Distributed XGBoost with Dask

Dask is a parallel computing library built on Python. Dask allows easy management of distributed workers and excels at handling large distributed data science workflows. The implementation in XGBoost originates from dask-xgboost with some extended functionalities and a different interface. The tutorial here focuses on basic usage of dask with CPU tree algorithms. For an overview of GPU based training and internal workings, see A New, Official Dask API for XGBoost.

Contents

Requirements

Dask can be installed using either pip or conda (see the dask installation documentation for more information). For accelerating XGBoost with GPUs, dask-cuda is recommended for creating GPU clusters.

Overview

A dask cluster consists of three different components: a centralized scheduler, one or more workers, and one or more clients which act as the user-facing entry point for submitting tasks to the cluster. When using XGBoost with dask, one needs to call the XGBoost dask interface from the client side. Below is a small example which illustrates basic usage of running XGBoost on a dask cluster:

from xgboost import dask as dxgb

import dask.array as da
import dask.distributed

if __name__ == "__main__":
    cluster = dask.distributed.LocalCluster()
    client = dask.distributed.Client(cluster)

    # X and y must be Dask dataframes or arrays
    num_obs = 1e5
    num_features = 20
    X = da.random.random(size=(num_obs, num_features), chunks=(1000, num_features))
    y = da.random.random(size=(num_obs, 1), chunks=(1000, 1))

    dtrain = dxgb.DaskDMatrix(client, X, y)
    # or
    # dtrain = dxgb.DaskQuantileDMatrix(client, X, y)

    output = dxgb.train(
        client,
        {"verbosity": 2, "tree_method": "hist", "objective": "reg:squarederror"},
        dtrain,
        num_boost_round=4,
        evals=[(dtrain, "train")],
    )

Here we first create a cluster in single-node mode with distributed.LocalCluster, then connect a distributed.Client to this cluster, setting up an environment for later computation. Notice that the cluster construction is guarded by __name__ == "__main__", which is necessary otherwise there might be obscure errors.

We then create a xgboost.dask.DaskDMatrix object and pass it to xgboost.dask.train(), along with some other parameters, much like XGBoost’s normal, non-dask interface. Unlike that interface, data and label must be either Dask DataFrame or Dask Array instances.

The primary difference with XGBoost’s dask interface is we pass our dask client as an additional argument for carrying out the computation. Note that if client is set to None, XGBoost will use the default client returned by dask.

There are two sets of APIs implemented in XGBoost. The first set is functional API illustrated in above example. Given the data and a set of parameters, the train function returns a model and the computation history as a Python dictionary:

{
  "booster": Booster,
  "history": dict,
}

For prediction, pass the output returned by train into xgboost.dask.predict():

prediction = dxgb.predict(client, output, dtrain)
# Or equivalently, pass ``output['booster']``:
prediction = dxgb.predict(client, output['booster'], dtrain)

Eliminating the construction of DaskDMatrix is also possible, this can make the computation a bit faster when meta information like base_margin is not needed:

prediction = dxgb.predict(client, output, X)
# Use inplace version.
prediction = dxgb.inplace_predict(client, output, X)

Here prediction is a dask Array object containing predictions from model if input is a DaskDMatrix or da.Array. When putting dask collection directly into the predict function or using xgboost.dask.inplace_predict(), the output type depends on input data. See next section for details.

Alternatively, XGBoost also implements the Scikit-Learn interface with DaskXGBClassifier, DaskXGBRegressor, DaskXGBRanker and 2 random forest variances. This wrapper is similar to the single node Scikit-Learn interface in xgboost, with dask collection as inputs and has an additional client attribute. See following sections and XGBoost Dask Feature Walkthrough for more examples.

Running prediction

In previous example we used DaskDMatrix as input to predict function. In practice, it’s also possible to call predict function directly on dask collections like Array and DataFrame and might have better prediction performance. When DataFrame is used as prediction input, the result is a dask Series instead of array. Also, there’s in-place predict support on dask interface, which can help reducing both memory usage and prediction time.

