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From Igor Berman <igor.ber...@gmail.com>
Subject Re: Spark on Yarn: Kryo throws ClassNotFoundException for class included in fat jar
Date Tue, 08 Sep 2015 15:25:48 GMT
hmm...out of ideas.
can you check in spark ui environment tab that this jar is not somehow
appears 2 times or more...? or more generally - any 2 jars that can contain
this class by any chance

regarding your question about classloader - no idea, probably there is, I
remember stackoverflow has some examples on how to print all classes, but
how to print all classes of kryo classloader - no idea.

On 8 September 2015 at 16:43, Nick Peterson <nrpeterson@gmail.com> wrote:

> Yes, the jar contains the class:
>
> $ jar -tf lumiata-evaluation-assembly-1.0.jar | grep 2028/Document/Document
> com/i2028/Document/Document$1.class
> com/i2028/Document/Document.class
>
> What else can I do?  Is there any way to get more information about the
> classes available to the particular classloader kryo is using?
>
> On Tue, Sep 8, 2015 at 6:34 AM Igor Berman <igor.berman@gmail.com> wrote:
>
>> java.lang.ClassNotFoundException: com.i2028.Document.Document
>>
>> 1. so have you checked that jar that you create(fat jar) contains this class?
>>
>> 2. might be there is some stale cache issue...not sure though
>>
>>
>> On 8 September 2015 at 16:12, Nicholas R. Peterson <nrpeterson@gmail.com>
>> wrote:
>>
>>> Here is the stack trace:  (Sorry for the duplicate, Igor -- I forgot to include
the list.)
>>>
>>>
>>> 15/09/08 05:56:43 WARN scheduler.TaskSetManager: Lost task 183.0 in stage 41.0
(TID 193386, ds-compute2.lumiata.com): java.io.IOException: com.esotericsoftware.kryo.KryoException:
Error constructing instance of class: com.lumiata.patientanalysis.utils.CachedGraph
>>> 	at org.apache.spark.util.Utils$.tryOrIOException(Utils.scala:1257)
>>> 	at org.apache.spark.broadcast.TorrentBroadcast.readBroadcastBlock(TorrentBroadcast.scala:165)
>>> 	at org.apache.spark.broadcast.TorrentBroadcast._value$lzycompute(TorrentBroadcast.scala:64)
>>> 	at org.apache.spark.broadcast.TorrentBroadcast._value(TorrentBroadcast.scala:64)
>>> 	at org.apache.spark.broadcast.TorrentBroadcast.getValue(TorrentBroadcast.scala:88)
>>> 	at org.apache.spark.broadcast.Broadcast.value(Broadcast.scala:70)
>>> 	at com.lumiata.evaluation.analysis.prod.ProductionAnalyzer$$anonfun$apply$1.apply(ProductionAnalyzer.scala:44)
>>> 	at com.lumiata.evaluation.analysis.prod.ProductionAnalyzer$$anonfun$apply$1.apply(ProductionAnalyzer.scala:43)
>>> 	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$17.apply(RDD.scala:686)
>>> 	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$17.apply(RDD.scala:686)
>>> 	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
>>> 	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
>>> 	at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
>>> 	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
>>> 	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
>>> 	at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
>>> 	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
>>> 	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
>>> 	at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
>>> 	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:63)
>>> 	at org.apache.spark.scheduler.Task.run(Task.scala:70)
>>> 	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
>>> 	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>> 	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>> 	at java.lang.Thread.run(Thread.java:745)
>>> Caused by: com.esotericsoftware.kryo.KryoException: Error constructing instance
of class: com.lumiata.patientanalysis.utils.CachedGraph
>>> 	at com.twitter.chill.Instantiators$$anon$1.newInstance(KryoBase.scala:126)
>>> 	at com.esotericsoftware.kryo.Kryo.newInstance(Kryo.java:1065)
>>> 	at com.esotericsoftware.kryo.serializers.FieldSerializer.create(FieldSerializer.java:228)
>>> 	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:217)
>>> 	at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729)
>>> 	at org.apache.spark.serializer.KryoDeserializationStream.readObject(KryoSerializer.scala:182)
>>> 	at org.apache.spark.broadcast.TorrentBroadcast$.unBlockifyObject(TorrentBroadcast.scala:217)
