hadoop - Spark Shell - __spark_libs__.zip does not exist

Question

I'm new to Spark and I'm busy setting up a Spark Cluster with HA enabled.

When starting a spark shell for testing via: bash spark-shell --master yarn --deploy-mode client

I receive the following error (See full error bellow): file:/tmp/spark-126d2844-5b37-461b-98a4-3f3de5ece91b/__spark_libs__3045590511279655158.zip does not exist

The application is marked as failed on the yarn web app and no containers are started.

When starting a shell via: spark-shell --master local it opens without errors.

I have noticed that files are only being written to the tmp folder on the node where the shell is created.

Any help will be much appreciated. Let me know if more information is required.

Environment Variables:

HADOOP_CONF_DIR=/opt/hadoop-2.7.3/etc/hadoop/

YARN_CONF_DIR=/opt/hadoop-2.7.3/etc/hadoop/

SPARK_HOME=/opt/spark-2.0.2-bin-hadoop2.7/

Full error message:

16/11/30 21:08:47 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 
16/11/30 21:08:49 WARN yarn.Client: Neither spark.yarn.jars nor spark.yarn.archive is set, falling back to uploading libraries under SPARK_HOME. 
16/11/30 21:09:03 WARN cluster.YarnSchedulerBackend$YarnSchedulerEndpoint: Container marked as failed: container_e14_1480532715390_0001_02_000003 on host: slave2. Exit status: -1000. Diagnostics: File file:/tmp/spark-126d2844-5b37-461b-98a4-3f3de5ece91b/__spark_libs__3045590511279655158.zip does not exist 
java.io.FileNotFoundException: File file:/tmp/spark-126d2844-5b37-461b-98a4-3f3de5ece91b/__spark_libs__3045590511279655158.zip
does not exist
        at org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:611)
        at org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:824)
        at org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:601)
        at org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:421)
        at org.apache.hadoop.yarn.util.FSDownload.copy(FSDownload.java:253)
        at org.apache.hadoop.yarn.util.FSDownload.access$000(FSDownload.java:63)
        at org.apache.hadoop.yarn.util.FSDownload$2.run(FSDownload.java:361)
        at org.apache.hadoop.yarn.util.FSDownload$2.run(FSDownload.java:359)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.security.auth.Subject.doAs(Subject.java:422)
        at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1698)
        at org.apache.hadoop.yarn.util.FSDownload.call(FSDownload.java:358)
        at org.apache.hadoop.yarn.util.FSDownload.call(FSDownload.java:62)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)

16/11/30 22:29:28 ERROR cluster.YarnClientSchedulerBackend: Yarn application has already exited with state FINISHED! 16/11/30 22:29:28 ERROR spark.SparkContext: Error initializing SparkContext. java.lang.IllegalStateException: Spark context stopped while waiting for backend
        at org.apache.spark.scheduler.TaskSchedulerImpl.waitBackendReady(TaskSchedulerImpl.scala:584)
        at org.apache.spark.scheduler.TaskSchedulerImpl.postStartHook(TaskSchedulerImpl.scala:162)
        at org.apache.spark.SparkContext.<init>(SparkContext.scala:546)
        at org.apache.spark.SparkContext$.getOrCreate(SparkContext.scala:2258)
        at org.apache.spark.sql.SparkSession$Builder$$anonfun$8.apply(SparkSession.scala:831)
        at org.apache.spark.sql.SparkSession$Builder$$anonfun$8.apply(SparkSession.scala:823)
        at scala.Option.getOrElse(Option.scala:121)
        at org.apache.spark.sql.SparkSession$Builder.getOrCreate(SparkSession.scala:823)
        at org.apache.spark.repl.Main$.createSparkSession(Main.scala:95)
        at $line3.$read$$iw$$iw.<init>(<console>:15)
        at $line3.$read$$iw.<init>(<console>:31)
        at $line3.$read.<init>(<console>:33)
        at $line3.$read$.<init>(<console>:37)
        at $line3.$read$.<clinit>(<console>)
        at $line3.$eval$.$print$lzycompute(<console>:7)
        at $line3.$eval$.$print(<console>:6)
        at $line3.$eval.$print(<console>)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at scala.tools.nsc.interpreter.IMain$ReadEvalPrint.call(IMain.scala:786)
        at scala.tools.nsc.interpreter.IMain$Request.loadAndRun(IMain.scala:1047)
        at scala.tools.nsc.interpreter.IMain$WrappedRequest$$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:94)
        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:736)
        at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:185)
        at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:210)
        at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:124)
        at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)

