Kryo IndexOutofBoundsException in MapReferenceResolver

[tenstriker]

I see people are facing this issue quite often. I am facing this as well during deserialization. Looks like MapReferenceResolver.getReadObject trying to access incorrect index.

Job aborted due to stage failure: Task 16 in stage 9.0 failed 10 times, most recent failure: Lost task 16.9 in stage 9.0 (TID 28614, hdn10.mycorptcorporation.local): com.esotericsoftware.kryo.KryoException: java.lang.IndexOutOfBoundsException: Index: 100, Size: 6
Serialization trace:
familyMap (org.apache.hadoop.hbase.client.Put)
at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:626)
at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729)
at com.twitter.chill.Tuple2Serializer.read(TupleSerializers.scala:42)
at com.twitter.chill.Tuple2Serializer.read(TupleSerializers.scala:33)
at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729)
at org.apache.spark.serializer.KryoDeserializationStream.readObject(KryoSerializer.scala:192)
at org.apache.spark.serializer.DeserializationStream$$anon$1.getNext(Serializer.scala:181)
at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73)
at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at scala.collection.Iterator$GroupedIterator.fill(Iterator.scala:966)
at scala.collection.Iterator$GroupedIterator.hasNext(Iterator.scala:972)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at com.mycorpt.myprojjobs.spark.jobs.hbase.HbaseUtils$$anonfun$writeRddToHBase2$1.apply(HbaseUtils.scala:80)
at com.mycorpt.myprojjobs.spark.jobs.hbase.HbaseUtils$$anonfun$writeRddToHBase2$1.apply(HbaseUtils.scala:75)
at org.apache.spark.rdd.RDD$$anonfun$foreachPartition$1$$anonfun$apply$29.apply(RDD.scala:902)
at org.apache.spark.rdd.RDD$$anonfun$foreachPartition$1$$anonfun$apply$29.apply(RDD.scala:902)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1850)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1850)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
Caused by: java.lang.IndexOutOfBoundsException: Index: 100, Size: 6
at java.util.ArrayList.rangeCheck(ArrayList.java:635)
at java.util.ArrayList.get(ArrayList.java:411)
at com.esotericsoftware.kryo.util.MapReferenceResolver.getReadObject(MapReferenceResolver.java:42)
at com.esotericsoftware.kryo.Kryo.readReferenceOrNull(Kryo.java:773)
at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:727)
at com.esotericsoftware.kryo.serializers.MapSerializer.read(MapSerializer.java:134)
at com.esotericsoftware.kryo.serializers.MapSerializer.read(MapSerializer.java:17)
at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)
at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)
... 26 more

[magro]

I guess we don't need to reopen #255 then, right?
Can you provide an sscce?

[tenstriker]

I use kryo as a part of spark 1.5.2 library which uses twitter-chill underneath. From my spark application point of view it just configurations and almost no code to register classes to kryo. Could this be related to reading particular serialized object - org.apache.hadoop.hbase.client.Put? It does throws exception reading back that object.

[SiphonSquirrel]

I ran in to this earlier using Spark 1.5 + HBase 1.0. The version of Kryo that is bring brought in for our CDH 5.5 version of Spark is 2.21. Inside of the HBase Put object is a TreeMap, which led me to find #112 which was fixed in commit 00ffc7e . I believe what might be happening is a race condition where the TreeMap serializer is messing with setReferences (setting it to false, then setting it back).

So I worked around this by setting references to false using the Spark property spark.kryo.referenceTracking (found here: http://spark.apache.org/docs/latest/configuration.html ) to false. This seems to have fixed the problem for now.

[magro]

@SiphonSquirrel great, thanks for stepping in! Btw, there was also #312 reported for 2.21 which we merged and released as 2.21.1 (which might make sense to use of you can change the pulled in kryo version).

[tenstriker]

thanks @SiphonSquirrel for workaround. I found my spark assembly jar uses kryo 2.21. Will try to override that somehow as well with latest one.

[magro]

@tenstriker spark upgraded recently to the latest kryo version, not sure if that's released already. See apache/spark#12076

[magro]

Is this still an issue that needs a resolution from kryo, or can we close it?

