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From Julien Laurenceau <julien.laurenc...@pepitedata.com>
Subject Re: intermittent Kryo serialization failures in Spark
Date Fri, 20 Sep 2019 14:00:38 GMT
Hi,
Did you try without the broadcast ?
Regards
JL

Le jeu. 19 sept. 2019 à 06:41, Vadim Semenov <vadim@datadoghq.com.invalid>
a écrit :

> Pre-register your classes:
>
> ```
> import com.esotericsoftware.kryo.Kryo
> import org.apache.spark.serializer.KryoRegistrator
>
> class MyKryoRegistrator extends KryoRegistrator {
>   override def registerClasses(kryo: Kryo): Unit = {
>     kryo.register(Class.forName("[[B")) // byte[][]
>     kryo.register(classOf[java.lang.Class[_]])
>   }
> }
> ```
>
> then run with
>
> 'spark.kryo.referenceTracking': 'false',
> 'spark.kryo.registrationRequired': 'false',
> 'spark.kryo.registrator': 'com.datadog.spark.MyKryoRegistrator',
> 'spark.kryo.unsafe': 'false',
> 'spark.kryoserializer.buffer.max': '256m',
>
> On Tue, Sep 17, 2019 at 10:38 AM Jerry Vinokurov <grapesmoker@gmail.com>
> wrote:
>
>> Hi folks,
>>
>> Posted this some time ago but the problem continues to bedevil us. I'm
>> including a (slightly edited) stack trace that results from this error. If
>> anyone can shed any light on what exactly is happening here and what we can
>> do to avoid it, that would be much appreciated.
>>
>> org.apache.spark.SparkException: Failed to register classes with Kryo
>>> 	at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:140)
>>> 	at org.apache.spark.serializer.KryoSerializerInstance.borrowKryo(KryoSerializer.scala:324)
>>> 	at org.apache.spark.serializer.KryoSerializerInstance.<init>(KryoSerializer.scala:309)
>>> 	at org.apache.spark.serializer.KryoSerializer.newInstance(KryoSerializer.scala:218)
>>> 	at org.apache.spark.broadcast.TorrentBroadcast$.blockifyObject(TorrentBroadcast.scala:288)
>>> 	at org.apache.spark.broadcast.TorrentBroadcast.writeBlocks(TorrentBroadcast.scala:127)
>>> 	at org.apache.spark.broadcast.TorrentBroadcast.<init>(TorrentBroadcast.scala:88)
>>> 	at org.apache.spark.broadcast.TorrentBroadcastFactory.newBroadcast(TorrentBroadcastFactory.scala:34)
>>> 	at org.apache.spark.broadcast.BroadcastManager.newBroadcast(BroadcastManager.scala:62)
>>> 	at org.apache.spark.SparkContext.broadcast(SparkContext.scala:1489)
>>> 	at org.apache.spark.sql.execution.datasources.csv.CSVFileFormat.buildReader(CSVFileFormat.scala:103)
>>> 	at org.apache.spark.sql.execution.datasources.FileFormat$class.buildReaderWithPartitionValues(FileFormat.scala:129)
>>> 	at org.apache.spark.sql.execution.datasources.TextBasedFileFormat.buildReaderWithPartitionValues(FileFormat.scala:165)
>>> 	at org.apache.spark.sql.execution.FileSourceScanExec.inputRDD$lzycompute(DataSourceScanExec.scala:309)
>>> 	at org.apache.spark.sql.execution.FileSourceScanExec.inputRDD(DataSourceScanExec.scala:305)
>>> 	at org.apache.spark.sql.execution.FileSourceScanExec.inputRDDs(DataSourceScanExec.scala:327)
>>> 	at org.apache.spark.sql.execution.FilterExec.inputRDDs(basicPhysicalOperators.scala:121)
>>> 	at org.apache.spark.sql.execution.ProjectExec.inputRDDs(basicPhysicalOperators.scala:41)
>>> 	at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:627)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:131)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:156)
>>> 	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
>>> 	at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:152)
>>> 	at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec.prepareShuffleDependency(ShuffleExchangeExec.scala:92)
>>> 	at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec$$anonfun$doExecute$1.apply(ShuffleExchangeExec.scala:128)
>>> 	at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec$$anonfun$doExecute$1.apply(ShuffleExchangeExec.scala:119)
>>> 	at org.apache.spark.sql.catalyst.errors.package$.attachTree(package.scala:52)
>>> 	at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec.doExecute(ShuffleExchangeExec.scala:119)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:131)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:156)
>>> 	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
>>> 	at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:152)
>>> 	at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.InputAdapter.inputRDDs(WholeStageCodegenExec.scala:391)
>>> 	at org.apache.spark.sql.execution.SortExec.inputRDDs(SortExec.scala:121)
>>> 	at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:627)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:131)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:156)
>>> 	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
>>> 	at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:152)
>>> 	at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.window.WindowExec.doExecute(WindowExec.scala:302)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:131)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:156)
>>> 	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
>>> 	at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:152)
>>> 	at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.InputAdapter.inputRDDs(WholeStageCodegenExec.scala:391)
>>> 	at org.apache.spark.sql.execution.ProjectExec.inputRDDs(basicPhysicalOperators.scala:41)
>>> 	at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:627)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:131)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:156)
>>> 	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
>>> 	at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:152)
>>> 	at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.columnar.CachedRDDBuilder.buildBuffers(InMemoryRelation.scala:83)
>>> 	at org.apache.spark.sql.execution.columnar.CachedRDDBuilder.cachedColumnBuffers(InMemoryRelation.scala:59)
>>> 	at org.apache.spark.sql.execution.columnar.InMemoryTableScanExec.filteredCachedBatches(InMemoryTableScanExec.scala:276)
>>> 	at org.apache.spark.sql.execution.columnar.InMemoryTableScanExec.inputRDD$lzycompute(InMemoryTableScanExec.scala:105)
