java.lang.OutOfMemoryError: GC overhead limit exceeded

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via Google Groups by Jaeki Hong, 10 months ago
java.lang.OutOfMemoryError: GC overhead limit exceeded
at scala.collection.immutable.HashMap$HashMap1.get0(HashMap.scala:183)
at scala.collection.immutable.HashMap$HashTrieMap.get0(HashMap.scala:314)
at scala.collection.immutable.HashMap$HashTrieMap.get0(HashMap.scala:314)
at scala.collection.immutable.HashMap.get(HashMap.scala:51)
at scala.collection.MapLike$class.apply(MapLike.scala:140)
at scala.collection.AbstractMap.apply(Map.scala:58)
at org.bdgenomics.adam.rdd.GenomicPositionPartitioner.getPart$1(GenomicPartitioners.scala:68)
at org.bdgenomics.adam.rdd.GenomicPositionPartitioner.getPartition(GenomicPartitioners.scala:84)
at org.apache.spark.util.collection.ExternalSorter.org$apache$spark$util$collection$ExternalSorter$$getPartition(ExternalSorter.scala:113)
at org.apache.spark.util.collection.ExternalSorter$$anonfun$insertAll$1.apply(ExternalSorter.scala:212)
at org.apache.spark.util.collection.ExternalSorter.spillToPartitionFiles(ExternalSorter.scala:366)
at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:211)
at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:63)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:68)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:56)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)

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