setup/run spark (spark-shell) on yarn client mode - apache-spark

Question

I am trying to make spark-shell working with YARN, however when I try to run the code like below:
spark-shell \
--master yarn \
--deploy-mode client \
--driver-memory 1g \
--executor-memory 1g \
--executor-cores 1
The stacktrace I got is:
17/02/07 01:52:41 ERROR spark.SparkContext: Error initializing SparkContext.
org.apache.spark.SparkException: Yarn application has already ended! It might have been killed or unable to launch application master.
at org.apache.spark.scheduler.cluster.YarnClientSchedulerBackend.waitForApplication(YarnClientSchedulerBackend.scala:85)
at org.apache.spark.scheduler.cluster.YarnClientSchedulerBackend.start(YarnClientSchedulerBackend.scala:62)
at org.apache.spark.scheduler.TaskSchedulerImpl.start(TaskSchedulerImpl.scala:156)
at org.apache.spark.SparkContext.<init>(SparkContext.scala:509)
at org.apache.spark.SparkContext$.getOrCreate(SparkContext.scala:2313)
at org.apache.spark.sql.SparkSession$Builder$$anonfun$6.apply(SparkSession.scala:868)
at org.apache.spark.sql.SparkSession$Builder$$anonfun$6.apply(SparkSession.scala:860)
at scala.Option.getOrElse(Option.scala:121)
at org.apache.spark.sql.SparkSession$Builder.getOrCreate(SparkSession.scala:860)
at org.apache.spark.repl.Main$.createSparkSession(Main.scala:95)
at $line3.$read$$iw$$iw.<init>(<console>:15)
at $line3.$read$$iw.<init>(<console>:42)
at $line3.$read.<init>(<console>:44)
at $line3.$read$.<init>(<console>:48)
at $line3.$read$.<clinit>(<console>)
at $line3.$eval$.$print$lzycompute(<console>:7)
at $line3.$eval$.$print(<console>:6)
at $line3.$eval.$print(<console>)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at scala.tools.nsc.interpreter.IMain$ReadEvalPrint.call(IMain.scala:786)
at scala.tools.nsc.interpreter.IMain$Request.loadAndRun(IMain.scala:1047)
at scala.tools.nsc.interpreter.IMain$WrappedRequest$$anonfun$loadAndRunReq$1.apply(IMain.scala:638)
at scala.tools.nsc.interpreter.IMain$WrappedRequest$$anonfun$loadAndRunReq$1.apply(IMain.scala:637)
at scala.reflect.internal.util.ScalaClassLoader$class.asContext(ScalaClassLoader.scala:31)
at scala.reflect.internal.util.AbstractFileClassLoader.asContext(AbstractFileClassLoader.scala:19)
at scala.tools.nsc.interpreter.IMain$WrappedRequest.loadAndRunReq(IMain.scala:637)
at scala.tools.nsc.interpreter.IMain.interpret(IMain.scala:569)
at scala.tools.nsc.interpreter.IMain.interpret(IMain.scala:565)
at scala.tools.nsc.interpreter.ILoop.interpretStartingWith(ILoop.scala:807)
at scala.tools.nsc.interpreter.ILoop.command(ILoop.scala:681)
at scala.tools.nsc.interpreter.ILoop.processLine(ILoop.scala:395)
at org.apache.spark.repl.SparkILoop$$anonfun$initializeSpark$1.apply$mcV$sp(SparkILoop.scala:38)
at org.apache.spark.repl.SparkILoop$$anonfun$initializeSpark$1.apply(SparkILoop.scala:37)
at org.apache.spark.repl.SparkILoop$$anonfun$initializeSpark$1.apply(SparkILoop.scala:37)
at scala.tools.nsc.interpreter.IMain.beQuietDuring(IMain.scala:214)
at org.apache.spark.repl.SparkILoop.initializeSpark(SparkILoop.scala:37)
at org.apache.spark.repl.SparkILoop.loadFiles(SparkILoop.scala:105)
at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply$mcZ$sp(ILoop.scala:920)
at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply(ILoop.scala:909)
at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply(ILoop.scala:909)
at scala.reflect.internal.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:97)
at scala.tools.nsc.interpreter.ILoop.process(ILoop.scala:909)
at org.apache.spark.repl.Main$.doMain(Main.scala:68)
at org.apache.spark.repl.Main$.main(Main.scala:51)
at org.apache.spark.repl.Main.main(Main.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:738)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:187)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:212)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:126)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
17/02/07 01:52:42 ERROR client.TransportClient: Failed to send RPC 7605279734171920371 to /172.17.0.2:35136: java.nio.channels.ClosedChannelException
java.nio.channels.ClosedChannelException
at io.netty.channel.AbstractChannel$AbstractUnsafe.write(...)(Unknown Source)
17/02/07 01:52:42 ERROR cluster.YarnSchedulerBackend$YarnSchedulerEndpoint: Sending RequestExecutors(0,0,Map()) to AM was unsuccessful