yarn-site.xml

<configuration>
  <property>
    <name>yarn.resourcemanager.connect.retry-interval.ms</name>
    <value>2000</value>
  </property>
  <property>
    <name>yarn.resourcemanager.ha.enabled</name>
    <value>true</value>
  </property>
  <property>
    <name>yarn.resourcemanager.ha.automatic-failover.enabled</name>
    <value>true</value>
  </property>
  <property>
    <name>yarn.resourcemanager.ha.automatic-failover.embedded</name>
    <value>true</value>
  </property>
  <property>
    <name>yarn.resourcemanager.cluster-id</name>
    <value>yarn-cluster</value>
  </property>
  <property>
    <name>yarn.resourcemanager.ha.rm-ids</name>
    <value>rm1,rm2</value>
  </property>
  <property>
    <name>yarn.resourcemanager.ha.id</name>
    <value>rm1</value>
  </property>
  <property>
    <name>yarn.resourcemanager.scheduler.class</name>
    <value>org.apache.hadoop.yarn.server.resourcemanager.scheduler.fair.FairScheduler</value>
  </property>
  <property>
    <name>yarn.resourcemanager.recovery.enabled</name>
    <value>true</value>
  </property>
  <property>
    <name>yarn.resourcemanager.store.class</name>
    <value>org.apache.hadoop.yarn.server.resourcemanager.recovery.ZKRMStateStore</value>
  </property>
  <property>
    <name>yarn.resourcemanager.zk-address</name>
    <value>master:2181,slave1:2181,slave2:2181</value>
  </property>
  <property>
    <name>yarn.app.mapreduce.am.scheduler.connection.wait.interval-ms</name>
    <value>5000</value>
  </property>
  <property>
    <name>yarn.resourcemanager.work-preserving-recovery.enabled</name>
    <value>true</value>
  </property>

  <property>
    <name>yarn.resourcemanager.address.rm1</name>
    <value>master:23140</value>
  </property>
  <property>
    <name>yarn.resourcemanager.scheduler.address.rm1</name>
    <value>master:23130</value>
  </property>
  <property>
    <name>yarn.resourcemanager.webapp.https.address.rm1</name>
    <value>master:23189</value>
  </property>
  <property>
    <name>yarn.resourcemanager.webapp.address.rm1</name>
    <value>master:23188</value>
  </property>
  <property>
    <name>yarn.resourcemanager.resource-tracker.address.rm1</name>
    <value>master:23125</value>
  </property>
  <property>
    <name>yarn.resourcemanager.admin.address.rm1</name>
    <value>master:23141</value>
  </property>

  <property>
    <name>yarn.resourcemanager.address.rm2</name>
    <value>slave1:23140</value>
  </property>
  <property>
    <name>yarn.resourcemanager.scheduler.address.rm2</name>
    <value>slave1:23130</value>
  </property>
  <property>
    <name>yarn.resourcemanager.webapp.https.address.rm2</name>
    <value>slave1:23189</value>
  </property>
  <property>
    <name>yarn.resourcemanager.webapp.address.rm2</name>
    <value>slave1:23188</value>
  </property>
  <property>
    &lt

Answer 1

This error was due to the config in the core-site.xml file.

Please note that to find this file your HADOOP_CONF_DIR env variable must be set.

In my case I added HADOOP_CONF_DIR=/opt/hadoop-2.7.3/etc/hadoop/ to ./conf/spark-env.sh

See: Spark Job running on Yarn Cluster java.io.FileNotFoundException: File does not exits , eventhough the file exits on the master node

core-site.xml

<configuration>
    <property>
        <name>fs.default.name</name>
        <value>hdfs://master:9000</value>
    </property> 
</configuration>

If this endpoint is unreachable, or if Spark detects that the file system is the same as the current system, the lib files will not be distributed to the other nodes in your cluster causing the errors above.

In my situation the node I was on couldn't reach port 9000 on the specified host.

Debugging

Turn the log level up to info. You can do this by:

1. Copy ./conf/log4j.properties.template to ./conf/log4j.properties

2. In the file set log4j.logger.org.apache.spark.repl.Main = INFO

Start your Spark Shell as normal. If your issue is the same as mine, you should see an info message such as: INFO Client: Source and destination file systems are the same. Not copying file:/tmp/spark-c1a6cdcd-d348-4253-8755-5086a8931e75/__spark_libs__1391186608525933727.zip

This should lead you to the problem as it starts the train reaction that results from the missing files.