>>> 	at org.apache.spark.sql.execution.columnar.InMemoryTableScanExec.inputRDD(InMemoryTableScanExec.scala:104)
>>> 	at org.apache.spark.sql.execution.columnar.InMemoryTableScanExec.doExecute(InMemoryTableScanExec.scala:310)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:131)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:156)
>>> 	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
>>> 	at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:152)
>>> 	at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.InputAdapter.inputRDDs(WholeStageCodegenExec.scala:391)
>>> 	at org.apache.spark.sql.execution.FilterExec.inputRDDs(basicPhysicalOperators.scala:121)
>>> 	at org.apache.spark.sql.execution.ProjectExec.inputRDDs(basicPhysicalOperators.scala:41)
>>> 	at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:627)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:131)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:156)
>>> 	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
>>> 	at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:152)
>>> 	at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:143)
>>> 	at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:159)
>>> 	at org.apache.spark.sql.execution.command.DataWritingCommandExec.sideEffectResult$lzycompute(commands.scala:104)
>>> 	at org.apache.spark.sql.execution.command.DataWritingCommandExec.sideEffectResult(commands.scala:102)
>>> 	at org.apache.spark.sql.execution.command.DataWritingCommandExec.doExecute(commands.scala:122)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:131)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:156)
>>> 	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
>>> 	at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:152)
>>> 	at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:127)
>>> 	at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:80)
>>> 	at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:80)
>>> 	at org.apache.spark.sql.DataFrameWriter$$anonfun$runCommand$1.apply(DataFrameWriter.scala:676)
>>> 	at org.apache.spark.sql.DataFrameWriter$$anonfun$runCommand$1.apply(DataFrameWriter.scala:676)
>>> 	at org.apache.spark.sql.execution.SQLExecution$$anonfun$withNewExecutionId$1.apply(SQLExecution.scala:78)
>>> 	at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:125)
>>> 	at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:73)
>>> 	at org.apache.spark.sql.DataFrameWriter.runCommand(DataFrameWriter.scala:676)
>>> 	at org.apache.spark.sql.DataFrameWriter.saveToV1Source(DataFrameWriter.scala:285)
>>> 	at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:271)
>>> 	at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:229)
>>> 	at org.apache.spark.sql.DataFrameWriter.csv(DataFrameWriter.scala:664)
>>>         [our code that writes data to CSV]	
>>> Caused by: java.lang.ClassNotFoundException: com.mycompany.models.MyModel
>>> 	at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
>>> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>> 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
>>> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>> 	at java.lang.Class.forName0(Native Method)
>>> 	at java.lang.Class.forName(Class.java:348)
>>> 	at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$4.apply(KryoSerializer.scala:132)
>>> 	at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$4.apply(KryoSerializer.scala:132)
>>> 	at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
>>> 	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186)
>>> 	at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:132)
>>> 	... 132 more
>>>
>>>
>> On Wed, Jul 10, 2019 at 12:50 PM Jerry Vinokurov <grapesmoker@gmail.com>
>> wrote:
>>
>>> Hi all,
>>>
>>> I am experiencing a strange intermittent failure of my Spark job that
>>> results from serialization issues in Kryo. Here is the stack trace:
>>>
>>> Caused by: java.lang.ClassNotFoundException: com.mycompany.models.MyModel
>>>> 	at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
>>>> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>> 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
>>>> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>> 	at java.lang.Class.forName0(Native Method)
>>>> 	at java.lang.Class.forName(Class.java:348)
>>>> 	at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$4.apply(KryoSerializer.scala:132)
>>>> 	at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$4.apply(KryoSerializer.scala:132)
>>>> 	at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
>>>> 	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186)
>>>> 	at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:132)
>>>> 	... 204 more
>>>>
>>>> (I've edited the company and model name since this is proprietary code)
>>>
>>> This error does not surface every time the job is run; I would say it
>>> probably shows up once in every 10 runs or so, and there isn't anything
>>> about the input data that triggers this, as I've been able to
>>> (nondeterministically) reproduce the error by simply rerunning the job with
>>> the same inputs over and over again. The model itself is just a plain Scala
>>> case class whose fields are strings and integers, so there's no custom
>>> serialization logic or anything like that. As I understand, this is seems
>>> related to an issue previously documented here
>>> <https://issues.apache.org/jira/browse/SPARK-21928>but allegedly this
>>> was fixed long ago. I'm running this job on an AWS EMR cluster and have
>>> confirmed that the version of Spark running there is 2.4.0, with the patch
>>> that is linked in the above issue being part of the code.
>>>
>>> A suggested solution has been to set the extraClasspath config settings
>>> on the driver and executor, but that has not fixed the problem. I'm out of
>>> ideas for how to tackle this and would love to hear if anyone has any
>>> suggestions or strategies for fixing this.
>>>
>>> thanks,
>>> Jerry
>>>
>>> --
>>> http://www.google.com/profiles/grapesmoker
>>>
>>
>>
>> --
>> http://www.google.com/profiles/grapesmoker
>>
>
>
> --
> Sent from my iPhone
>

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