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Posted to issues@flink.apache.org by "Vishal Palla (Jira)" <ji...@apache.org> on 2023/12/07 10:16:00 UTC
[jira] [Updated] (FLINK-33769) ExternalSorter hits "java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted" when using custom serializer
[ https://issues.apache.org/jira/browse/FLINK-33769?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Vishal Palla updated FLINK-33769:
---------------------------------
Description:
The [NormalizedKeySorter library|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/operators/sort/NormalizedKeySorter.java] is used to sort records in-memory. It internally uses a [SimpleCollectingOutputView|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/io/disk/SimpleCollectingOutputView.java] instantiated using a fixed chunk of managed memory to store the records. When the SimpleCollectingOutputView runs out of memory segments, it [throws an EOFException|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/io/disk/SimpleCollectingOutputView.java#L76] which [should be caught by the sorter in the write method
|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/operators/sort/NormalizedKeySorter.java#L298]and a {{false}} indicating that the sort buffer was full (javadoc). The issue here is that the EOFException thrown by the SimpleCollectingOutputView is first caught by the record serializer which offers no guarantee on passing on the exception as it was caught upwards. In the case of Kryo and Thrift, the serializer wraps the caught exception in their own exception classes and throw them upwards which the sorter doesn't catch and the job crashes.
Example stacktrace -
{{java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:487)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:357)
at org.apache.flink.runtime.taskmanager.Task.runWithSystemExitMonitoring(Task.java:935)
at org.apache.flink.runtime.taskmanager.Task.restoreAndInvoke(Task.java:914)
at org.apache.flink.runtime.taskmanager.Task.doRun(Task.java:728)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:550)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: org.apache.flink.util.WrappingRuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
at org.apache.flink.runtime.operators.sort.ExternalSorter.getIterator(ExternalSorter.java:262)
at org.apache.flink.runtime.operators.BatchTask.getInput(BatchTask.java:1222)
at org.apache.flink.runtime.operators.GroupReduceDriver.prepare(GroupReduceDriver.java:105)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:479)
... 6 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
at java.base/java.util.concurrent.CompletableFuture.reportGet(CompletableFuture.java:395)
at java.base/java.util.concurrent.CompletableFuture.get(CompletableFuture.java:1999)
at org.apache.flink.runtime.operators.sort.ExternalSorter.getIterator(ExternalSorter.java:259)
... 9 more
Caused by: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
at org.apache.flink.runtime.operators.sort.ExternalSorter.lambda$getIterator$1(ExternalSorter.java:256)
at java.base/java.util.concurrent.CompletableFuture.uniExceptionally(CompletableFuture.java:986)
at java.base/java.util.concurrent.CompletableFuture$UniExceptionally.tryFire(CompletableFuture.java:970)
at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:506)
at java.base/java.util.concurrent.CompletableFuture.completeExceptionally(CompletableFuture.java:2088)
at org.apache.flink.runtime.operators.sort.ExternalSorterBuilder.lambda$doBuild$1(ExternalSorterBuilder.java:397)
at org.apache.flink.runtime.operators.sort.ThreadBase.internalHandleException(ThreadBase.java:121)
at org.apache.flink.runtime.operators.sort.ThreadBase.run(ThreadBase.java:75)
Caused by: java.io.IOException: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
at org.apache.flink.runtime.operators.sort.ThreadBase.run(ThreadBase.java:80)
Caused by: com.esotericsoftware.kryo.KryoException: java.io.EOFException: Can't collect further: memorySource depleted
at com.esotericsoftware.kryo.io.Output.flush(Output.java:165)
at com.esotericsoftware.kryo.io.OutputChunked.flush(OutputChunked.java:45)
at com.esotericsoftware.kryo.io.OutputChunked.endChunks(OutputChunked.java:82)
at com.twitter.beam.coder.scala.ChillCoder.encode(ChillCoder.scala:101)
at com.twitter.eventwrangler.core.attribution.AttributionEventCoder.encode(AttributionEvent.scala:40)
at com.twitter.eventwrangler.core.attribution.AttributionEventCoder.encode(AttributionEvent.scala:22)
at org.apache.beam.sdk.coders.Coder.encode(Coder.java:136)
at org.apache.beam.sdk.transforms.join.UnionCoder.encode(UnionCoder.java:74)
