Piotr Kołaczkowski created SPARK-27018:
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Summary: 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: 2.4.0, 2.2.2
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
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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