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https://issues.apache.org/jira/browse/SPARK-10679?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Reynold Xin resolved SPARK-10679.
---------------------------------
Resolution: Fixed
Fix Version/s: 1.6.0
> javax.jdo.JDOFatalUserException in executor
> -------------------------------------------
>
> Key: SPARK-10679
> URL: https://issues.apache.org/jira/browse/SPARK-10679
> Project: Spark
> Issue Type: Bug
> Components: Spark Core
> Reporter: Navis
> Priority: Minor
> Fix For: 1.6.0
>
>
> HadoopRDD throws exception in executor, something like below.
> {noformat}
> 5/09/17 18:51:21 INFO metastore.HiveMetaStore: 0: Opening raw store with
> implemenation class:org.apache.hadoop.hive.metastore.ObjectStore
> 15/09/17 18:51:21 INFO metastore.ObjectStore: ObjectStore, initialize called
> 15/09/17 18:51:21 WARN metastore.HiveMetaStore: Retrying creating default
> database after error: Class
> org.datanucleus.api.jdo.JDOPersistenceManagerFactory was not found.
> javax.jdo.JDOFatalUserException: Class
> org.datanucleus.api.jdo.JDOPersistenceManagerFactory was not found.
> 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: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.plan.PlanUtils.configureJobPropertiesForStorageHandler(PlanUtils.java:803)
> at
> org.apache.hadoop.hive.ql.plan.PlanUtils.configureInputJobPropertiesForStorageHandler(PlanUtils.java:782)
> at
> org.apache.spark.sql.hive.HadoopTableReader$.initializeLocalJobConfFunc(TableReader.scala:298)
> at
> org.apache.spark.sql.hive.HadoopTableReader$$anonfun$12.apply(TableReader.scala:274)
> at
> org.apache.spark.sql.hive.HadoopTableReader$$anonfun$12.apply(TableReader.scala:274)
> at
> org.apache.spark.rdd.HadoopRDD$$anonfun$getJobConf$6.apply(HadoopRDD.scala:176)
> at
> org.apache.spark.rdd.HadoopRDD$$anonfun$getJobConf$6.apply(HadoopRDD.scala:176)
> at scala.Option.map(Option.scala:145)
> at org.apache.spark.rdd.HadoopRDD.getJobConf(HadoopRDD.scala:176)
> at org.apache.spark.rdd.HadoopRDD$$anon$1.<init>(HadoopRDD.scala:220)
> at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:216)
> at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:101)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
> at
> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
> at
> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
> at org.apache.spark.rdd.UnionRDD.compute(UnionRDD.scala:87)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
> at
> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
> at
> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
> at org.apache.spark.scheduler.Task.run(Task.scala:88)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at java.lang.Thread.run(Thread.java:745)
> {noformat}
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