java.lang.OutOfMemoryError: Java heap space

GitHub | car2008 | 2 months ago
  1. 0

    GitHub comment 572#249369489

    GitHub | 2 months ago | car2008
    java.lang.OutOfMemoryError: Java heap space
  2. 0

    Re: Spark Application Master on Yarn client mode - Virtual memory limit

    spark-user | 10 months ago | Olivier Girardot
    java.lang.OutOfMemoryError: Java heap space
  3. 0

    Re: Spark Application Master on Yarn client mode - Virtual memory limit

    spark-user | 10 months ago | Olivier Girardot
    java.lang.OutOfMemoryError: Java heap space
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  5. 0

    Re: Spark Application Master on Yarn client mode - Virtual memory limit

    spark-user | 10 months ago | Olivier Girardot
    java.lang.OutOfMemoryError: Java heap space
  6. 0

    Re: Spark Application Master on Yarn client mode - Virtual memory limit

    incubator-spark-user | 10 months ago | Olivier Girardot
    java.lang.OutOfMemoryError: Java heap space

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    Root Cause Analysis

    1. java.lang.OutOfMemoryError

      Java heap space

      at java.util.IdentityHashMap.resize()
    2. Java RT
      IdentityHashMap.put
      1. java.util.IdentityHashMap.resize(IdentityHashMap.java:471)
      2. java.util.IdentityHashMap.put(IdentityHashMap.java:440)
      2 frames
    3. Spark
      SizeEstimator$$anonfun$visitSingleObject$1.apply
      1. org.apache.spark.util.SizeEstimator$SearchState.enqueue(SizeEstimator.scala:176)
      2. org.apache.spark.util.SizeEstimator$$anonfun$visitSingleObject$1.apply(SizeEstimator.scala:224)
      3. org.apache.spark.util.SizeEstimator$$anonfun$visitSingleObject$1.apply(SizeEstimator.scala:223)
      3 frames
    4. Scala
      List.foreach
      1. scala.collection.immutable.List.foreach(List.scala:318)
      1 frame
    5. Spark
      SparkContext.broadcast
      1. org.apache.spark.util.SizeEstimator$.visitSingleObject(SizeEstimator.scala:223)
      2. org.apache.spark.util.SizeEstimator$.org$apache$spark$util$SizeEstimator$$estimate(SizeEstimator.scala:203)
      3. org.apache.spark.util.SizeEstimator$.estimate(SizeEstimator.scala:70)
      4. org.apache.spark.util.collection.SizeTracker$class.takeSample(SizeTracker.scala:78)
      5. org.apache.spark.util.collection.SizeTracker$class.afterUpdate(SizeTracker.scala:70)
      6. org.apache.spark.util.collection.SizeTrackingVector.$plus$eq(SizeTrackingVector.scala:31)
      7. org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:285)
      8. org.apache.spark.storage.MemoryStore.putIterator(MemoryStore.scala:169)
      9. org.apache.spark.storage.MemoryStore.putIterator(MemoryStore.scala:147)
      10. org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:798)
      11. org.apache.spark.storage.BlockManager.putIterator(BlockManager.scala:645)
      12. org.apache.spark.storage.BlockManager.putSingle(BlockManager.scala:1003)
      13. org.apache.spark.broadcast.TorrentBroadcast.writeBlocks(TorrentBroadcast.scala:99)
      14. org.apache.spark.broadcast.TorrentBroadcast.<init>(TorrentBroadcast.scala:85)
      15. org.apache.spark.broadcast.TorrentBroadcastFactory.newBroadcast(TorrentBroadcastFactory.scala:34)
      16. org.apache.spark.broadcast.BroadcastManager.newBroadcast(BroadcastManager.scala:63)
      17. org.apache.spark.SparkContext.broadcast(SparkContext.scala:1326)
      17 frames
    6. org.hammerlab.guacamole
      Main$.main
      1. org.hammerlab.guacamole.readsets.rdd.PartitionedRegions$.compute(PartitionedRegions.scala:199)
      2. org.hammerlab.guacamole.readsets.rdd.PartitionedRegions$.apply(PartitionedRegions.scala:184)
      3. org.hammerlab.guacamole.readsets.rdd.PartitionedRegions$.apply(PartitionedRegions.scala:146)
      4. org.hammerlab.guacamole.commands.SomaticJoint$.makeCalls(SomaticJointCaller.scala:166)
      5. org.hammerlab.guacamole.commands.SomaticJoint$Caller$.run(SomaticJointCaller.scala:91)
      6. org.hammerlab.guacamole.commands.SomaticJoint$Caller$.run(SomaticJointCaller.scala:56)
      7. org.hammerlab.guacamole.commands.SparkCommand.run(SparkCommand.scala:12)
      8. org.hammerlab.guacamole.commands.Command.run(Command.scala:27)
      9. org.hammerlab.guacamole.Main$.main(Main.scala:49)
      9 frames