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From Eugen Cepoi <cepoi.eu...@gmail.com>
Subject Re: Spark 0.9.1 java.lang.outOfMemoryError: Java Heap Space
Date Fri, 20 Jun 2014 20:46:15 GMT
In short, ADD_JARS will add the jar to your driver classpath and also send
it to the workers (similar to what you are doing when you do sc.addJars).

ex: MASTER=master/url ADD_JARS=/path/to/myJob.jar ./bin/spark-shell


You also have SPARK_CLASSPATH var but it does not distribute the code, it
is only used to compute the driver classpath.


BTW, you are not supposed to change the compute_classpath.script


2014-06-20 19:45 GMT+02:00 Shivani Rao <raoshivani@gmail.com>:

> Hello Eugene,
>
> You are right about this. I did encounter the "pergmgenspace" in the spark
> shell. Can you tell me a little more about "ADD_JARS". In order to ensure
> my spark_shell has all required jars, I added the jars to the "$CLASSPATH"
> in the compute_classpath.sh script. is there another way of doing it?
>
> Shivani
>
>
> On Fri, Jun 20, 2014 at 9:47 AM, Eugen Cepoi <cepoi.eugen@gmail.com>
> wrote:
>
>> In my case it was due to a case class I was defining in the spark-shell
>> and not being available on the workers. So packaging it in a jar and adding
>> it with ADD_JARS solved the problem. Note that I don't exactly remember if
>> it was an out of heap space exception or pergmen space. Make sure your
>> jarsPath is correct.
>>
>> Usually to debug this kind of problems I am using the spark-shell (you
>> can do the same in your job but its more time constuming to repackage,
>> deploy, run, iterate). Try for example
>> 1) read the lines (without any processing) and count them
>> 2) apply processing and count
>>
>>
>>
>> 2014-06-20 17:15 GMT+02:00 Shivani Rao <raoshivani@gmail.com>:
>>
>> Hello Abhi, I did try that and it did not work
>>>
>>> And Eugene, Yes I am assembling the argonaut libraries in the fat jar.
>>> So how did you overcome this problem?
>>>
>>> Shivani
>>>
>>>
>>> On Fri, Jun 20, 2014 at 1:59 AM, Eugen Cepoi <cepoi.eugen@gmail.com>
>>> wrote:
>>>
>>>>
>>>> Le 20 juin 2014 01:46, "Shivani Rao" <raoshivani@gmail.com> a écrit
:
>>>>
>>>> >
>>>> > Hello Andrew,
>>>> >
>>>> > i wish I could share the code, but for proprietary reasons I can't.
>>>> But I can give some idea though of what i am trying to do. The job reads
a
>>>> file and for each line of that file and processors these lines. I am not
>>>> doing anything intense in the "processLogs" function
>>>> >
>>>> > import argonaut._
>>>> > import argonaut.Argonaut._
>>>> >
>>>> >
>>>> > /* all of these case classes are created from json strings extracted
>>>> from the line in the processLogs() function
>>>> > *
>>>> > */
>>>> > case class struct1…
>>>> > case class struct2…
>>>> > case class value1(struct1, struct2)
>>>> >
>>>> > def processLogs(line:String): Option[(key1, value1)] {…
>>>> > }
>>>> >
>>>> > def run(sparkMaster, appName, executorMemory, jarsPath) {
>>>> >   val sparkConf = new SparkConf()
>>>> >    sparkConf.setMaster(sparkMaster)
>>>> >    sparkConf.setAppName(appName)
>>>> >    sparkConf.set("spark.executor.memory", executorMemory)
>>>> >     sparkConf.setJars(jarsPath) // This includes all the jars
>>>> relevant jars..
>>>> >    val sc = new SparkContext(sparkConf)
>>>> >   val rawLogs =
>>>> sc.textFile("hdfs://<my-hadoop-namenode:8020:myfile.txt")
>>>> >
>>>> rawLogs.saveAsTextFile("hdfs://<my-hadoop-namenode:8020:writebackForTesting")
>>>> >
>>>> rawLogs.flatMap(processLogs).saveAsTextFile("hdfs://<my-hadoop-namenode:8020:outfile.txt")
>>>> > }
>>>> >
>>>> > If I switch to "local" mode, the code runs just fine, it fails with
>>>> the error I pasted above. In the cluster mode, even writing back the file
>>>> we just read fails
>>>> (rawLogs.saveAsTextFile("hdfs://<my-hadoop-namenode:8020:writebackForTesting")
>>>> >
>>>> > I still believe this is a classNotFound error in disguise
>>>> >
>>>>
>>>> Indeed you are right, this can be the reason. I had similar errors when
>>>> defining case classes in the shell and trying to use them in the RDDs. Are
>>>> you shading argonaut in the fat jar ?
>>>>
>>>> > Thanks
>>>> > Shivani
>>>> >
>>>> >
>>>> >
>>>> > On Wed, Jun 18, 2014 at 2:49 PM, Andrew Ash <andrew@andrewash.com>
>>>> wrote:
>>>> >>
>>>> >> Wait, so the file only has four lines and the job running out of
>>>> heap space?  Can you share the code you're running that does the
>>>> processing?  I'd guess that you're doing some intense processing on every
>>>> line but just writing parsed case classes back to disk sounds very
>>>> lightweight.
>>>> >>
>>>> >> I
>>>> >>
>>>> >>
>>>> >> On Wed, Jun 18, 2014 at 5:17 PM, Shivani Rao <raoshivani@gmail.com>
>>>> wrote:
>>>> >>>
>>>> >>> I am trying to process a file that contains 4 log lines (not
very
>>>> long) and then write my parsed out case classes to a destination folder,
