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Posted to issues@spark.apache.org by "Fabian Boehnlein (JIRA)" <ji...@apache.org> on 2016/08/17 11:42:20 UTC
[jira] [Commented] (SPARK-10872) Derby error (XSDB6) when creating
new HiveContext after restarting SparkContext
[ https://issues.apache.org/jira/browse/SPARK-10872?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15424335#comment-15424335 ]
Fabian Boehnlein commented on SPARK-10872:
------------------------------------------
Seeing that exception on 1.6.* and 2.0.0 - can someone confirm to update the affected versions?
Isn't this a problem for every batch job using HiveContext which repeatedly runs in the same file system location?
> Derby error (XSDB6) when creating new HiveContext after restarting SparkContext
> -------------------------------------------------------------------------------
>
> Key: SPARK-10872
> URL: https://issues.apache.org/jira/browse/SPARK-10872
> Project: Spark
> Issue Type: Bug
> Components: PySpark, SQL
> Affects Versions: 1.4.0, 1.4.1, 1.5.0
> Reporter: Dmytro Bielievtsov
>
> Starting from spark 1.4.0 (works well on 1.3.1), the following code fails with "XSDB6: Another instance of Derby may have already booted the database ~/metastore_db":
> {code:python}
> from pyspark import SparkContext, HiveContext
> sc = SparkContext("local[*]", "app1")
> sql = HiveContext(sc)
> sql.createDataFrame([[1]]).collect()
> sc.stop()
> sc = SparkContext("local[*]", "app2")
> sql = HiveContext(sc)
> sql.createDataFrame([[1]]).collect() # Py4J error
> {code}
> This is related to [#SPARK-9539], and I intend to restart spark context several times for isolated jobs to prevent cache cluttering and GC errors.
> Here's a larger part of the full error trace:
> {noformat}
> Failed to start database 'metastore_db' with class loader org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1@13015ec0, see the next exception for details.
> org.datanucleus.exceptions.NucleusDataStoreException: Failed to start database 'metastore_db' with class loader org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1@13015ec0, see the next exception for details.
> at org.datanucleus.store.rdbms.ConnectionFactoryImpl$ManagedConnectionImpl.getConnection(ConnectionFactoryImpl.java:516)
> at org.datanucleus.store.rdbms.RDBMSStoreManager.<init>(RDBMSStoreManager.java:298)
> 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.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:57)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at javax.jdo.JDOHelper$16.run(JDOHelper.java:1965)
> at java.security.AccessController.doPrivileged(Native Method)
> at javax.jdo.JDOHelper.invoke(JDOHelper.java:1960)
> at javax.jdo.JDOHelper.invokeGetPersistenceManagerFactoryOnImplementation(JDOHelper.java:1166)
> at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:808)
> at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:701)
> at org.apache.hadoop.hive.metastore.ObjectStore.getPMF(ObjectStore.java:365)
> at org.apache.hadoop.hive.metastore.ObjectStore.getPersistenceManager(ObjectStore.java:394)
> at org.apache.hadoop.hive.metastore.ObjectStore.initialize(ObjectStore.java:291)
> at org.apache.hadoop.hive.metastore.ObjectStore.setConf(ObjectStore.java:258)
> at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:73)
> at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:133)
> at org.apache.hadoop.hive.metastore.RawStoreProxy.<init>(RawStoreProxy.java:57)
> at org.apache.hadoop.hive.metastore.RawStoreProxy.getProxy(RawStoreProxy.java:66)
> at org.apache.hadoop.hive.metastore.HiveMetaStore$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: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: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:171)
> 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.spark.sql.hive.client.IsolatedClientLoader.liftedTree1$1(IsolatedClientLoader.scala:183)
> at org.apache.spark.sql.hive.client.IsolatedClientLoader.<init>(IsolatedClientLoader.scala:179)
> at org.apache.spark.sql.hive.HiveContext.metadataHive$lzycompute(HiveContext.scala:227)
> at org.apache.spark.sql.hive.HiveContext.metadataHive(HiveContext.scala:186)
> at org.apache.spark.sql.hive.HiveContext.setConf(HiveContext.scala:393)
> at org.apache.spark.sql.hive.HiveContext.defaultOverrides(HiveContext.scala:175)
> at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:178)
> 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 py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:234)
> at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:379)
> at py4j.Gateway.invoke(Gateway.java:214)
> at py4j.commands.ConstructorCommand.invokeConstructor(ConstructorCommand.java:79)
> at py4j.commands.ConstructorCommand.execute(ConstructorCommand.java:68)
> at py4j.GatewayConnection.run(GatewayConnection.java:207)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.sql.SQLException: Failed to start database 'metastore_db' with class loader org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1@13015ec0, see the next exception for details.
