Unable to run Spark Job in clutser mode

[#1]

Hi,

I'm able to run the job in client mode but unable to run the same job in cluster mode. Can someone please help me? Below is the error message.

16/06/22 21:57:10 ERROR yarn.ApplicationMaster: User class threw exception: java.lang.RuntimeException: java.lang.RuntimeException: Unable to instantiate org.apache.hadoop.hive.metastore.HiveMetaStoreClient
java.lang.RuntimeException: java.lang.RuntimeException: Unable to instantiate org.apache.hadoop.hive.metastore.HiveMetaStoreClient
        at org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:346)
        at org.apache.spark.sql.hive.client.ClientWrapper.<init>(ClientWrapper.scala:117)
        at org.apache.spark.sql.hive.HiveContext.executionHive$lzycompute(HiveContext.scala:165)
        at org.apache.spark.sql.hive.HiveContext.executionHive(HiveContext.scala:163)
        at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:170)
        at DisplayAnalysisForecast$.main(DisplayAnalysisForecast.scala:35)
        at DisplayAnalysisForecast.main(DisplayAnalysisForecast.scala)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.spark.deploy.yarn.ApplicationMaster$$anon$2.run(ApplicationMaster.scala:486)
Caused by: java.lang.RuntimeException: Unable to instantiate org.apache.hadoop.hive.metastore.HiveMetaStoreClient
        at org.apache.hadoop.hive.metastore.MetaStoreUtils.newInstance(MetaStoreUtils.java:1412)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.<init>(RetryingMetaStoreClient.java:62)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:72)
        at org.apache.hadoop.hive.ql.metadata.Hive.createMetaStoreClient(Hive.java:2453)
        at org.apache.hadoop.hive.ql.metadata.Hive.getMSC(Hive.java:2465)
        at org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:340)
        ... 11 more
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
        at org.apache.hadoop.hive.metastore.MetaStoreUtils.newInstance(MetaStoreUtils.java:1410)
        ... 16 more
Caused by: javax.jdo.JDOFatalUserException: Class org.datanucleus.api.jdo.JDOPersistenceManagerFactory was not found.
NestedThrowables:
java.lang.ClassNotFoundException: org.datanucleus.api.jdo.JDOPersistenceManagerFactory
        at javax.jdo.JDOHelper.invokeGetPersistenceManagerFactoryOnImplementation(JDOHelper.java:1175)
        at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:808)
        at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:701)
        at org.apache.hadoop.hive.metastore.ObjectStore.getPMF(ObjectStore.java:310)
        at org.apache.hadoop.hive.metastore.ObjectStore.getPersistenceManager(ObjectStore.java:339)
        at org.apache.hadoop.hive.metastore.ObjectStore.initialize(ObjectStore.java:248)
        at org.apache.hadoop.hive.metastore.ObjectStore.setConf(ObjectStore.java:223)
        at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:76)
        at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:136)
        at org.apache.hadoop.hive.metastore.RawStoreProxy.<init>(RawStoreProxy.java:58)
        at org.apache.hadoop.hive.metastore.RawStoreProxy.getProxy(RawStoreProxy.java:67)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.newRawStore(HiveMetaStore.java:497)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.getMS(HiveMetaStore.java:475)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.createDefaultDB(HiveMetaStore.java:523)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.init(HiveMetaStore.java:397)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.<init>(HiveMetaStore.java:356)
        at org.apache.hadoop.hive.metastore.RetryingHMSHandler.<init>(RetryingHMSHandler.java:54)
        at org.apache.hadoop.hive.metastore.RetryingHMSHandler.getProxy(RetryingHMSHandler.java:59)
        at org.apache.hadoop.hive.metastore.HiveMetaStore.newHMSHandler(HiveMetaStore.java:4944)
        at org.apache.hadoop.hive.metastore.HiveMetaStoreClient.<init>(HiveMetaStoreClient.java:171)
        ... 21 more
Caused by: java.lang.ClassNotFoundException: org.datanucleus.api.jdo.JDOPersistenceManagerFactory
        at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:270)
        at javax.jdo.JDOHelper$18.run(JDOHelper.java:2018)
        at javax.jdo.JDOHelper$18.run(JDOHelper.java:2016)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.jdo.JDOHelper.forName(JDOHelper.java:2015)
        at javax.jdo.JDOHelper.invokeGetPersistenceManagerFactoryOnImplementation(JDOHelper.java:1162)
        ... 40 more
16/06/22 21:57:10 INFO yarn.ApplicationMaster: Final app status: FAILED, exitCode: 15, (reason: User class threw exception: java.lang.RuntimeException: java.lang.RuntimeException: Unable to instantiate org.apache.hadoop.hive.metastore.HiveMetaStoreClient)
16/06/22 21:57:18 ERROR yarn.ApplicationMaster: SparkContext did not initialize after waiting for 100000 ms. Please check earlier log output for errors. Failing the application.
16/06/22 21:57:18 INFO spark.SparkContext: Invoking stop() from shutdown hook