java.io.IOException: Failed to send RPC 7605279734171920371 to /172.17.0.2:35136: java.nio.channels.ClosedChannelException
at org.apache.spark.network.client.TransportClient$3.operationComplete(TransportClient.java:249)
at org.apache.spark.network.client.TransportClient$3.operationComplete(TransportClient.java:233)
at io.netty.util.concurrent.DefaultPromise.notifyListener0(DefaultPromise.java:514)
at io.netty.util.concurrent.DefaultPromise.notifyListenersNow(DefaultPromise.java:488)
at io.netty.util.concurrent.DefaultPromise.access$000(DefaultPromise.java:34)
at io.netty.util.concurrent.DefaultPromise$1.run(DefaultPromise.java:438)
at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:408)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:455)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:140)
at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.nio.channels.ClosedChannelException
at io.netty.channel.AbstractChannel$AbstractUnsafe.write(...)(Unknown Source)
17/02/07 01:52:42 ERROR util.Utils: Uncaught exception in thread main
org.apache.spark.SparkException: Exception thrown in awaitResult
at org.apache.spark.rpc.RpcTimeout$$anonfun$1.applyOrElse(RpcTimeout.scala:77)
at org.apache.spark.rpc.RpcTimeout$$anonfun$1.applyOrElse(RpcTimeout.scala:75)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:59)
at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:59)
at scala.PartialFunction$OrElse.apply(PartialFunction.scala:167)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:83)
at org.apache.spark.scheduler.cluster.CoarseGrainedSchedulerBackend.requestTotalExecutors(CoarseGrainedSchedulerBackend.scala:512)
at org.apache.spark.scheduler.cluster.YarnSchedulerBackend.stop(YarnSchedulerBackend.scala:93)
at org.apache.spark.scheduler.cluster.YarnClientSchedulerBackend.stop(YarnClientSchedulerBackend.scala:151)
at org.apache.spark.scheduler.TaskSchedulerImpl.stop(TaskSchedulerImpl.scala:467)
at org.apache.spark.scheduler.DAGScheduler.stop(DAGScheduler.scala:1588)
at org.apache.spark.SparkContext$$anonfun$stop$8.apply$mcV$sp(SparkContext.scala:1826)
at org.apache.spark.util.Utils$.tryLogNonFatalError(Utils.scala:1283)
at org.apache.spark.SparkContext.stop(SparkContext.scala:1825)
at org.apache.spark.SparkContext.<init>(SparkContext.scala:587)
at org.apache.spark.SparkContext$.getOrCreate(SparkContext.scala:2313)
at org.apache.spark.sql.SparkSession$Builder$$anonfun$6.apply(SparkSession.scala:868)
at org.apache.spark.sql.SparkSession$Builder$$anonfun$6.apply(SparkSession.scala:860)
at scala.Option.getOrElse(Option.scala:121)
at org.apache.spark.sql.SparkSession$Builder.getOrCreate(SparkSession.scala:860)
at org.apache.spark.repl.Main$.createSparkSession(Main.scala:95)
at $line3.$read$$iw$$iw.<init>(<console>:15)
at $line3.$read$$iw.<init>(<console>:42)
at $line3.$read.<init>(<console>:44)
at $line3.$read$.<init>(<console>:48)
at $line3.$read$.<clinit>(<console>)
at $line3.$eval$.$print$lzycompute(<console>:7)
at $line3.$eval$.$print(<console>:6)
at $line3.$eval.$print(<console>)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at scala.tools.nsc.interpreter.IMain$ReadEvalPrint.call(IMain.scala:786)
at scala.tools.nsc.interpreter.IMain$Request.loadAndRun(IMain.scala:1047)
at scala.tools.nsc.interpreter.IMain$WrappedRequest$$anonfun$loadAndRunReq$1.apply(IMain.scala:638)
at scala.tools.nsc.interpreter.IMain$WrappedRequest$$anonfun$loadAndRunReq$1.apply(IMain.scala:637)
at scala.reflect.internal.util.ScalaClassLoader$class.asContext(ScalaClassLoader.scala:31)
at scala.reflect.internal.util.AbstractFileClassLoader.asContext(AbstractFileClassLoader.scala:19)
at scala.tools.nsc.interpreter.IMain$WrappedRequest.loadAndRunReq(IMain.scala:637)
at scala.tools.nsc.interpreter.IMain.interpret(IMain.scala:569)
at scala.tools.nsc.interpreter.IMain.interpret(IMain.scala:565)
at scala.tools.nsc.interpreter.ILoop.interpretStartingWith(ILoop.scala:807)
at scala.tools.nsc.interpreter.ILoop.command(ILoop.scala:681)
at scala.tools.nsc.interpreter.ILoop.processLine(ILoop.scala:395)
at org.apache.spark.repl.SparkILoop$$anonfun$initializeSpark$1.apply$mcV$sp(SparkILoop.scala:38)
at org.apache.spark.repl.SparkILoop$$anonfun$initializeSpark$1.apply(SparkILoop.scala:37)
at org.apache.spark.repl.SparkILoop$$anonfun$initializeSpark$1.apply(SparkILoop.scala:37)
at scala.tools.nsc.interpreter.IMain.beQuietDuring(IMain.scala:214)
at org.apache.spark.repl.SparkILoop.initializeSpark(SparkILoop.scala:37)
