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python - MultiGPU Kmeans 聚类与 RAPID 冻结

问题描述

我是 Python 和 Rapids.AI 的新手，我正在尝试使用 Dask 和 RAPIDs 在多节点 GPU（我有 2 个 GPU）中重新创建 SKLearn KMeans（我正在使用带有它的 docker 的 rapids，它也安装了一个 Jupyter Notebook）。

我在下面显示的代码（也显示了 Iris 数据集的示例）冻结并且 jupyter notebook 单元永远不会结束。我尝试使用%debug魔法键和 Dask 仪表板，但我没有得出任何明确的结论（我认为可能是唯一的结论device_m_csv.iloc，但我不确定）。另一件事可能是我忘记了一些wait()或compute()或persistent()（真的，我不确定在什么情况下应该正确使用它们）。

我将解释代码，以便更好地阅读：

很抱歉无法提供更多数据，但我无法获得。任何需要解决疑问的东西我都会很乐意提供。

您认为问题出在哪里或是什么？

非常感谢您提前。

%%time

# Import libraries and show its versions
import numpy as np; print('NumPy Version:', np.__version__)
import pandas as pd; print('Pandas Version:', pd.__version__)
import sklearn; print('Scikit-Learn Version:', sklearn.__version__)
import nvstrings, nvcategory
import cupy; print('cuPY Version:', cupy.__version__)
import cudf; print('cuDF Version:', cudf.__version__)
import cuml; print('cuML Version:', cuml.__version__)
import dask; print('Dask Version:', dask.__version__)
import dask_cuda; print('DaskCuda Version:', dask_cuda.__version__)
import dask_cudf; print('DaskCuDF Version:', dask_cudf.__version__)
import matplotlib; print('MatPlotLib Version:', matplotlib.__version__)
import seaborn as sns; print('SeaBorn Version:', sns.__version__)
#import timeimport warnings

from dask import delayed
import dask.dataframe as dd
from dask.distributed import Client, LocalCluster, wait
from dask_ml.cluster import KMeans as skmKMeans
from dask_cuda import LocalCUDACluster

from sklearn import metrics
from sklearn.cluster import KMeans as skKMeans
from sklearn.metrics import adjusted_rand_score as sk_adjusted_rand_score, silhouette_score as sk_silhouette_score
from cuml.cluster import KMeans as cuKMeans
from cuml.dask.cluster.kmeans import KMeans as cumKMeans
from cuml.metrics import adjusted_rand_score as cu_adjusted_rand_score

# Configure matplotlib library
import matplotlib.pyplot as plt
%matplotlib inline

# Configure seaborn library
sns.set()
#sns.set(style="white", color_codes=True)
%config InlineBackend.figure_format = 'svg'

# Configure warnings
#warnings.filterwarnings("ignore")


####################################### KMEANS #############################################################
# Create local cluster
cluster = LocalCUDACluster(n_workers=2, threads_per_worker=1)
client = Client(cluster)

# Identify number of workers
n_workers = len(client.has_what().keys())

# Read data in host memory
device_m_csv = dask_cudf.read_csv('./DataSet/iris.csv', header = 0, delimiter = ',', chunksize='2kB') # Get complete CSV. Chunksize is 2kb for getting 2 partitions
#x = host_data.iloc[:, [0,1,2,3]].values
device_m_data = device_m_csv.iloc[:, [0, 1, 2, 3]] # Get data columns
device_m_labels = device_m_csv.iloc[:, 4] # Get labels column

# Plot data
#sns.pairplot(device_csv.to_pandas(), hue='variety');

# Define variables
label_type = { 'Setosa': 1, 'Versicolor': 2, 'Virginica': 3 } # Dictionary of variables type

# Create KMeans
cu_m_kmeans = cumKMeans(init = 'k-means||',
                     n_clusters = len(device_m_labels.unique()),
                     oversampling_factor = 40,
                     random_state = 0)
# Fit data in KMeans
cu_m_kmeans.fit(device_m_data)

# Predict data
cu_m_kmeans_labels_predicted = cu_m_kmeans.predict(device_m_data).compute()

# Check score
#print('Cluster centers:\n',cu_m_kmeans.cluster_centers_)
#print('adjusted_rand_score: ', sk_adjusted_rand_score(device_m_labels, cu_m_kmeans.labels_))
#print('silhouette_score: ', sk_silhouette_score(device_m_data.to_pandas(), cu_m_kmeans_labels_predicted))

# Close local cluster
client.close()
cluster.close()

鸢尾花数据集示例：

鸢尾花数据集示例

编辑 1

@Corey，这是我使用您的代码的输出：

NumPy Version: 1.17.5
Pandas Version: 0.25.3
Scikit-Learn Version: 0.22.1
cuPY Version: 6.7.0
cuDF Version: 0.12.0
cuML Version: 0.12.0
Dask Version: 2.10.1
DaskCuda Version: 0+unknown
DaskCuDF Version: 0.12.0
MatPlotLib Version: 3.1.3
SeaBorn Version: 0.10.0
Cluster centers:
           0         1         2         3
0  5.006000  3.428000  1.462000  0.246000
1  5.901613  2.748387  4.393548  1.433871
2  6.850000  3.073684  5.742105  2.071053
adjusted_rand_score:  0.7302382722834697
silhouette_score:  0.5528190123564102

