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Version: 1.0.4

LightGBM on Apache Spark


LightGBM is an open-source, distributed, high-performance gradient boosting (GBDT, GBRT, GBM, or MART) framework. This framework specializes in creating high-quality and GPU enabled decision tree algorithms for ranking, classification, and many other machine learning tasks. LightGBM is part of Microsoft's DMTK project.

Advantages of LightGBM through SynapseML

  • Composability: LightGBM models can be incorporated into existing SparkML Pipelines, and used for batch, streaming, and serving workloads.
  • Performance: LightGBM on Spark is 10-30% faster than SparkML on the Higgs dataset, and achieves a 15% increase in AUC. Parallel experiments have verified that LightGBM can achieve a linear speed-up by using multiple machines for training in specific settings.
  • Functionality: LightGBM offers a wide array of tunable parameters, that one can use to customize their decision tree system. LightGBM on Spark also supports new types of problems such as quantile regression.
  • Cross platform LightGBM on Spark is available on Spark, PySpark, and SparklyR


In PySpark, you can run the LightGBMClassifier via:

from import LightGBMClassifier
model = LightGBMClassifier(learningRate=0.3,

Similarly, you can run the LightGBMRegressor by setting the application and alpha parameters:

from import LightGBMRegressor
model = LightGBMRegressor(application='quantile',

For an end to end application, check out the LightGBM notebook example.


SynapseML exposes getters/setters for many common LightGBM parameters. In python, you can use property-value pairs, or in Scala use fluent setters. Examples of both are shown in this section.

val classifier = new LightGBMClassifier()

LightGBM has far more parameters than SynapseML exposes. For cases where you need to set some parameters that SynapseML doesn't expose a setter for, use passThroughArgs. This argument is just a free string that you can use to add extra parameters to the command SynapseML sends to configure LightGBM.

In python:

from import LightGBMClassifier
model = LightGBMClassifier(passThroughArgs="force_row_wise=true min_sum_hessian_in_leaf=2e-3",

In Scala:

val classifier = new LightGBMClassifier()
.setPassThroughArgs("force_row_wise=true min_sum_hessian_in_leaf=2e-3")

For formatting options and specific argument documentation, see LightGBM docs. SynapseML sets some parameters specifically for the Spark distributed environment and shouldn't be changed. Some parameters are for CLI mode only, and don't work within Spark.

You can mix passThroughArgs and explicit args, as shown in the example. SynapseML merges them to create one argument string to send to LightGBM. If you set a parameter in both places, passThroughArgs takes precedence.


LightGBM on Spark uses the Simple Wrapper and Interface Generator (SWIG) to add Java support for LightGBM. These Java Binding use the Java Native Interface call into the distributed C++ API.

We initialize LightGBM by calling LGBM_NetworkInit with the Spark executors within a MapPartitions call. We then pass each workers partitions into LightGBM to create the in-memory distributed dataset for LightGBM. We can then train LightGBM to produce a model that can then be used for inference.

The LightGBMClassifier and LightGBMRegressor use the SparkML API, inherit from the same base classes, integrate with SparkML pipelines, and can be tuned with SparkML's cross validators.

Models built can be saved as SparkML pipeline with native LightGBM model using saveNativeModel(). Additionally, they're fully compatible with PMML and can be converted to PMML format through the JPMML-SparkML-LightGBM plugin.

Dynamic Allocation Limitations

The native LightGBM library has a distributed mode that allows the algorithm to work over multiple machines. SynapseML uses this mode to call LightGBM from Spark. SynapseML first gathers all the Spark executor networking information, passes that to LightGBM, and then waits for LightGBM to complete its work. However, the native LightGBM algorithm implementation assumes all networking is constant over the time period of a single training or scoring session. The native LightGBM distributed mode was designed this way and isn't a limitation of SynapseML by itself.

Dynamic compute changes can cause LightGBM problems if the Spark executors change during data processing. Spark can naturally take advantage of cluster autoscaling and can also dynamically replace any failed executor with another, but LightGBM can't handle these networking changes. Large datasets are affected in particular since they're more likely to cause executor scaling or have a single executor fail during a single processing pass.

If you're experiencing problems with LightGBM as exposed through SynapseML due to executor changes (for example, occasional Task failures or networking hangs), there are several options.

  1. In the Spark platform, turn off any autoscaling on the cluster you have provisioned.
  2. Set numTasks manually to be smaller so that fewer executors are used (reducing probability of single executor failure).
  3. Turn off dynamic executor scaling with configuration in a notebook cell. In Synapse and Fabric, you can use:
"spark.dynamicAllocation.enabled": "false"

Note: setting any custom configuration can affect cluster startup time if your compute platform takes advantage of "live pools" to improve notebook performance.

If you still have problems, you can consider splitting your data into smaller segments using numBatches. Splitting into multiple batches increases total processing time, but can potentially be used to increase reliability.

