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From Hao Wang <wh.s...@gmail.com>
Subject Re: long GC pause during file.cache()
Date Sun, 15 Jun 2014 16:13:01 GMT
Hi, Wei

You may try to set JVM opts in *spark-env.sh* as follow to prevent or
mitigate GC pause:

export SPARK_JAVA_OPTS="-XX:-UseGCOverheadLimit -XX:+UseConcMarkSweepGC
-Xmx2g -XX:MaxPermSize=256m"

There are more options you could add, please just Google :)


Regards,
Wang Hao(王灏)

CloudTeam | School of Software Engineering
Shanghai Jiao Tong University
Address:800 Dongchuan Road, Minhang District, Shanghai, 200240
Email:wh.sjtu@gmail.com


On Sun, Jun 15, 2014 at 10:24 AM, Wei Tan <wtan@us.ibm.com> wrote:

> Hi,
>
>   I have a single node (192G RAM) stand-alone spark, with memory
> configuration like this in spark-env.sh
>
> SPARK_WORKER_MEMORY=180g
> SPARK_MEM=180g
>
>
>  In spark-shell I have a program like this:
>
> val file = sc.textFile("/localpath") //file size is 40G
> file.cache()
>
>
> val output = file.map(line => extract something from line)
>
> output.saveAsTextFile (...)
>
>
> When I run this program again and again, or keep trying file.unpersist()
> --> file.cache() --> output.saveAsTextFile(), the run time varies a lot,
> from 1 min to 3 min to 50+ min. Whenever the run-time is more than 1 min,
> from the stage monitoring GUI I observe big GC pause (some can be 10+ min).
> Of course when run-time is "normal", say ~1 min, no significant GC is
> observed. The behavior seems somewhat random.
>
> Is there any JVM tuning I should do to prevent this long GC pause from
> happening?
>
>
>
> I used java-1.6.0-openjdk.x86_64, and my spark-shell process is something
> like this:
>
> root     10994  1.7  0.6 196378000 1361496 pts/51 Sl+ 22:06   0:12
> /usr/lib/jvm/java-1.6.0-openjdk.x86_64/bin/java -cp
> ::/home/wtan/scala/spark-1.0.0-bin-hadoop1/conf:/home/wtan/scala/spark-1.0.0-bin-hadoop1/lib/spark-assembly-1.0.0-hadoop1.0.4.jar:/home/wtan/scala/spark-1.0.0-bin-hadoop1/lib/datanucleus-core-3.2.2.jar:/home/wtan/scala/spark-1.0.0-bin-hadoop1/lib/datanucleus-rdbms-3.2.1.jar:/home/wtan/scala/spark-1.0.0-bin-hadoop1/lib/datanucleus-api-jdo-3.2.1.jar
> -XX:MaxPermSize=128m -Djava.library.path= -Xms180g -Xmx180g
> org.apache.spark.deploy.SparkSubmit spark-shell --class
> org.apache.spark.repl.Main
>
> Best regards,
> Wei
>
> ---------------------------------
> Wei Tan, PhD
> Research Staff Member
> IBM T. J. Watson Research Center
> *http://researcher.ibm.com/person/us-wtan*
> <http://researcher.ibm.com/person/us-wtan>

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