Spark runs on Yarn cluster exitCode=13:

Question

I am a spark/yarn newbie, run into exitCode=13 when I submit a spark job on yarn cluster. When the spark job is running in local mode, everything is fine.

The command I used is:

/usr/hdp/current/spark-client/bin/spark-submit --class com.test.sparkTest --master yarn --deploy-mode cluster --num-executors 40 --executor-cores 4 --driver-memory 17g --executor-memory 22g --files /usr/hdp/current/spark-client/conf/hive-site.xml /home/user/sparkTest.jar*

Spark Error Log:

16/04/12 17:59:30 INFO Client:
         client token: N/A
         diagnostics: Application application_1459460037715_23007 failed 2 times due to AM Container for appattempt_1459460037715_23007_000002 exited with  exitCode: 13
For more detailed output, check application tracking page:http://b-r06f2-prod.phx2.cpe.net:8088/cluster/app/application_1459460037715_23007Then, click on links to logs of each attempt.
Diagnostics: Exception from container-launch.
Container id: container_e40_1459460037715_23007_02_000001
Exit code: 13
Stack trace: ExitCodeException exitCode=13:
        at org.apache.hadoop.util.Shell.runCommand(Shell.java:576)
        at org.apache.hadoop.util.Shell.run(Shell.java:487)
        at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:753)
        at org.apache.hadoop.yarn.server.nodemanager.DefaultContainerExecutor.launchContainer(DefaultContainerExecutor.java:211)
        at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:302)
        at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:82)


**Yarn logs**

    16/04/12 23:55:35 INFO mapreduce.TableInputFormatBase: Input split length: 977 M bytes.
16/04/12 23:55:41 INFO yarn.ApplicationMaster: Waiting for spark context initialization ...
16/04/12 23:55:51 INFO yarn.ApplicationMaster: Waiting for spark context initialization ...
16/04/12 23:56:01 INFO yarn.ApplicationMaster: Waiting for spark context initialization ...
16/04/12 23:56:11 INFO yarn.ApplicationMaster: Waiting for spark context initialization ...
16/04/12 23:56:11 INFO client.ConnectionManager$HConnectionImplementation: Closing zookeeper sessionid=0x152f0b4fc0e7488
16/04/12 23:56:11 INFO zookeeper.ZooKeeper: Session: 0x152f0b4fc0e7488 closed
16/04/12 23:56:11 INFO zookeeper.ClientCnxn: EventThread shut down
16/04/12 23:56:11 INFO executor.Executor: Finished task 0.0 in stage 1.0 (TID 2). 2003 bytes result sent to driver
16/04/12 23:56:11 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 1.0 (TID 2) in 82134 ms on localhost (2/3)
16/04/12 23:56:17 INFO client.ConnectionManager$HConnectionImplementation: Closing zookeeper sessionid=0x4508c270df0980316/04/12 23:56:17 INFO zookeeper.ZooKeeper: Session: 0x4508c270df09803 closed *
...
    16/04/12 23:56:21 ERROR yarn.ApplicationMaster: SparkContext did not initialize after waiting for 100000 ms. Please check earlier log output for errors. Failing the application.
16/04/12 23:56:21 INFO yarn.ApplicationMaster: Final app status: FAILED, exitCode: 13, (reason: Timed out waiting for SparkContext.)
16/04/12 23:56:21 INFO spark.SparkContext: Invoking stop() from shutdown hook *

Answer 1

It seems that you have set the master in your code to be local

SparkConf.setMaster("local[*]")

You have to let the master unset in the code, and set it later when you issue spark-submit

spark-submit --master yarn-client ...

Answer 2

If it helps someone

Another possibility of this error is when you put incorrectly the --class param

Answer 3

I had exactly the same problem but the above answer didn't work. Alternatively, when I ran this with spark-submit --deploy-mode client everything worked fine.

Answer 4

I got this same error running a SparkSQL job in cluster mode. None of the other solutions worked for me but looking in the job history server logs in Hadoop I found this stack trace.

20/02/05 23:01:24 INFO hive.metastore: Connected to metastore.
20/02/05 23:03:03 ERROR yarn.ApplicationMaster: Uncaught exception: 
java.util.concurrent.TimeoutException: Futures timed out after [100000 milliseconds]
    at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:223)
    at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:227)
    at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:220)
    at org.apache.spark.deploy.yarn.ApplicationMaster.runDriver(ApplicationMaster.scala:468)
    at org.apache.spark.deploy.yarn.ApplicationMaster.org$apache$spark$deploy$yarn$ApplicationMaster$$runImpl(ApplicationMaster.scala:305)
    at org.apache.spark.deploy.yarn.ApplicationMaster$$anonfun$run$1.apply$mcV$sp(ApplicationMaster.scala:245)
    at org.apache.spark.deploy.yarn.ApplicationMaster$$anonfun$run$1.apply(ApplicationMaster.scala:245)
    at org.apache.spark.deploy.yarn.ApplicationMaster$$anonfun$run$1.apply(ApplicationMaster.scala:245)
...

and looking at the Spark source code you'll find that basically the AM timed out waiting for the spark.driver.port property to be set by the Thread executing the user class.
So it could either be a transient issue or you should investigate your code for the reason for a timeout.

Answer 5

This exit code 13 is a tricky one...

For me it was SyntaxError: invalid syntax that was in one of the scripts imports downstream to the spark-submit call.

When debugging this on aws, if the spark-submit was not initialized properly, you will not find the error on Spark History Server, you will have to find it on the Spark logs: EMR UI Console -> Summary -> Log URI -> Containers -> application_xxx_xxx -> container_yyy_yy_yy -> stdout.gz.