# dtrain is the DaskDMatrix defined above.
prediction = dxgb.predict(client, booster, dtrain)

or equivalently:

# where X is a dask DataFrame or dask Array.
prediction = dxgb.predict(client, booster, X)

Also for inplace prediction:

# where X is a dask DataFrame or dask Array backed by cupy or cuDF.
booster.set_param({"device": "cuda"})
prediction = dxgb.inplace_predict(client, booster, X)

When input is da.Array object, output is always da.Array. However, if the input type is dd.DataFrame, output can be dd.Series, dd.DataFrame or da.Array, depending on output shape. For example, when SHAP-based prediction is used, the return value can have 3 or 4 dimensions , in such cases an Array is always returned.

The performance of running prediction, either using predict or inplace_predict, is sensitive to number of blocks. Internally, it’s implemented using da.map_blocks and dd.map_partitions. When number of partitions is large and each of them have only small amount of data, the overhead of calling predict becomes visible. On the other hand, if not using GPU, the number of threads used for prediction on each block matters. Right now, xgboost uses single thread for each partition. If the number of blocks on each workers is smaller than number of cores, then the CPU workers might not be fully utilized.

One simple optimization for running consecutive predictions is using distributed.Future:

dataset = [X_0, X_1, X_2]
booster_f = client.scatter(booster, broadcast=True)
futures = []
for X in dataset:
    # Here we pass in a future instead of concrete booster
    shap_f = dxgb.predict(client, booster_f, X, pred_contribs=True)
    futures.append(shap_f)

results = client.gather(futures)

This is only available on functional interface, as the Scikit-Learn wrapper doesn’t know how to maintain a valid future for booster. To obtain the booster object from Scikit-Learn wrapper object:

cls = dxgb.DaskXGBClassifier()
cls.fit(X, y)

booster = cls.get_booster()

Scikit-Learn Estimator Interface

As mentioned previously, there’s another interface that mimics the scikit-learn estimators with higher level of of abstraction. The interface is easier to use compared to the functional interface but with more constraints. It’s worth mentioning that, although the interface mimics scikit-learn estimators, it doesn’t work with normal scikit-learn utilities like GridSearchCV as scikit-learn doesn’t understand distributed dask data collection.

from distributed import LocalCluster, Client
from xgboost import dask as dxgb


def main(client: Client) -> None:
    X, y = load_data()
    clf = dxgb.DaskXGBClassifier(n_estimators=100, tree_method="hist")
    clf.client = client  # assign the client
    clf.fit(X, y, eval_set=[(X, y)])
    proba = clf.predict_proba(X)


if __name__ == "__main__":
    with LocalCluster() as cluster:
        with Client(cluster) as client:
            main(client)

GPU acceleration

For most of the use cases with GPUs, the Dask-CUDA project should be used to create the cluster, which automatically configures the correct device ordinal for worker processes. As a result, users should NOT specify the ordinal (good: device=cuda, bad: device=cuda:1). See Example of training with Dask on GPU and Use scikit-learn regressor interface with GPU histogram tree method for worked examples.

Working with other clusters

Using Dask’s LocalCluster is convenient for getting started quickly on a local machine. Once you’re ready to scale your work, though, there are a number of ways to deploy Dask on a distributed cluster. You can use Dask-CUDA, for example, for GPUs and you can use Dask Cloud Provider to deploy Dask clusters in the cloud. See the Dask documentation for a more comprehensive list.

In the example below, a KubeCluster is used for deploying Dask on Kubernetes:

from dask_kubernetes.operator import KubeCluster  # Need to install the ``dask-kubernetes`` package
from dask_kubernetes.operator.kubecluster.kubecluster import CreateMode

from dask.distributed import Client
from xgboost import dask as dxgb
import dask.array as da


def main():
  '''Connect to a remote kube cluster with GPU nodes and run training on it.'''
    m = 1000
    n = 10
    kWorkers = 2                # assuming you have 2 GPU nodes on that cluster.
    # You need to work out the worker-spec yourself.  See document in dask_kubernetes for
    # its usage.  Here we just want to show that XGBoost works on various clusters.

