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 ...