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.ber...@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 <nrpeter...@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.ber...@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 <
>>>> nrpeter...@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
>>>>>
>>>>
>>>>
>>