Using Spark 1.4 and running on Hadoop cluster only. Any help is highly appreciated and thanks in advance.

[#2]

@Sri Bandaru

1. Check the hive-site.xml contents. Should be like as below for spark.
2. Add hive-site.xml to the driver-classpath so that spark can read hive configuration. Make sure —files must come before you .jar file
3. Add the datanucleus jars using --jars option when you submit
4. Check the contents of hive-site.xml

5.  <configuration>
       <property>
         <name>hive.metastore.uris</name>
         <value>thrift://sandbox.hortonworks.com:9083</value>
       </property>
     </configuration>

6. The Seq. of command

1. spark-submit \
2. --class <Your.class.name> \
3. --master yarn-cluster \
4. --num-executors 1 \
5. --driver-memory 1g \
6. --executor-memory 1g \
7. --executor-cores 1 \
8. --files /usr/hdp/current/spark-client/conf/hive-site.xml \
9. --jars /usr/hdp/current/spark-client/lib/datanucleus-api-jdo-3.2.6.jar,/usr/hdp/current/spark-client/lib/datanucleus-rdbms-3.2.9.jar,/usr/hdp/current/spark-client/lib/datanucleus-core-3.2.10.jar \
10. target/YOUR_JAR-1.0.0-SNAPSHOT.jar "show tables""select * from your_table"

[#3]

@Gangadhar Kadam

Thanks for the quick response, HA is enabled for HiveServer2 and we are pointing to two thrift servers at hive.metastore.uris

I have already followed all the steps, but that doesn't help my scenario. I'm able to run the same job in client mode.

[#4]

can you share your code.

[#5]

@Gangadhar Kadam

spark-submit --class org.apache.spark.examples.SparkPi --master yarn --deploy-mode cluster --executor-memory 1G --num-executors 1 -driver-memory 2G --executor-memory 2G --jars /usr/hdp/current/spark-client/lib/datanucleus-api-jdo-3.2.6.jar,/usr/hdp/current/spark-client/lib/datanucleus-rdbms-3.2.9.jar,/usr/hdp/current/spark-client/lib/datanucleus-core-3.2.10.jar  --files /usr/hdp/current/spark-client/conf/hive-site.xml /usr/hdp/current/spark-client/lib/spark-examples-1.4.1.2.3.2.0-2950-hadoop2.7.1.2.3.2.0-2950.jar 10

[#6]

did you tried --file before the --jar?

[#7]

@Gangadhar Kadam

Yes, this time I got different error,

ERROR yarn.ApplicationMaster: SparkContext did not initialize after waiting for 100000 ms. Please check earlier log output for errors. Failing the application.

[#8 · Accepted solution]

Suggest solution:

1. As discovered, we are hitting a bug with HDP 2.3.2 with Ambari 2.2.1 :https://hortonworks.jira.com/browse/BUG-56393 where starting from Ambari 2.2.1 , it does not manage the spark version if HDP stack is < HDP 2.3.4

spark.driver.extraJavaOptions =-Dhdp.version={{hdp_full_version}}
spark.yarn.am.extraJavaOptions=-Dhdp.version={{hdp_full_version}}

2. Right now we have a workaround where we have modified the property value and hard coded the right HDP version.

spark.driver.extraJavaOptions =-Dhdp.version=2.3.2.0-2950
spark.yarn.am.extraJavaOptions=-Dhdp.version=2.3.2.0-2950

Currently, Spark pi jobs are running fine

[#9]

@Gangadhar Kadam Thank you.. Steps you mentioned help me to resolve the problem

,

Thank you @Gangadhar Kadam ..Steps you provided help us to resolve the issue