    # See notes below for why we use pre-allocated cluster.
    with KubeCluster(
        name="xgboost-test",
        image="my-image-name:latest",
        n_workers=kWorkers,
        create_mode=CreateMode.CONNECT_ONLY,
        shutdown_on_close=False,
    ) as cluster:
        with Client(cluster) as client:
            X = da.random.random(size=(m, n), chunks=100)
            y = X.sum(axis=1)

            regressor = dxgb.DaskXGBRegressor(n_estimators=10, missing=0.0)
            regressor.client = client
            regressor.set_params(tree_method='hist', device="cuda")
            regressor.fit(X, y, eval_set=[(X, y)])


if __name__ == '__main__':
    # Launch the kube cluster on somewhere like GKE, then run this as client process.
    # main function will connect to that cluster and start training xgboost model.
    main()

Different cluster classes might have subtle differences like network configuration, or specific cluster implementation might contains bugs that we are not aware of. Open an issue if such case is found and there’s no documentation on how to resolve it in that cluster implementation.

An interesting aspect of the Kubernetes cluster is that the pods may become available after the Dask workflow has begun, which can cause issues with distributed XGBoost since XGBoost expects the nodes used by input data to remain unchanged during training. To use Kubernetes clusters, it is necessary to wait for all the pods to be online before submitting XGBoost tasks. One can either create a wait function in Python or simply pre-allocate a cluster with k8s tools (like kubectl) before running dask workflows. To pre-allocate a cluster, we can first generate the cluster spec using dask kubernetes:

import json

from dask_kubernetes.operator import make_cluster_spec

spec = make_cluster_spec(name="xgboost-test", image="my-image-name:latest", n_workers=16)
with open("cluster-spec.json", "w") as fd:
    json.dump(spec, fd, indent=2)

kubectl apply -f ./cluster-spec.json

Check whether the pods are available:

kubectl get pods

Once all pods have been initialized, the Dask XGBoost workflow can be run, as in the previous example. It is important to ensure that the cluster sets the parameter create_mode=CreateMode.CONNECT_ONLY and optionally shutdown_on_close=False if you do not want to shut down the cluster after a single job.

Threads

XGBoost has built in support for parallel computation through threads by the setting nthread parameter (n_jobs for scikit-learn). If these parameters are set, they will override the configuration in Dask. For example:

with dask.distributed.LocalCluster(n_workers=7, threads_per_worker=4) as cluster:

There are 4 threads allocated for each dask worker. Then by default XGBoost will use 4 threads in each process for training. But if nthread parameter is set:

output = dxgb.train(
    client,
    {"verbosity": 1, "nthread": 8, "tree_method": "hist"},
    dtrain,
    num_boost_round=4,
    evals=[(dtrain, "train")],
)

XGBoost will use 8 threads in each training process.

Working with asyncio

Added in version 1.2.0.

XGBoost’s dask interface supports the new asyncio in Python and can be integrated into asynchronous workflows. For using dask with asynchronous operations, please refer to this dask example and document in distributed. To use XGBoost’s dask interface asynchronously, the client which is passed as an argument for training and prediction must be operating in asynchronous mode by specifying asynchronous=True when the client is created (example below). All functions (including DaskDMatrix) provided by the functional interface will then return coroutines which can then be awaited to retrieve their result.