at org.apache.beam.sdk.transforms.join.UnionCoder.encode(UnionCoder.java:32)
at org.apache.beam.sdk.coders.KvCoder.encode(KvCoder.java:73)
at org.apache.beam.sdk.coders.KvCoder.encode(KvCoder.java:37)
at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.encode(WindowedValue.java:607)
at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.encode(WindowedValue.java:598)
at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.encode(WindowedValue.java:558)
at org.apache.beam.runners.flink.translation.types.CoderTypeSerializer.serialize(CoderTypeSerializer.java:110)
at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.serialize(TupleSerializer.java:140)
at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.serialize(TupleSerializer.java:37)
at org.apache.flink.runtime.operators.sort.NormalizedKeySorter.write(NormalizedKeySorter.java:297)
at org.apache.flink.runtime.operators.sort.SorterInputGateway.writeRecord(SorterInputGateway.java:77)
at org.apache.flink.runtime.operators.sort.ReadingThread.go(ReadingThread.java:69)
at org.apache.flink.runtime.operators.sort.ThreadBase.run(ThreadBase.java:73)
Caused by: java.io.EOFException: Can't collect further: memorySource depleted
at org.apache.flink.runtime.io.disk.SimpleCollectingOutputView.nextSegment(SimpleCollectingOutputView.java:76)
at org.apache.flink.runtime.memory.AbstractPagedOutputView.advance(AbstractPagedOutputView.java:139)
at org.apache.flink.runtime.memory.AbstractPagedOutputView.write(AbstractPagedOutputView.java:205)
at org.apache.beam.runners.flink.translation.wrappers.DataOutputViewWrapper.write(DataOutputViewWrapper.java:44)
at com.esotericsoftware.kryo.io.Output.flush(Output.java:163)
... 20 more}}
was:
The [NormalizedKeySorter library|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/operators/sort/NormalizedKeySorter.java] is used to sort records in-memory. It internally uses a [SimpleCollectingOutputView|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/io/disk/SimpleCollectingOutputView.java] instantiated using a fixed chunk of managed memory to store the records. When the SimpleCollectingOutputView runs out of memory segments, it [throws an EOFException|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/io/disk/SimpleCollectingOutputView.java#L76] which [should be caught by the sorter in the write method
|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/operators/sort/NormalizedKeySorter.java#L298]and a {{false}} indicating that the sort buffer was full (javadoc). The issue here is that the EOFException thrown by the SimpleCollectingOutputView is first caught by the record serializer which offers no guarantee on passing on the exception as it was caught upwards. In the case of Kryo and Thrift for example, the serializer wraps the caught exception in their own exception classes and throw them upwards which the sorter doesn't catch and the job crashes.
Example stacktrace -
{{java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:487)
at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:357)
at org.apache.flink.runtime.taskmanager.Task.runWithSystemExitMonitoring(Task.java:935)
at org.apache.flink.runtime.taskmanager.Task.restoreAndInvoke(Task.java:914)
at org.apache.flink.runtime.taskmanager.Task.doRun(Task.java:728)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:550)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: org.apache.flink.util.WrappingRuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
at org.apache.flink.runtime.operators.sort.ExternalSorter.getIterator(ExternalSorter.java:262)
at org.apache.flink.runtime.operators.BatchTask.getInput(BatchTask.java:1222)
at org.apache.flink.runtime.operators.GroupReduceDriver.prepare(GroupReduceDriver.java:105)
at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:479)
... 6 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
at java.base/java.util.concurrent.CompletableFuture.reportGet(CompletableFuture.java:395)
at java.base/java.util.concurrent.CompletableFuture.get(CompletableFuture.java:1999)
at org.apache.flink.runtime.operators.sort.ExternalSorter.getIterator(ExternalSorter.java:259)
... 9 more
Caused by: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
at org.apache.flink.runtime.operators.sort.ExternalSorter.lambda$getIterator$1(ExternalSorter.java:256)
at java.base/java.util.concurrent.CompletableFuture.uniExceptionally(CompletableFuture.java:986)
at java.base/java.util.concurrent.CompletableFuture$UniExceptionally.tryFire(CompletableFuture.java:970)
at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:506)
