Unable to run Spark Job in clutser mode

Question

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.

Answer 1

Best Answer

Answer by Sridhar Reddy · Jul 29, 2016 at 03:19 PM

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

0 · Share

Answer 2

Answer by Gangadhar Kadam · Jun 23, 2016 at 03:31 AM

@Sri Bandaru

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

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

The Seq. of command

spark-submit \
--class <Your.class.name> \
--master yarn-cluster \
--num-executors 1 \
--driver-memory 1g \
--executor-memory 1g \
--executor-cores 1 \
--files /usr/hdp/current/spark-client/conf/hive-site.xml \
--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 \
target/YOUR_JAR-1.0.0-SNAPSHOT.jar "show tables""select * from your_table"

0 Show 5 · Share

Sridhar Reddy · Jun 23, 2016 at 04:14 AM 0

Share

@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.

Gangadhar Kadam Sridhar Reddy · Jun 23, 2016 at 04:18 AM 0

Share

can you share your code.

Sridhar Reddy Gangadhar Kadam · Jun 23, 2016 at 04:36 AM 0

Share

@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

Show more comments

Answer 3

Answer by Gurjeet Singh · Jan 10 at 05:19 PM

@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

0 · Share

Unable to run Spark Job in clutser mode

3 Replies

Your answer