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[dask] dask cudf inplace prediction. #5512

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merged 22 commits into from
Apr 15, 2020
Merged

[dask] dask cudf inplace prediction. #5512

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8689170
dask cudf inplace prediction.
trivialfis Apr 10, 2020
12b31c5
Change CI script.
trivialfis Apr 12, 2020
bd50317
Remove Dockerfile.release, since it's not used anywhere
hcho3 Apr 14, 2020
e94fe52
Use latest Miniconda version
hcho3 Apr 14, 2020
e044d8f
Use Conda exclusively in CUDF and GPU containers
hcho3 Apr 14, 2020
1576332
Merge remote-tracking branch 'upstream/master' into dask-cudf-inplace
hcho3 Apr 14, 2020
73f073b
Correct pytest mark.
trivialfis Apr 14, 2020
7eca412
Merge branch 'dask-cudf-inplace' of https://github.com/trivialfis/xgb…
trivialfis Apr 14, 2020
76cbef7
Use `python-kubernetes`.
trivialfis Apr 14, 2020
9e20bb7
Use kubernetes with pip
hcho3 Apr 14, 2020
269c9f1
Do not install 'cudatoolkit' conda package for GPU container, as cuDF…
hcho3 Apr 14, 2020
4288462
Strict device id checks.
trivialfis Apr 14, 2020
e1ebde0
Fix latest cudf.
trivialfis Apr 14, 2020
c652cc0
Add skip marks.
trivialfis Apr 14, 2020
f8ed0c4
Don't use raw memcpy.
trivialfis Apr 14, 2020
30f792e
Revert installation.
trivialfis Apr 14, 2020
d503aac
type mapping.
trivialfis Apr 14, 2020
cfbc3cd
Just run all of them.
trivialfis Apr 14, 2020
07467aa
File name.
trivialfis Apr 14, 2020
bc2aa18
Add back cuDF tests that need multi-GPU
hcho3 Apr 15, 2020
58ca057
Add mgpu-cudf category
hcho3 Apr 15, 2020
3dd595d
Just run all of test_gpu_with_dask.py
hcho3 Apr 15, 2020
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2 changes: 0 additions & 2 deletions python-package/xgboost/dask.py
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Expand Up @@ -623,8 +623,6 @@ 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:
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4 changes: 2 additions & 2 deletions tests/ci_build/Dockerfile.cpu
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Expand Up @@ -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

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16 changes: 6 additions & 10 deletions tests/ci_build/Dockerfile.cudf
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Expand Up @@ -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 kubernetes urllib3 graphviz

ENV GOSU_VERSION 1.10

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10 changes: 5 additions & 5 deletions tests/ci_build/Dockerfile.gpu
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Expand Up @@ -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 cudatoolkit=$CUDA_VERSION dask dask-cuda numpy pytest scipy \
scikit-learn pandas matplotlib wheel kubernetes urllib3 graphviz

ENV GOSU_VERSION 1.10

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4 changes: 2 additions & 2 deletions tests/ci_build/Dockerfile.gpu_build
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Expand Up @@ -17,8 +17,8 @@ RUN \
$DEVTOOLSET_URL_ROOT/devtoolset-4-runtime-4.1-3.sc1.el6.x86_64.rpm \
$DEVTOOLSET_URL_ROOT/devtoolset-4-libstdc++-devel-5.3.1-6.1.el6.x86_64.rpm && \
# Python
wget https://repo.continuum.io/miniconda/Miniconda3-4.5.12-Linux-x86_64.sh && \
bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/python && \
wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
bash Miniconda3.sh -b -p /opt/python && \
# CMake
wget -nv -nc https://cmake.org/files/v3.13/cmake-3.13.0-Linux-x86_64.sh --no-check-certificate && \
bash cmake-3.13.0-Linux-x86_64.sh --skip-license --prefix=/usr
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4 changes: 2 additions & 2 deletions tests/ci_build/Dockerfile.jvm
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Expand Up @@ -8,8 +8,8 @@ RUN \
yum -y update && \
yum install -y devtoolset-6-gcc devtoolset-6-binutils devtoolset-6-gcc-c++ && \
# Python
wget https://repo.continuum.io/miniconda/Miniconda3-4.5.12-Linux-x86_64.sh && \
bash Miniconda3-4.5.12-Linux-x86_64.sh -b -p /opt/python && \
wget -O Miniconda3.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
bash Miniconda3.sh -b -p /opt/python && \
# CMake
wget -nv -nc https://cmake.org/files/v3.13/cmake-3.13.0-Linux-x86_64.sh --no-check-certificate && \
bash cmake-3.13.0-Linux-x86_64.sh --skip-license --prefix=/usr && \
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4 changes: 2 additions & 2 deletions tests/ci_build/Dockerfile.jvm_cross
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Expand Up @@ -13,8 +13,8 @@ RUN \
apt-get update && \
apt-get install -y tar unzip wget openjdk-$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 && \
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31 changes: 0 additions & 31 deletions tests/ci_build/Dockerfile.release
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This file was deleted.

5 changes: 4 additions & 1 deletion tests/ci_build/test_python.sh
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Expand Up @@ -28,11 +28,13 @@ 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
;;

mgpu)
source activate gpu_test
install_xgboost
pytest -v -s --fulltrace -m "mgpu" tests/python-gpu
cd tests/distributed
Expand All @@ -44,7 +46,8 @@ case "$suite" in
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 --fulltrace -m "not mgpu" tests/python-gpu/test_from_cudf.py tests/python-gpu/test_from_cupy.py \
tests/python-gpu/test_gpu_with_dask.py::TestDistributedGPU::test_dask_dataframe
;;

cpu)
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10 changes: 4 additions & 6 deletions tests/python-gpu/test_gpu_with_dask.py
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Expand Up @@ -51,16 +51,14 @@ 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())
def test_dask_array(self):
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