Spark submit - yarn-cluster giving derby exception

Question

I am using HDP 2.4 distribution that is using spark 1.6 and I am trying to submit spark job on yarn-cluster.

As I submit job on yarn-client and local, it is working. But when submitting job with yarn-cluster gives below error.

java.lang.RuntimeException: Unable to instantiate org.apache.hadoop.hive.ql.metadata.SessionHiveMetaStoreClient

Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.apache.derby.jdbc.EmbeddedDriver

Full stack trace as below :

<code>    

16/04/28 13:06:15 INFO YarnClusterScheduler: YarnClusterScheduler.postStartHook done
16/04/28 13:06:16 INFO HiveContext: Initializing execution hive, version 1.2.1
    16/04/28 13:06:16 INFO ClientWrapper: Inspected Hadoop version: 2.7.1.2.4.0.0-169
    16/04/28 13:06:16 INFO ClientWrapper: Loaded org.apache.hadoop.hive.shims.Hadoop23Shims for Hadoop version 2.7.1.2.4.0.0-169
    16/04/28 13:06:16 INFO HiveMetaStore: 0: Opening raw store with implemenation class:org.apache.hadoop.hive.metastore.ObjectStore
    16/04/28 13:06:16 INFO ObjectStore: ObjectStore, initialize called
    16/04/28 13:06:16 INFO Persistence: Property hive.metastore.integral.jdo.pushdown unknown - will be ignored
    16/04/28 13:06:16 INFO Persistence: Property datanucleus.cache.level2 unknown - will be ignored
    16/04/28 13:06:17 WARN HiveMetaStore: Retrying creating default database after error: Error creating transactional connection factory
    javax.jdo.JDOFatalInternalException: Error creating transactional connection factory
        at org.datanucleus.api.jdo.NucleusJDOHelper.getJDOExceptionForNucleusException(NucleusJDOHelper.java:587)
        at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.freezeConfiguration(JDOPersistenceManagerFactory.java:788)
        at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.createPersistenceManagerFactory(JDOPersistenceManagerFactory.java:333)
        at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.getPersistenceManagerFactory(JDOPersistenceManagerFactory.java:202)
        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:483)
        at javax.jdo.JDOHelper$16.run(JDOHelper.java:1965)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.jdo.JDOHelper.invoke(JDOHelper.java:1960)
        at javax.jdo.JDOHelper.invokeGetPersistenceManagerFactoryOnImplementation(JDOHelper.java:1166)
        at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:808)
        at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:701)
        at org.apache.hadoop.hive.metastore.ObjectStore.getPMF(ObjectStore.java:365)
        at org.apache.hadoop.hive.metastore.ObjectStore.getPersistenceManager(ObjectStore.java:394)
        at org.apache.hadoop.hive.metastore.ObjectStore.initialize(ObjectStore.java:291)
        at org.apache.hadoop.hive.metastore.ObjectStore.setConf(ObjectStore.java:258)
        at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:76)
        at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:136)
        at org.apache.hadoop.hive.metastore.RawStoreProxy.<init>(RawStoreProxy.java:57)
        at org.apache.hadoop.hive.metastore.RawStoreProxy.getProxy(RawStoreProxy.java:66)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.newRawStore(HiveMetaStore.java:593)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.getMS(HiveMetaStore.java:571)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.createDefaultDB(HiveMetaStore.java:620)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.init(HiveMetaStore.java:461)
        at org.apache.hadoop.hive.metastore.RetryingHMSHandler.<init>(RetryingHMSHandler.java:66)
        at org.apache.hadoop.hive.metastore.RetryingHMSHandler.getProxy(RetryingHMSHandler.java:72)
        at org.apache.hadoop.hive.metastore.HiveMetaStore.newRetryingHMSHandler(HiveMetaStore.java:5762)
        at org.apache.hadoop.hive.metastore.HiveMetaStoreClient.<init>(HiveMetaStoreClient.java:199)
        at org.apache.hadoop.hive.ql.metadata.SessionHiveMetaStoreClient.<init>(SessionHiveMetaStoreClient.java:74)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
