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From "Jungtaek Lim (Jira)" <j...@apache.org>
Subject [jira] [Commented] (SPARK-29055) Memory leak in Spark
Date Tue, 01 Oct 2019 19:35:00 GMT

    [ https://issues.apache.org/jira/browse/SPARK-29055?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16942267#comment-16942267
] 

Jungtaek Lim commented on SPARK-29055:
--------------------------------------

Looks like I can update the title and description, but then the information of "possible memory
leak" is lost.
I could also clone the issue but it changes the reporter to me (as I don't have privilege
to modify reporter) which is not desired.

[~Geopap] [~vanzin] [~viirya] Could anyone clone this issue? After cloning I'll update this
issue accordingly.

> Memory leak in Spark
> --------------------
>
>                 Key: SPARK-29055
>                 URL: https://issues.apache.org/jira/browse/SPARK-29055
>             Project: Spark
>          Issue Type: Bug
>          Components: Block Manager, Spark Core
>    Affects Versions: 2.3.3
>            Reporter: George Papa
>            Assignee: Jungtaek Lim
>            Priority: Major
>             Fix For: 2.4.5, 3.0.0
>
>         Attachments: test_csvs.zip
>
>
> I used Spark 2.1.1 and I upgraded into new versions. After Spark version 2.3.3,  I observed
from Spark UI that the driver memory is{color:#ff0000} increasing continuously.{color}
> In more detail, the driver memory and executors memory have the same used memory storage
and after each iteration the storage memory is increasing. You can reproduce this behavior
by running the following snippet code. The following example, is very simple, without any
dataframe persistence, but the memory consumption is not stable as it was in former Spark
versions (Specifically until Spark 2.3.2).
> Also, I tested with Spark streaming and structured streaming API and I had the same behavior.
I tested with an existing application which reads from Kafka source and do some aggregations,
persist dataframes and then unpersist them. The persist and unpersist it works correct, I
see the dataframes in the storage tab in Spark UI and after the unpersist, all dataframe have
removed. But, after the unpersist the executors memory is not zero, BUT has the same value
with the driver memory. This behavior also affects the application performance because the
memory of the executors is increasing as the driver increasing and after a while the persisted
dataframes are not fit in the executors memory and  I have spill to disk.
> Another error which I had after a long running, was {color:#ff0000}java.lang.OutOfMemoryError:
GC overhead limit exceeded, but I don't know if its relevant with the above behavior or not.{color}
>  
> *HOW TO REPRODUCE THIS BEHAVIOR:*
> Create a very simple application(streaming count_file.py) in order to reproduce this
behavior. This application reads CSV files from a directory, count the rows and then remove
the processed files.
> {code:java}
> import time
> import os
> from pyspark.sql import SparkSession
> from pyspark.sql import functions as F
> from pyspark.sql import types as T
> target_dir = "..."
> spark=SparkSession.builder.appName("DataframeCount").getOrCreate()
> while True:
>     for f in os.listdir(target_dir):
>         df = spark.read.load(target_dir + f, format="csv")
>         print("Number of records: {0}".format(df.count()))
>         time.sleep(15){code}
> Submit code:
> {code:java}
> spark-submit 
> --master spark://xxx.xxx.xx.xxx
> --deploy-mode client
> --executor-memory 4g
> --executor-cores 3
> streaming count_file.py
> {code}
>  
> *TESTED CASES WITH THE SAME BEHAVIOUR:*
>  * I tested with default settings (spark-defaults.conf)
>  * Add spark.cleaner.periodicGC.interval 1min (or less)
>  * {{Turn spark.cleaner.referenceTracking.blocking}}=false
>  * Run the application in cluster mode
>  * Increase/decrease the resources of the executors and driver
>  * I tested with extraJavaOptions in driver and executor -XX:+UseG1GC -XX:InitiatingHeapOccupancyPercent=35
-XX:ConcGCThreads=12
>   
> *DEPENDENCIES*
>  * Operation system: Ubuntu 16.04.3 LTS
>  * Java: jdk1.8.0_131 (tested also with jdk1.8.0_221)
>  * Python: Python 2.7.12
>  
> *NOTE:* In Spark 2.1.1 the driver memory consumption (Storage Memory tab) was extremely
low and after the run of ContextCleaner and BlockManager the memory was decreasing.



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