[magro]

Closed for now, please reopen if still relevant.

[David-hod]

I am facing same issue. Does upgrade solved this issue of serializing hbase 'Put' objects ? any recommended workaround ?

[mooncake020]

I am facing same issue too

[kratos1308]

Same issue. Does not seem the problem was solved anywhere. What's up since September 2017 ?

[tjormola]

Hi,

I just encountered this problem, too, while experimenting with distributed state machine support of Spring State Machine. I'm using org.springframework.statemachine:spring-statemachine-zookeeper:2.0.1.RELEASE which pulls com.esotericsoftware:kryo-shaded:3.0.3. I also tried with compiling and running against Kryo 4.0.2 but the problem remains unfixed.

I have no idea what might be going on regarding the root cause in Kryo and I have no interest in digging the Kryo internals any further but here's some screenshots showing how this is triggered for me and some notes made during debugging. Hopefully someone finds this useful...

• The docs how distributed Spring State Machine relates to Kryo here: https://docs.spring.io/spring-statemachine/docs/2.0.1.RELEASE/reference/htmlsingle/#sm-distributed
• TLDR; SSM uses Kryo to serialize/deserialize the internal representation of the user built state machine and its metadata after each update in the model/state machine action and then stores/restores the blob in/from a node in Zookeeper thus implementing a distributed state machine engine assisted by Zookeeper.
  • The model
  • Kryo custom serializer
  • The Zookeeper stuff here and here
• Environment: macOS 10.13.4, Oracle JDK 9.0.4, Zookeeper 3.4.10 from Homebrew with empty data/node structure, everything is as initialized and managed by SSM

1. https://drive.google.com/open?id=1Q4e2YL4LJA-jpdYkHrXJ7eRwjNMlweF1 We start here in the SSM code, the intention is to restore the state machine state from the blob read from Zookeeper.
2. https://drive.google.com/open?id=1Dfj0hdTblAv4BFAxuwoLcA9Vajyano71 SSM Zookeeper code that pulls the blob from Zookeeper and deserializes eventually using Kryo
3. https://drive.google.com/open?id=1BJbOC8R4FOQ6aHatcL0E7s0eKll7Xl78 ...Continues
4. https://drive.google.com/open?id=1n56GXkKYN4SJFtBVXDFIm9aJ1FldmDHB Jump to Kryo deserialization code
5. https://drive.google.com/open?id=1cLHTmUAlbk3Z68T4l_sPTmjT8HNUy1nO ...Continues. The breakpoint here is interesting because this subroutine returns the initial id value that is eventually used as an index/key to a list that triggers the exception in question.
6. https://drive.google.com/open?id=1oZz5_v2J0IaMNul7JWAQPS7gwwiQBirR Code that returns the id integer value discussed above
7. https://drive.google.com/open?id=1ituv53jtgQW1SggkQzCVyXccX6ieYzJq About to call the Kryo code that uses the id
8. https://drive.google.com/open?id=1An3wNzb4KDlW24Iop8CniLIRSW7K7Xdj Bang, the integer id is used as a list index with an empty list and naturally this is triggering the IndexOutOfBoundsException in question. What is this referenceResolver thing and why it is empty at this stage? Supposedly org.springframework.statemachine.StateMachineContext should be stored there and retrievable by the id but it isn't. How so, that I do not know and have no desire to research ;)
9. https://drive.google.com/open?id=1esesZf_GSpMw8_hJm6r8FfRNNPp-Iaod After throwing the exception, we're back to SSM code, exception handler to be more precise.
10. https://drive.google.com/open?id=1L-zADRBO8-IuRQhjd2VM_JNmNRlcAKys Finally, the SSM code happily continues with broken internal reference objects... The state wrapper object currentStateWrapper is never created due to this exception thus the reference objects stateRef and notifyRef continue referencing to null instead of the state object initialized with the data load from Zookeeper and wrapped for use. The state machine engine will try continuing anyway, but naturally problems will ensue down the road.

[tjormola]

Reopen the issue, please?