Spark-sql: Unable to instantiate org.apache.hadoop.hive.metastore.HiveMetaStoreClient - apache-spark

Question

After quite some time, can't figure out how to identify root cause of below error when running spark-sql binary:
15/12/08 14:48:41 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Exception in thread "main" 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.thriftserver.SparkSQLCLIDriver$.main(SparkSQLCLIDriver.scala:109)
at org.apache.spark.sql.hive.thriftserver.SparkSQLCLIDriver.main(SparkSQLCLIDriver.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:665)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:170)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:193)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:112)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
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:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
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:73)
at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:133)
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.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
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

Answer 1

You are missing datanucleus-api-jdo.jar in your class path. This jar is used by hive. Try to figure out which version of this jar you need (probably latest will do). You can download it then from here: http://repo1.maven.org/maven2/org/datanucleus/datanucleus-api-jdo/
And add it to hive permanently by adding this to your .hiverc file:
add jar datanucleus-api-jdo.jar

Answer 2

For spark versions > 2.0, you can approach below solutions:
Make sure the $HIVE_HOME/conf/hive-site.xml configuration which is pointing to complete path of metastore.
javax.jdo.option.ConnectionURL
jdbc:derby:;databaseName=/home/hive/metastore_db;create=true
JDBC connect string for a JDBC metastore
Place the hive-site.xml file in $SPARK_HOME/confto point SparkR to the same metastore as Hive Hope this solves your issue.