Implementing a custom serialization approach with Flink's CopyableValue (instead of relying on Flink to automatically use Kryo) solved the issue. As a side benefit, this also reduced the serialized size of my object by about half.
From: Stephan Ewen <se...@apache.org<mailto:se...@apache.org>> Date: Friday, September 30, 2016 at 3:58 AM To: <user@flink.apache.org<mailto:user@flink.apache.org>> Cc: Stephan Ewen <se...@apache.org<mailto:se...@apache.org>> Subject: Re: Error while adding data to RocksDB: No more bytes left Agree with Stefan, let's see if the fully async snapshot mode helps. It looks suspiciously RocksDB related... On Fri, Sep 30, 2016 at 10:30 AM, Stefan Richter <s.rich...@data-artisans.com<mailto:s.rich...@data-artisans.com>> wrote: Hi Shannon, from your new stack trace and the bogus class names, I agree with Stephan that either serialization or the database itself is corrupted in some way. Could you please check if this problem only happens if checkpointing is enabled? If yes, does switching to fully async snapshots change the behavior? Best, Stefan Am 29.09.2016 um 21:12 schrieb Shannon Carey <sca...@expedia.com<mailto:sca...@expedia.com>>: Hi Stephan! The failure appeared to occur every 10 minutes, which is also the interval for checkpointing. However, I agree with you that the stack trace appears to be independent. Could this perhaps be an issue with multithreading, where the checkpoint mechanism is somehow interfering with ongoing operation of the state backend? I've never seen this problem until now, so I am a little suspicious that it might be due to something in my code, but so far it's been difficult to figure out what that might be. I am using the default, SemiAsync snapshot mode. The classes of the data flow are a bit too large to put here in their entirety. We are using Scala case classes, Java classes generated by Avro, Tuples, Scala Option, java.util.UUID and Scala mutable.Map. The majority of these classes have been operational in other jobs before. I added a unit test for the class which contains a mutable.Map to see whether that was causing a problem. Does this look like a reasonable unit test to verify Flink serializability to you? it("roundtrip serializes in Flink") { val millis: Long = TimeUnit.DAYS.toMillis(2) val original: PreferredAirportDailySum = new PreferredAirportDailySum(millis) original.add("a", TimestampedAirportCount(4, 6)) original.add("b", TimestampedAirportCount(7, 8)) val deserialized: PreferredAirportDailySum = serializationRoundTrip(original, 100) deserialized.timestamp shouldBe millis deserialized.immutableItems("a") shouldBe TimestampedAirportCount(4, 6) deserialized.immutableItems("b") shouldBe TimestampedAirportCount(7, 8) } def serializationRoundTrip[T : ClassTag : TypeInformation](original: T, expectedMaxBytes: Int): T = { val typeInfo = implicitly[TypeInformation[T]] val serializer: TypeSerializer[T] = typeInfo.createSerializer(new ExecutionConfig) val out: ByteArrayOutputStream = new ByteArrayOutputStream(expectedMaxBytes) val outputView: DataOutputView = new DataOutputViewStreamWrapper(out) serializer.serialize(original, outputView) out.size() should be <= expectedMaxBytes val inputView: DataInputViewStreamWrapper = new DataInputViewStreamWrapper(new ByteArrayInputStream(out.toByteArray)) val deserialized: T = serializer.deserialize(inputView) deserialized } I tried running my job in a local one-slot cluster with RocksDB enabled but checkpointing to local filesystem. Similar errors occur, but are more sporadic. I have not yet been able to capture the error while debugging, but if I do I will provide additional information. I noticed that locally, execution only reaches DefaultClassResolver#readName(Input)->Class.forName() when a checkpoint completes. Also, the timing of checkpointing a bit odd: in the example below the checkpoint takes 200s to complete after being triggered even though RocksDB reports that it only took ~100ms. 2016-09-29 12:56:17,619 INFO CheckpointCoordinator - Triggering checkpoint 2 @ 1475171777619 2016-09-29 12:59:38,079 INFO RocksDBStateBackend - RocksDB (/var/folders/…./WindowOperator_38_0/dummy_state/730773a2-bb33-4021-aa9e-9b4e3cb172f3/db) backup (synchronous part) took 7 ms. 2016-09-29 12:59:38,214 INFO RocksDBStateBackend - RocksDB materialization from /var/folders/…/WindowOperator_38_0/dummy_state/730773a2-bb33-4021-aa9e-9b4e3cb172f3/local-chk-2 to file:/var/flinkstate/…/WindowOperator_38_0/dummy_state/chk-2 (asynchronous part) took 96 ms. 2016-09-29 12:59:38,333 INFO CheckpointCoordinator - Completed checkpoint 2 (in 200621 ms) Do you have any other advice? Exceptions from local execution: java.lang.RuntimeException: Error while adding data to RocksDB at