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Posted to issues@spark.apache.org by "Virgil Palanciuc (JIRA)" <ji...@apache.org> on 2015/08/19 13:59:45 UTC
[jira] [Created] (SPARK-10109) NPE when saving Parquet To HDFS
Virgil Palanciuc created SPARK-10109:
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Summary: NPE when saving Parquet To HDFS
Key: SPARK-10109
URL: https://issues.apache.org/jira/browse/SPARK-10109
Project: Spark
Issue Type: Bug
Components: SQL
Affects Versions: 1.4.1
Environment: Sparc-ec2, standalone cluster on amazon
Reporter: Virgil Palanciuc
Very simple code, trying to save a dataframe
I get this in the driver
{quote}
15/08/19 11:21:41 INFO TaskSetManager: Lost task 9.2 in stage 217.0 (TID 4748) on executor 172.xx.xx.xx: java.lang.NullPointerException (null)
and (not for that task):
15/08/19 11:21:46 WARN TaskSetManager: Lost task 5.0 in stage 543.0 (TID 5607, 172.yy.yy.yy): java.lang.NullPointerException
at parquet.hadoop.InternalParquetRecordWriter.flushRowGroupToStore(InternalParquetRecordWriter.java:146)
at parquet.hadoop.InternalParquetRecordWriter.close(InternalParquetRecordWriter.java:112)
at parquet.hadoop.ParquetRecordWriter.close(ParquetRecordWriter.java:73)
at org.apache.spark.sql.parquet.ParquetOutputWriter.close(newParquet.scala:88)
at org.apache.spark.sql.sources.DynamicPartitionWriterContainer$$anonfun$clearOutputWriters$1.apply(commands.scala:536)
at org.apache.spark.sql.sources.DynamicPartitionWriterContainer$$anonfun$clearOutputWriters$1.apply(commands.scala:536)
at scala.collection.mutable.HashMap$$anon$2$$anonfun$foreach$3.apply(HashMap.scala:107)
at scala.collection.mutable.HashMap$$anon$2$$anonfun$foreach$3.apply(HashMap.scala:107)
at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:226)
at scala.collection.mutable.HashMap.foreachEntry(HashMap.scala:39)
at scala.collection.mutable.HashMap$$anon$2.foreach(HashMap.scala:107)
at org.apache.spark.sql.sources.DynamicPartitionWriterContainer.clearOutputWriters(commands.scala:536)
at org.apache.spark.sql.sources.DynamicPartitionWriterContainer.abortTask(commands.scala:552)
at org.apache.spark.sql.sources.InsertIntoHadoopFsRelation.org$apache$spark$sql$sources$InsertIntoHadoopFsRelation$$writeRows$2(commands.scala:269)
at org.apache.spark.sql.sources.InsertIntoHadoopFsRelation$$anonfun$insertWithDynamicPartitions$3.apply(commands.scala:229)
at org.apache.spark.sql.sources.InsertIntoHadoopFsRelation$$anonfun$insertWithDynamicPartitions$3.apply(commands.scala:229)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:63)
at org.apache.spark.scheduler.Task.run(Task.scala:70)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
{quote}
I get this in the executor log:
{quote}
15/08/19 11:21:41 WARN DFSClient: DataStreamer Exception
org.apache.hadoop.ipc.RemoteException(org.apache.hadoop.hdfs.server.namenode.LeaseExpiredException): No lease on /gglogs/2015-07-27/_temporary/_attempt_201508191119_0217_m_000009_2/dpid=18432/pid=1109/part-r-00009-46ac3a79-a95c-4d9c-a2f1-b3ee76f6a46c.snappy.parquet File does not exist. Holder DFSClient_NONMAPREDUCE_1730998114_63 does not have any open files.
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.checkLease(FSNamesystem.java:2396)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.checkLease(FSNamesystem.java:2387)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:2183)
at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.addBlock(NameNodeRpcServer.java:481)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.addBlock(ClientNamenodeProtocolServerSideTranslatorPB.java:297)
at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44080)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1695)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1691)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:415)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1408)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1689)
at org.apache.hadoop.ipc.Client.call(Client.java:1225)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.invoke(ProtobufRpcEngine.java:202)
at com.sun.proxy.$Proxy14.addBlock(Unknown Source)
at sun.reflect.GeneratedMethodAccessor33.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:164)
at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:83)
at com.sun.proxy.$Proxy14.addBlock(Unknown Source)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.addBlock(ClientNamenodeProtocolTranslatorPB.java:290)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.locateFollowingBlock(DFSOutputStream.java:1150)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.nextBlockOutputStream(DFSOutputStream.java:1003)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.run(DFSOutputStream.java:463)
15/08/19 11:21:41 ERROR InsertIntoHadoopFsRelation: Aborting task.