Data Transfer Mode

SynapseML must pass data from Spark partitions to LightGBM native Datasets before turning over control to the actual LightGBM execution code for training and inference. SynapseML has two modes that control how this data is transferred: streaming and bulk. This mode doesn't affect training but can affect memory usage and overall fit/transform time.

Bulk Execution mode

The "Bulk" mode is older and requires accumulating all data in executor memory before creating Datasets. This mode can cause OOM errors for large data, especially since the data must be accumulated in its original uncompressed double-format size. For now, "bulk" mode is the default since "streaming" is new, but SynapseML will eventually make streaming the default.

For bulk mode, native LightGBM Datasets can either be created per partition (useSingleDatasetMode=false), or per executor (useSingleDatasetMode=true). Generally, one Dataset per executor is more efficient since it reduces LightGBM network size and complexity during training or fitting. It also avoids using slow network protocols on partitions that are actually on the same executor node.

Streaming Execution Mode

The "streaming" execution mode uses new native LightGBM APIs created just for SynapseML that don't require loading extra copies of the data into memory. In particular, data is passed directly from partitions to Datasets in small "micro-batches", similar to Spark streaming. The microBatchSize parameter controls the size of these micro-batches. Smaller micro-batch sizes reduce memory overhead, but larger sizes avoid overhead from repeatedly transferring data to the native layer. The default 100, uses far less memory than bulk mode since only 100 rows of data will be loaded at a time. If your dataset has few columns, you can increase the batch size. Alternatively, if your dataset has a large number of columns you can decrease the micro-batch size to avoid OOM issues.

These new streaming APIs in LightGBM are thread-safe, and allow all partitions in the same executor to push data into a shared Dataset in parallel. Because of this, streaming mode always uses the more efficient "useSingleDatasetMode=true", creating only one Dataset per executor.

You can explicitly specify Execution Mode and MicroBatch size as parameters.

val lgbm = new LightGBMClassifier()
<train classifier>

For streaming mode, only one Dataset is created per partition, so useSingleDataMode has no effect. It's effectively always true.

Data Sampling

In order for LightGBM algorithm to work, it must first create a set of bin boundaries for optimization. It does this calculation by first sampling the data before any training or inferencing starts. (LightGBM docs). The number of samples to use is set using binSampleCount, which must be a minimal percent of the data or LightGBM rejects it.

For bulk mode, this sampling is automatically done over the entire data, and each executor uses its own partitions to calculate samples for only a subset of the features. This distributed sampling can have subtle effects since partitioning can affect the calculated bins. Also, all data is sampled no matter what.

For streaming mode, there are more explicit user controls for this sampling, and it's all done from the driver. The samplingMode property controls the behavior. The efficiency of these methods increases from first to last.

  • global - Like bulk mode, the random sample is calculated by iterating over entire data (hence data is traversed twice)
  • subset - (default) Samples only from the first samplingSubsetSize elements. Assumes this subset is representative.
  • fixed - There's no random sample. The first binSampleSize rows are used. Assumes randomized data. For large row counts, subset and fixed modes can save a first iteration over the entire data.

Reference Dataset

The sampling of the data to calculate bin boundaries happens every fit call. If repeating a fit many times (for example, hyperparameter tuning), this calculation is duplicated effort.

For streaming mode, there's an optimization that a client can set to use the previously calculated bin boundaries. The sampling calculation results in a reference dataset, which can be reused. After a fit, there will be a referenceDataset property on the estimator that was calculated and used for that fit. If that is set on the next estimator (or you reuse the same one), it will use that instead of resampling the data.

from import LightGBMClassifier
classifier = LightGBMClassifier(learningRate=0.3,
model1 =

classifier.learningRate = 0.4
model2 =

The 'model2' call to 'fit' doesn't resample the data and uses the same bin boundaries as 'model1'.

Caution: Some parameters actually affect the bin boundary calculation and require the use of a new reference dataset every time. These parameters include isEnableSparse, useMissing, and zeroAsMissing that you can set from SynapseML. If you manually set some parameters with passThroughArgs, you should look at LightGBM docs to see if they affect bin boundaries. If you're setting any parameter that affects bin boundaries and reusing the same estimator, you should set referenceDataset to an empty array between calls.

Barrier Execution Mode

By default LightGBM uses the regular spark paradigm for launching tasks and communicates with the driver to coordinate task execution. The driver thread aggregates all task host:port information and then communicates the full list back to the workers in order for NetworkInit to be called. This procedure requires the driver to know how many tasks there are, and a mismatch between the expected number of tasks and the actual number causes the initialization to deadlock.

If you're experiencing network issues, you can try using Spark's barrier execution mode. SynapseML provides a UseBarrierExecutionMode flag, to use Apache Spark's barrier() stage to ensure all tasks execute at the same time. Barrier execution mode changes the logic to aggregate host:port information across all tasks in a synchronized way. To use it in scala, you can call setUseBarrierExecutionMode(true), for example:

val lgbm = new LightGBMClassifier()
<train classifier>

Note: barrier execution mode can also cause complicated issues, so use it only if needed.