Spark Shell - __spark_libs__.zip does not exist

10
votes

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>
    <name>yarn.resourcemanager.resource-tracker.address.rm2</name>
    <value>slave1:23125</value>
  </property>
  <property>
    <name>yarn.resourcemanager.admin.address.rm2</name>
    <value>slave1:23141</value>
  </property>

  <property>
    <description>Address where the localizer IPC is.</description>
    <name>yarn.nodemanager.localizer.address</name>
    <value>0.0.0.0:23344</value>
  </property>
  <property>
    <description>NM Webapp address.</description>
    <name>yarn.nodemanager.webapp.address</name>
    <value>0.0.0.0:23999</value>
  </property>
  <property>
    <name>yarn.nodemanager.aux-services</name>
    <value>mapreduce_shuffle</value>
  </property>
  <property>
    <name>yarn.nodemanager.local-dirs</name>
    <value>/tmp/pseudo-dist/yarn/local</value>
  </property>
  <property>
    <name>yarn.nodemanager.log-dirs</name>
    <value>/tmp/pseudo-dist/yarn/log</value>
  </property>
  <property>
    <name>mapreduce.shuffle.port</name>
    <value>23080</value>
  </property>
  <property>
    <name>yarn.resourcemanager.work-preserving-recovery.enabled</name>
    <value>true</value>
  </property>
</configuration>
4
hadoopapache-sparkhadoop-yarn
is /tmp path in all datanodes have rwx permission – Nirmal Ram
I've just confirmed, the /tmp directory has rwx permissions on all nodes. Do you think this is a problem writing the file or that the file can't be retrieved? – Ryan Nel
it might be. try directly creating a file in /tmp/spark-126d2844-5b37-461b-98a4-3f3de5ece91b/ path. does it show any permission issue? – Nirmal Ram
possible duplicate of stackoverflow.com/questions/36753546/… – Nirmal Ram
@NirmalRam I tried the fix suggested in stackoverflow.com/questions/36753546/…. I've placed my HADOOP_CONF_DIR in my question. I believe it's set correctly. I've also created the directory as recommended, no problems there. – Ryan Nel

4 Answers

6
votes

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.

1
votes

You must have set your configuration to master("local[*]") from spark session.I have removed and it worked.

0
votes

I do not see any errors in your logs, there are only warnings that you can avoid by adding the environment variables :

export HADOOP_COMMON_LIB_NATIVE_DIR=$HADOOP_HOME/lib/native
export HADOOP_OPTS="-Djava.library.path=$HADOOP_HOME/lib"

For the exception : try to set manually the spark configuration for yarn : http://badrit.com/blog/2015/2/29/running-spark-on-yarn#.WD_e66IrJsM

hdfs dfs -mkdir -p  /user/spark/share/lib<br>
hdfs dfs -put $SPARK_HOME/assembly/lib/spark-assembly_*.jar        /user/spark/share/lib/spark-assembly.jar<br>
export SPARK_JAR=hdfs://your-server:port/user/spark/share/lib/spark-assembly.jar

Hope this help.

0
votes

In my case, the spark user account was not able to read/recurse into the HADOOP_HOME, hence unable to read the core-site.xml.

spark@ubuntu$ ls -lrt /opt/hadoop/
ls: cannot open directory '/opt/hadoop/': Permission denied    <--- Cannot read the directory

spark@ubuntu$ ls -lrt /opt
total 20
drwxrwx--- 3 hadoop  1003 4096 Jun 18 20:38 hadoop             <---- Invalid group
drwxr-xr-x 3 spark  spark 4096 Jun 19 04:24 spark

Would recommend to run ls -la $HADOOP_CONF_DIR to make sure the account that submits the Spark job can read the core-site.xml.