I have been running into NegativeArraySizeException's when doing joins on
data with very skewed key distributions in Spark 1.2.0. I found a previous
post that mentioned that this exception arises when the size of the blocks
spilled during the shuffle exceeds 2GB. The post recommended increasing the
number of partitions. I tried increasing the number of partitions, and using
the RangePartitioner instead of the HashPartitioner but still encountered
the problem.
Does Spark support skewed joins similar to Pig?
com.esotericsoftware.kryo.KryoException:
java.lang.NegativeArraySizeException
Serialization trace:
otherElements (org.apache.spark.util.collection.CompactBuffer)
at
com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.write(FieldSerializer.java:585)
at
com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:213)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:568)
at
com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:318)
at
com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:293)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:501)
at
com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.write(FieldSerializer.java:564)
at
com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:213)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:568)
at
com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:318)
at
com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:293)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:568)
at
com.twitter.chill.Tuple2Serializer.write(TupleSerializers.scala:37)
at
com.twitter.chill.Tuple2Serializer.write(TupleSerializers.scala:33)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:568)
at
org.apache.spark.serializer.KryoSerializationStream.writeObject(KryoSerializer.scala:128)
at
org.apache.spark.storage.DiskBlockObjectWriter.write(BlockObjectWriter.scala:195)
at
org.apache.spark.util.collection.ExternalAppendOnlyMap.spill(ExternalAppendOnlyMap.scala:176)
at
org.apache.spark.util.collection.ExternalAppendOnlyMap.spill(ExternalAppendOnlyMap.scala:63)
at
org.apache.spark.util.collection.Spillable$class.maybeSpill(Spillable.scala:87)
at
org.apache.spark.util.collection.ExternalAppendOnlyMap.maybeSpill(ExternalAppendOnlyMap.scala:63)
at
org.apache.spark.util.collection.ExternalAppendOnlyMap.insertAll(ExternalAppendOnlyMap.scala:127)
at
org.apache.spark.rdd.CoGroupedRDD$$anonfun$compute$5.apply(CoGroupedRDD.scala:160)
at
org.apache.spark.rdd.CoGroupedRDD$$anonfun$compute$5.apply(CoGroupedRDD.scala:159)
at
scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:772)
at
scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at
scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
at
scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:771)
at org.apache.spark.rdd.CoGroupedRDD.compute(CoGroupedRDD.scala:159)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
at
org.apache.spark.rdd.MappedValuesRDD.compute(MappedValuesRDD.scala:31)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
at
org.apache.spark.rdd.FlatMappedValuesRDD.compute(FlatMappedValuesRDD.scala:31)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
at
org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:68)
at
org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:56)
at
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:196)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NegativeArraySizeException
at
com.esotericsoftware.kryo.util.IdentityObjectIntMap.resize(IdentityObjectIntMap.java:409)
at
com.esotericsoftware.kryo.util.IdentityObjectIntMap.putStash(IdentityObjectIntMap.java:227)
at
com.esotericsoftware.kryo.util.IdentityObjectIntMap.push(IdentityObjectIntMap.java:221)
at
com.esotericsoftware.kryo.util.IdentityObjectIntMap.put(IdentityObjectIntMap.java:117)
at
com.esotericsoftware.kryo.util.IdentityObjectIntMap.putStash(IdentityObjectIntMap.java:228)
at
com.esotericsoftware.kryo.util.IdentityObjectIntMap.push(IdentityObjectIntMap.java:221)
at
com.esotericsoftware.kryo.util.IdentityObjectIntMap.put(IdentityObjectIntMap.java:117)
at
com.esotericsoftware.kryo.util.MapReferenceResolver.addWrittenObject(MapReferenceResolver.java:23)
at
com.esotericsoftware.kryo.Kryo.writeReferenceOrNull(Kryo.java:598)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:499)
at
com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.write(FieldSerializer.java:564)
... 46 more
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