RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: null

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RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: null

Kaepke, Marc
Hi everyone,

what does mean that following exception, if I run my gelly program?

Exception in thread "main" org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply$mcV$sp(JobManager.scala:900)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply(JobManager.scala:843)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply(JobManager.scala:843)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$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.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: null
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger.getIterator(UnilateralSortMerger.java:619)
at org.apache.flink.runtime.operators.BatchTask.getInput(BatchTask.java:1094)
at org.apache.flink.runtime.operators.CoGroupWithSolutionSetSecondDriver.run(CoGroupWithSolutionSetSecondDriver.java:203)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:490)
at org.apache.flink.runtime.iterative.task.AbstractIterativeTask.run(AbstractIterativeTask.java:146)
at org.apache.flink.runtime.iterative.task.IterationTailTask.run(IterationTailTask.java:107)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:355)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:655)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: Thread 'SortMerger Reading Thread' terminated due to an exception: null
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:799)
Caused by: java.lang.NullPointerException
at java.util.ArrayList$SubList.checkForComodification(ArrayList.java:1230)
at java.util.ArrayList$SubList.size(ArrayList.java:1040)
at java.util.AbstractList.add(AbstractList.java:108)
at com.esotericsoftware.kryo.serializers.CollectionSerializer.read(CollectionSerializer.java:116)
at com.esotericsoftware.kryo.serializers.CollectionSerializer.read(CollectionSerializer.java:22)
at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:761)
at org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.deserialize(KryoSerializer.java:232)
at org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.deserialize(KryoSerializer.java:246)
at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.deserialize(TupleSerializer.java:144)
at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.deserialize(TupleSerializer.java:30)
at org.apache.flink.runtime.plugable.ReusingDeserializationDelegate.read(ReusingDeserializationDelegate.java:57)
at org.apache.flink.runtime.io.network.api.serialization.SpillingAdaptiveSpanningRecordDeserializer.getNextRecord(SpillingAdaptiveSpanningRecordDeserializer.java:109)
at org.apache.flink.runtime.io.network.api.reader.AbstractRecordReader.getNextRecord(AbstractRecordReader.java:72)
at org.apache.flink.runtime.io.network.api.reader.MutableRecordReader.next(MutableRecordReader.java:42)
at org.apache.flink.runtime.operators.util.ReaderIterator.next(ReaderIterator.java:59)
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ReadingThread.go(UnilateralSortMerger.java:973)
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:796)

Process finished with exit code 1
—————————————————————

During an iteration (GatherFunction) I will update a custom class

if(!allNewSemiClusters.isEmpty()) {
for(SemiCluster semiCluster : allNewSemiClusters) {
existingSemiClusters.add(semiCluster);
}
I don’t get the error above, if I comment out the second to last line.


Any ideas?


Best,
Marc


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Re: RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: null

Kaepke, Marc
Hi,

did some had an answer or solution?

Best
Marc

Am 05.05.2017 um 20:05 schrieb Kaepke, Marc <[hidden email]>:

Hi everyone,

what does mean that following exception, if I run my gelly program?

Exception in thread "main" org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply$mcV$sp(JobManager.scala:900)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply(JobManager.scala:843)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply(JobManager.scala:843)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$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.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: null
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger.getIterator(UnilateralSortMerger.java:619)
at org.apache.flink.runtime.operators.BatchTask.getInput(BatchTask.java:1094)
at org.apache.flink.runtime.operators.CoGroupWithSolutionSetSecondDriver.run(CoGroupWithSolutionSetSecondDriver.java:203)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:490)
at org.apache.flink.runtime.iterative.task.AbstractIterativeTask.run(AbstractIterativeTask.java:146)
at org.apache.flink.runtime.iterative.task.IterationTailTask.run(IterationTailTask.java:107)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:355)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:655)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: Thread 'SortMerger Reading Thread' terminated due to an exception: null
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:799)
Caused by: java.lang.NullPointerException
at java.util.ArrayList$SubList.checkForComodification(ArrayList.java:1230)
at java.util.ArrayList$SubList.size(ArrayList.java:1040)
at java.util.AbstractList.add(AbstractList.java:108)
at com.esotericsoftware.kryo.serializers.CollectionSerializer.read(CollectionSerializer.java:116)
at com.esotericsoftware.kryo.serializers.CollectionSerializer.read(CollectionSerializer.java:22)
at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:761)
at org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.deserialize(KryoSerializer.java:232)
at org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.deserialize(KryoSerializer.java:246)
at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.deserialize(TupleSerializer.java:144)
at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.deserialize(TupleSerializer.java:30)
at org.apache.flink.runtime.plugable.ReusingDeserializationDelegate.read(ReusingDeserializationDelegate.java:57)
at org.apache.flink.runtime.io.network.api.serialization.SpillingAdaptiveSpanningRecordDeserializer.getNextRecord(SpillingAdaptiveSpanningRecordDeserializer.java:109)
at org.apache.flink.runtime.io.network.api.reader.AbstractRecordReader.getNextRecord(AbstractRecordReader.java:72)
at org.apache.flink.runtime.io.network.api.reader.MutableRecordReader.next(MutableRecordReader.java:42)
at org.apache.flink.runtime.operators.util.ReaderIterator.next(ReaderIterator.java:59)
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ReadingThread.go(UnilateralSortMerger.java:973)
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:796)