>>>> and I get the following error:
>>>> >>>
>>>> >>>
>>>> >>> java.lang.OutOfMemoryError: Java heap space
>>>> >>>
>>>> >>> at
>>>> org.apache.hadoop.io.WritableUtils.readCompressedStringArray(WritableUtils.java:183)
>>>> >>>
>>>> >>> at
>>>> org.apache.hadoop.conf.Configuration.readFields(Configuration.java:2244)
>>>> >>>
>>>> >>> at
>>>> org.apache.hadoop.io.ObjectWritable.readObject(ObjectWritable.java:280)
>>>> >>>
>>>> >>> at
>>>> org.apache.hadoop.io.ObjectWritable.readFields(ObjectWritable.java:75)
>>>> >>>
>>>> >>> at
>>>> org.apache.spark.SerializableWritable.readObject(SerializableWritable.scala:39)
>>>> >>>
>>>> >>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>> >>>
>>>> >>> at
>>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>> >>>
>>>> >>> at
>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>> >>>
>>>> >>> at java.lang.reflect.Method.invoke(Method.java:597)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:974)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1848)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1752)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1328)
>>>> >>>
>>>> >>> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:350)
>>>> >>>
>>>> >>> at
>>>> org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:40)
>>>> >>>
>>>> >>> at
>>>> org.apache.spark.broadcast.HttpBroadcast$.read(HttpBroadcast.scala:165)
>>>> >>>
>>>> >>> at
>>>> org.apache.spark.broadcast.HttpBroadcast.readObject(HttpBroadcast.scala:56)
>>>> >>>
>>>> >>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>> >>>
>>>> >>> at
>>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>> >>>
>>>> >>> at
>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>> >>>
>>>> >>> at java.lang.reflect.Method.invoke(Method.java:597)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:974)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1848)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1752)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1328)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1946)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1870)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1752)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1328)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1946)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1870)
>>>> >>>
>>>> >>> at
>>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1752)
>>>> >>>
>>>> >>>
>>>> >>> Sadly, there are several folks that have faced this error while
>>>> trying to execute Spark jobs and there are various solutions, none of which
>>>> work for me
>>>> >>>
>>>> >>>
>>>> >>> a) I tried (
>>>> http://apache-spark-user-list.1001560.n3.nabble.com/Spark-1-0-0-java-lang-outOfMemoryError-Java-Heap-Space-td7735.html#a7736)
>>>> changing the number of partitions in my RDD by using coalesce(8) and the
>>>> error persisted
>>>> >>>
>>>> >>> b)  I tried changing SPARK_WORKER_MEM=2g,
>>>> SPARK_EXECUTOR_MEMORY=10g, and both did not work
>>>> >>>
>>>> >>> c) I strongly suspect there is a class path error (
>>>> http://apache-spark-user-list.1001560.n3.nabble.com/how-to-set-spark-executor-memory-and-heap-size-td4719.html)
>>>> Mainly because the call stack is repetitive. Maybe the OOM error is a
>>>> disguise ?
>>>> >>>
>>>> >>> d) I checked that i am not out of disk space and that i do not
have
>>>> too many open files (ulimit -u << sudo ls
>>>> /proc/<spark_master_process_id>/fd | wc -l)
>>>> >>>
>>>> >>>
>>>> >>> I am also noticing multiple reflections happening to find the
right
>>>> "class" i guess, so it could be "class Not Found: error disguising itself
>>>> as a memory error.
>>>> >>>
>>>> >>>
>>>> >>> Here are other threads that are encountering same situation
.. but
>>>> have not been resolved in any way so far..
>>>> >>>
>>>> >>>
>>>> >>>
>>>> http://apache-spark-user-list.1001560.n3.nabble.com/no-response-in-spark-web-UI-td4633.html
>>>> >>>
>>>> >>>
>>>> http://apache-spark-user-list.1001560.n3.nabble.com/Spark-program-thows-OutOfMemoryError-td4268.html
>>>> >>>
>>>> >>>
>>>> >>> Any help is greatly appreciated. I am especially calling out
on
>>>> creators of Spark and Databrick folks. This seems like a "known bug"
>>>> waiting to happen.
>>>> >>>
>>>> >>>
>>>> >>> Thanks,
>>>> >>>
>>>> >>> Shivani
>>>> >>>
>>>> >>>
>>>> >>> --
>>>> >>> Software Engineer
>>>> >>> Analytics Engineering Team@ Box
>>>> >>> Mountain View, CA
>>>> >>
>>>> >>
>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > Software Engineer
>>>> > Analytics Engineering Team@ Box
>>>> > Mountain View, CA
>>>>
>>>
>>>
>>>
>>> --
>>> Software Engineer
>>> Analytics Engineering Team@ Box
>>> Mountain View, CA
>>>
>>
>>
>
>
> --
> Software Engineer
> Analytics Engineering Team@ Box
> Mountain View, CA
>

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