        at org.apache.hadoop.hive.metastore.MetaStoreUtils.newInstance(MetaStoreUtils.java:1521)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.<init>(RetryingMetaStoreClient.java:86)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:132)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:104)
        at org.apache.hadoop.hive.ql.metadata.Hive.createMetaStoreClient(Hive.java:3005)
        at org.apache.hadoop.hive.ql.metadata.Hive.getMSC(Hive.java:3024)
        at org.apache.hadoop.hive.ql.metadata.Hive.getAllDatabases(Hive.java:1234)
        at org.apache.hadoop.hive.ql.metadata.Hive.reloadFunctions(Hive.java:174)
        at org.apache.hadoop.hive.ql.metadata.Hive.<clinit>(Hive.java:166)
        at org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:503)
        at org.apache.spark.sql.hive.client.ClientWrapper.<init>(ClientWrapper.scala:194)
        at org.apache.spark.sql.hive.client.IsolatedClientLoader.createClient(IsolatedClientLoader.scala:238)
        at org.apache.spark.sql.hive.HiveContext.executionHive$lzycompute(HiveContext.scala:218)
        at org.apache.spark.sql.hive.HiveContext.executionHive(HiveContext.scala:208)
        at org.apache.spark.sql.hive.HiveContext.functionRegistry$lzycompute(HiveContext.scala:462)
        at org.apache.spark.sql.hive.HiveContext.functionRegistry(HiveContext.scala:461)
        at org.apache.spark.sql.UDFRegistration.<init>(UDFRegistration.scala:40)
        at org.apache.spark.sql.SQLContext.<init>(SQLContext.scala:330)
        at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:90)
        at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:101)
        at com.bhartiinfotech.bigdata.job.CsvToHiveSparkJob.execute(CsvToHiveSparkJob.java:39)
        at com.bhartiinfotech.bigdata.job.CsvToHiveSparkJob.main(CsvToHiveSparkJob.java:89)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:483)
        at org.apache.spark.deploy.yarn.ApplicationMaster$anon$2.run(ApplicationMaster.scala:546)
    NestedThrowablesStackTrace:
    java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
        at org.datanucleus.plugin.NonManagedPluginRegistry.createExecutableExtension(NonManagedPluginRegistry.java:631)
        at org.datanucleus.plugin.PluginManager.createExecutableExtension(PluginManager.java:325)
        at org.datanucleus.store.AbstractStoreManager.registerConnectionFactory(AbstractStoreManager.java:282)
        at org.datanucleus.store.AbstractStoreManager.<init>(AbstractStoreManager.java:240)
        at org.datanucleus.store.rdbms.RDBMSStoreManager.<init>(RDBMSStoreManager.java:286)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
        at org.datanucleus.plugin.NonManagedPluginRegistry.createExecutableExtension(NonManagedPluginRegistry.java:631)
        at org.datanucleus.plugin.PluginManager.createExecutableExtension(PluginManager.java:301)
        at org.datanucleus.NucleusContext.createStoreManagerForProperties(NucleusContext.java:1187)
        at org.datanucleus.NucleusContext.initialise(NucleusContext.java:356)
        at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.freezeConfiguration(JDOPersistenceManagerFactory.java:775)
        at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.createPersistenceManagerFactory(JDOPersistenceManagerFactory.java:333)
        at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.getPersistenceManagerFactory(JDOPersistenceManagerFactory.java:202)
        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:483)
        at javax.jdo.JDOHelper$16.run(JDOHelper.java:1965)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.jdo.JDOHelper.invoke(JDOHelper.java:1960)
        at javax.jdo.JDOHelper.invokeGetPersistenceManagerFactoryOnImplementation(JDOHelper.java:1166)
        at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:808)
        at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:701)
        at org.apache.hadoop.hive.metastore.ObjectStore.getPMF(ObjectStore.java:365)
        at org.apache.hadoop.hive.metastore.ObjectStore.getPersistenceManager(ObjectStore.java:394)
        at org.apache.hadoop.hive.metastore.ObjectStore.initialize(ObjectStore.java:291)
        at org.apache.hadoop.hive.metastore.ObjectStore.setConf(ObjectStore.java:258)
