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Commit 713e4f44 authored by navis.ryu's avatar navis.ryu Committed by Reynold Xin
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[SPARK-10679] [CORE] javax.jdo.JDOFatalUserException in executor 

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}

Author: navis.ryu <navis@apache.org>

Closes #8804 from navis/SPARK-10679.
parent c14aee4d
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sql/hive/src/main/scala/org/apache/spark/sql/hive/TableReader.scala
+ 28
− 3
View file @ 713e4f44
......@@ -17,12 +17,14 @@
package org.apache.spark.sql.hive
import java.util
import org.apache.hadoop.fs.{Path, PathFilter}
import org.apache.hadoop.hive.conf.HiveConf
import org.apache.hadoop.hive.metastore.api.hive_metastoreConstants._
import org.apache.hadoop.hive.ql.exec.Utilities
import org.apache.hadoop.hive.ql.metadata.{Partition => HivePartition, Table => HiveTable}
import org.apache.hadoop.hive.ql.plan.{PlanUtils, TableDesc}
import org.apache.hadoop.hive.ql.metadata.{Partition => HivePartition, Table => HiveTable, Hive, HiveUtils, HiveStorageHandler}
import org.apache.hadoop.hive.ql.plan.TableDesc
import org.apache.hadoop.hive.serde2.Deserializer
import org.apache.hadoop.hive.serde2.objectinspector.primitive._
import org.apache.hadoop.hive.serde2.objectinspector.{ObjectInspectorConverters, StructObjectInspector}
......@@ -287,6 +289,29 @@ class HadoopTableReader(
}
}
private[hive] object HiveTableUtil {
// copied from PlanUtils.configureJobPropertiesForStorageHandler(tableDesc)
// that calls Hive.get() which tries to access metastore, but it's not valid in runtime
// it would be fixed in next version of hive but till then, we should use this instead
def configureJobPropertiesForStorageHandler(
tableDesc: TableDesc, jobConf: JobConf, input: Boolean) {
val property = tableDesc.getProperties.getProperty(META_TABLE_STORAGE)
val storageHandler = HiveUtils.getStorageHandler(jobConf, property)
if (storageHandler != null) {
val jobProperties = new util.LinkedHashMap[String, String]
if (input) {
storageHandler.configureInputJobProperties(tableDesc, jobProperties)
} else {
storageHandler.configureOutputJobProperties(tableDesc, jobProperties)
}
if (!jobProperties.isEmpty) {
tableDesc.setJobProperties(jobProperties)
}
}
}
}
private[hive] object HadoopTableReader extends HiveInspectors with Logging {
/**
* Curried. After given an argument for 'path', the resulting JobConf => Unit closure is used to
......@@ -295,7 +320,7 @@ private[hive] object HadoopTableReader extends HiveInspectors with Logging {
def initializeLocalJobConfFunc(path: String, tableDesc: TableDesc)(jobConf: JobConf) {
FileInputFormat.setInputPaths(jobConf, Seq[Path](new Path(path)): _*)
if (tableDesc != null) {
PlanUtils.configureInputJobPropertiesForStorageHandler(tableDesc)
HiveTableUtil.configureJobPropertiesForStorageHandler(tableDesc, jobConf, true)
Utilities.copyTableJobPropertiesToConf(tableDesc, jobConf)
}
val bufferSize = System.getProperty("spark.buffer.size", "65536")
......
sql/hive/src/main/scala/org/apache/spark/sql/hive/hiveWriterContainers.scala
+ 2
− 2
View file @ 713e4f44
......@@ -26,7 +26,7 @@ import org.apache.hadoop.fs.Path
import org.apache.hadoop.hive.conf.HiveConf.ConfVars
import org.apache.hadoop.hive.ql.exec.{FileSinkOperator, Utilities}
import org.apache.hadoop.hive.ql.io.{HiveFileFormatUtils, HiveOutputFormat}
import org.apache.hadoop.hive.ql.plan.{PlanUtils, TableDesc}
import org.apache.hadoop.hive.ql.plan.TableDesc
import org.apache.hadoop.io.Writable
import org.apache.hadoop.mapred._
import org.apache.hadoop.hive.common.FileUtils
......@@ -55,7 +55,7 @@ private[hive] class SparkHiveWriterContainer(
// Add table properties from storage handler to jobConf, so any custom storage
// handler settings can be set to jobConf
if (tableDesc != null) {
PlanUtils.configureOutputJobPropertiesForStorageHandler(tableDesc)
HiveTableUtil.configureJobPropertiesForStorageHandler(tableDesc, jobConf, false)
Utilities.copyTableJobPropertiesToConf(tableDesc, jobConf)
}
protected val conf = new SerializableJobConf(jobConf)
......
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