org.apache.flink.contrib.streaming.state.RocksDBFoldingState.add(RocksDBFoldingState.java:125) at org.apache.flink.streaming.runtime.operators.windowing.WindowOperator.processElement(WindowOperator.java:382) at org.apache.flink.streaming.runtime.io<http://runtime.io>.StreamInputProcessor.processInput(StreamInputProcessor.java:176) at org.apache.flink.streaming.runtime.tasks.OneInputStreamTask.run(OneInputStreamTask.java:66) at org.apache.flink.streaming.runtime.tasks.StreamTask.invoke(StreamTask.java:266) at org.apache.flink.runtime.taskmanager.Task.run(Task.java:584) at java.lang.Thread.run(Thread.java:745) Caused by: com.esotericsoftware.kryo.KryoException: Unable to find class: 'CLE at com.esotericsoftware.kryo.util.DefaultClassResolver.readName(DefaultClassResolver.java:138) at com.esotericsoftware.kryo.util.DefaultClassResolver.readClass(DefaultClassResolver.java:115) at com.esotericsoftware.kryo.Kryo.readClass(Kryo.java:641) at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:752) 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.scala.typeutils.CaseClassSerializer.deserialize(CaseClassSerializer.scala:113) at org.apache.flink.api.scala.typeutils.CaseClassSerializer.deserialize(CaseClassSerializer.scala:30) at org.apache.flink.contrib.streaming.state.RocksDBFoldingState.add(RocksDBFoldingState.java:118) ... 6 more Caused by: java.lang.ClassNotFoundException: 'CLE at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at com.esotericsoftware.kryo.util.DefaultClassResolver.readName(DefaultClassResolver.java:136) ... 16 more After that one happened, this one happened many times: java.lang.RuntimeException: Failed to deserialize state handle and setup initial operator state. at org.apache.flink.runtime.taskmanager.Task.run(Task.java:547) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.IOException: Unable to deserialize default value. at org.apache.flink.api.common.state.StateDescriptor.readObject(StateDescriptor.java:285) at sun.reflect.GeneratedMethodAccessor34.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1058) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1900) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:371) at java.util.ArrayList.readObject(ArrayList.java:791) at sun.reflect.GeneratedMethodAccessor11.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1058) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1900) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:371) at java.util.HashMap.readObject(HashMap.java:1396) at sun.reflect.GeneratedMethodAccessor9.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1058) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1900) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1707) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1345) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:371) at org.apache.flink.util.InstantiationUtil.deserializeObject(InstantiationUtil.java:291) at org.apache.flink.util.SerializedValue.deserializeValue(SerializedValue.java:58) at org.apache.flink.runtime.taskmanager.Task.run(Task.java:542) ... 1 more Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -2 at java.lang.String.<init>(String.java:196) at com.esotericsoftware.kryo.io<http://com.esotericsoftware.kryo.io>.Input.readString(Input.java:466) at com.esotericsoftware.kryo.util.DefaultClassResolver.readName(DefaultClassResolver.java:132) at com.esotericsoftware.kryo.util.DefaultClassResolver.readClass(DefaultClassResolver.java:115) at com.esotericsoftware.kryo.Kryo.readClass(Kryo.java:641) at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:752) 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.scala.typeutils.CaseClassSerializer.deserialize(CaseClassSerializer.scala:113) at org.apache.flink.api.scala.typeutils.CaseClassSerializer.deserialize(CaseClassSerializer.scala:30) at org.apache.flink.api.common.state.StateDescriptor.readObject(StateDescriptor.java:282) ... 44 more During another execution, this one occurred several times: java.lang.RuntimeException: Failed to deserialize state handle and setup initial operator state. at org.apache.flink.runtime.taskmanager.Task.run(Task.java:547) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.IOException: Unable to deserialize default value. at org.apache.flink.api.common.state.StateDescriptor.readObject(StateDescriptor.java:285) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1058) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1900) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:371) at java.util.ArrayList.readObject(ArrayList.java:791) at sun.reflect.GeneratedMethodAccessor42.