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Posted to issues@spark.apache.org by "Neville Li (JIRA)" <ji...@apache.org> on 2014/06/04 10:46:03 UTC
[jira] [Comment Edited] (SPARK-1977) mutable.BitSet in ALS not
serializable with KryoSerializer
[ https://issues.apache.org/jira/browse/SPARK-1977?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14017508#comment-14017508 ]
Neville Li edited comment on SPARK-1977 at 6/4/14 8:45 AM:
-----------------------------------------------------------
We submit 1 spark-assembly and 1 job assembly jar via spark-submit and there are no other obvious scala/spark/kryo jars in the global classpath. I can reproduce the same exception locally with the following snippet, when kryo.register() is commented out.
I just added mutable BitSet to Twitter chill: https://github.com/twitter/chill/pull/185
{code}
import com.twitter.chill._
import org.apache.spark.serializer.{KryoSerializer, KryoRegistrator}
import org.apache.spark.SparkConf
import scala.collection.mutable
class MyRegistrator extends KryoRegistrator {
override def registerClasses(kryo: Kryo) {
// kryo.register(classOf[mutable.BitSet])
}
}
case class OutLinkBlock(elementIds: Array[Int], shouldSend: Array[mutable.BitSet])
object KryoTest {
def main(args: Array[String]) {
println("hello")
val conf = new SparkConf()
.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
.set("spark.kryo.registrator", classOf[MyRegistrator].getName)
val serializer = new KryoSerializer(conf).newInstance()
val bytes = serializer.serialize(OutLinkBlock(Array(1, 2, 3), Array(mutable.BitSet(2, 4, 6))))
serializer.deserialize(bytes).asInstanceOf[OutLinkBlock]
}
}
{code}
was (Author: sinisa_lyh):
We submit 1 spark-assembly and 1 job assembly jar via spark-submit and there are no other obvious scala/spark/kryo jars in the global classpath. I can reproduce the same exception locally with the following snippet, when kryo.register() is commented out.
I just added mutable BitSet to Twitter chill: https://github.com/twitter/chill/pull/185
{{code}}
import com.twitter.chill._
import org.apache.spark.serializer.{KryoSerializer, KryoRegistrator}
import org.apache.spark.SparkConf
import scala.collection.mutable
class MyRegistrator extends KryoRegistrator {
override def registerClasses(kryo: Kryo) {
// kryo.register(classOf[mutable.BitSet])
}
}
case class OutLinkBlock(elementIds: Array[Int], shouldSend: Array[mutable.BitSet])
object KryoTest {
def main(args: Array[String]) {
println("hello")
val conf = new SparkConf()
.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
.set("spark.kryo.registrator", classOf[MyRegistrator].getName)
val serializer = new KryoSerializer(conf).newInstance()
val bytes = serializer.serialize(OutLinkBlock(Array(1, 2, 3), Array(mutable.BitSet(2, 4, 6))))
serializer.deserialize(bytes).asInstanceOf[OutLinkBlock]
}
}
{{code}}
> mutable.BitSet in ALS not serializable with KryoSerializer
> ----------------------------------------------------------
>
> Key: SPARK-1977
> URL: https://issues.apache.org/jira/browse/SPARK-1977
> Project: Spark
> Issue Type: Bug
> Components: MLlib
> Affects Versions: 1.0.0
> Reporter: Neville Li
> Priority: Minor
>
> OutLinkBlock in ALS.scala has an Array[mutable.BitSet] member.
> KryoSerializer uses AllScalaRegistrar from Twitter chill but it doesn't register mutable.BitSet.
> Right now we have to register mutable.BitSet manually. A proper fix would be using immutable.BitSet in ALS or register mutable.BitSet in upstream chill.
> {code}
> Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 1724.0:9 failed 4 times, most recent failure: Exception failure in TID 68548 on host lon4-hadoopslave-b232.lon4.spotify.net: com.esotericsoftware.kryo.KryoException: java.lang.ArrayStoreException: scala.collection.mutable.HashSet
> Serialization trace:
> shouldSend (org.apache.spark.mllib.recommendation.OutLinkBlock)
> com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:626)
> com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
> com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:732)
> com.twitter.chill.Tuple2Serializer.read(TupleSerializers.scala:43)
> com.twitter.chill.Tuple2Serializer.read(TupleSerializers.scala:34)
> com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:732)
> org.apache.spark.serializer.KryoDeserializationStream.readObject(KryoSerializer.scala:115)
> org.apache.spark.serializer.DeserializationStream$$anon$1.getNext(Serializer.scala:125)
> org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:71)
> org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
> org.apache.spark.rdd.CoGroupedRDD$$anonfun$compute$4.apply(CoGroupedRDD.scala:155)
> org.apache.spark.rdd.CoGroupedRDD$$anonfun$compute$4.apply(CoGroupedRDD.scala:154)
> scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
> scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
> org.apache.spark.rdd.CoGroupedRDD.compute(CoGroupedRDD.scala:154)
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262)
> org.apache.spark.rdd.RDD.iterator(RDD.scala:229)
> org.apache.spark.rdd.MappedValuesRDD.compute(MappedValuesRDD.scala:31)
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262)
> org.apache.spark.rdd.RDD.iterator(RDD.scala:229)
> org.apache.spark.rdd.FlatMappedValuesRDD.compute(FlatMappedValuesRDD.scala:31)
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262)
> org.apache.spark.rdd.RDD.iterator(RDD.scala:229)
> org.apache.spark.rdd.FlatMappedRDD.compute(FlatMappedRDD.scala:33)
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262)
> org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:77)
> org.apache.spark.rdd.RDD.iterator(RDD.scala:227)
> org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:111)
> org.apache.spark.scheduler.Task.run(Task.scala:51)
> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:187)
> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
> java.lang.Thread.run(Thread.java:662)
> Driver stacktrace:
> at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1033)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1017)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1015)
> at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
> at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
> at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1015)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:633)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:633)
> at scala.Option.foreach(Option.scala:236)
> at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:633)
> at org.apache.spark.scheduler.DAGSchedulerEventProcessActor$$anonfun$receive$2.applyOrElse(DAGScheduler.scala:1207)
> at akka.actor.ActorCell.receiveMessage(ActorCell.scala:498)
> at akka.actor.ActorCell.invoke(ActorCell.scala:456)
> at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:237)
> at akka.dispatch.Mailbox.run(Mailbox.scala:219)
> at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:386)
> at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
> at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
> at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
> at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
> {code}
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