sql-pyspark-pandas-with-arrow.md

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Apache Arrow in PySpark

Apache Arrow is an in-memory columnar data format that is used in Spark to efficiently transfer data between JVM and Python processes. This currently is most beneficial to Python users that work with Pandas/NumPy data. Its usage is not automatic and might require some minor changes to configuration or code to take full advantage and ensure compatibility. This guide will give a high-level description of how to use Arrow in Spark and highlight any differences when working with Arrow-enabled data.

Ensure PyArrow Installed

To use Apache Arrow in PySpark, the recommended version of PyArrow should be installed. If you install PySpark using pip, then PyArrow can be brought in as an extra dependency of the SQL module with the command pip install pyspark[sql]. Otherwise, you must ensure that PyArrow is installed and available on all cluster nodes. You can install using pip or conda from the conda-forge channel. See PyArrow installation for details.

Enabling for Conversion to/from Pandas

Arrow is available as an optimization when converting a Spark DataFrame to a Pandas DataFrame using the call toPandas() and when creating a Spark DataFrame from a Pandas DataFrame with createDataFrame(pandas_df). To use Arrow when executing these calls, users need to first set the Spark configuration spark.sql.execution.arrow.pyspark.enabled to true. This is disabled by default.

In addition, optimizations enabled by spark.sql.execution.arrow.pyspark.enabled could fallback automatically to non-Arrow optimization implementation if an error occurs before the actual computation within Spark. This can be controlled by spark.sql.execution.arrow.pyspark.fallback.enabled.

{% include_example dataframe_with_arrow python/sql/arrow.py %}

Using the above optimizations with Arrow will produce the same results as when Arrow is not enabled. Note that even with Arrow, toPandas() results in the collection of all records in the DataFrame to the driver program and should be done on a small subset of the data. Not all Spark data types are currently supported and an error can be raised if a column has an unsupported type, see Supported SQL Types. If an error occurs during createDataFrame(), Spark will fall back to create the DataFrame without Arrow.

Pandas UDFs (a.k.a. Vectorized UDFs)

Pandas UDFs are user defined functions that are executed by Spark using Arrow to transfer data and Pandas to work with the data, which allows vectorized operations. A Pandas UDF is defined using the pandas_udf as a decorator or to wrap the function, and no additional configuration is required. A Pandas UDF behaves as a regular PySpark function API in general.

Before Spark 3.0, Pandas UDFs used to be defined with PandasUDFType. From Spark 3.0 with Python 3.6+, you can also use Python type hints. Using Python type hints are preferred and using PandasUDFType will be deprecated in the future release.

Note that the type hint should use pandas.Series in all cases but there is one variant that pandas.DataFrame should be used for its input or output type hint instead when the input or output column is of StructType. The following example shows a Pandas UDF which takes long column, string column and struct column, and outputs a struct column. It requires the function to specify the type hints of pandas.Series and pandas.DataFrame as below:

{% include_example ser_to_frame_pandas_udf python/sql/arrow.py %}

In the following sections, it describes the combinations of the supported type hints. For simplicity, pandas.DataFrame variant is omitted.

Series to Series

The type hint can be expressed as pandas.Series, ... -> pandas.Series.

By using pandas_udf with the function having such type hints above, it creates a Pandas UDF where the given function takes one or more pandas.Series and outputs one pandas.Series. The output of the function should always be of the same length as the input. Internally, PySpark will execute a Pandas UDF by splitting columns into batches and calling the function for each batch as a subset of the data, then concatenating the results together.

The following example shows how to create this Pandas UDF that computes the product of 2 columns.

{% include_example ser_to_ser_pandas_udf python/sql/arrow.py %}

For detailed usage, please see pyspark.sql.functions.pandas_udf

Iterator of Series to Iterator of Series

The type hint can be expressed as Iterator[pandas.Series] -> Iterator[pandas.Series].

By using pandas_udf with the function having such type hints above, it creates a Pandas UDF where the given function takes an iterator of pandas.Series and outputs an iterator of pandas.Series. The length of the entire output from the function should be the same length of the entire input; therefore, it can prefetch the data from the input iterator as long as the lengths are the same. In this case, the created Pandas UDF requires one input column when the Pandas UDF is called. To use multiple input columns, a different type hint is required. See Iterator of Multiple Series to Iterator of Series.

It is also useful when the UDF execution requires initializing some states although internally it works identically as Series to Series case. The pseudocode below illustrates the example.

