4

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()compute()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:

  • 首先,做需要的进口
  • 接下来,从 KMeans 算法开始(分隔符:#######################...)
  • 创建一个 CUDA 集群,有 2 个工作人员,每个 GPU 一个(我有 2 个 GPU)和 1 个工作线程(我已阅读这是推荐值)并启动一个客户端
  • 从 CSV 读取数据集制作 2 个分区 ( chunksize = '2kb')
  • 将以前的数据集拆分为数据(更称为X)和标签((更称为y
  • 使用 Dask 实例化 cu_KMeans
  • 适合模型
  • 预测值
  • 检查获得的分数

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
4

2 回答 2

3

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。

于 2020-03-06T20:55:38.570 回答
1

Dask 文档非常好且内容广泛,尽管我承认有时如果提供的功能的灵活性和数量可能会有点压倒性。我认为将 Dask 视为分布式计算的 API 有助于用户控制几个不同的执行层,每一层都提供更细粒度的控制。

compute()wait()并且persist()是来自一系列分布式计算下的任务在一组工作人员上调度的方式的概念。所有这些计算的共同点是一个表示远程任务及其相互依赖关系的执行图。在某些时候,这个执行图会被安排在一组工作人员上。Dask 提供了两个 API,这取决于图底层的任务是立即调度(急切地)还是计算需要手动触发(懒惰地)。

当创建依赖于其他任务结果的任务时,这两个 API 都会构建执行图。前者使用dask.futuresAPI 进行即时异步执行,有时您可能希望wait()在执行其他操作之前先执行其结果。该dask.delayedAPI 用于延迟执行,需要调用类似compute()or的方法persist()才能开始计算。

大多数情况下,像 RAPIDS 这样的库的用户更关心操作他们的数据,而不关心如何在一组工作人员上安排这些操作。和对象构建在 和dask.dataframeAPI之上dask.array。大多数用户与这些数据结构交互而不是与对象交互,但如果您需要在分布式对象和对象提供的功能之外进行一些数据转换,那么了解它们并不是一个坏主意。delayedfuturesdelayedfuturesdataframearray

dask.dataframe并且dask.array都尽可能构建惰性执行图,并提供一种compute()方法来实现图并将结果返回给客户端。它们都提供了persist()一种在后台异步启动计算的方法。wait()如果您想在后台开始计算但不想将结果返回给客户端,这很有用。

我希望这是有帮助的。

于 2020-03-12T14:51:23.840 回答