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Posted to issues@spark.apache.org by "zhengruifeng (JIRA)" <ji...@apache.org> on 2019/06/10 10:12:00 UTC
[jira] [Commented] (SPARK-27018) Checkpointed RDD deleted
prematurely when using GBTClassifier
[ https://issues.apache.org/jira/browse/SPARK-27018?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16859889#comment-16859889 ]
zhengruifeng commented on SPARK-27018:
--------------------------------------
[~pkolaczk] With the codes you provided, I reproduced this failure.
moreover, I doubt that this bug may also affect the computation on distributed env.
I also encountered a similar case on a cluster, I will look into this.
{code:java}
java.io.FileNotFoundException: File does not exist: /tmp/sparkGBM/application_1551338088092_2518369/checkpoints/edbd13db-b61f-445a-8703-691acd595d62/rdd-46484/_partitioner
at org.apache.hadoop.hdfs.server.namenode.INodeFile.valueOf(INodeFile.java:71)
at org.apache.hadoop.hdfs.server.namenode.INodeFile.valueOf(INodeFile.java:61)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocationsInt(FSNamesystem.java:1929)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocations(FSNamesystem.java:1900)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocations(FSNamesystem.java:1803)
at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.getBlockLocations(NameNodeRpcServer.java:604)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.getBlockLocations(ClientNamenodeProtocolServerSideTranslatorPB.java:388)
at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:624)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:969)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2094)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2090)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/javax.security.auth.Subject.doAs(Subject.java:423)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1803)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:2090)
at sun.reflect.GeneratedConstructorAccessor79.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at org.apache.hadoop.ipc.RemoteException.instantiateException(RemoteException.java:106)
at org.apache.hadoop.ipc.RemoteException.unwrapRemoteException(RemoteException.java:73)
at org.apache.hadoop.hdfs.DFSClient.callGetBlockLocations(DFSClient.java:1268)
at org.apache.hadoop.hdfs.DFSClient.getLocatedBlocks(DFSClient.java:1253)
at org.apache.hadoop.hdfs.DFSClient.getLocatedBlocks(DFSClient.java:1241)
at org.apache.hadoop.hdfs.DFSInputStream.fetchLocatedBlocksAndGetLastBlockLength(DFSInputStream.java:303)
at org.apache.hadoop.hdfs.DFSInputStream.openInfo(DFSInputStream.java:269)
at org.apache.hadoop.hdfs.DFSInputStream.<init>(DFSInputStream.java:261)
at org.apache.hadoop.hdfs.DFSClient.open(DFSClient.java:1566)
at org.apache.hadoop.hdfs.DistributedFileSystem$3.doCall(DistributedFileSystem.java:303)
at org.apache.hadoop.hdfs.DistributedFileSystem$3.doCall(DistributedFileSystem.java:299)
at org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81)
at org.apache.hadoop.hdfs.DistributedFileSystem.open(DistributedFileSystem.java:299)
at org.apache.spark.rdd.ReliableCheckpointRDD$.org$apache$spark$rdd$ReliableCheckpointRDD$$readCheckpointedPartitionerFile(ReliableCheckpointRDD.scala:255)
at org.apache.spark.rdd.ReliableCheckpointRDD$$anonfun$3.apply(ReliableCheckpointRDD.scala:59)
at org.apache.spark.rdd.ReliableCheckpointRDD$$anonfun$3.apply(ReliableCheckpointRDD.scala:59)
at scala.Option.orElse(Option.scala:289)
at org.apache.spark.rdd.ReliableCheckpointRDD.<init>(ReliableCheckpointRDD.scala:58)
at org.apache.spark.rdd.ReliableCheckpointRDD$.writeRDDToCheckpointDirectory(ReliableCheckpointRDD.scala:151)
at org.apache.spark.rdd.ReliableRDDCheckpointData.doCheckpoint(ReliableRDDCheckpointData.scala:58)
at org.apache.spark.rdd.RDDCheckpointData.checkpoint(RDDCheckpointData.scala:75)
at org.apache.spark.rdd.RDD$$anonfun$doCheckpoint$1.apply$mcV$sp(RDD.scala:1734)
at org.apache.spark.rdd.RDD$$anonfun$doCheckpoint$1.apply(RDD.scala:1724)
at org.apache.spark.rdd.RDD$$anonfun$doCheckpoint$1.apply(RDD.scala:1724){code}
> Checkpointed RDD deleted prematurely when using GBTClassifier
> -------------------------------------------------------------
>
> Key: SPARK-27018
> URL: https://issues.apache.org/jira/browse/SPARK-27018
> Project: Spark
> Issue Type: Bug
> Components: ML
> Affects Versions: 2.2.2, 2.2.3, 2.3.3, 2.4.0
> Environment: OS: Ubuntu Linux 18.10
> Java: java version "1.8.0_201"
> Java(TM) SE Runtime Environment (build 1.8.0_201-b09)
> Java HotSpot(TM) 64-Bit Server VM (build 25.201-b09, mixed mode)
> Reproducible with a single-node Spark in standalone mode.