Functional interface:

async with dask.distributed.Client(scheduler_address, asynchronous=True) as client:
    X, y = generate_array()
    m = await dxgb.DaskDMatrix(client, X, y)
    output = await dxgb.train(client, {}, dtrain=m)

    with_m = await dxgb.predict(client, output, m)
    with_X = await dxgb.predict(client, output, X)
    inplace = await dxgb.inplace_predict(client, output, X)

    # Use ``client.compute`` instead of the ``compute`` method from dask collection
    print(await client.compute(with_m))

While for the Scikit-Learn interface, trivial methods like set_params and accessing class attributes like evals_result() do not require await. Other methods involving actual computation will return a coroutine and hence require awaiting:

async with dask.distributed.Client(scheduler_address, asynchronous=True) as client:
    X, y = generate_array()
    regressor = await dxgb.DaskXGBRegressor(verbosity=1, n_estimators=2)
    regressor.set_params(tree_method='hist')  # trivial method, synchronous operation
    regressor.client = client  #  accessing attribute, synchronous operation
    regressor = await regressor.fit(X, y, eval_set=[(X, y)])
    prediction = await regressor.predict(X)

    # Use `client.compute` instead of the `compute` method from dask collection
    print(await client.compute(prediction))

Evaluation and Early Stopping

Added in version 1.3.0.

The Dask interface allows the use of validation sets that are stored in distributed collections (Dask DataFrame or Dask Array). These can be used for evaluation and early stopping.

To enable early stopping, pass one or more validation sets containing DaskDMatrix objects.

import dask.array as da
from xgboost import dask as dxgb

num_rows = 1e6
num_features = 100
num_partitions = 10
rows_per_chunk = num_rows / num_partitions

data = da.random.random(
    size=(num_rows, num_features),
    chunks=(rows_per_chunk, num_features)
)

labels = da.random.random(
    size=(num_rows, 1),
    chunks=(rows_per_chunk, 1)
)

X_eval = da.random.random(
    size=(num_rows, num_features),
    chunks=(rows_per_chunk, num_features)
)

y_eval = da.random.random(
    size=(num_rows, 1),
    chunks=(rows_per_chunk, 1)
)

dtrain = dxgb.DaskDMatrix(
    client=client,
    data=data,
    label=labels
)

dvalid = dxgb.DaskDMatrix(
    client=client,
    data=X_eval,
    label=y_eval
)

result = dxgb.train(
    client=client,
    params={
        "objective": "reg:squarederror",
    },
    dtrain=dtrain,
    num_boost_round=10,
    evals=[(dvalid, "valid1")],
    early_stopping_rounds=3
)

When validation sets are provided to xgboost.dask.train() in this way, the model object returned by xgboost.dask.train() contains a history of evaluation metrics for each validation set, across all boosting rounds.

print(result["history"])
# {'valid1': OrderedDict([('rmse', [0.28857, 0.28858, 0.288592, 0.288598])])}

If early stopping is enabled by also passing early_stopping_rounds, you can check the best iteration in the returned booster.

booster = result["booster"]
print(booster.best_iteration)
best_model = booster[: booster.best_iteration]

Other customization

XGBoost dask interface accepts other advanced features found in single node Python interface, including callback functions, custom evaluation metric and objective:

def eval_error_metric(predt, dtrain: xgb.DMatrix):
    label = dtrain.get_label()
    r = np.zeros(predt.shape)
    gt = predt > 0.5
    r[gt] = 1 - label[gt]
    le = predt <= 0.5
    r[le] = label[le]
    return 'CustomErr', np.sum(r)

# custom callback
early_stop = xgb.callback.EarlyStopping(
    rounds=early_stopping_rounds,
    metric_name="CustomErr",
    data_name="Train",
    save_best=True,
)

booster = dxgb.train(
    client,
    params={
        "objective": "binary:logistic",
        "eval_metric": ["error", "rmse"],
        "tree_method": "hist",
    },
    dtrain=D_train,
    evals=[(D_train, "Train"), (D_valid, "Valid")],
    feval=eval_error_metric,  # custom evaluation metric
    num_boost_round=100,
    callbacks=[early_stop],
)

Hyper-parameter tuning

See https://github.com/coiled/dask-xgboost-nyctaxi for a set of examples of using XGBoost with dask and optuna.

