PySpark Usage Guide for Pandas with Apache Arrow
- Apache Arrow in Spark
- Enabling for Conversion to/from Pandas
- Pandas UDFs (a.k.a. Vectorized UDFs)
- Usage Notes
Apache Arrow in Spark
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
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. The current supported version is 0.8.0.
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
true. This is disabled by default.
In addition, optimizations enabled by
spark.sql.execution.arrow.enabled could fallback automatically
to non-Arrow optimization implementation if an error occurs before the actual computation within Spark.
This can be controlled by
import numpy as np import pandas as pd # Enable Arrow-based columnar data transfers spark.conf.set("spark.sql.execution.arrow.enabled", "true") # Generate a Pandas DataFrame pdf = pd.DataFrame(np.random.rand(100, 3)) # Create a Spark DataFrame from a Pandas DataFrame using Arrow df = spark.createDataFrame(pdf) # Convert the Spark DataFrame back to a Pandas DataFrame using Arrow result_pdf = df.select("*").toPandas()
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
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. A Pandas UDF is defined using the keyword
pandas_udf as a decorator
or to wrap the function, no additional configuration is required. Currently, there are two types of
Pandas UDF: Scalar and Grouped Map.
Scalar Pandas UDFs are used for vectorizing scalar operations. They can be used with functions such
withColumn. The Python function should take
pandas.Series as inputs and return
pandas.Series of the same length. Internally, Spark 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 a scalar Pandas UDF that computes the product of 2 columns.
import pandas as pd from pyspark.sql.functions import col, pandas_udf from pyspark.sql.types import LongType # Declare the function and create the UDF def multiply_func(a, b): return a * b multiply = pandas_udf(multiply_func, returnType=LongType()) # The function for a pandas_udf should be able to execute with local Pandas data x = pd.Series([1, 2, 3]) print(multiply_func(x, x)) # 0 1 # 1 4 # 2 9 # dtype: int64 # Create a Spark DataFrame, 'spark' is an existing SparkSession df = spark.createDataFrame(pd.DataFrame(x, columns=["x"])) # Execute function as a Spark vectorized UDF df.select(multiply(col("x"), col("x"))).show() # +-------------------+ # |multiply_func(x, x)| # +-------------------+ # | 1| # | 4| # | 9| # +-------------------+
Grouped map Pandas UDFs are used with
groupBy().apply() which implements the “split-apply-combine” pattern.
Split-apply-combine consists of three steps:
- Split the data into groups by using
- 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
groupBy().apply(), the user needs to define the following:
- A Python function that defines the computation for each group.
StructTypeobject or a string that defines the schema of the output
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
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().apply() to subtract the mean from each value in the group.
from pyspark.sql.functions import pandas_udf, PandasUDFType df = spark.createDataFrame( [(1, 1.0), (1, 2.0), (2, 3.0), (2, 5.0), (2, 10.0)], ("id", "v")) @pandas_udf("id long, v double", PandasUDFType.GROUPED_MAP) def subtract_mean(pdf): # pdf is a pandas.DataFrame v = pdf.v return pdf.assign(v=v - v.mean()) df.groupby("id").apply(subtract_mean).show() # +---+----+ # | id| v| # +---+----+ # | 1|-0.5| # | 1| 0.5| # | 2|-3.0| # | 2|-1.0| # | 2| 4.0| # +---+----+
Grouped aggregate Pandas UDFs are similar to Spark aggregate functions. Grouped aggregate Pandas UDFs are used with
pyspark.sql.Window. It defines an aggregation from one or more
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 groupBy and window operations:
from pyspark.sql.functions import pandas_udf, PandasUDFType from pyspark.sql import Window df = spark.createDataFrame( [(1, 1.0), (1, 2.0), (2, 3.0), (2, 5.0), (2, 10.0)], ("id", "v")) @pandas_udf("double", PandasUDFType.GROUPED_AGG) def mean_udf(v): return v.mean() df.groupby("id").agg(mean_udf(df['v'])).show() # +---+-----------+ # | id|mean_udf(v)| # +---+-----------+ # | 1| 1.5| # | 2| 6.0| # +---+-----------+ w = Window \ .partitionBy('id') \ .rowsBetween(Window.unboundedPreceding, Window.unboundedFollowing) df.withColumn('mean_v', mean_udf(df['v']).over(w)).show() # +---+----+------+ # | id| v|mean_v| # +---+----+------+ # | 1| 1.0| 1.5| # | 1| 2.0| 1.5| # | 2| 3.0| 6.0| # | 2| 5.0| 6.0| # | 2|10.0| 6.0| # +---+----+------+
For detailed usage, please see
Supported SQL Types
Currently, all Spark SQL data types are supported by Arrow-based conversion except
TimestampType, and nested
BinaryType is supported only when
installed PyArrow is equal to or higher then 0.10.0.
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
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
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.
Compatibiliy 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:
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
toPandas() with Arrow enabled. More information about the Arrow IPC change can
be read on the Arrow 0.15.0 release blog.