at java.base/java.util.concurrent.CompletableFuture.completeExceptionally(CompletableFuture.java:2088)
at org.apache.flink.runtime.operators.sort.ExternalSorterBuilder.lambda$doBuild$1(ExternalSorterBuilder.java:397)
at org.apache.flink.runtime.operators.sort.ThreadBase.internalHandleException(ThreadBase.java:121)
at org.apache.flink.runtime.operators.sort.ThreadBase.run(ThreadBase.java:75)
Caused by: java.io.IOException: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
at org.apache.flink.runtime.operators.sort.ThreadBase.run(ThreadBase.java:80)
Caused by: com.esotericsoftware.kryo.KryoException: java.io.EOFException: Can't collect further: memorySource depleted
at com.esotericsoftware.kryo.io.Output.flush(Output.java:165)
at com.esotericsoftware.kryo.io.OutputChunked.flush(OutputChunked.java:45)
at com.esotericsoftware.kryo.io.OutputChunked.endChunks(OutputChunked.java:82)
at com.twitter.beam.coder.scala.ChillCoder.encode(ChillCoder.scala:101)
at com.twitter.eventwrangler.core.attribution.AttributionEventCoder.encode(AttributionEvent.scala:40)
at com.twitter.eventwrangler.core.attribution.AttributionEventCoder.encode(AttributionEvent.scala:22)
at org.apache.beam.sdk.coders.Coder.encode(Coder.java:136)
at org.apache.beam.sdk.transforms.join.UnionCoder.encode(UnionCoder.java:74)
at org.apache.beam.sdk.transforms.join.UnionCoder.encode(UnionCoder.java:32)
at org.apache.beam.sdk.coders.KvCoder.encode(KvCoder.java:73)
at org.apache.beam.sdk.coders.KvCoder.encode(KvCoder.java:37)
at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.encode(WindowedValue.java:607)
at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.encode(WindowedValue.java:598)
at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.encode(WindowedValue.java:558)
at org.apache.beam.runners.flink.translation.types.CoderTypeSerializer.serialize(CoderTypeSerializer.java:110)
at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.serialize(TupleSerializer.java:140)
at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.serialize(TupleSerializer.java:37)
at org.apache.flink.runtime.operators.sort.NormalizedKeySorter.write(NormalizedKeySorter.java:297)
at org.apache.flink.runtime.operators.sort.SorterInputGateway.writeRecord(SorterInputGateway.java:77)
at org.apache.flink.runtime.operators.sort.ReadingThread.go(ReadingThread.java:69)
at org.apache.flink.runtime.operators.sort.ThreadBase.run(ThreadBase.java:73)
Caused by: java.io.EOFException: Can't collect further: memorySource depleted
at org.apache.flink.runtime.io.disk.SimpleCollectingOutputView.nextSegment(SimpleCollectingOutputView.java:76)
at org.apache.flink.runtime.memory.AbstractPagedOutputView.advance(AbstractPagedOutputView.java:139)
at org.apache.flink.runtime.memory.AbstractPagedOutputView.write(AbstractPagedOutputView.java:205)
at org.apache.beam.runners.flink.translation.wrappers.DataOutputViewWrapper.write(DataOutputViewWrapper.java:44)
at com.esotericsoftware.kryo.io.Output.flush(Output.java:163)
... 20 more}}
> ExternalSorter hits "java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted" when using custom serializer
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Key: FLINK-33769
> URL: https://issues.apache.org/jira/browse/FLINK-33769
> Project: Flink
> Issue Type: Bug
> Components: Runtime / Task
> Affects Versions: 1.17.2
> Reporter: Vishal Palla
> Priority: Major
>
> The [NormalizedKeySorter library|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/operators/sort/NormalizedKeySorter.java] is used to sort records in-memory. It internally uses a [SimpleCollectingOutputView|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/io/disk/SimpleCollectingOutputView.java] instantiated using a fixed chunk of managed memory to store the records. When the SimpleCollectingOutputView runs out of memory segments, it [throws an EOFException|https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/io/disk/SimpleCollectingOutputView.java#L76] which [should be caught by the sorter in the write method
> |https://github.com/twitter-forks/flink/blob/master/flink-runtime/src/main/java/org/apache/flink/runtime/operators/sort/NormalizedKeySorter.java#L298]and a {{false}} indicating that the sort buffer was full (javadoc). The issue here is that the EOFException thrown by the SimpleCollectingOutputView is first caught by the record serializer which offers no guarantee on passing on the exception as it was caught upwards. In the case of Kryo and Thrift, the serializer wraps the caught exception in their own exception classes and throw them upwards which the sorter doesn't catch and the job crashes.