Troubleshooting

In some environments XGBoost might fail to resolve the IP address of the scheduler, a symptom is user receiving OSError: [Errno 99] Cannot assign requested address error during training. A quick workaround is to specify the address explicitly. To do that dask config is used:

Added in version 1.6.0.

import dask
from distributed import Client
from xgboost import dask as dxgb
# let xgboost know the scheduler address
dask.config.set({"xgboost.scheduler_address": "192.0.0.100"})

with Client(scheduler_file="sched.json") as client:
    reg = dxgb.DaskXGBRegressor()

# We can specify the port for XGBoost as well
with dask.config.set({"xgboost.scheduler_address": "192.0.0.100:12345"}):
    reg = dxgb.DaskXGBRegressor()

Please note that XGBoost requires a different port than dask. By default, on a unix-like system XGBoost uses the port 0 to find available ports, which may fail if a user is running in a restricted docker environment. In this case, please open additional ports in the container and specify it as in the above snippet.
If you encounter a NCCL system error while training with GPU enabled, which usually includes the error message NCCL failure: unhandled system error, you can specify its network configuration using one of the environment variables listed in the NCCL document such as the NCCL_SOCKET_IFNAME. In addition, you can use NCCL_DEBUG to obtain debug logs.
If NCCL fails to initialize in a container environment, it might be caused by limited system shared memory. With docker, one can try the flag: –shm-size=4g.
MIG (Multi-Instance GPU) is not yet supported by NCCL. You will receive an error message that includes Multiple processes within a communication group … upon initialization.

Starting from version 2.1.0, to reduce the size of the binary wheel, the XGBoost package (installed using pip) loads NCCL from the environment instead of bundling it directly. This means that if you encounter an error message like “Failed to load nccl …”, it indicates that NCCL is not installed or properly configured in your environment.

To resolve this issue, you can install NCCL using pip:
```
pip install nvidia-nccl-cu12 # (or with any compatible CUDA version)
```
The default conda installation of XGBoost should not encounter this error. If you are using a customized XGBoost, please make sure one of the followings is true:
- XGBoost is NOT compiled with the USE_DLOPEN_NCCL flag.
- The dmlc_nccl_path parameter is set to full NCCL path when initializing the collective.
Here are some additional tips for troubleshooting NCCL dependency issues:
- Check the NCCL installation path and verify that it’s installed correctly. We try to find NCCL by using from nvidia.nccl import lib in Python when XGBoost is installed using pip.
- Ensure that you have the correct CUDA version installed. NCCL requires a compatible CUDA version to function properly.
- If you are not using distributed training with XGBoost and yet see this error, please open an issue on GitHub.
- If you continue to encounter NCCL dependency issues, please open an issue on GitHub.

IPv6 Support

Added in version 1.7.0.

XGBoost has initial IPv6 support for the dask interface on Linux. Due to most of the cluster support for IPv6 is partial (dual stack instead of IPv6 only), we require additional user configuration similar to Troubleshooting to help XGBoost obtain the correct address information:

import dask
from distributed import Client
from xgboost import dask as dxgb
# let xgboost know the scheduler address, use the same bracket format as dask.
with dask.config.set({"xgboost.scheduler_address": "[fd20:b6f:f759:9800::]"}):
    with Client("[fd20:b6f:f759:9800::]") as client:
        reg = dxgb.DaskXGBRegressor(tree_method="hist")

When GPU is used, XGBoost employs NCCL as the underlying communication framework, which may require some additional configuration via environment variable depending on the setting of the cluster. Please note that IPv6 support is Unix only.

