196 lines
8.2 KiB
ReStructuredText
196 lines
8.2 KiB
ReStructuredText
#####################################
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Using XGBoost External Memory Version
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#####################################
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When working with large datasets, training XGBoost models can be challenging as the entire
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dataset needs to be loaded into memory. This can be costly and sometimes
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infeasible. Staring from 1.5, users can define a custom iterator to load data in chunks
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for running XGBoost algorithms. External memory can be used for both training and
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prediction, but training is the primary use case and it will be our focus in this
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tutorial. For prediction and evaluation, users can iterate through the data themseleves
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while training requires the full dataset to be loaded into the memory.
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During training, there are two different modes for external memory support available in
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XGBoost, one for CPU-based algorithms like ``hist`` and ``approx``, another one for the
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GPU-based training algorithm. We will introduce them in the following sections.
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.. note::
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Training on data from external memory is not supported by the ``exact`` tree method.
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.. note::
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The feature is still experimental as of 2.0. The performance is not well optimized.
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*************
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Data Iterator
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*************
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Starting from XGBoost 1.5, users can define their own data loader using Python or C
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interface. There are some examples in the ``demo`` directory for quick start. This is a
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generalized version of text input external memory, where users no longer need to prepare a
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text file that XGBoost recognizes. To enable the feature, users need to define a data
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iterator with 2 class methods: ``next`` and ``reset``, then pass it into the ``DMatrix``
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constructor.
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.. code-block:: python
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import os
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from typing import List, Callable
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import xgboost
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from sklearn.datasets import load_svmlight_file
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class Iterator(xgboost.DataIter):
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def __init__(self, svm_file_paths: List[str]):
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self._file_paths = svm_file_paths
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self._it = 0
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# XGBoost will generate some cache files under current directory with the prefix
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# "cache"
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super().__init__(cache_prefix=os.path.join(".", "cache"))
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def next(self, input_data: Callable):
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"""Advance the iterator by 1 step and pass the data to XGBoost. This function is
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called by XGBoost during the construction of ``DMatrix``
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"""
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if self._it == len(self._file_paths):
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# return 0 to let XGBoost know this is the end of iteration
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return 0
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# input_data is a function passed in by XGBoost who has the exact same signature of
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# ``DMatrix``
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X, y = load_svmlight_file(self._file_paths[self._it])
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input_data(data=X, label=y)
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self._it += 1
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# Return 1 to let XGBoost know we haven't seen all the files yet.
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return 1
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def reset(self):
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"""Reset the iterator to its beginning"""
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self._it = 0
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it = Iterator(["file_0.svm", "file_1.svm", "file_2.svm"])
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Xy = xgboost.DMatrix(it)
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# Other tree methods including ``hist`` and ``gpu_hist`` also work, but has some caveats
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# as noted in following sections.
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booster = xgboost.train({"tree_method": "hist"}, Xy)
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The above snippet is a simplified version of :ref:`sphx_glr_python_examples_external_memory.py`.
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For an example in C, please see ``demo/c-api/external-memory/``. The iterator is the
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common interface for using external memory with XGBoost, you can pass the resulting
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``DMatrix`` object for training, prediction, and evaluation.
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It is important to set the batch size based on the memory available. A good starting point
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is to set the batch size to 10GB per batch if you have 64GB of memory. It is *not*
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recommended to set small batch sizes like 32 samples per batch, as this can seriously hurt
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performance in gradient boosting.
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***********
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CPU Version
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***********
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In the previous section, we demonstrated how to train a tree-based model using the
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``hist`` tree method on a CPU. This method involves iterating through data batches stored
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in a cache during tree construction. For optimal performance, we recommend using the
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``grow_policy=depthwise`` setting, which allows XGBoost to build an entire layer of tree
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nodes with only a few batch iterations. Conversely, using the ``lossguide`` policy
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requires XGBoost to iterate over the data set for each tree node, resulting in slower
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performance.
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If external memory is used, the performance of CPU training is limited by IO
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(input/output) speed. This means that the disk IO speed primarily determines the training
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speed. During benchmarking, we used an NVMe connected to a PCIe-4 slot, other types of
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storage can be too slow for practical usage. In addition, your system may perform caching
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to reduce the overhead of file reading.
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**********************************
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GPU Version (GPU Hist tree method)
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**********************************
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External memory is supported by GPU algorithms (i.e. when ``tree_method`` is set to
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``gpu_hist``). However, the algorithm used for GPU is different from the one used for
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CPU. When training on a CPU, the tree method iterates through all batches from external
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memory for each step of the tree construction algorithm. On the other hand, the GPU
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algorithm concatenates all batches into one and stores it in GPU memory. To reduce overall
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memory usage, users can utilize subsampling. The good news is that the GPU hist tree
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method supports gradient-based sampling, enabling users to set a low sampling rate without
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compromising accuracy.
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.. code-block:: python
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param = {
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...
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'subsample': 0.2,
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'sampling_method': 'gradient_based',
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}
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For more information about the sampling algorithm and its use in external memory training,
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see `this paper <https://arxiv.org/abs/2005.09148>`_.
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.. warning::
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When GPU is running out of memory during iteration on external memory, user might
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recieve a segfault instead of an OOM exception.
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*******
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Remarks
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*******
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When using external memory with XBGoost, data is divided into smaller chunks so that only
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a fraction of it needs to be stored in memory at any given time. It's important to note
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that this method only applies to the predictor data (``X``), while other data, like labels
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and internal runtime structures are concatenated. This means that memory reduction is most
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effective when dealing with wide datasets where ``X`` is larger compared to other data
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like ``y``, while it has little impact on slim datasets.
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Starting with XGBoost 2.0, the implementation of external memory uses ``mmap``. It is not
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yet tested against system errors like disconnected network devices (`SIGBUS`). Also, it's
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worth noting that most tests have been conducted on Linux distributions.
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Another important point to keep in mind is that creating the initial cache for XGBoost may
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take some time. The interface to external memory is through custom iterators, which may or
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may not be thread-safe. Therefore, initialization is performed sequentially.
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****************
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Text File Inputs
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****************
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This is the original form of external memory support, users are encouraged to use custom
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data iterator instead. There is no big difference between using external memory version of
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text input and the in-memory version. The only difference is the filename format.
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The external memory version takes in the following `URI
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<https://en.wikipedia.org/wiki/Uniform_Resource_Identifier>`_ format:
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.. code-block:: none
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filename?format=libsvm#cacheprefix
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The ``filename`` is the normal path to LIBSVM format file you want to load in, and
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``cacheprefix`` is a path to a cache file that XGBoost will use for caching preprocessed
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data in binary form.
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To load from csv files, use the following syntax:
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.. code-block:: none
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filename.csv?format=csv&label_column=0#cacheprefix
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where ``label_column`` should point to the csv column acting as the label.
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If you have a dataset stored in a file similar to ``demo/data/agaricus.txt.train`` with LIBSVM
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format, the external memory support can be enabled by:
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.. code-block:: python
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dtrain = DMatrix('../data/agaricus.txt.train?format=libsvm#dtrain.cache')
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XGBoost will first load ``agaricus.txt.train`` in, preprocess it, then write to a new file named
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``dtrain.cache`` as an on disk cache for storing preprocessed data in an internal binary format. For
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more notes about text input formats, see :doc:`/tutorials/input_format`.
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For CLI version, simply add the cache suffix, e.g. ``"../data/agaricus.txt.train?format=libsvm#dtrain.cache"``.
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