        at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:76)
        at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:136)
        at org.apache.hadoop.hive.metastore.RawStoreProxy.<init>(RawStoreProxy.java:57)
        at org.apache.hadoop.hive.metastore.RawStoreProxy.getProxy(RawStoreProxy.java:66)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.newRawStore(HiveMetaStore.java:593)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.getMS(HiveMetaStore.java:571)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.createDefaultDB(HiveMetaStore.java:620)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.init(HiveMetaStore.java:461)
        at org.apache.hadoop.hive.metastore.RetryingHMSHandler.<init>(RetryingHMSHandler.java:66)
        at org.apache.hadoop.hive.metastore.RetryingHMSHandler.getProxy(RetryingHMSHandler.java:72)
        at org.apache.hadoop.hive.metastore.HiveMetaStore.newRetryingHMSHandler(HiveMetaStore.java:5762)
        at org.apache.hadoop.hive.metastore.HiveMetaStoreClient.<init>(HiveMetaStoreClient.java:199)
        at org.apache.hadoop.hive.ql.metadata.SessionHiveMetaStoreClient.<init>(SessionHiveMetaStoreClient.java:74)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
        at org.apache.hadoop.hive.metastore.MetaStoreUtils.newInstance(MetaStoreUtils.java:1521)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.<init>(RetryingMetaStoreClient.java:86)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:132)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:104)
        at org.apache.hadoop.hive.ql.metadata.Hive.createMetaStoreClient(Hive.java:3005)
        at org.apache.hadoop.hive.ql.metadata.Hive.getMSC(Hive.java:3024)
        at org.apache.hadoop.hive.ql.metadata.Hive.getAllDatabases(Hive.java:1234)
        at org.apache.hadoop.hive.ql.metadata.Hive.reloadFunctions(Hive.java:174)
        at org.apache.hadoop.hive.ql.metadata.Hive.<clinit>(Hive.java:166)
        at org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:503)
        at org.apache.spark.sql.hive.client.ClientWrapper.<init>(ClientWrapper.scala:194)
        at org.apache.spark.sql.hive.client.IsolatedClientLoader.createClient(IsolatedClientLoader.scala:238)
        at org.apache.spark.sql.hive.HiveContext.executionHive$lzycompute(HiveContext.scala:218)
        at org.apache.spark.sql.hive.HiveContext.executionHive(HiveContext.scala:208)
        at org.apache.spark.sql.hive.HiveContext.functionRegistry$lzycompute(HiveContext.scala:462)
        at org.apache.spark.sql.hive.HiveContext.functionRegistry(HiveContext.scala:461)
        at org.apache.spark.sql.UDFRegistration.<init>(UDFRegistration.scala:40)
        at org.apache.spark.sql.SQLContext.<init>(SQLContext.scala:330)
        at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:90)
        at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:101)
        at com.bhartiinfotech.bigdata.job.CsvToHiveSparkJob.execute(CsvToHiveSparkJob.java:39)
        at com.bhartiinfotech.bigdata.job.CsvToHiveSparkJob.main(CsvToHiveSparkJob.java:89)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:483)
        at org.apache.spark.deploy.yarn.ApplicationMaster$anon$2.run(ApplicationMaster.scala:546)
    Caused by: java.lang.ExceptionInInitializerError
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
        at java.lang.Class.newInstance(Class.java:433)
        at org.datanucleus.store.rdbms.connectionpool.AbstractConnectionPoolFactory.loadDriver(AbstractConnectionPoolFactory.java:47)
        at org.datanucleus.store.rdbms.connectionpool.BoneCPConnectionPoolFactory.createConnectionPool(BoneCPConnectionPoolFactory.java:54)
        at org.datanucleus.store.rdbms.ConnectionFactoryImpl.generateDataSources(ConnectionFactoryImpl.java:238)
        at org.datanucleus.store.rdbms.ConnectionFactoryImpl.initialiseDataSources(ConnectionFactoryImpl.java:131)
        at org.datanucleus.store.rdbms.ConnectionFactoryImpl.<init>(ConnectionFactoryImpl.java:85)
        ... 78 more
    Caused by: java.lang.SecurityException: sealing violation: package org.apache.derby.impl.services.timer is sealed