标签： pythonk-meansdaskrapids

解决方案

我稍微修改了您的可重现示例，并且能够在最近的 RAPIDS 夜间生成输出。

这是脚本的输出。

(cuml_dev_2) cjnolet@deeplearn ~ $ python ~/kmeans_mnmg_reproduce.py 
NumPy Version: 1.18.1
Pandas Version: 0.25.3
Scikit-Learn Version: 0.22.2.post1
cuPY Version: 7.2.0
cuDF Version: 0.13.0a+3237.g61e4d9c
cuML Version: 0.13.0a+891.g4f44f7f
Dask Version: 2.11.0+28.g10db6ba
DaskCuda Version: 0+unknown
DaskCuDF Version: 0.13.0a+3237.g61e4d9c
MatPlotLib Version: 3.2.0
SeaBorn Version: 0.10.0
/share/software/miniconda3/envs/cuml_dev_2/lib/python3.7/site-packages/dask/array/random.py:27: FutureWarning: dask.array.random.doc_wraps is deprecated and will be removed in a future version
  FutureWarning,
/share/software/miniconda3/envs/cuml_dev_2/lib/python3.7/site-packages/distributed/dashboard/core.py:79: UserWarning: 
Port 8787 is already in use. 
Perhaps you already have a cluster running?
Hosting the diagnostics dashboard on a random port instead.
  warnings.warn("\n" + msg)
bokeh.server.util - WARNING - Host wildcard '*' will allow connections originating from multiple (or possibly all) hostnames or IPs. Use non-wildcard values to restrict access explicitly
Cluster centers:
           0         1         2         3
0  5.883607  2.740984  4.388525  1.434426
1  5.006000  3.428000  1.462000  0.246000
2  6.853846  3.076923  5.715385  2.053846
adjusted_rand_score:  0.7163421126838475
silhouette_score:  0.5511916046195927

这是产生此输出的修改后的脚本：

    # Import libraries and show its versions
    import numpy as np; print('NumPy Version:', np.__version__)
    import pandas as pd; print('Pandas Version:', pd.__version__)
    import sklearn; print('Scikit-Learn Version:', sklearn.__version__)
    import nvstrings, nvcategory
    import cupy; print('cuPY Version:', cupy.__version__)
    import cudf; print('cuDF Version:', cudf.__version__)
    import cuml; print('cuML Version:', cuml.__version__)
    import dask; print('Dask Version:', dask.__version__)
    import dask_cuda; print('DaskCuda Version:', dask_cuda.__version__)
    import dask_cudf; print('DaskCuDF Version:', dask_cudf.__version__)
    import matplotlib; print('MatPlotLib Version:', matplotlib.__version__)
    import seaborn as sns; print('SeaBorn Version:', sns.__version__)
    #import timeimport warnings

    from dask import delayed
    import dask.dataframe as dd
    from dask.distributed import Client, LocalCluster, wait
    from dask_ml.cluster import KMeans as skmKMeans
    from dask_cuda import LocalCUDACluster

    from sklearn import metrics
    from sklearn.cluster import KMeans as skKMeans
    from sklearn.metrics import adjusted_rand_score as sk_adjusted_rand_score, silhouette_score as sk_silhouette_score
    from cuml.cluster import KMeans as cuKMeans
    from cuml.dask.cluster.kmeans import KMeans as cumKMeans
    from cuml.metrics import adjusted_rand_score as cu_adjusted_rand_score
    # Configure matplotlib library
    import matplotlib.pyplot as plt

    # Configure seaborn library
    sns.set()
    #sns.set(style="white", color_codes=True)
    # Configure warnings
    #warnings.filterwarnings("ignore")


    ####################################### KMEANS #############################################################
    # Create local cluster
    cluster = LocalCUDACluster(n_workers=2, threads_per_worker=1)
    client = Client(cluster)

    # Identify number of workers
    n_workers = len(client.has_what().keys())

    # Read data in host memory
    from sklearn.datasets import load_iris

    loader = load_iris()

    #x = host_data.iloc[:, [0,1,2,3]].values
    device_m_data = dask_cudf.from_cudf(cudf.from_pandas(pd.DataFrame(loader.data)), npartitions=2) # Get data columns
    device_m_labels = dask_cudf.from_cudf(cudf.from_pandas(pd.DataFrame(loader.target)), npartitions=2)

    # Plot data
    #sns.pairplot(device_csv.to_pandas(), hue='variety');

    # Define variables
    label_type = { 'Setosa': 1, 'Versicolor': 2, 'Virginica': 3 } # Dictionary of variables type

    # Create KMeans
    cu_m_kmeans = cumKMeans(init = 'k-means||',
                     n_clusters = len(np.unique(loader.target)),
                     oversampling_factor = 40,
                     random_state = 0)
    # Fit data in KMeans
    cu_m_kmeans.fit(device_m_data)

    # Predict data
    cu_m_kmeans_labels_predicted = cu_m_kmeans.predict(device_m_data).compute()

    # Check score
    print('Cluster centers:\n',cu_m_kmeans.cluster_centers_)
    print('adjusted_rand_score: ', sk_adjusted_rand_score(loader.target, cu_m_kmeans_labels_predicted.values.get()))
    print('silhouette_score: ', sk_silhouette_score(device_m_data.compute().to_pandas(), cu_m_kmeans_labels_predicted))

    # Close local cluster
    client.close()
    cluster.close()

您能否提供这些库版本的输出？我建议还运行修改后的脚本，看看它是否为您成功运行。如果不是，我们可以进一步深入了解它是否与 Docker 相关、RAPIDS 版本相关或其他。

如果您有权访问运行 Jupyter 笔记本的命令提示符，则在verbose=True构造KMeans对象时通过传入启用日志记录可能会有所帮助。这可以帮助我们隔离出问题所在。

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