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From Stephan Ewen <se...@apache.org>
Subject Re: Flink - Avro - AvroTypeInfo issue - Index out of bounds exception
Date Tue, 21 Apr 2015 17:03:23 GMT
Hi!

>From a quick look at the code it seems that this is a followup exception
that occurs because the task has been shut down and the buffer pools
destroyed.

Is there another root exception that is the root cause of the failure?

Greetings,
Stephan


On Tue, Apr 21, 2015 at 5:46 PM, Filip Łęczycki <filipleczycki@gmail.com>
wrote:

> Hi guys,
>
> Thank you very much for you help, upgarding to the 0.9.0-milestone
> resolved the issue but the new one arised. While trying to run the
> following code:
>
> val job = Job.getInstance(new Configuration(true))
> ParquetInputFormat.setReadSupportClass(job,
> classOf[AvroReadSupport[AlignmentRecord]])
> val file=env.readHadoopFile[Void, AlignmentRecord](new
>  ParquetInputFormat[AlignmentRecord],classOf[Void],classOf[AlignmentRecord],path1,
> job)
> file.map(R=>R._2.getCigar()).first(1000).print()
>
> I receive following error:
> Exception in thread "main"
> org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
> at
> org.apache.flink.runtime.jobmanager.JobManager$$anonfun$receiveWithLogMessages$1.applyOrElse(JobManager.scala:306)
> at
> scala.runtime.AbstractPartialFunction$mcVL$sp.apply$mcVL$sp(AbstractPartialFunction.scala:33)
> at
> scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:33)
> at
> scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:25)
> at
> org.apache.flink.runtime.ActorLogMessages$$anon$1.apply(ActorLogMessages.scala:37)
> at
> org.apache.flink.runtime.ActorLogMessages$$anon$1.apply(ActorLogMessages.scala:30)
> at scala.PartialFunction$class.applyOrElse(PartialFunction.scala:118)
> at
> org.apache.flink.runtime.ActorLogMessages$$anon$1.applyOrElse(ActorLogMessages.scala:30)
> at akka.actor.Actor$class.aroundReceive(Actor.scala:465)
> at
> org.apache.flink.runtime.jobmanager.JobManager.aroundReceive(JobManager.scala:91)
> at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516)
> at akka.actor.ActorCell.invoke(ActorCell.scala:487)
> at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:254)
> at akka.dispatch.Mailbox.run(Mailbox.scala:221)
> at akka.dispatch.Mailbox.exec(Mailbox.scala:231)
> 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)
> Caused by: java.lang.NullPointerException
> at
> org.apache.flink.runtime.io.network.api.serialization.SpanningRecordSerializer.setNextBuffer(SpanningRecordSerializer.java:93)
> at
> org.apache.flink.runtime.io.network.api.writer.RecordWriter.emit(RecordWriter.java:92)
> at
> org.apache.flink.runtime.operators.shipping.OutputCollector.collect(OutputCollector.java:65)
> at
> org.apache.flink.runtime.operators.chaining.ChainedMapDriver.collect(ChainedMapDriver.java:78)
> at
> org.apache.flink.runtime.operators.DataSourceTask.invoke(DataSourceTask.java:174)
> at
> org.apache.flink.runtime.execution.RuntimeEnvironment.run(RuntimeEnvironment.java:217)
> at java.lang.Thread.run(Thread.java:744)
>
> The file is loaded properly, I am able to print out it's conent but when I
> try to do anything more complex (like .getCigar) the above exception
> arrives. Moreover, code that worked in the previous version, simple mapping:
> seqQualSet.map(R=>R.qual.get).map(R=>(R.sum[Int]/R.size, 1L))
>     .groupBy(0).sum(1)
>     .map(R=>(1,R._1,R._2))
>     .groupBy(0)
>     .sortGroup(1, Order.ASCENDING)
>     .first(100)
>     .map(R=>(R._2,R._3))
>
> after upgrade doesn't work and causes the same error as above.
>
> Could you please advise me on that? If you need more information to
> determine the issue I will gladly provide.
>
> Regards,
> Filip Łęczycki
>
> Pozdrawiam,
> Filip Łęczycki
>
> 2015-04-14 11:43 GMT+02:00 Maximilian Michels <mxm@apache.org>:
>
>> Hi Filip,
>>
>> I think your issue is best dealt with on the user mailing list.
>> Unfortunately, you can't use attachments on the mailing lists. So if you
>> want to post a screenshot you'll have to upload it somewhere else (e.g.
>> http://imgur.com/).
>>
>> I can confirm your error. Would you mind using the 0.9.0-milestone
>> release? Just change the Flink version in the Maven pom.xml to
>> 0.9.0-milestone-1. Your example works with this version.
>>
>> Best regards,
>> Max
>>
>>
>> On Mon, Apr 13, 2015 at 6:42 PM, Filip Łęczycki <filipleczycki@gmail.com>
>> wrote:
>>
>>> Hi
>>>
>>> I have an issue while running the following line while usig flink v
>>> 0.8.1 (:
>>>     val asdf = new
>>> AvroTypeInfo[AlignmentRecord](classOf[AlignmentRecord])
>>>
>>> Alignment record belongs to the package :
>>> org.bdgenomics.formats.avro.AlignmentRecord
>>>
>>> http://mvnrepository.com/artifact/org.bdgenomics.bdg-formats/bdg-formats/0.4.0
>>>
>>> While trying to run I am receivng following exception:
>>>
>>> Exception in thread "main" java.lang.IndexOutOfBoundsException
>>> at
>>> org.apache.flink.api.java.typeutils.PojoTypeInfo.getPojoFieldAt(PojoTypeInfo.java:178)
>>> at
>>> org.apache.flink.api.java.typeutils.AvroTypeInfo.generateFieldsFromAvroSchema(AvroTypeInfo.java:52)
>>> at
>>> org.apache.flink.api.java.typeutils.AvroTypeInfo.<init>(AvroTypeInfo.java:38)
>>> at flinkTest.FlinkBAMReader$.main(FlinkBAMReader.scala:74)
>>>
>>> While debugging I have noticed that the generated AvroTypeInfo class has
>>> a fields array with 42 elements, while the totalFIelds property has value
>>> 52 (please find screenshot attached) which seems to be the cause of the
>>> exception. Could you please help me o determine what may be the issue with
>>> the parser? Is this some bug in AvroTypeInfo class or the AlignmentRecord
>>> class is somehow corrupted?
>>>
>>> Best Regards/Pozdrawiam,
>>> Filip Łęczycki
>>>
>>>
>>>
>>
>

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