Process finished with exit code 1
—————————————————————

During an iteration (GatherFunction) I will update a custom class

if(!allNewSemiClusters.isEmpty()) {
for(SemiCluster semiCluster : allNewSemiClusters) {
existingSemiClusters.add(semiCluster);
}
I don’t get the error above, if I comment out the second to last line.


Any ideas?


Best,
Marc



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Re: RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: null

Aljoscha Krettek
Hi Marc,

Does the problem still persist? Could you try running it with the custom Kryo serialiser that Flavio posted here: http://apache-flink-user-mailing-list-archive.2336050.n4.nabble.com/com-esotericsoftware-kryo-KryoException-and-java-lang-IndexOutOfBoundsException-tp7459p7461.html

Or, better yet. Try implementing your custom type in such a way that it doesn’t need to Kryo serialiser but can work with the PojoSerializer. For this you need to ensure that the type as a zero-argument constructor and that all fields are either public or have public getters/setters.

Best,
Aljoscha

On 8. May 2017, at 19:39, Kaepke, Marc <[hidden email]> wrote:

Hi,

did some had an answer or solution?

Best
Marc

Am 05.05.2017 um 20:05 schrieb Kaepke, Marc <[hidden email]>:

Hi everyone,

what does mean that following exception, if I run my gelly program?

Exception in thread "main" org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply$mcV$sp(JobManager.scala:900)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply(JobManager.scala:843)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply(JobManager.scala:843)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$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.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: null
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger.getIterator(UnilateralSortMerger.java:619)
at org.apache.flink.runtime.operators.BatchTask.getInput(BatchTask.java:1094)
at org.apache.flink.runtime.operators.CoGroupWithSolutionSetSecondDriver.run(CoGroupWithSolutionSetSecondDriver.java:203)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:490)
at org.apache.flink.runtime.iterative.task.AbstractIterativeTask.run(AbstractIterativeTask.java:146)
at org.apache.flink.runtime.iterative.task.IterationTailTask.run(IterationTailTask.java:107)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:355)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:655)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: Thread 'SortMerger Reading Thread' terminated due to an exception: null
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:799)
Caused by: java.lang.NullPointerException
at java.util.ArrayList$SubList.checkForComodification(ArrayList.java:1230)
at java.util.ArrayList$SubList.size(ArrayList.java:1040)
at java.util.AbstractList.add(AbstractList.java:108)
at com.esotericsoftware.kryo.serializers.CollectionSerializer.read(CollectionSerializer.java:116)
at com.esotericsoftware.kryo.serializers.CollectionSerializer.read(CollectionSerializer.java:22)
at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:761)
at org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.deserialize(KryoSerializer.java:232)
at org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.deserialize(KryoSerializer.java:246)
at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.deserialize(TupleSerializer.java:144)
at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.deserialize(TupleSerializer.java:30)
at org.apache.flink.runtime.plugable.ReusingDeserializationDelegate.read(ReusingDeserializationDelegate.java:57)
at org.apache.flink.runtime.io.network.api.serialization.SpillingAdaptiveSpanningRecordDeserializer.getNextRecord(SpillingAdaptiveSpanningRecordDeserializer.java:109)
at org.apache.flink.runtime.io.network.api.reader.AbstractRecordReader.getNextRecord(AbstractRecordReader.java:72)
at org.apache.flink.runtime.io.network.api.reader.MutableRecordReader.next(MutableRecordReader.java:42)
at org.apache.flink.runtime.operators.util.ReaderIterator.next(ReaderIterator.java:59)
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ReadingThread.go(UnilateralSortMerger.java:973)
at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:796)

Process finished with exit code 1
—————————————————————

During an iteration (GatherFunction) I will update a custom class

if(!allNewSemiClusters.isEmpty()) {
for(SemiCluster semiCluster : allNewSemiClusters) {
existingSemiClusters.add(semiCluster);
}
I don’t get the error above, if I comment out the second to last line.


Any ideas?


Best,
Marc




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