{% highlight python %} @pandas_udf("long") def calculate(iterator: Iterator[pd.Series]) -> Iterator[pd.Series]: # Do some expensive initialization with a state state = very_expensive_initialization() for x in iterator: # Use that state for whole iterator. yield calculate_with_state(x, state)

df.select(calculate("value")).show() {% endhighlight %}

The following example shows how to create this Pandas UDF:

{% include_example iter_ser_to_iter_ser_pandas_udf python/sql/arrow.py %}

For detailed usage, please see pyspark.sql.functions.pandas_udf

Iterator of Multiple Series to Iterator of Series

The type hint can be expressed as Iterator[Tuple[pandas.Series, ...]] -> Iterator[pandas.Series].

By using pandas_udf with the function having such type hints above, it creates a Pandas UDF where the given function takes an iterator of a tuple of multiple pandas.Series and outputs an iterator of pandas.Series. In this case, the created pandas UDF requires multiple input columns as many as the series in the tuple when the Pandas UDF is called. Otherwise, it has the same characteristics and restrictions as Iterator of Series to Iterator of Series case.

The following example shows how to create this Pandas UDF:

{% include_example iter_sers_to_iter_ser_pandas_udf python/sql/arrow.py %}

For detailed usage, please see pyspark.sql.functions.pandas_udf

Series to Scalar

The type hint can be expressed as pandas.Series, ... -> Any.

By using pandas_udf with the function having such type hints above, it creates a Pandas UDF similar to PySpark's aggregate functions. The given function takes pandas.Series and returns a scalar value. The return type should be a primitive data type, and the returned scalar can be either a python primitive type, e.g., int or float or a numpy data type, e.g., numpy.int64 or numpy.float64. Any should ideally be a specific scalar type accordingly.

This UDF can be also used with groupBy().agg() and pyspark.sql.Window. It defines an aggregation from one or more pandas.Series to a scalar value, where each pandas.Series represents a column within the group or window.

Note that this type of UDF does not support partial aggregation and all data for a group or window will be loaded into memory. Also, only unbounded window is supported with Grouped aggregate Pandas UDFs currently. The following example shows how to use this type of UDF to compute mean with a group-by and window operations:

{% include_example ser_to_scalar_pandas_udf python/sql/arrow.py %}

For detailed usage, please see pyspark.sql.functions.pandas_udf

Pandas Function APIs

Pandas Function APIs can directly apply a Python native function against the whole DataFrame by using Pandas instances. Internally it works similarly with Pandas UDFs by using Arrow to transfer data and Pandas to work with the data, which allows vectorized operations. However, A Pandas Function API behaves as a regular API under PySpark DataFrame instead of Column, and Python type hints in Pandas Functions APIs are optional and do not affect how it works internally at this moment although they might be required in the future.

From Spark 3.0, grouped map pandas UDF is now categorized as a separate Pandas Function API, DataFrame.groupby().applyInPandas(). It is still possible to use it with PandasUDFType and DataFrame.groupby().apply() as it was; however, it is preferred to use DataFrame.groupby().applyInPandas() directly. Using PandasUDFType will be deprecated in the future.

Grouped Map

Grouped map operations with Pandas instances are supported by DataFrame.groupby().applyInPandas() which requires a Python function that takes a pandas.DataFrame and return another pandas.DataFrame. It maps each group to each pandas.DataFrame in the Python function.

This API implements the "split-apply-combine" pattern which consists of three steps:

• Split the data into groups by using DataFrame.groupBy.
• Apply a function on each group. The input and output of the function are both pandas.DataFrame. The input data contains all the rows and columns for each group.
• Combine the results into a new PySpark DataFrame.

To use groupBy().applyInPandas(), the user needs to define the following:

• A Python function that defines the computation for each group.
• A StructType object or a string that defines the schema of the output PySpark DataFrame.

The column labels of the returned pandas.DataFrame must either match the field names in the defined output schema if specified as strings, or match the field data types by position if not strings, e.g. integer indices. See pandas.DataFrame on how to label columns when constructing a pandas.DataFrame.

Note that all data for a group will be loaded into memory before the function is applied. This can lead to out of memory exceptions, especially if the group sizes are skewed. The configuration for maxRecordsPerBatch is not applied on groups and it is up to the user to ensure that the grouped data will fit into the available memory.

The following example shows how to use groupby().applyInPandas() to subtract the mean from each value in the group.

{% include_example grouped_apply_in_pandas python/sql/arrow.py %}

For detailed usage, please see pyspark.sql.GroupedData.applyInPandas.

Map

Map operations with Pandas instances are supported by DataFrame.mapInPandas() which maps an iterator of pandas.DataFrames to another iterator of pandas.DataFrames that represents the current PySpark DataFrame and returns the result as a PySpark DataFrame. The functions takes and outputs an iterator of pandas.DataFrame. It can return the output of arbitrary length in contrast to some Pandas UDFs although internally it works similarly with Series to Series Pandas UDF.

