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From Vadim Semenov <va...@datadoghq.com.INVALID>
Subject Re: intermittent Kryo serialization failures in Spark
Date Tue, 17 Sep 2019 20:34:42 GMT
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
>


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