Zeppelin throws java.lang.OutOfMemoryError: Java heap space - apache-spark

Question

I am trying to use Zeppelin with the following code:
val dataText = sc.parallelize(IOUtils.toString(new URL("http://XXX.XX.XXX.121:8090/my_data.txt"),Charset.forName("utf8")).split("\n"))
case class Data(id: string, time: long, value1: Double, value2: int, mode: int)
val dat = dataText .map(s => s.split("\t")).filter(s => s(0) != "Header:").map(
s => Data(s(0),
s(1).toLong,
s(2).toDouble,
s(3).toInt,
s(4).toInt
)
).toDF()
dat.registerTempTable("mydatatable")
this keeps throwing me following error :
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:2367)
at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:535)
at java.lang.StringBuilder.append(StringBuilder.java:204)
at org.apache.commons.io.output.StringBuilderWriter.write(StringBuilderWriter.java:138)
at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:2002)
at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:1980)
at org.apache.commons.io.IOUtils.copy(IOUtils.java:1957)
at org.apache.commons.io.IOUtils.copy(IOUtils.java:1907)
at org.apache.commons.io.IOUtils.toString(IOUtils.java:778)
at org.apache.commons.io.IOUtils.toString(IOUtils.java:896)
at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:38)
at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:43)
at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:45)
at $iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:47)
at $iwC$$iwC$$iwC$$iwC.<init>(<console>:49)
at $iwC$$iwC$$iwC.<init>(<console>:51)
at $iwC$$iwC.<init>(<console>:53)
at $iwC.<init>(<console>:55)
at <init>(<console>:57)
at .<init>(<console>:61)
at .<clinit>(<console>)
at .<init>(<console>:7)
at .<clinit>(<console>)
at $print(<console>)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.repl.SparkIMain$ReadEvalPrint.call(SparkIMain.scala:1065)
at org.apache.spark.repl.SparkIMain$Request.loadAndRun(SparkIMain.scala:1338)
I have already set the following in the zeppelin-env.sh
export ZEPPELIN_JAVA_OPTS="-Dhdp.version=2.3.0.0-2557 -Dspark.executor.memory=4g"
any idea what I may be missing. File I am parsing my_data.txt is about 200MB
BTW I am using the Hortonworks Sandbox if that matters
EDIT 1
Here is my zeppelin-env.sh
export HADOOP_CONF_DIR=/etc/hadoop/conf
export ZEPPELIN_PORT=9995
export ZEPPELIN_JAVA_OPTS="-Dhdp.version=2.3.0.0-2557 -Dspark.executor.memory=4g"
export SPARK_SUBMIT_OPTIONS="--driver-java-options -Xmx4g"
export ZEPPELIN_INT_MEM="-Xmx4g"
export SPARK_HOME=/usr/hdp/2.3.0.0-2557/spark
Regards
Kiran

Answer 1

Can you try increasing the memory in SPARK_SUBMIT_OPTIONS in conf/zeppelin-env.sh:
export SPARK_SUBMIT_OPTIONS="--driver-java-options -Xmx20g"
This thread may help
http://apache-zeppelin-users-incubating-mailing-list.75479.x6.nabble.com/Can-not-configure-driver-memory-size-td1513.html

Answer 2

Increasing the memory for the following zeppelin-env.sh var, did the trick for me. The default is 1/0.5GB, I increased it to 10/5GB
ZEPPELIN_MEM": "-Xmx10024m -XX:MaxPermSize=5120m

Answer 3

I was getting below error while trying to bring up Zeppelin notebook
INFO [2021-05-04 15:16:22,015] ({main} Folder.java[addNote]:185) - Add note 2G7CAFXX7 to folder /
INFO [2021-05-04 15:16:22,016] ({main} Notebook.java[<init>]:127) - Notebook indexing started...
WARN [2021-05-04 15:16:32,045] ({main} ContextHandler.java[log]:2355) - unavailable
MultiException stack 1 of 1
java.lang.OutOfMemoryError: Java heap space
at org.apache.lucene.store.RAMFile.newBuffer(RAMFile.java:80)
at org.apache.lucene.store.RAMFile.addBuffer(RAMFile.java:53)
To resolve this issue I tuned the ZEPPELIN_MEM parameter in zeppelin-env.sh file like this,
export ZEPPELIN_MEM="-Xmx5024m -XX:MaxPermSize=5120m"
Then restart zeppelin
sudo systemctl stop zeppelin; sudo systemctl start zeppelin
Result
INFO [2021-05-04 18:51:02,939] ({main} Folder.java[addNote]:185) - Add note 2G7CAFXX7 to folder /
INFO [2021-05-04 18:51:02,940] ({main} Notebook.java[<init>]:127) - Notebook indexing started...
INFO [2021-05-04 18:51:05,793] ({main} LuceneSearch.java[addIndexDocs]:305) - Indexing 905 notebooks took 2853ms
INFO [2021-05-04 18:51:05,793] ({main} Notebook.java[<init>]:129) - Notebook indexing finished: 905 indexed in -2s
INFO [2021-05-04 18:51:05,795] ({main} Helium.java[loadConf]:103) - Add helium local registry /usr/lib/zeppelin/helium
INFO [2021-05-04 18:51:05,797] ({main} Helium.java[loadConf]:100) - Add helium
INFO [2021-05-04 18:51:06,631] ({main} Server.java[doStart]:407) - Started #131632ms
INFO [2021-05-04 18:51:06,631] ({main} ZeppelinServer.java[main]:249) - Done, zeppelin server started

Answer 4

The only thing that worked for me (using Spark 2) was to add to conf/zeppelin-env.sh:
export SPARK_SUBMIT_OPTIONS="... --driver-memory 4g ..."
Then restart Zeppelin interpreter (In the Zeppelin for Spark 2, click on the settings button on the top right and then click on the Interpreter link, scroll down and click the Restart button of the Spark section).