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qcri / Arabesque

Scalable Graph Mining
http://arabesque.io
Apache License 2.0
61 stars 33 forks source link

Encounter kyro serialization error when calculating maximum cliques #17

Open HongHuangNeu opened 5 years ago

HongHuangNeu commented 5 years ago

When I launch maximum clique computation on spark, I encounter the following errors(I bump spark version from 2.0.0 to 2.1.0):

Exception,java.lang.NullPointerException Serialization trace: vertexPositions (io.arabesque.pattern.JBlissPattern),[Ljava.lang.StackTraceElement;@106a45fa,com.esotericsoftware.kryo.KryoException: java.lang.NullPointerException Serialization trace: vertexPositions (io.arabesque.pattern.JBlissPattern) at com.esotericsoftware.kryo.serializers.ObjectField.read(ObjectField.java:144) at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:551) at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:790) at com.twitter.chill.Tuple2Serializer.read(TupleSerializers.scala:41) at com.twitter.chill.Tuple2Serializer.read(TupleSerializers.scala:33) at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:790) at org.apache.spark.serializer.KryoDeserializationStream.readObject(KryoSerializer.scala:244) at org.apache.spark.serializer.DeserializationStream.readKey(Serializer.scala:157) at org.apache.spark.serializer.DeserializationStream$$anon$2.getNext(Serializer.scala:189) at org.apache.spark.serializer.DeserializationStream$$anon$2.getNext(Serializer.scala:186) at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73) at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:438) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) at org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32) at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39) at org.apache.spark.util.collection.ExternalAppendOnlyMap.insertAll(ExternalAppendOnlyMap.scala:154) at org.apache.spark.Aggregator.combineCombinersByKey(Aggregator.scala:50) at org.apache.spark.shuffle.BlockStoreShuffleReader.read(BlockStoreShuffleReader.scala:85) at org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:109) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323) at org.apache.spark.rdd.RDD.iterator(RDD.scala:287) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323) at org.apache.spark.rdd.RDD.iterator(RDD.scala:287) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53) at org.apache.spark.scheduler.Task.run(Task.scala:99) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: java.lang.NullPointerException at com.koloboke.collect.impl.hash.MutableLHashParallelKVIntIntMapGO.put(MutableLHashParallelKVIntIntMapGO.java:474) at com.koloboke.collect.impl.hash.MutableLHashParallelKVIntIntMapGO.put(MutableLHashParallelKVIntIntMapGO.java:45) at com.esotericsoftware.kryo.serializers.MapSerializer.read(MapSerializer.java:162) at com.esotericsoftware.kryo.serializers.MapSerializer.read(MapSerializer.java:39) at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:708) at com.esotericsoftware.kryo.serializers.ObjectField.read(ObjectField.java:125) ... 30 more ,Some(org.apache.spark.ThrowableSerializationWrapper@5d417398),Vector(AccumulableInfo(1974,Some(internal.metrics.executorRunTime),Some(354),None,true,true,None), AccumulableInfo(1976,Some(internal.metrics.resultSize),Some(0),None,true,true,None), AccumulableInfo(1977,Some(internal.metrics.jvmGCTime),Some(27),None,true,true,None)),Vector(LongAccumulator(id: 1974, name: Some(internal.metrics.executorRunTime), value: 354), LongAccumulator(id: 1976, name: Some(internal.metrics.resultSize), value: 0), LongAccumulator(id: 1977, name: Some(internal.metrics.jvmGCTime), value: 27))),org.apache.spark.scheduler.TaskInfo@ab7ac0e,org.apache.spark.executor.TaskMetrics@2c4b63fc)

Does the spark version of Arabesque work with spark 2.1.0?

ghanemabdo commented 5 years ago

Arabesque is tested only with Spark 2.0. We faced several stability and memory issues when we tried upgrading to Spark 2.1+ (this NPE is one of them). We strongly recommend sticking to Spark 2.0 in order to get the expected outcomes.

HongHuangNeu commented 5 years ago

I fixed the issue by forcing Spark to use Java serializer. In Spark 2.1+ kyro serializer is used by default in some of the shuffling stages, which destroys the serialization process. In the implementation most classes inherits Java serializer.