        at java.net.URLClassLoader.getAndVerifyPackage(URLClassLoader.java:394)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:423)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:367)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:760)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:455)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:367)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:259)
        at org.apache.derby.impl.services.monitor.BaseMonitor.getImplementations(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.getDefaultImplementations(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.runWithState(Unknown Source)
        at org.apache.derby.impl.services.monitor.FileMonitor.<init>(Unknown Source)
        at org.apache.derby.iapi.services.monitor.Monitor.startMonitor(Unknown Source)
        at org.apache.derby.iapi.jdbc.JDBCBoot.boot(Unknown Source)
        at org.apache.derby.jdbc.EmbeddedDriver.boot(Unknown Source)
        at org.apache.derby.jdbc.EmbeddedDriver.<clinit>(Unknown Source)
        ... 88 more
    16/04/28 13:06:17 INFO HiveMetaStore: 0: Opening raw store with implemenation class:org.apache.hadoop.hive.metastore.ObjectStore
    16/04/28 13:06:17 INFO ObjectStore: ObjectStore, initialize called
    16/04/28 13:06:17 INFO Persistence: Property hive.metastore.integral.jdo.pushdown unknown - will be ignored
    16/04/28 13:06:17 INFO Persistence: Property datanucleus.cache.level2 unknown - will be ignored
    16/04/28 13:06:17 WARN Hive: Failed to access metastore. This class should not accessed in runtime.
    org.apache.hadoop.hive.ql.metadata.HiveException: java.lang.RuntimeException: Unable to instantiate org.apache.hadoop.hive.ql.metadata.SessionHiveMetaStoreClient
        at org.apache.hadoop.hive.ql.metadata.Hive.getAllDatabases(Hive.java:1236)
        at org.apache.hadoop.hive.ql.metadata.Hive.reloadFunctions(Hive.java:174)
        at org.apache.hadoop.hive.ql.metadata.Hive.<clinit>(Hive.java:166)
        at org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:503)
        at org.apache.spark.sql.hive.client.ClientWrapper.<init>(ClientWrapper.scala:194)
        at org.apache.spark.sql.hive.client.IsolatedClientLoader.createClient(IsolatedClientLoader.scala:238)
        at org.apache.spark.sql.hive.HiveContext.executionHive$lzycompute(HiveContext.scala:218)
        at org.apache.spark.sql.hive.HiveContext.executionHive(HiveContext.scala:208)
        at org.apache.spark.sql.hive.HiveContext.functionRegistry$lzycompute(HiveContext.scala:462)
        at org.apache.spark.sql.hive.HiveContext.functionRegistry(HiveContext.scala:461)
        at org.apache.spark.sql.UDFRegistration.<init>(UDFRegistration.scala:40)
        at org.apache.spark.sql.SQLContext.<init>(SQLContext.scala:330)
        at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:90)
        at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:101)
        at com.bhartiinfotech.bigdata.job.CsvToHiveSparkJob.execute(CsvToHiveSparkJob.java:39)
        at com.bhartiinfotech.bigdata.job.CsvToHiveSparkJob.main(CsvToHiveSparkJob.java:89)
        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:483)
        at org.apache.spark.deploy.yarn.ApplicationMaster$anon$2.run(ApplicationMaster.scala:546)
    Caused by: java.lang.RuntimeException: Unable to instantiate org.apache.hadoop.hive.ql.metadata.SessionHiveMetaStoreClient
        at org.apache.hadoop.hive.metastore.MetaStoreUtils.newInstance(MetaStoreUtils.java:1523)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.<init>(RetryingMetaStoreClient.java:86)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:132)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:104)
        at org.apache.hadoop.hive.ql.metadata.Hive.createMetaStoreClient(Hive.java:3005)
        at org.apache.hadoop.hive.ql.metadata.Hive.getMSC(Hive.java:3024)
        at org.apache.hadoop.hive.ql.metadata.Hive.getAllDatabases(Hive.java:1234)
        ... 20 more
    Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
        at org.apache.hadoop.hive.metastore.MetaStoreUtils.newInstance(MetaStoreUtils.java:1521)
        ... 26 more
    Caused by: javax.jdo.JDOFatalInternalException: Error creating transactional connection factory
NestedThrowables:
java.lang.reflect.InvocationTargetException
    at org.datanucleus.api.jdo.NucleusJDOHelper.getJDOExceptionForNucleusException(NucleusJDOHelper.java:587)
    at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.freezeConfiguration(JDOPersistenceManagerFactory.java:788)
    at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.createPersistenceManagerFactory(JDOPersistenceManagerFactory.java:333)
    at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.getPersistenceManagerFactory(JDOPersistenceManagerFactory.java:202)
    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:483)
    at javax.jdo.JDOHelper$16.run(JDOHelper.java:1965)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.jdo.JDOHelper.invoke(JDOHelper.java:1960)
    at javax.jdo.JDOHelper.invokeGetPersistenceManagerFactoryOnImplementation(JDOHelper.java:1166)
    at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:808)
    at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:701)
    at org.apache.hadoop.hive.metastore.ObjectStore.getPMF(ObjectStore.java:365)
    at org.apache.hadoop.hive.metastore.ObjectStore.getPersistenceManager(ObjectStore.java:394)
    at org.apache.hadoop.hive.metastore.ObjectStore.initialize(ObjectStore.java:291)
    at org.apache.hadoop.hive.metastore.ObjectStore.setConf(ObjectStore.java:258)
    at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:76)
    at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:136)
    at org.apache.hadoop.hive.metastore.RawStoreProxy.<init>(RawStoreProxy.java:57)
    at org.apache.hadoop.hive.metastore.RawStoreProxy.getProxy(RawStoreProxy.java:66)
    at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.newRawStore(HiveMetaStore.java:593)
    at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.getMS(HiveMetaStore.java:571)
    at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.createDefaultDB(HiveMetaStore.java:624)
    at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.init(HiveMetaStore.java:461)
    at org.apache.hadoop.hive.metastore.RetryingHMSHandler.<init>(RetryingHMSHandler.java:66)
    at org.apache.hadoop.hive.metastore.RetryingHMSHandler.getProxy(RetryingHMSHandler.java:72)
    at org.apache.hadoop.hive.metastore.HiveMetaStore.newRetryingHMSHandler(HiveMetaStore.java:5762)
    at org.apache.hadoop.hive.metastore.HiveMetaStoreClient.<init>(HiveMetaStoreClient.java:199)
    at org.apache.hadoop.hive.ql.metadata.SessionHiveMetaStoreClient.<init>(SessionHiveMetaStoreClient.java:74)
    ... 31 more
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
    at org.datanucleus.plugin.NonManagedPluginRegistry.createExecutableExtension(NonManagedPluginRegistry.java:631)
    at org.datanucleus.plugin.PluginManager.createExecutableExtension(PluginManager.java:325)
    at org.datanucleus.store.AbstractStoreManager.registerConnectionFactory(AbstractStoreManager.java:282)
    at org.datanucleus.store.AbstractStoreManager.<init>(AbstractStoreManager.java:240)
    at org.datanucleus.store.rdbms.RDBMSStoreManager.<init>(RDBMSStoreManager.java:286)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
    at org.datanucleus.plugin.NonManagedPluginRegistry.createExecutableExtension(NonManagedPluginRegistry.java:631)
    at org.datanucleus.plugin.PluginManager.createExecutableExtension(PluginManager.java:301)
    at org.datanucleus.NucleusContext.createStoreManagerForProperties(NucleusContext.java:1187)
    at org.datanucleus.NucleusContext.initialise(NucleusContext.java:356)
    at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.freezeConfiguration(JDOPersistenceManagerFactory.java:775)
    ... 60 more
Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.apache.derby.jdbc.EmbeddedDriver
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
    at java.lang.Class.newInstance(Class.java:433)
    at org.datanucleus.store.rdbms.connectionpool.AbstractConnectionPoolFactory.loadDriver(AbstractConnectionPoolFactory.java:47)
    at org.datanucleus.store.rdbms.connectionpool.BoneCPConnectionPoolFactory.createConnectionPool(BoneCPConnectionPoolFactory.java:54)
    at org.datanucleus.store.rdbms.ConnectionFactoryImpl.generateDataSources(ConnectionFactoryImpl.java:238)
    at 

