predict(data, is_df):
  if is_df:
  if lazy_isinstance(data, 'cudf.core.dataframe', 'DataFrame'):
  import cudf # pylint: disable=import-error
- # There's an error with cudf saying `concat_cudf` got an
- # expected argument `ignore_index`. So this is not yet working.
  prediction = cudf.DataFrame({'prediction': prediction},
  dtype=numpy.float32)
  else:

tests/ci_build/Dockerfile.cpu

@@ -12,8 +12,8 @@ RUN \
  wget -nv -nc https://cmake.org/files/v3.13/cmake-3.13.0-Linux-x86_64.sh --no-check-certificate && \
  bash cmake-3.13.0-Linux-x86_64.sh --skip-license --prefix=/usr && \
  # Python
- wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
- bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/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
 

tests/ci_build/Dockerfile.cudf

@@ -10,20 +10,16 @@ RUN \
  apt-get update && \
  apt-get install -y wget unzip bzip2 libgomp1 build-essential && \
  # Python
- wget https://repo.continuum.io/miniconda/Miniconda3-4.5.12-Linux-x86_64.sh && \
- bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/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 and dask
+# Create new Conda environment with cuDF, Dask, and cuPy
 RUN \
- conda create -n cudf_test -c rapidsai -c nvidia -c numba -c conda-forge -c anaconda \
- cudf=0.9 python=3.7 anaconda::cudatoolkit=$CUDA_VERSION dask dask-cuda cupy
-
-# Install other Python packages
-RUN \
- source activate cudf_test && \
- pip install numpy pytest scipy scikit-learn pandas matplotlib wheel kubernetes urllib3 graphviz
+ conda create -n cudf_test -c rapidsai -c nvidia -c conda-forge -c defaults \
+ python=3.7 cudf cudatoolkit=$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
 

tests/ci_build/Dockerfile.gpu

@@ -9,16 +9,16 @@ RUN \
  apt-get update && \
  apt-get install -y wget unzip bzip2 libgomp1 build-essential && \
  # Python
- wget https://repo.continuum.io/miniconda/Miniconda3-4.5.12-Linux-x86_64.sh && \
- bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/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
 
 # Install Python packages
 RUN \
- pip install numpy pytest scipy scikit-learn pandas matplotlib wheel kubernetes urllib3 graphviz && \
- pip install "dask[complete]" && \
- conda install -c rapidsai -c nvidia -c numba -c conda-forge -c anaconda dask-cuda
+ 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 \
+  matplotlib wheel python-kubernetes urllib3 graphviz
 
 ENV GOSU_VERSION 1.10
 

tests/ci_build/Dockerfile.gpu_build

@@ -17,8 +17,8 @@ RUN \
  $DEVTOOLSET_URL_ROOT/devtoolset-4-runtime-4.1-3.sc1.el6.x86_64.rpm \
  $DEVTOOLSET_URL_ROOT/devtoolset-4-libstdc++-devel-5.3.1-6.1.el6.x86_64.rpm && \
  # Python
- wget https://repo.continuum.io/miniconda/Miniconda3-4.5.12-Linux-x86_64.sh && \
- bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/python && \
+ wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+ bash Miniconda3.sh -b -p /opt/python && \
  # CMake
  wget -nv -nc https://cmake.org/files/v3.13/cmake-3.13.0-Linux-x86_64.sh --no-check-certificate && \
  bash cmake-3.13.0-Linux-x86_64.sh --skip-license --prefix=/usr

tests/ci_build/Dockerfile.jvm

@@ -8,8 +8,8 @@ RUN \
  yum -y update && \
  yum install -y devtoolset-6-gcc devtoolset-6-binutils devtoolset-6-gcc-c++ && \
  # Python
- wget https://repo.continuum.io/miniconda/Miniconda3-4.5.12-Linux-x86_64.sh && \
- bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/python && \
+ wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+ bash Miniconda3.sh -b -p /opt/python && \
  # CMake
  wget -nv -nc https://cmake.org/files/v3.13/cmake-3.13.0-Linux-x86_64.sh --no-check-certificate && \
  bash cmake-3.13.0-Linux-x86_64.sh --skip-license --prefix=/usr && \

tests/ci_build/Dockerfile.jvm_cross

@@ -13,8 +13,8 @@ RUN \
  apt-get update && \
  apt-get install -y tar unzip wget openjdk-$JDK_VERSION-jdk libgomp1 && \
  # Python
- wget https://repo.continuum.io/miniconda/Miniconda3-4.5.12-Linux-x86_64.sh && \
- bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/python && \
+ wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+ bash Miniconda3.sh -b -p /opt/python && \
  /opt/python/bin/pip install awscli && \
  # Maven
  wget https://archive.apache.org/dist/maven/maven-3/3.6.1/binaries/apache-maven-3.6.1-bin.tar.gz && \

tests/ci_build/test_python.sh

@@ -28,23 +28,33 @@ function install_xgboost {
 # Run specified test suite
 case "$suite" in
  gpu)
+ source activate gpu_test
  install_xgboost
- pytest -v -s --fulltrace -m "not mgpu" tests/python-gpu
+ pytest -v -s -rxXs --fulltrace -m "not mgpu" tests/python-gpu
  ;;
 
  mgpu)
+ source activate gpu_test
  install_xgboost
- pytest -v -s --fulltrace -m "mgpu" tests/python-gpu
+ pytest -v -s -rxXs --fulltrace -m "mgpu" tests/python-gpu
+
  cd tests/distributed
  ./runtests-gpu.sh
  cd -
- pytest -v -s --fulltrace -m "mgpu" tests/python-gpu/test_gpu_with_dask.py
  ;;
 
  cudf)
  source activate cudf_test
  install_xgboost
- pytest -v -s --fulltrace -m "not mgpu" tests/python-gpu/test_from_cudf.py tests/python-gpu/test_from_cupy.py
+ 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)

tests/python-gpu/test_gpu_prediction.py

@@ -62,6 +62,7 @@ def non_decreasing(self, L):
 