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1058) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1900) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:371) at java.util.HashMap.readObject(HashMap.java:1396) at sun.reflect.GeneratedMethodAccessor41.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1058) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1900) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1707) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1345) at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2000) at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1924) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1801) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1351) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:371) at org.apache.flink.util.InstantiationUtil.deserializeObject(InstantiationUtil.java:291) at org.apache.flink.util.SerializedValue.deserializeValue(SerializedValue.java:58) at org.apache.flink.runtime.taskmanager.Task.run(Task.java:542) ... 1 more Caused by: com.esotericsoftware.kryo.KryoException: Unable to find class: # at com.esotericsoftware.kryo.util.DefaultClassResolver.readName(DefaultClassResolver.java:138) at com.esotericsoftware.kryo.util.DefaultClassResolver.readClass(DefaultClassResolver.java:115) at com.esotericsoftware.kryo.Kryo.readClass(Kryo.java:641) at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:752) at org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.deserialize(KryoSerializer.java:232) at org.apache.flink.api.scala.typeutils.CaseClassSerializer.deserialize(CaseClassSerializer.scala:113) at org.apache.flink.api.scala.typeutils.CaseClassSerializer.deserialize(CaseClassSerializer.scala:30) at org.apache.flink.api.common.state.StateDescriptor.readObject(StateDescriptor.java:282) ... 45 more Caused by: java.lang.ClassNotFoundException: # at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at com.esotericsoftware.kryo.util.DefaultClassResolver.readName(DefaultClassResolver.java:136) ... 52 more From: Stephan Ewen <se...@apache.org<mailto:se...@apache.org>> Date: Wednesday, September 28, 2016 at 1:18 PM To: <user@flink.apache.org<mailto:user@flink.apache.org>> Subject: Re: Error while adding data to RocksDB: No more bytes left Hi Shannon! The stack trace you pasted is independent of checkpointing - it seems to be from the regular processing. Does this only happen when checkpoints are activated? Can you also share which checkpoint method you use? - FullyAsynchronous - SemiAsynchronous I think there are two possibilities for what can happen - There is a serialization inconsistency in the Serializers. If that is the case, this error should occur almost in a deterministic fashion. To debug that, would be good to know which data types you are using. - There is a bug in RocksDB (or Flink's wrapping of it) where data gets corrupted when using the snapshot feature. That would explain why this only occurs when checkpoints are happening. Greetings, Stephan On Wed, Sep 28, 2016 at 7:28 PM, Shannon Carey <sca...@expedia.com<mailto:sca...@expedia.com>> wrote: It appears that when one of my jobs tries to checkpoint, the following exception is triggered. I am using Flink 1.1.1 in Scala 2.11. RocksDB checkpoints are being saved to S3. java.lang.RuntimeException: Error while adding data to RocksDB at org.apache.flink.contrib.streaming.state.RocksDBFoldingState.add(RocksDBFoldingState.java:125) at org.apache.flink.streaming.runtime.operators.windowing.WindowOperator.processElement(WindowOperator.java:382) at org.apache.flink.streaming.runtime.io<http://runtime.io/>.StreamInputProcessor.processInput(StreamInputProcessor.java:176) at org.apache.flink.streaming.runtime.tasks.OneInputStreamTask.run(OneInputStreamTask.java:66) at org.apache.flink.streaming.runtime.tasks.StreamTask.invoke(StreamTask.java:266) at org.apache.flink.runtime.taskmanager.Task.run(Task.java:584) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.EOFException: No more bytes left. at org.apache.flink.api.java.typeutils.runtime.NoFetchingInput.require(NoFetchingInput.java:77) at com.esotericsoftware.kryo.io<http://com.esotericsoftware.kryo.io/>.Input.readVarLong(Input.java:690) at com.esotericsoftware.kryo.io<http://com.esotericsoftware.kryo.io/>.Input.readLong(Input.java:685) at com.esotericsoftware.kryo.serializers.UnsafeCacheFields$UnsafeLongField.read(UnsafeCacheFields.java:160) at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:528) 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.scala.typeutils.CaseClassSerializer.deserialize(CaseClassSerializer.scala:113) at org.apache.flink.api.scala.typeutils.CaseClassSerializer.deserialize(CaseClassSerializer.scala:30) at org.apache.flink.contrib.streaming.state.RocksDBFoldingState.add(RocksDBFoldingState.java:118) ... 6 more Thanks for any help! Shannon