    org.datanucleus.store.rdbms.ConnectionFactoryImpl.initialiseDataSources(ConnectionFactoryImpl.java:131)
        at org.datanucleus.store.rdbms.ConnectionFactoryImpl.<init>(ConnectionFactoryImpl.java:85)
        ... 78 more
    16/04/28 13:06:17 INFO HiveMetaStore: 0: Opening raw store with implemenation class:org.apache.hadoop.hive.metastore.ObjectStore
    16/04/28 13:06:17 INFO ObjectStore: ObjectStore, initialize called
    16/04/28 13:06:17 INFO Persistence: Property hive.metastore.integral.jdo.pushdown unknown - will be ignored
16/04/28 13:06:17 INFO Persistence: Property datanucleus.cache.level2 unknown - will be ignored

I found this bug in hive for derby jar issues for older version of spark and hive https://issues.apache.org/jira/browse/HIVE-9198,

but I am not able to figure it out how can I fix it for my environment.

Can anybody help me ?

Thanks

Answer 1

Answer by Jitendra Yadav · Apr 29, 2016 at 08:18 PM

@Ankit A

NoClassDefFoundError is always been an interesting issue, lets try below step and share the result please?

bash# find /usr/hdp/ -name "*.jar" -exec sh -c 'jar -tf {}|grep -H --label {} 'org.apache.derby.jdbc.EmbeddedDriver'' \;

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Ankit A · Apr 30, 2016 at 02:00 AM 0

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I am assuming this command will will fetch available 'org.apache.derby.jdbc.EmbeddedDriver' classes from jar..

I have executed in one of my node and full result is :

java.io.FileNotFoundException: /usr/hdp/2.4.0.0-169/kafka/libs/zookeeper.jar (No such file or directory)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:220)
at java.util.zip.ZipFile.<init>(ZipFile.java:150)
at java.util.zip.ZipFile.<init>(ZipFile.java:121)
at sun.tools.jar.Main.list(Main.java:1060)
at sun.tools.jar.Main.run(Main.java:291)
at sun.tools.jar.Main.main(Main.java:1233)
java.io.FileNotFoundException: /usr/hdp/2.4.0.0-169/kafka/libs/ojdbc6.jar (No such file or directory)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:220)
at java.util.zip.ZipFile.<init>(ZipFile.java:150)
at java.util.zip.ZipFile.<init>(ZipFile.java:121)
at sun.tools.jar.Main.list(Main.java:1060)
at sun.tools.jar.Main.run(Main.java:291)
at sun.tools.jar.Main.main(Main.java:1233)
/usr/hdp/2.4.0.0-169/oozie/libtools/derby-10.10.1.1.jar:org/apache/derby/jdbc/EmbeddedDriver.class
/usr/hdp/2.4.0.0-169/oozie/libserver/derby-10.10.1.1.jar:org/apache/derby/jdbc/EmbeddedDriver.class
java.io.FileNotFoundException: /usr/hdp/2.4.0.0-169/hbase/lib/ojdbc6.jar (No such file or directory)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:220)
at java.util.zip.ZipFile.<init>(ZipFile.java:150)
at java.util.zip.ZipFile.<init>(ZipFile.java:121)
at sun.tools.jar.Main.list(Main.java:1060)
at sun.tools.jar.Main.run(Main.java:291)
at sun.tools.jar.Main.main(Main.java:1233)
java.io.FileNotFoundException: /usr/hdp/2.4.0.0-169/hive/lib/ojdbc6.jar (No such file or directory)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:220)
at java.util.zip.ZipFile.<init>(ZipFile.java:150)
at java.util.zip.ZipFile.<init>(ZipFile.java:121)
at sun.tools.jar.Main.list(Main.java:1060)
at sun.tools.jar.Main.run(Main.java:291)
at sun.tools.jar.Main.main(Main.java:1233)
/usr/hdp/2.4.0.0-169/hive/lib/derby-10.10.2.0.jar:org/apache/derby/jdbc/EmbeddedDriver.class
java.io.FileNotFoundException: /usr/hdp/2.4.0.0-169/hadoop/lib/ojdbc6.jar (No such file or directory)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:220)
at java.util.zip.ZipFile.<init>(ZipFile.java:150)
at java.util.zip.ZipFile.<init>(ZipFile.java:121)
at sun.tools.jar.Main.list(Main.java:1060)
at sun.tools.jar.Main.run(Main.java:291)
at sun.tools.jar.Main.main(Main.java:1233)
java.io.FileNotFoundException: /usr/hdp/2.4.0.0-169/phoenix/lib/hbase-testing-util.jar (No such file or directory)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:220)
at java.util.zip.ZipFile.<init>(ZipFile.java:150)
at java.util.zip.ZipFile.<init>(ZipFile.java:121)
at sun.tools.jar.Main.list(Main.java:1060)
at sun.tools.jar.Main.run(Main.java:291)
at sun.tools.jar.Main.main(Main.java:1233)
/usr/hdp/2.4.0.0-169/spark/lib/spark-examples-1.6.0.2.4.0.0-169-hadoop2.7.1.2.4.0.0-169.jar:org/apache/derby/jdbc/EmbeddedDriver.class
/usr/hdp/2.4.0.0-169/spark/lib/spark-hdp-assembly.jar:org/apache/derby/jdbc/EmbeddedDriver.class
/usr/hdp/2.4.0.0-169/spark/lib/spark-assembly-1.6.0.2.4.0.0-169-hadoop2.7.1.2.4.0.0-169.jar:org/apache/derby/jdbc/EmbeddedDriver.class

