Improve Pandas UDF in Pyspark

Question

I must perform an aggregation within a sliding window in Pyspark. In particular, I must do the following operations:

Consider 100 days worth data at a time
GroupBy a given column of ID
Take the last value of the aggregation
Sum the values and return the result

These tasks must be computed in a sliding window with .rangeBetween(-100 days, 0)

I can easily achieve this result by constructing a Pandas UDF that takes as input some columns of the Pyspark DF, transform them into a Pandas DataFrame, and then compute the aggregation and return the scalar result. The UDF is then applied over the desired sliding Window.

Even though this solution works fine, it takes a lot of time (3-4 hours) to complete the task since the DFs contain millions of rows. Is there a way to improve the computational time of such operation? I am working with Pyspark in Databricks.

My pandas UDF is:

@pandas_udf(FloatType(), PandasUDFType.GROUPED_AGG)
def method2(analyst: pd.Series, revisions: pd.Series) -> float:
  df = pd.DataFrame({
    'analyst': analyst,
    'revisions': revisions
  })
  return df.groupby('analyst').last()['revisions'].sum() / df.groupby('analyst').last()['revisions'].abs().sum()

And is applied in:

days = lambda x: x*60*60*24
w = Window.partitionBy('csecid').orderBy(F.col('date').cast('timestamp').cast('long')).rangeBetween(-days(100), 0)
df = df.withColumn('new_col', method2(F.col('analystid'), F.col('revisions_improved')).over(w))

EDIT: I know that this kind of aggregation could be achieved by using numpy arrays and PySpark UDF are much more faster working with numpy structure. However, I would like to avoid this solution because I need to apply in the same framework functions tht are much more complex than the one showed and that are hardly replicable with numpy.

user_377118 · Answer

I recently had to implement a similar aggregation and my first attempt was to use Pandas UDF with Sliding windows. The performance was quite bad and I managed to improve it by using the following approach.

Try to use collect_list to compose the sliding window vectors and then map them with your UDF. Note that this only works if your sliding window can fit into a workers memory (which usually does).

Here is my test code. The first part is just your code but as a complete reproducible example.

import pandas as pd
import pyspark.sql.functions as F
from pyspark.sql import Window
from pyspark.sql.functions import pandas_udf, PandasUDFType, udf
from pyspark.sql.types import FloatType, StructType, StructField, IntegerType, StringType

df = spark.createDataFrame(
  [(1, "2021-04-01", 10, -30),
   (1, "2021-03-01", 10, 20),
   (1, "2021-02-01", 10, -1),
   (1, "2021-01-01", 10, 10),
   (1, "2020-12-01", 10, 5),
   (1, "2021-04-01", 20, -5),
   (1, "2021-03-01", 20, -4),
   (1, "2021-02-01", 20, -3),
   (2, "2021-03-01", 10, 5),
   (2, "2021-02-01", 10, 6),
  ], 
  StructType([
    StructField("csecid", StringType(), True), 
    StructField("date", StringType(), True), 
    StructField("analystid", IntegerType(), True), 
    StructField("revisions_improved", IntegerType(), True)
  ]))

### Baseline
@pandas_udf(FloatType(), PandasUDFType.GROUPED_AGG)
def method2(analyst: pd.Series, revisions: pd.Series) -> float:
  df = pd.DataFrame({
    'analyst': analyst,
    'revisions': revisions
  })
  return df.groupby('analyst').last()['revisions'].sum() / df.groupby('analyst').last()['revisions'].abs().sum()

days = lambda x: x*60*60*24
w = Window.partitionBy('csecid').orderBy(F.col('date').cast('timestamp').cast('long')).rangeBetween(-days(100), 0)

# df.withColumn('new_col', method2(F.col('analystid'), F.col('revisions_improved')).over(w))

Proposed alternative:

### Method 3
from typing import List

@udf(FloatType())
def method3(analyst: List[int], revisions: List[int]) -> float:
  df = pd.DataFrame({
    'analyst': analyst,
    'revisions': revisions
  })
  return float(df.groupby('analyst').last()['revisions'].sum() / df.groupby('analyst').last()['revisions'].abs().sum())

(df
.withColumn('new_col', method2(F.col('analystid'), F.col('revisions_improved')).over(w))

.withColumn('analyst_win', F.collect_list("analystid").over(w))
.withColumn('revisions_win', F.collect_list("revisions_improved").over(w))

.withColumn('method3', method3(F.collect_list("analystid").over(w), 
                               F.collect_list("revisions_improved").over(w)))
.orderBy("csecid", "date", "analystid")
.show(truncate=False))

Result:

+------+----------+---------+------------------+---------+----------------------------+-----------------------------+---------+
|csecid|date      |analystid|revisions_improved|new_col  |analyst_win                 |revisions_win                |method3  |
+------+----------+---------+------------------+---------+----------------------------+-----------------------------+---------+
|1     |2020-12-01|10       |5                 |1.0      |[10]                        |[5]                          |1.0      |
|1     |2021-01-01|10       |10                |1.0      |[10, 10]                    |[5, 10]                      |1.0      |
|1     |2021-02-01|10       |-1                |-1.0     |[10, 10, 10, 20]            |[5, 10, -1, -3]              |-1.0     |
|1     |2021-02-01|20       |-3                |-1.0     |[10, 10, 10, 20]            |[5, 10, -1, -3]              |-1.0     |
|1     |2021-03-01|10       |20                |0.6666667|[10, 10, 10, 20, 10, 20]    |[5, 10, -1, -3, 20, -4]      |0.6666667|
|1     |2021-03-01|20       |-4                |0.6666667|[10, 10, 10, 20, 10, 20]    |[5, 10, -1, -3, 20, -4]      |0.6666667|
|1     |2021-04-01|10       |-30               |-1.0     |[10, 10, 20, 10, 20, 10, 20]|[10, -1, -3, 20, -4, -30, -5]|-1.0     |
|1     |2021-04-01|20       |-5                |-1.0     |[10, 10, 20, 10, 20, 10, 20]|[10, -1, -3, 20, -4, -30, -5]|-1.0     |
|2     |2021-02-01|10       |6                 |1.0      |[10]                        |[6]                          |1.0      |
|2     |2021-03-01|10       |5                 |1.0      |[10, 10]                    |[6, 5]                       |1.0      |
+------+----------+---------+------------------+---------+----------------------------+-----------------------------+---------+

analyst_win and revisions_win are just there to show how the sliding windows are created and passed into the UDF. They should be removed in production.

Moving the Pandas groupby outside of the UDF would probably improve the performance. Spark can take care of that step. However, I did not question that part because you mentioned the function is not representative of the actual tasks.

Check out the performance in SparkUI, specially the time statistics for the tasks that apply the UDF. If the times are high, try increasing the number of partitions with repartition so that each tasks does a smaller subset of the data.

Improve Pandas UDF in Pyspark

1 Answers