java.lang.OutOfMemoryError: GC overhead limit exceeded

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    Root Cause Analysis

    1. java.lang.OutOfMemoryError

      GC overhead limit exceeded

      at scala.collection.immutable.HashMap$HashMap1.get0()
    2. Scala
      AbstractMap.apply
      1. scala.collection.immutable.HashMap$HashMap1.get0(HashMap.scala:183)
      2. scala.collection.immutable.HashMap$HashTrieMap.get0(HashMap.scala:314)
      3. scala.collection.immutable.HashMap$HashTrieMap.get0(HashMap.scala:314)
      4. scala.collection.immutable.HashMap.get(HashMap.scala:51)
      5. scala.collection.MapLike$class.apply(MapLike.scala:140)
      6. scala.collection.AbstractMap.apply(Map.scala:58)
      6 frames
    3. org.bdgenomics.adam
      GenomicPositionPartitioner.getPartition
      1. org.bdgenomics.adam.rdd.GenomicPositionPartitioner.getPart$1(GenomicPartitioners.scala:68)
      2. org.bdgenomics.adam.rdd.GenomicPositionPartitioner.getPartition(GenomicPartitioners.scala:84)
      2 frames
    4. Spark
      ExternalSorter$$anonfun$insertAll$1.apply
      1. org.apache.spark.util.collection.ExternalSorter.org$apache$spark$util$collection$ExternalSorter$$getPartition(ExternalSorter.scala:113)
      2. org.apache.spark.util.collection.ExternalSorter$$anonfun$insertAll$1.apply(ExternalSorter.scala:212)
      3. org.apache.spark.util.collection.ExternalSorter$$anonfun$insertAll$1.apply(ExternalSorter.scala:211)
      3 frames
    5. Scala
      Iterator$$anon$11.next
      1. scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
      1 frame
    6. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.util.collection.ExternalSorter.spillToPartitionFiles(ExternalSorter.scala:366)
      2. org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:211)
      3. org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:63)
      4. org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:68)
      5. org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
      6. org.apache.spark.scheduler.Task.run(Task.scala:56)
      7. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:198)
      7 frames
    7. Java RT
      Thread.run
      1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
      2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
      3. java.lang.Thread.run(Thread.java:722)
      3 frames