java.lang.RuntimeException: Failed to commit task
at org.apache.spark.sql.sources.DynamicPartitionWriterContainer.commitTask(commands.scala:546)
at org.apache.spark.sql.sources.InsertIntoHadoopFsRelation.org$apache$spark$sql$sources$InsertIntoHadoopFsRelation$$writeRows$2(commands.scala:266)
at org.apache.spark.sql.sources.InsertIntoHadoopFsRelation$$anonfun$insertWithDynamicPartitions$3.apply(commands.scala:229)
at org.apache.spark.sql.sources.InsertIntoHadoopFsRelation$$anonfun$insertWithDynamicPartitions$3.apply(commands.scala:229)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:63)
at org.apache.spark.scheduler.Task.run(Task.scala:70)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
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)
Caused by: org.apache.hadoop.ipc.RemoteException(org.apache.hadoop.hdfs.server.namenode.LeaseExpiredException): No lease on /gglogs/2015-07-27/_temporary/_attempt_201508191119_0217_m_000009_2/dpid=18432/pid=1109/part-r-00009-46ac3a79-a95c-4d9c-a2f1-b3ee76f6a46c.snappy.parquet File does not exist. Holder DFSClient_NONMAPREDUCE_1730998114_63 does not have any open files.
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.checkLease(FSNamesystem.java:2396)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.checkLease(FSNamesystem.java:2387)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:2183)
at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.addBlock(NameNodeRpcServer.java:481)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.addBlock(ClientNamenodeProtocolServerSideTranslatorPB.java:297)
at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44080)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1695)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1691)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:415)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1408)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1689)
at org.apache.hadoop.ipc.Client.call(Client.java:1225)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.invoke(ProtobufRpcEngine.java:202)
at com.sun.proxy.$Proxy14.addBlock(Unknown Source)
at sun.reflect.GeneratedMethodAccessor33.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:164)
at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:83)
at com.sun.proxy.$Proxy14.addBlock(Unknown Source)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.addBlock(ClientNamenodeProtocolTranslatorPB.java:290)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.locateFollowingBlock(DFSOutputStream.java:1150)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.nextBlockOutputStream(DFSOutputStream.java:1003)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.run(DFSOutputStream.java:463)
15/08/19 11:21:41 ERROR DynamicPartitionWriterContainer: Task attempt attempt_201508191119_0217_m_000009_2 aborted.
15/08/19 11:21:41 ERROR Executor: Exception in task 9.2 in stage 217.0 (TID 4748)
java.lang.NullPointerException
at parquet.hadoop.InternalParquetRecordWriter.flushRowGroupToStore(InternalParquetRecordWriter.java:146)
at parquet.hadoop.InternalParquetRecordWriter.close(InternalParquetRecordWriter.java:112)
at parquet.hadoop.ParquetRecordWriter.close(ParquetRecordWriter.java:73)
at org.apache.spark.sql.parquet.ParquetOutputWriter.close(newParquet.scala:88)
at org.apache.spark.sql.sources.DynamicPartitionWriterContainer$$anonfun$clearOutputWriters$1.apply(commands.scala:536)
at org.apache.spark.sql.sources.DynamicPartitionWriterContainer$$anonfun$clearOutputWriters$1.apply(commands.scala:536)
at scala.collection.mutable.HashMap$$anon$2$$anonfun$foreach$3.apply(HashMap.scala:107)
at scala.collection.mutable.HashMap$$anon$2$$anonfun$foreach$3.apply(HashMap.scala:107)
at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:226)
at scala.collection.mutable.HashMap.foreachEntry(HashMap.scala:39)
at scala.collection.mutable.HashMap$$anon$2.foreach(HashMap.scala:107)
at org.apache.spark.sql.sources.DynamicPartitionWriterContainer.clearOutputWriters(commands.scala:536)
at org.apache.spark.sql.sources.DynamicPartitionWriterContainer.abortTask(commands.scala:552)
at org.apache.spark.sql.sources.InsertIntoHadoopFsRelation.org$apache$spark$sql$sources$InsertIntoHadoopFsRelation$$writeRows$2(commands.scala:269)
at org.apache.spark.sql.sources.InsertIntoHadoopFsRelation$$anonfun$insertWithDynamicPartitions$3.apply(commands.scala:229)
at org.apache.spark.sql.sources.InsertIntoHadoopFsRelation$$anonfun$insertWithDynamicPartitions$3.apply(commands.scala:229)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:63)
at org.apache.spark.scheduler.Task.run(Task.scala:70)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
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)
{quote}
this is the code that I'm using:
{quote}
val ppRDD=
sparkContext
.sequenceFile[Array[Byte], String](inputPath)
.values
.repartition(numPartitions)
.filter( <criteria>)
.flatMap(line => parseGGLogLine(<params; including 2 broadcasted variables, one a "Set" and one a "Map">)
if(ppRDD.isEmpty())
logInfo(s"<message>")
else
ppRDD.toDF().write
.partitionBy("dpid","pid")
.mode( SaveMode.Append )
.parquet(outputPath)
{quote}
possibly relevant configuration:
{quote}
"spark.sql.parquet" {
cacheMetadata = "true",
compression.codec = "snappy"
}
"spark.serializer" = "org.apache.spark.serializer.KryoSerializer",
{quote}
I didn't modify the speculation setting, so I'm assuming it's disabled.
Input path is s3n://<path>
Output path is hdfs:///<path> (i.e. ephemeral hdfs)
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