I extracted result for embeddedDriver.class as below

/usr/hdp/2.4.0.0-169/hive/lib/derby-10.10.2.0.jar:org/apache/derby/jdbc/EmbeddedDriver.class
.
.
/usr/hdp/2.4.0.0-169/oozie/libtools/derby-10.10.1.1.jar:org/apache/derby/jdbc/EmbeddedDriver.class
/usr/hdp/2.4.0.0-169/oozie/libserver/derby-10.10.1.1.jar:org/apache/derby/jdbc/EmbeddedDriver.class
.
.
/usr/hdp/2.4.0.0-169/spark/lib/spark-examples-1.6.0.2.4.0.0-169-hadoop2.7.1.2.4.0.0-169.jar:org/apache/derby/jdbc/EmbeddedDriver.class
/usr/hdp/2.4.0.0-169/spark/lib/spark-hdp-assembly.jar:org/apache/derby/jdbc/EmbeddedDriver.class
/usr/hdp/2.4.0.0-169/spark/lib/spark-assembly-1.6.0.2.4.0.0-169-hadoop2.7.1.2.4.0.0-169.jar:org/apache/derby/jdbc/EmbeddedDriver.class

Answer 2

Answer by Mukund V · Aug 23, 2017 at 01:30 PM

I copied the latest derby jar into the /user/oozie/share/lib/lib_<ts>/spark folder and it started to work

Earlier I was copying the same file into /user/oozie/share/lib/lib_<ts>/oozie folder but the error was prevailing. Then understood that the oozie application triggers a spark application. The oozie app refer to the /user/oozie/share/lib/lib_<ts>/oozie folder and the spark job refers to /user/oozie/share/lib/lib_<ts>/spark folder.

However jitendras command helped me to identify the jar files folder and the solution. Thank u Jitendra

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Answer 3

Answer by bkosaraju · Aug 23, 2017 at 03:05 AM

Hi @Ankit,

Are you using Derby DB for Hive ? If Not(in case MySQL or Postgres) then it is the issue is with spark configuration to identify the metadata for thrift server.

in case you can do two things

1. copy the /etc/hive/conf/hive-site.xml and /etc/hadoop/conf/core-site.xml,hdfs-site.xml to the common library path

2. include the same file in --flies option in spark-submit argument list, so that it will have the configuration details and points to right config.

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