[SPARK-18181] Huge managed memory leak (2.7G) when running reduceByKey

• Type: Bug
• Status: Closed
• Priority: Major
• Resolution: Information Provided
• Affects Version/s: 1.6.2
• Component/s: Spark Core
• Assignee: Unassigned
• Reporter: Barry Becker
• Created: 31/Oct/16 18:40
• Updated: 10/Jan/17 20:56
• Resolved: 10/Jan/17 20:56

Description

For a while now, I have noticed messages like
16/10/31 09:44:25 ERROR Executor: Managed memory leak detected; size = 5251642 bytes, TID = 64204
when running jobs with spark 1.6.2.
I have seen others post bugs on this, but they are all marked fixed in earlier versions. I am certain that the issue still exists in 1.6.2.

In the following case, I can even get it to leak 2.7G all at once.
The message is:
16/10/31 11:12:47 ERROR Executor: Managed memory leak detected; size = 2724723111 bytes, TID = 18

The code snippet causing it is:

val nonZeros: RDD[((Int, Float), Array[Long])] =
      featureValues.map(y => (y._1._1 + "," + y._1._2, y._2)).reduceByKey { case (v1, v2) =>
      (v1, v2).zipped.map(_ + _)
    }.map(y => {
      val s = y._1.split(",")
      ((s(0).toInt, s(1).toFloat), y._2)
    })

and the stack trace is:

16/10/31 11:12:47 ERROR Executor: Exception in task 0.0 in stage 11.0 (TID 18)
java.lang.OutOfMemoryError: Java heap space
	at scala.collection.mutable.ArrayBuilder$ofLong.mkArray(ArrayBuilder.scala:388)
	at scala.collection.mutable.ArrayBuilder$ofLong.resize(ArrayBuilder.scala:394)
	at scala.collection.mutable.ArrayBuilder$ofLong.sizeHint(ArrayBuilder.scala:399)
	at scala.collection.mutable.Builder$class.sizeHint(Builder.scala:69)
	at scala.collection.mutable.ArrayBuilder.sizeHint(ArrayBuilder.scala:22)
	at scala.runtime.Tuple2Zipped$.map$extension(Tuple2Zipped.scala:41)
	at org.apache.spark.mllib.feature.MDLPDiscretizer$$anonfun$11.apply(MDLPDiscretizer.scala:151)
	at org.apache.spark.mllib.feature.MDLPDiscretizer$$anonfun$11.apply(MDLPDiscretizer.scala:150)
	at org.apache.spark.util.collection.ExternalSorter$$anonfun$5.apply(ExternalSorter.scala:187)
	at org.apache.spark.util.collection.ExternalSorter$$anonfun$5.apply(ExternalSorter.scala:186)
	at org.apache.spark.util.collection.AppendOnlyMap.changeValue(AppendOnlyMap.scala:144)
	at org.apache.spark.util.collection.SizeTrackingAppendOnlyMap.changeValue(SizeTrackingAppendOnlyMap.scala:32)
	at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:192)
	at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:64)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
	at org.apache.spark.scheduler.Task.run(Task.scala:89)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:227)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
16/10/31 11:12:47 ERROR SparkUncaughtExceptionHandler: Uncaught exception in thread Thread[Executor task launch worker-0,5,main]
java.lang.OutOfMemoryError: Java heap space
	at scala.collection.mutable.ArrayBuilder$ofLong.mkArray(ArrayBuilder.scala:388)
	at scala.collection.mutable.ArrayBuilder$ofLong.resize(ArrayBuilder.scala:394)
	at scala.collection.mutable.ArrayBuilder$ofLong.sizeHint(ArrayBuilder.scala:399)
	at scala.collection.mutable.Builder$class.sizeHint(Builder.scala:69)
	at scala.collection.mutable.ArrayBuilder.sizeHint(ArrayBuilder.scala:22)
	at scala.runtime.Tuple2Zipped$.map$extension(Tuple2Zipped.scala:41)
	at org.apache.spark.mllib.feature.MDLPDiscretizer$$anonfun$11.apply(MDLPDiscretizer.scala:151)
	at org.apache.spark.mllib.feature.MDLPDiscretizer$$anonfun$11.apply(MDLPDiscretizer.scala:150)
	at org.apache.spark.util.collection.ExternalSorter$$anonfun$5.apply(ExternalSorter.scala:187)
	at org.apache.spark.util.collection.ExternalSorter$$anonfun$5.apply(ExternalSorter.scala:186)
	at org.apache.spark.util.collection.AppendOnlyMap.changeValue(AppendOnlyMap.scala:144)
	at org.apache.spark.util.collection.SizeTrackingAppendOnlyMap.changeValue(SizeTrackingAppendOnlyMap.scala:32)
	at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:192)
	at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:64)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
	at org.apache.spark.scheduler.Task.run(Task.scala:89)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:227)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
16/10/31 11:12:47 WARN TaskSetManager: Lost task 0.0 in stage 11.0 (TID 18, localhost): java.lang.OutOfMemoryError: Java heap space
	at scala.collection.mutable.ArrayBuilder$ofLong.mkArray(ArrayBuilder.scala:388)
	at scala.collection.mutable.ArrayBuilder$ofLong.resize(ArrayBuilder.scala:394)
	at scala.collection.mutable.ArrayBuilder$ofLong.sizeHint(ArrayBuilder.scala:399)
	at scala.collection.mutable.Builder$class.sizeHint(Builder.scala:69)
	at scala.collection.mutable.ArrayBuilder.sizeHint(ArrayBuilder.scala:22)
	at scala.runtime.Tuple2Zipped$.map$extension(Tuple2Zipped.scala:41)
	at org.apache.spark.mllib.feature.MDLPDiscretizer$$anonfun$11.apply(MDLPDiscretizer.scala:151)
	at org.apache.spark.mllib.feature.MDLPDiscretizer$$anonfun$11.apply(MDLPDiscretizer.scala:150)
	at org.apache.spark.util.collection.ExternalSorter$$anonfun$5.apply(ExternalSorter.scala:187)
	at org.apache.spark.util.collection.ExternalSorter$$anonfun$5.apply(ExternalSorter.scala:186)
	at org.apache.spark.util.collection.AppendOnlyMap.changeValue(AppendOnlyMap.scala:144)
	at org.apache.spark.util.collection.SizeTrackingAppendOnlyMap.changeValue(SizeTrackingAppendOnlyMap.scala:32)
	at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:192)
	at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:64)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
	at org.apache.spark.scheduler.Task.run(Task.scala:89)

If you want to run the example, you can checkout this branch of the MDLP project
https://github.com/barrybecker4/spark-MDLP-discretization/tree/ISSUE-14-performance
and going to commit cd9c797 and running the MDLPDiscretizerHugeSuite.

Issue Links

• is related to: SPARK-14363 Executor OOM due to a memory leak in Sorter