>>> 	at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$readBroadcastBlock$1.apply(TorrentBroadcast.scala:178)
>>> 	at org.apache.spark.util.Utils$.tryOrIOException(Utils.scala:1254)
>>> 	... 24 more
>>> Caused by: java.lang.reflect.InvocationTargetException
>>> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>> 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>>> 	at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
>>> 	at com.twitter.chill.Instantiators$$anonfun$normalJava$1.apply(KryoBase.scala:160)
>>> 	at com.twitter.chill.Instantiators$$anon$1.newInstance(KryoBase.scala:123)
>>> 	... 32 more
>>> Caused by: com.esotericsoftware.kryo.KryoException: Unable to find class: com.i2028.Document.Document
>>> 	at com.esotericsoftware.kryo.util.DefaultClassResolver.readName(DefaultClassResolver.java:138)
>>> 	at com.esotericsoftware.kryo.util.DefaultClassResolver.readClass(DefaultClassResolver.java:115)
>>> 	at com.esotericsoftware.kryo.Kryo.readClass(Kryo.java:610)
>>> 	at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:721)
>>> 	at com.esotericsoftware.kryo.serializers.MapSerializer.read(MapSerializer.java:134)
>>> 	at com.esotericsoftware.kryo.serializers.MapSerializer.read(MapSerializer.java:17)
>>> 	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:626)
>>> 	at com.lumiata.patientanalysis.utils.CachedGraph.loadCacheFromSerializedData(CachedGraph.java:221)
>>> 	at com.lumiata.patientanalysis.utils.CachedGraph.<init>(CachedGraph.java:182)
>>> 	at com.lumiata.patientanalysis.utils.CachedGraph.<init>(CachedGraph.java:178)
>>> 	... 38 more
>>> Caused by: java.lang.ClassNotFoundException: com.i2028.Document.Document
>>> 	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
>>> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>> 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
>>> 	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)
>>> 	... 47 more
>>>
>>>
>>>
>>>> On Tue, Sep 8, 2015 at 6:01 AM Igor Berman <igor.berman@gmail.com>
>>>> wrote:
>>>>
>>>>> I wouldn't build on this. local mode & yarn are different so that
jars
>>>>> you use in spark submit are handled differently
>>>>>
>>>>> On 8 September 2015 at 15:43, Nicholas R. Peterson <
>>>>> nrpeterson@gmail.com> wrote:
>>>>>
>>>>>> Thans, Igor; I've got it running again right now, and can attach
the
>>>>>> stack trace when it finishes.
>>>>>>
>>>>>> In the mean time, I've noticed something interesting: in the Spark
>>>>>> UI, the application jar that I submit is not being included on the
>>>>>> classpath.  It has been successfully uploaded to the nodes -- in
the
>>>>>> nodemanager directory for the application, I see __app__.jar and
>>>>>> __spark__.jar.  The directory itself is on the classpath, and __spark__.jar
>>>>>> and __hadoop_conf__ are as well.  When I do everything the same but
>>>>>> switch the master to local[*], the jar I submit IS added to the classpath.
>>>>>>
>>>>>> This seems like a likely culprit.  What could cause this, and how
can
>>>>>> I fix it?
>>>>>>
>>>>>> Best,
>>>>>> Nick
>>>>>>
>>>>>> On Tue, Sep 8, 2015 at 1:14 AM Igor Berman <igor.berman@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> as a starting point, attach your stacktrace...
>>>>>>> ps: look for duplicates in your classpath, maybe you include
another
>>>>>>> jar with same class
>>>>>>>
>>>>>>> On 8 September 2015 at 06:38, Nicholas R. Peterson <
>>>>>>> nrpeterson@gmail.com> wrote:
>>>>>>>
>>>>>>>> I'm trying to run a Spark 1.4.1 job on my CDH5.4 cluster,
through
>>>>>>>> Yarn. Serialization is set to use Kryo.
>>>>>>>>
>>>>>>>> I have a large object which I send to the executors as a
Broadcast.
>>>>>>>> The object seems to serialize just fine. When it attempts
to deserialize,
>>>>>>>> though, Kryo throws a ClassNotFoundException... for a class
that I include
>>>>>>>> in the fat jar that I spark-submit.
>>>>>>>>
>>>>>>>> What could be causing this classpath issue with Kryo on the
>>>>>>>> executors? Where should I even start looking to try to diagnose
the
>>>>>>>> problem? I appreciate any help you can provide.
>>>>>>>>
>>>>>>>> Thank you!
>>>>>>>>
>>>>>>>> -- Nick
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>

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