>
> Example stacktrace -
> {{java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
> at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:487)
> at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:357)
> at org.apache.flink.runtime.taskmanager.Task.runWithSystemExitMonitoring(Task.java:935)
> at org.apache.flink.runtime.taskmanager.Task.restoreAndInvoke(Task.java:914)
> at org.apache.flink.runtime.taskmanager.Task.doRun(Task.java:728)
> at org.apache.flink.runtime.taskmanager.Task.run(Task.java:550)
> at java.base/java.lang.Thread.run(Thread.java:829)
> Caused by: org.apache.flink.util.WrappingRuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
> at org.apache.flink.runtime.operators.sort.ExternalSorter.getIterator(ExternalSorter.java:262)
> at org.apache.flink.runtime.operators.BatchTask.getInput(BatchTask.java:1222)
> at org.apache.flink.runtime.operators.GroupReduceDriver.prepare(GroupReduceDriver.java:105)
> at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:479)
> ... 6 more
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
> at java.base/java.util.concurrent.CompletableFuture.reportGet(CompletableFuture.java:395)
> at java.base/java.util.concurrent.CompletableFuture.get(CompletableFuture.java:1999)
> at org.apache.flink.runtime.operators.sort.ExternalSorter.getIterator(ExternalSorter.java:259)
> ... 9 more
> Caused by: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
> at org.apache.flink.runtime.operators.sort.ExternalSorter.lambda$getIterator$1(ExternalSorter.java:256)
> at java.base/java.util.concurrent.CompletableFuture.uniExceptionally(CompletableFuture.java:986)
> at java.base/java.util.concurrent.CompletableFuture$UniExceptionally.tryFire(CompletableFuture.java:970)
> at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:506)
> at java.base/java.util.concurrent.CompletableFuture.completeExceptionally(CompletableFuture.java:2088)
> at org.apache.flink.runtime.operators.sort.ExternalSorterBuilder.lambda$doBuild$1(ExternalSorterBuilder.java:397)
> at org.apache.flink.runtime.operators.sort.ThreadBase.internalHandleException(ThreadBase.java:121)
> at org.apache.flink.runtime.operators.sort.ThreadBase.run(ThreadBase.java:75)
> Caused by: java.io.IOException: Thread 'SortMerger Reading Thread' terminated due to an exception: java.io.EOFException: Can't collect further: memorySource depleted
> at org.apache.flink.runtime.operators.sort.ThreadBase.run(ThreadBase.java:80)
> Caused by: com.esotericsoftware.kryo.KryoException: java.io.EOFException: Can't collect further: memorySource depleted
> at com.esotericsoftware.kryo.io.Output.flush(Output.java:165)
> at com.esotericsoftware.kryo.io.OutputChunked.flush(OutputChunked.java:45)
> at com.esotericsoftware.kryo.io.OutputChunked.endChunks(OutputChunked.java:82)
> at com.twitter.beam.coder.scala.ChillCoder.encode(ChillCoder.scala:101)
> at com.twitter.eventwrangler.core.attribution.AttributionEventCoder.encode(AttributionEvent.scala:40)
> at com.twitter.eventwrangler.core.attribution.AttributionEventCoder.encode(AttributionEvent.scala:22)
> at org.apache.beam.sdk.coders.Coder.encode(Coder.java:136)
> at org.apache.beam.sdk.transforms.join.UnionCoder.encode(UnionCoder.java:74)
> at org.apache.beam.sdk.transforms.join.UnionCoder.encode(UnionCoder.java:32)
> at org.apache.beam.sdk.coders.KvCoder.encode(KvCoder.java:73)
> at org.apache.beam.sdk.coders.KvCoder.encode(KvCoder.java:37)
> at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.encode(WindowedValue.java:607)
> at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.encode(WindowedValue.java:598)
> at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.encode(WindowedValue.java:558)
> at org.apache.beam.runners.flink.translation.types.CoderTypeSerializer.serialize(CoderTypeSerializer.java:110)
> at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.serialize(TupleSerializer.java:140)
> at org.apache.flink.api.java.typeutils.runtime.TupleSerializer.serialize(TupleSerializer.java:37)
> at org.apache.flink.runtime.operators.sort.NormalizedKeySorter.write(NormalizedKeySorter.java:297)
> at org.apache.flink.runtime.operators.sort.SorterInputGateway.writeRecord(SorterInputGateway.java:77)
> at org.apache.flink.runtime.operators.sort.ReadingThread.go(ReadingThread.java:69)
> at org.apache.flink.runtime.operators.sort.ThreadBase.run(ThreadBase.java:73)
> Caused by: java.io.EOFException: Can't collect further: memorySource depleted
> at org.apache.flink.runtime.io.disk.SimpleCollectingOutputView.nextSegment(SimpleCollectingOutputView.java:76)
> at org.apache.flink.runtime.memory.AbstractPagedOutputView.advance(AbstractPagedOutputView.java:139)
> at org.apache.flink.runtime.memory.AbstractPagedOutputView.write(AbstractPagedOutputView.java:205)
> at org.apache.beam.runners.flink.translation.wrappers.DataOutputViewWrapper.write(DataOutputViewWrapper.java:44)
> at com.esotericsoftware.kryo.io.Output.flush(Output.java:163)
> ... 20 more}}
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