at org.apache.spark.repl.SparkILoop.loadFiles(SparkILoop.scala:105)
at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply$mcZ$sp(ILoop.scala:920)
at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply(ILoop.scala:909)
at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply(ILoop.scala:909)
at scala.reflect.internal.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:97)
at scala.tools.nsc.interpreter.ILoop.process(ILoop.scala:909)
at org.apache.spark.repl.Main$.doMain(Main.scala:68)
at org.apache.spark.repl.Main$.main(Main.scala:51)
at org.apache.spark.repl.Main.main(Main.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:738)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:187)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:212)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:126)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.io.IOException: Failed to send RPC 7605279734171920371 to /172.17.0.2:35136: java.nio.channels.ClosedChannelException
at org.apache.spark.network.client.TransportClient$3.operationComplete(TransportClient.java:249)
at org.apache.spark.network.client.TransportClient$3.operationComplete(TransportClient.java:233)
at io.netty.util.concurrent.DefaultPromise.notifyListener0(DefaultPromise.java:514)
at io.netty.util.concurrent.DefaultPromise.notifyListenersNow(DefaultPromise.java:488)
at io.netty.util.concurrent.DefaultPromise.access$000(DefaultPromise.java:34)
at io.netty.util.concurrent.DefaultPromise$1.run(DefaultPromise.java:438)
at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:408)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:455)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:140)
at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.nio.channels.ClosedChannelException
at io.netty.channel.AbstractChannel$AbstractUnsafe.write(...)(Unknown Source)
17/02/07 01:52:42 WARN metrics.MetricsSystem: Stopping a MetricsSystem that is not running
org.apache.spark.SparkException: Yarn application has already ended! It might have been killed or unable to launch application master.
at org.apache.spark.scheduler.cluster.YarnClientSchedulerBackend.waitForApplication(YarnClientSchedulerBackend.scala:85)
at org.apache.spark.scheduler.cluster.YarnClientSchedulerBackend.start(YarnClientSchedulerBackend.scala:62)
at org.apache.spark.scheduler.TaskSchedulerImpl.start(TaskSchedulerImpl.scala:156)
at org.apache.spark.SparkContext.<init>(SparkContext.scala:509)
at org.apache.spark.SparkContext$.getOrCreate(SparkContext.scala:2313)
at org.apache.spark.sql.SparkSession$Builder$$anonfun$6.apply(SparkSession.scala:868)
at org.apache.spark.sql.SparkSession$Builder$$anonfun$6.apply(SparkSession.scala:860)
at scala.Option.getOrElse(Option.scala:121)
at org.apache.spark.sql.SparkSession$Builder.getOrCreate(SparkSession.scala:860)
at org.apache.spark.repl.Main$.createSparkSession(Main.scala:95)
... 47 elided
<console>:14: error: not found: value spark
import spark.implicits._
^
<console>:14: error: not found: value spark
import spark.sql
^
To me this looks more like YARN does not have spark libraries in it's context when running in client mode. I tried to add the $SPARK_HOME/jars into the yarn-site.xml file within the yarn.application.classpath configuration, but this seems not working either.
How this could work with spark-shell and yarn? I was trying to find an official instructions in terms of handling such issue, but no guidance about this is found.

Answer 1

It's actually the reverse way as I described. Due to the connection failure caused by Yarn + Java 8 problem(https://issues.apache.org/jira/browse/YARN-4714). The sparkContext failed to be created.
the change should be add the following section in the yarn-site.xml file:
<property>
<name>yarn.nodemanager.pmem-check-enabled</name>
<value>false</value>
</property>
<property>
<name>yarn.nodemanager.vmem-check-enabled</name>
<value>false</value>
</property>

Answer 2

I have fixed this as below:
ERROR spark.SparkContext: Error initializing SparkContext.
My cluster is spark 1.6.2 and hadoop 2.6. It gives same issue when I kick off
spark-shell --master yarn-client
Solution:
copy spark-assembly-1.6.2-hadoop2.6.0.jar from local to hdfs such as
hdfs://Master:9000/spark/spark-assembly-1.6.2-hadoop2.6.0.jar
in spark-defaults.conf add following parameter
spark.yarn.jars hdfs://Master:9000/spark/spark-assembly-1.6.2-hadoop2.6.0.jar
then the issue fixed.