The following example shows how to use mapInPandas():

{% include_example map_in_pandas python/sql/arrow.py %}

For detailed usage, please see pyspark.sql.DataFrame.mapsInPandas.

Co-grouped Map

Co-grouped map operations with Pandas instances are supported by DataFrame.groupby().cogroup().applyInPandas() which allows two PySpark DataFrames to be cogrouped by a common key and then a Python function applied to each cogroup. It consists of the following steps:

• Shuffle the data such that the groups of each dataframe which share a key are cogrouped together.
• Apply a function to each cogroup. The input of the function is two pandas.DataFrame (with an optional tuple representing the key). The output of the function is a pandas.DataFrame.
• Combine the pandas.DataFrames from all groups into a new PySpark DataFrame.

To use groupBy().cogroup().applyInPandas(), the user needs to define the following:

• A Python function that defines the computation for each cogroup.
• A StructType object or a string that defines the schema of the output PySpark DataFrame.

The column labels of the returned pandas.DataFrame must either match the field names in the defined output schema if specified as strings, or match the field data types by position if not strings, e.g. integer indices. See pandas.DataFrame on how to label columns when constructing a pandas.DataFrame.

Note that all data for a cogroup will be loaded into memory before the function is applied. This can lead to out of memory exceptions, especially if the group sizes are skewed. The configuration for maxRecordsPerBatch is not applied and it is up to the user to ensure that the cogrouped data will fit into the available memory.

The following example shows how to use groupby().cogroup().applyInPandas() to perform an asof join between two datasets.

{% include_example cogrouped_apply_in_pandas python/sql/arrow.py %}

For detailed usage, please see pyspark.sql.PandasCogroupedOps.applyInPandas().

Usage Notes

Supported SQL Types

Currently, all Spark SQL data types are supported by Arrow-based conversion except MapType, ArrayType of TimestampType, and nested StructType.

Setting Arrow Batch Size

Data partitions in Spark are converted into Arrow record batches, which can temporarily lead to high memory usage in the JVM. To avoid possible out of memory exceptions, the size of the Arrow record batches can be adjusted by setting the conf "spark.sql.execution.arrow.maxRecordsPerBatch" to an integer that will determine the maximum number of rows for each batch. The default value is 10,000 records per batch. If the number of columns is large, the value should be adjusted accordingly. Using this limit, each data partition will be made into 1 or more record batches for processing.

Timestamp with Time Zone Semantics

Spark internally stores timestamps as UTC values, and timestamp data that is brought in without a specified time zone is converted as local time to UTC with microsecond resolution. When timestamp data is exported or displayed in Spark, the session time zone is used to localize the timestamp values. The session time zone is set with the configuration 'spark.sql.session.timeZone' and will default to the JVM system local time zone if not set. Pandas uses a datetime64 type with nanosecond resolution, datetime64[ns], with optional time zone on a per-column basis.

When timestamp data is transferred from Spark to Pandas it will be converted to nanoseconds and each column will be converted to the Spark session time zone then localized to that time zone, which removes the time zone and displays values as local time. This will occur when calling toPandas() or pandas_udf with timestamp columns.

When timestamp data is transferred from Pandas to Spark, it will be converted to UTC microseconds. This occurs when calling createDataFrame with a Pandas DataFrame or when returning a timestamp from a pandas_udf. These conversions are done automatically to ensure Spark will have data in the expected format, so it is not necessary to do any of these conversions yourself. Any nanosecond values will be truncated.

Note that a standard UDF (non-Pandas) will load timestamp data as Python datetime objects, which is different than a Pandas timestamp. It is recommended to use Pandas time series functionality when working with timestamps in pandas_udfs to get the best performance, see here for details.

Recommended Pandas and PyArrow Versions

For usage with pyspark.sql, the supported versions of Pandas is 0.24.2 and PyArrow is 0.15.1. Higher versions may be used, however, compatibility and data correctness can not be guaranteed and should be verified by the user.

Compatibility Setting for PyArrow >= 0.15.0 and Spark 2.3.x, 2.4.x

Since Arrow 0.15.0, a change in the binary IPC format requires an environment variable to be compatible with previous versions of Arrow <= 0.14.1. This is only necessary to do for PySpark users with versions 2.3.x and 2.4.x that have manually upgraded PyArrow to 0.15.0. The following can be added to conf/spark-env.sh to use the legacy Arrow IPC format:

ARROW_PRE_0_15_IPC_FORMAT=1

This will instruct PyArrow >= 0.15.0 to use the legacy IPC format with the older Arrow Java that is in Spark 2.3.x and 2.4.x. Not setting this environment variable will lead to a similar error as described in SPARK-29367 when running pandas_udfs or toPandas() with Arrow enabled. More information about the Arrow IPC change can be read on the Arrow 0.15.0 release blog.