> at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
> at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)
> at org.apache.derby.impl.jdbc.Util.seeNextException(Unknown Source)
> at org.apache.derby.impl.jdbc.EmbedConnection.bootDatabase(Unknown Source)
> at org.apache.derby.impl.jdbc.EmbedConnection.<init>(Unknown Source)
> at org.apache.derby.impl.jdbc.EmbedConnection40.<init>(Unknown Source)
> at org.apache.derby.jdbc.Driver40.getNewEmbedConnection(Unknown Source)
> at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
> at org.apache.derby.jdbc.Driver20.connect(Unknown Source)
> at org.apache.derby.jdbc.AutoloadedDriver.connect(Unknown Source)
> at java.sql.DriverManager.getConnection(DriverManager.java:571)
> at java.sql.DriverManager.getConnection(DriverManager.java:187)
> at org.apache.commons.dbcp.DriverManagerConnectionFactory.createConnection(DriverManagerConnectionFactory.java:78)
> at org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
> at org.apache.commons.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:1148)
> at org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:106)
> at org.datanucleus.store.rdbms.ConnectionFactoryImpl$ManagedConnectionImpl.getConnection(ConnectionFactoryImpl.java:501)
> ... 76 more
> Caused by: java.sql.SQLException: Failed to start database 'metastore_db' with class loader org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1@13015ec0, see the next exception for details.
> at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
> at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)
> ... 93 more
> Caused by: java.sql.SQLException: Another instance of Derby may have already booted the database /home/dmytro/work/shared_store/integration/metastore_db.
> at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
> at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)
> at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
> at org.apache.derby.impl.jdbc.Util.generateCsSQLException(Unknown Source)
> ... 90 more
> Caused by: ERROR XSDB6: Another instance of Derby may have already booted the database /home/dmytro/work/shared_store/integration/metastore_db.
> at org.apache.derby.iapi.error.StandardException.newException(Unknown Source)
> at org.apache.derby.impl.store.raw.data.BaseDataFileFactory.privGetJBMSLockOnDB(Unknown Source)
> at org.apache.derby.impl.store.raw.data.BaseDataFileFactory.run(Unknown Source)
> at java.security.AccessController.doPrivileged(Native Method)
> at org.apache.derby.impl.store.raw.data.BaseDataFileFactory.getJBMSLockOnDB(Unknown Source)
> at org.apache.derby.impl.store.raw.data.BaseDataFileFactory.boot(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown Source)
> at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
> at org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
> at org.apache.derby.impl.store.raw.RawStore.boot(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown Source)
> at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
> at org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
> at org.apache.derby.impl.store.access.RAMAccessManager.boot(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown Source)
> at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
> at org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
> at org.apache.derby.impl.db.BasicDatabase.bootStore(Unknown Source)
> at org.apache.derby.impl.db.BasicDatabase.boot(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown Source)
> at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.bootService(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.startProviderService(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.findProviderAndStartService(Unknown Source)
> at org.apache.derby.impl.services.monitor.BaseMonitor.startPersistentService(Unknown Source)
> at org.apache.derby.iapi.services.monitor.Monitor.startPersistentService(Unknown Source)
> ... 90 more
> {noformat}
> Same happens in Scala.
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