Why is the initialization of `DaskDMatrix` so slow and throws weird errors

The dask API in XGBoost requires construction of DaskDMatrix. With the Scikit-Learn interface, DaskDMatrix is implicitly constructed for all input data during the fit or predict steps. You might have observed that DaskDMatrix construction can take large amounts of time, and sometimes throws errors that don’t seem to be relevant to DaskDMatrix. Here is a brief explanation for why. By default most dask computations are lazily evaluated, which means that computation is not carried out until you explicitly ask for a result by, for example, calling compute(). See the previous link for details in dask, and this wiki for information on the general concept of lazy evaluation. The DaskDMatrix constructor forces lazy computations to be evaluated, which means it’s where all your earlier computation actually being carried out, including operations like dd.read_csv(). To isolate the computation in DaskDMatrix from other lazy computations, one can explicitly wait for results of input data before constructing a DaskDMatrix. Also dask’s diagnostics dashboard can be used to monitor what operations are currently being performed.

Reproducible Result

In a single node mode, we can always expect the same training result between runs as along as the underlying platforms are the same. However, it’s difficult to obtain reproducible result in a distributed environment, since the tasks might get different machine allocation or have different amount of available resources during different sessions. There are heuristics and guidelines on how to achieve it but no proven method for guaranteeing such deterministic behavior. The Dask interface in XGBoost tries to provide reproducible result with best effort. This section highlights some known criteria and try to share some insights into the issue.

There are primarily two different tasks for XGBoost the carry out, training and inference. Inference is reproducible given the same software and hardware along with the same run-time configurations. The remaining of this section will focus on training.

Many of the challenges come from the fact that we are using approximation algorithms, The sketching algorithm used to find histogram bins is an approximation to the exact quantile algorithm, the AUC metric in a distributed environment is an approximation to the exact AUC score, and floating-point number is an approximation to real number. Floating-point is an issue as its summation is not associative, meaning \((a + b) + c\) does not necessarily equal to \(a + (b + c)\), even though this property holds true for real number. As a result, whenever we change the order of a summation, the result can differ. This imposes the requirement that, in order to have reproducible output from XGBoost, the entire pipeline needs to be reproducible.

The software stack is the same for each runs. This goes without saying. XGBoost might generate different outputs between different versions. This is expected as we might change the default value of hyper-parameter, or the parallel strategy that generates different floating-point result. We guarantee the correctness the algorithms, but there are lots of wiggle room for the final output. The situation is similar for many dependencies, for instance, the random number generator might differ from platform to platform.
The hardware stack is the same for each runs. This includes the number of workers, and the amount of available resources on each worker. XGBoost can generate different results using different number of workers. This is caused by the approximation issue mentioned previously.
Similar to the hardware constraint, the network topology is also a factor in final output. If we change topology the workers might be ordered differently, leading to different ordering of floating-point operations.
The random seed used in various place of the pipeline.
The partitioning of data needs to be reproducible. This is related to the available resources on each worker. Dask might partition the data differently for each run according to its own scheduling policy. For instance, if there are some additional tasks in the cluster while you are running the second training session for XGBoost, some of the workers might have constrained memory and Dask may not push the training data for XGBoost to that worker. This change in data partitioning can lead to different output models. If you are using a shared Dask cluster, then the result is likely to vary between runs.
The operations performed on dataframes need to be reproducible. There are some operations like DataFrame.merge not being deterministic on parallel hardwares like GPU where the order of the index might differ from run to run.

It’s expected to have different results when training the model in a distributed environment than training the model using a single node due to aforementioned criteria.

Memory Usage

Here are some practices on reducing memory usage with dask and xgboost.

In a distributed work flow, data is best loaded by dask collections directly instead of loaded by client process. When loading with client process is unavoidable, use client.scatter to distribute data from client process to workers. See [2] for a nice summary.
When using GPU input, like dataframe loaded by dask_cudf, you can try xgboost.dask.DaskQuantileDMatrix as a drop in replacement for DaskDMatrix to reduce overall memory usage. See Example of training with Dask on GPU for an example.
Use in-place prediction when possible.

References: