[dask] dask cudf inplace prediction. (#5512)

* Add inplace prediction for dask-cudf.

* Remove Dockerfile.release, since it's not used anywhere

* Use Conda exclusively in CUDF and GPU containers

* Improve cupy memory copying.

* Add skip marks to tests.

* Add mgpu-cudf category on the CI to run all distributed tests.

Co-authored-by: Hyunsu Cho <chohyu01@cs.washington.edu>

Jenkinsfile

@@ -307,19 +307,25 @@ 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
+    # pylint: disable=import-error
-    mem = cupy.zeros(length.value, dtype=dtype, order='C')
+    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(
+    device = cupy.cuda.runtime.pointerGetAttributes(addr).device
-        mem.__cuda_array_interface__['data'][0], addr,
+    # The owner field is just used to keep the memory alive with ref count.  As
-        length.value * ctypes.sizeof(ctypes.c_float),
+    # unowned's life time is scoped within this function we don't need that.
-        cupy.cuda.runtime.memcpyDeviceToDevice)
+    unownd = UnownedMemory(
-    return mem
+        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)
 
@@ -631,8 +636,6 @@ def inplace_predict(client, model, data,
         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 && \
+    wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/python
+    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 && \
+    wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/python
+    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 \
+    conda create -n cudf_test -c rapidsai -c nvidia -c conda-forge -c defaults \
-        cudf=0.9 python=3.7 anaconda::cudatoolkit=$CUDA_VERSION dask dask-cuda cupy
+        python=3.7 cudf cudatoolkit=$CUDA_VERSION dask dask-cuda dask-cudf cupy \
-
+        numpy pytest scipy scikit-learn pandas matplotlib wheel python-kubernetes urllib3 graphviz
-# Install other Python packages
-RUN \
-    source activate cudf_test && \
-    pip install numpy pytest scipy scikit-learn pandas matplotlib wheel 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 && \
+    wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/python
+    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 && \
+    conda create -n gpu_test -c rapidsai -c nvidia -c conda-forge -c defaults \
-    pip install "dask[complete]" && \
+        python=3.7 dask dask-cuda numpy pytest scipy  scikit-learn pandas \
-    conda install -c rapidsai -c nvidia -c numba -c conda-forge -c anaconda dask-cuda
+        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 && \
+    wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/python && \
+    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 && \
+    wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/python && \
+    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 && \
+    wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/python && \
+    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/Dockerfile.release

@@ -1,31 +0,0 @@
-FROM centos:6
-
-# Install all basic requirements
-RUN \
-    yum -y update && \
-    yum install -y graphviz tar unzip wget xz git && \
-    # Python
-    wget https://repo.continuum.io/miniconda/Miniconda2-4.3.27-Linux-x86_64.sh && \
-    bash Miniconda2-4.3.27-Linux-x86_64.sh -b -p /opt/python
-
-ENV PATH=/opt/python/bin:$PATH
-
-# Install Python packages
-RUN \
-    conda install numpy scipy pandas matplotlib pytest scikit-learn && \
-    pip install pytest wheel auditwheel graphviz
-
-ENV GOSU_VERSION 1.10
-
-# Install lightweight sudo (not bound to TTY)
-RUN set -ex; \
-    wget -O /usr/local/bin/gosu "https://github.com/tianon/gosu/releases/download/$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/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 @@ class TestGPUPredict(unittest.TestCase):
 
     # 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 @@ class TestGPUPredict(unittest.TestCase):
         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 @@ class TestDistributedGPU(unittest.TestCase):
                 predictions = dxgb.predict(client, out, dtrain).compute()
                 assert isinstance(predictions, np.ndarray)
 
-                # There's an error with cudf saying `concat_cudf` got an
+                series_predictions = dxgb.inplace_predict(client, out, X)
-                # expected argument `ignore_index`.  So the test here is just
+                assert isinstance(series_predictions, dd.Series)
-                # place holder.
+                series_predictions = series_predictions.compute()
-
-                # series_predictions = dxgb.inplace_predict(client, out, X)
-                # assert isinstance(series_predictions, dd.Series)
 
                 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 @@ class TestDistributedGPU(unittest.TestCase):
                 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)