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From "Cheng, Hao" <hao.ch...@intel.com>
Subject RE: Spark SQL Thrift Server start exception : java.lang.ClassNotFoundException: org.datanucleus.api.jdo.JDOPersistenceManagerFactory
Date Wed, 04 Mar 2015 00:45:44 GMT
Which version / distribution are you using? Please references this blog that Felix C posted
if you’re running on CDH.
http://eradiating.wordpress.com/2015/02/22/getting-hivecontext-to-work-in-cdh/

Or you may also need to download the datanucleus*.jar files try to add the option of “--jars”
while starting the spark shell.

From: Anusha Shamanur [mailto:anushasb11@gmail.com]
Sent: Wednesday, March 4, 2015 5:07 AM
To: Cheng, Hao
Subject: Re: Spark SQL Thrift Server start exception : java.lang.ClassNotFoundException: org.datanucleus.api.jdo.JDOPersistenceManagerFactory

Hi,

I am getting the same error. There is no lib folder in my $SPARK_HOME. But I included these
jars while calling spark-shell.

Now, I get this:

Caused by: org.datanucleus.exceptions.ClassNotResolvedException: Class "org.datanucleus.store.rdbms.RDBMSStoreManager"
was not found in the CLASSPATH. Please check your specification and your CLASSPATH.

               at org.datanucleus.ClassLoaderResolverImpl.classForName(ClassLoaderResolverImpl.java:218)



How do I solve this?

On Mon, Mar 2, 2015 at 11:04 PM, Cheng, Hao <hao.cheng@intel.com<mailto:hao.cheng@intel.com>>
wrote:
Copy those jars into the $SPARK_HOME/lib/

datanucleus-api-jdo-3.2.6.jar
datanucleus-core-3.2.10.jar
datanucleus-rdbms-3.2.9.jar

see https://github.com/apache/spark/blob/master/bin/compute-classpath.sh#L120


-----Original Message-----
From: fanooos [mailto:dev.fanooos@gmail.com<mailto:dev.fanooos@gmail.com>]
Sent: Tuesday, March 3, 2015 2:50 PM
To: user@spark.apache.org<mailto:user@spark.apache.org>
Subject: Spark SQL Thrift Server start exception : java.lang.ClassNotFoundException: org.datanucleus.api.jdo.JDOPersistenceManagerFactory

I have installed a hadoop cluster (version : 2.6.0), apache spark (version :
1.2.1 preBuilt for hadoop 2.4 and later), and hive (version 1.0.0).

When I try to start the spark sql thrift server I am getting the following exception.

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.HiveContext$$anonfun$4.apply(HiveContext.scala:235)
        at
org.apache.spark.sql.hive.HiveContext$$anonfun$4.apply(HiveContext.scala:231)
        at scala.Option.orElse(Option.scala:257)
        at
org.apache.spark.sql.hive.HiveContext.x$3$lzycompute(HiveContext.scala:231)
        at org.apache.spark.sql.hive.HiveContext.x$3(HiveContext.scala:229)
        at
org.apache.spark.sql.hive.HiveContext.hiveconf$lzycompute(HiveContext.scala:229)
        at org.apache.spark.sql.hive.HiveContext.hiveconf(HiveContext.scala:229)
        at org.apache.spark.sql.hive.HiveContext.runHive(HiveContext.scala:292)
        at org.apache.spark.sql.hive.HiveContext.runSqlHive(HiveContext.scala:276)
        at org.apache.spark.sql.hive.HiveContext.setConf(HiveContext.scala:248)
        at org.apache.spark.sql.SQLContext$$anonfun$2.apply(SQLContext.scala:91)
        at org.apache.spark.sql.SQLContext$$anonfun$2.apply(SQLContext.scala:90)
        at
scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
        at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
        at org.apache.spark.sql.SQLContext.<init>(SQLContext.scala:90)
        at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:72)
        at
org.apache.spark.sql.hive.thriftserver.SparkSQLEnv$.init(SparkSQLEnv.scala:51)
        at
org.apache.spark.sql.hive.thriftserver.HiveThriftServer2$.main(HiveThriftServer2.scala:56)
        at
org.apache.spark.sql.hive.thriftserver.HiveThriftServer2.main(HiveThriftServer2.scala)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.spark.deploy.SparkSubmit$.launch(SparkSubmit.scala:358)
        at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:75)
        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)
        ... 26 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)
        ... 31 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)
        ... 36 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:274)
        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)
        ... 55 more

As I understand from the exception, the datanucleus jars is not in the ClassPath so I added
the following line to my .profile

export $SPARK_OPTS="-Djava.library.path=$SPARK_HOME/lib"

but the same exception still thrown and the server does not run.

How can I solve this issue ?



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--
Regards,
Anusha
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