  # Test case for a bug where multiple batch predictions made on a
  # test set produce incorrect results
+ @pytest.mark.skipif(**tm.no_sklearn())
  def test_multi_predict(self):
  from sklearn.datasets import make_regression
  from sklearn.model_selection import train_test_split
@@ -89,6 +90,7 @@ def test_multi_predict(self):
  assert np.allclose(predict0, predict1)
  assert np.allclose(predict0, cpu_predict)
 
+ @pytest.mark.skipif(**tm.no_sklearn())
  def test_sklearn(self):
  m, n = 15000, 14
  tr_size = 2500

tests/python-gpu/test_gpu_with_dask.py

@@ -27,6 +27,7 @@ class TestDistributedGPU(unittest.TestCase):
  @pytest.mark.skipif(**tm.no_cudf())
  @pytest.mark.skipif(**tm.no_dask_cudf())
  @pytest.mark.skipif(**tm.no_dask_cuda())
+ @pytest.mark.mgpu
  def test_dask_dataframe(self):
  with LocalCUDACluster() as cluster:
  with Client(cluster) as client:
@@ -51,18 +52,18 @@ def test_dask_dataframe(self):
  predictions = dxgb.predict(client, out, dtrain).compute()
  assert isinstance(predictions, np.ndarray)
 
- # There's an error with cudf saying `concat_cudf` got an
- # expected argument `ignore_index`. So the test here is just
- # place holder.
-
- # series_predictions = dxgb.inplace_predict(client, out, X)
- # assert isinstance(series_predictions, dd.Series)
+ series_predictions = dxgb.inplace_predict(client, out, X)
+ assert isinstance(series_predictions, dd.Series)
+ series_predictions = series_predictions.compute()
 
  single_node = out['booster'].predict(
  xgboost.DMatrix(X.compute()))
+
  cupy.testing.assert_allclose(single_node, predictions)
+ cupy.testing.assert_allclose(single_node, series_predictions)
 
  @pytest.mark.skipif(**tm.no_cupy())
+ @pytest.mark.mgpu
  def test_dask_array(self):
  with LocalCUDACluster() as cluster:
  with Client(cluster) as client:
@@ -82,8 +83,12 @@ def test_dask_array(self):
  single_node = out['booster'].predict(
  xgboost.DMatrix(X.compute()))
  np.testing.assert_allclose(single_node, from_dmatrix)
+ device = cupy.cuda.runtime.getDevice()
+ assert device == inplace_predictions.device.id
+ single_node = cupy.array(single_node)
+ assert device == single_node.device.id
  cupy.testing.assert_allclose(
- cupy.array(single_node),
+ single_node,
  inplace_predictions)
 
 

tests/python-gpu/test_monotonic_constraints.py

@@ -1,12 +1,12 @@
-from __future__ import print_function
-
+import sys
 import numpy as np
-from sklearn.datasets import make_regression
 
 import unittest
 import pytest
 
 import xgboost as xgb
+sys.path.append("tests/python")
+import testing as tm
 
 rng = np.random.RandomState(1994)
 
@@ -20,6 +20,7 @@ def non_increasing(L):
 
 
 def assert_constraint(constraint, tree_method):
+ from sklearn.datasets import make_regression
  n = 1000
  X, y = make_regression(n, random_state=rng, n_features=1, n_informative=1)
  dtrain = xgb.DMatrix(X, y)
@@ -35,12 +36,13 @@ def assert_constraint(constraint, tree_method):
  assert non_increasing(pred)
 
 
-@pytest.mark.gpu
 class TestMonotonicConstraints(unittest.TestCase):
+ @pytest.mark.skipif(**tm.no_sklearn())
  def test_exact(self):
  assert_constraint(1, 'exact')
  assert_constraint(-1, 'exact')
 
+ @pytest.mark.skipif(**tm.no_sklearn())
  def test_gpu_hist(self):
  assert_constraint(1, 'gpu_hist')
  assert_constraint(-1, 'gpu_hist')

tests/python/test_predict.py

@@ -12,10 +12,10 @@ def run_threaded_predict(X, rows, predict_func):
  per_thread = 20
  with ThreadPoolExecutor(max_workers=10) as e:
  for i in range(0, rows, int(rows / per_thread)):
- try:
+ if hasattr(X, 'iloc'):
+ predictor = X.iloc[i:i+per_thread, :]
+ else:
  predictor = X[i:i+per_thread, ...]
- except TypeError:
- predictor = X.iloc[i:i+per_thread, ...]
  f = e.submit(predict_func, predictor)
  results.append(f)