> Reproducible with Zepellin or Spark shell.
>
> Reporter: Piotr Kołaczkowski
> Priority: Major
> Attachments: Fix_check_if_the_next_checkpoint_exists_before_deleting_the_old_one.patch
>
>
> Steps to reproduce:
> {noformat}
> import org.apache.spark.ml.linalg.Vectors
> import org.apache.spark.ml.classification.GBTClassifier
> case class Row(features: org.apache.spark.ml.linalg.Vector, label: Int)
> sc.setCheckpointDir("/checkpoints")
> val trainingData = sc.parallelize(1 to 2426874, 256).map(x => Row(Vectors.dense(x, x + 1, x * 2 % 10), if (x % 5 == 0) 1 else 0)).toDF
> val classifier = new GBTClassifier()
> .setLabelCol("label")
> .setFeaturesCol("features")
> .setProbabilityCol("probability")
> .setMaxIter(100)
> .setMaxDepth(10)
> .setCheckpointInterval(2)
> classifier.fit(trainingData){noformat}
>
> The last line fails with:
> {noformat}
> org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 56.0 failed 10 times, most recent failure: Lost task 0.9 in stage 56.0 (TID 12058, 127.0.0.1, executor 0): java.io.FileNotFoundException: /checkpoints/191c9209-0955-440f-8c11-f042bdf7f804/rdd-51
> at com.datastax.bdp.fs.hadoop.DseFileSystem$$anonfun$1.applyOrElse(DseFileSystem.scala:63)
> at com.datastax.bdp.fs.hadoop.DseFileSystem$$anonfun$1.applyOrElse(DseFileSystem.scala:61)
> at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
> at com.datastax.bdp.fs.hadoop.DseFileSystem.com$datastax$bdp$fs$hadoop$DseFileSystem$$translateToHadoopExceptions(DseFileSystem.scala:70)
> at com.datastax.bdp.fs.hadoop.DseFileSystem$$anonfun$6.apply(DseFileSystem.scala:264)
> at com.datastax.bdp.fs.hadoop.DseFileSystem$$anonfun$6.apply(DseFileSystem.scala:264)
> at com.datastax.bdp.fs.hadoop.DseFsInputStream.input(DseFsInputStream.scala:31)
> at com.datastax.bdp.fs.hadoop.DseFsInputStream.openUnderlyingDataSource(DseFsInputStream.scala:39)
> at com.datastax.bdp.fs.hadoop.DseFileSystem.open(DseFileSystem.scala:269)
> at org.apache.spark.rdd.ReliableCheckpointRDD$.readCheckpointFile(ReliableCheckpointRDD.scala:292)
> at org.apache.spark.rdd.ReliableCheckpointRDD.compute(ReliableCheckpointRDD.scala:100)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:322)
> at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:337)
> at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:335)
> at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165)
> at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156)
> at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091)
> at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156)
> at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882)
> at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:286)
> at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
> at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
> at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:337)
> at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:335)
> at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165)
> at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156)
> at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091)
> at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156)
> at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882)
> at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:286)
> at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
> at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
> at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:337)
> at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:335)
> at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165)
> at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156)
> at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091)
> at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156)
> at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882)
> at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:286)
> at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
> at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
> at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
> at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
> at org.apache.spark.scheduler.Task.run(Task.scala:121)
> at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:402)
> at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:408)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> at java.lang.Thread.run(Thread.java:748){noformat}
> The problem happens as well when checkpointing directory is placed on the local file system, on a single-node setup.
> Debugging at the FS level showed that the driver requests to recursively delete the checkpointed rdd-51 soon before the exception gets thrown by the task.
>
>
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