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From Jeremy Lewi <jer...@lewi.us>
Subject Re: Working with Avro Generic Records in the interactive scala shell
Date Tue, 27 May 2014 14:18:40 GMT
I was able to work around this by switching to the SpecificDatum interface
and following this example:
https://github.com/massie/spark-parquet-example/blob/master/src/main/scala/com/zenfractal/SerializableAminoAcid.java

As in the example, I defined a subclass of my Avro type which implemented
the Serializable interface using Avro serialization methods.

I also defined a copy constructor which converted from the actual avro type
to my subclass.

In spark, after reading the Avro file, I ran a map operation to convert
from the avro type to my serializable subclass.
This worked although I'm not sure its the most efficient solution.

Here's a gist of what I run in the console:
https://gist.github.com/jlewi/59b0dec90b639d5d568e#file-avrospecific

I haven't gotten Kryo registration to work yet but it seems like setting
the registrator before launching the console using the environment variable
SPARK_JAVA_OPTS might be better than shutting down and restarting the spark
context in the console.

J


On Sat, May 24, 2014 at 11:16 AM, Jeremy Lewi <jeremy@lewi.us> wrote:

> Hi Josh,
>
> Thanks for the help.
>
> The class should be on the path on all nodes. Here's what I did:
> 1) I built a jar from my scala code.
> 2) I copied that jar to a location on all nodes in my cluster
> (/usr/local/spark)
> 3) I edited bin/compute-classpath.sh  to add my jar to the class path.
> 4) I repeated the process with the avro mapreduce jar to provide AvroKey.
>
> I doubt this is the best way to set the classpath but it seems to work.
>
> J
>
>
> On Sat, May 24, 2014 at 9:26 AM, Josh Marcus <jmarcus@meetup.com> wrote:
>
>> Jeremy,
>>
>> Just to be clear, are you assembling a jar with that class compiled
>> (with its dependencies) and including the path to that jar on the command
>> line in an environment variable (e.g. SPARK_CLASSPATH=path ./spark-shell)?
>>
>> --j
>>
>>
>> On Saturday, May 24, 2014, Jeremy Lewi <jeremy@lewi.us> wrote:
>>
>>> Hi Spark Users,
>>>
>>> I'm trying to read and process an Avro dataset using the interactive
>>> spark scala shell. When my pipeline executes I get the
>>> ClassNotFoundException pasted at the end of this email.
>>> I'm trying to use the Generic Avro API (not the Specific API).
>>>
>>> Here's a gist of the commands I'm running in the spark console:
>>> https://gist.github.com/jlewi/2c853edddd0ceee5f00c
>>>
>>> Here's my registrator for kryo.
>>>
>>> https://github.com/jlewi/cloud/blob/master/spark/src/main/scala/contrail/AvroGenericRegistrator.scala
>>>
>>> Any help or suggestions would be greatly appreciated.
>>>
>>> Thanks
>>> Jeremy
>>>
>>> Here's the log message that is spewed out.
>>>
>>> 14/05/24 02:00:48 WARN TaskSetManager: Loss was due to
>>> java.lang.ClassNotFoundException
>>> java.lang.ClassNotFoundException:
>>> $line16.$read$$iwC$$iwC$$iwC$$iwC$$anonfun$1
>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>>>  at java.security.AccessController.doPrivileged(Native Method)
>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>>>  at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
>>>  at java.lang.Class.forName0(Native Method)
>>> at java.lang.Class.forName(Class.java:270)
>>> at
>>> org.apache.spark.serializer.JavaDeserializationStream$$anon$1.resolveClass(JavaSerializer.scala:37)
>>>  at
>>> java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1612)
>>> at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1517)
>>>  at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1771)
>>> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>>  at
>>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
>>> at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
>>>  at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
>>> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>>  at
>>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
>>> at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
>>>  at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
>>> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>>  at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)
>>> at scala.collection.immutable.$colon$colon.readObject(List.scala:362)
>>>  at sun.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
>>> at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>  at java.lang.reflect.Method.invoke(Method.java:606)
>>> at
>>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1017)
>>>  at
>>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1893)
>>> at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
>>>  at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>> at
>>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
>>>  at
>>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
>>> at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
>>>  at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>> at
>>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
>>>  at
>>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
>>> at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
>>>  at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)
>>>  at scala.collection.immutable.$colon$colon.readObject(List.scala:362)
>>> at sun.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
>>>  at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>> at java.lang.reflect.Method.invoke(Method.java:606)
>>>  at
>>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1017)
>>> at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1893)
>>>  at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
>>> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>>  at
>>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
>>> at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
>>>  at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
>>> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>>  at
>>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
>>> at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
>>>  at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
>>> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>>  at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)
>>> at scala.collection.immutable.$colon$colon.readObject(List.scala:362)
>>>  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>> at
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>>>  at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>> at java.lang.reflect.Method.invoke(Method.java:606)
>>>  at
>>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1017)
>>> at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1893)
>>>  at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
>>> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>>  at
>>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
>>> at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
>>>  at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
>>> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>>  at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)
>>> at
>>> org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:40)
>>>  at
>>> org.apache.spark.scheduler.ResultTask$.deserializeInfo(ResultTask.scala:63)
>>> at
>>> org.apache.spark.scheduler.ResultTask.readExternal(ResultTask.scala:139)
>>>  at
>>> java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1837)
>>> at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1796)
>>>  at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
>>> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)
>>>  at
>>> org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:40)
>>> at
>>> org.apache.spark.serializer.JavaSerializerInstance.deserialize(JavaSerializer.scala:62)
>>>  at
>>> org.apache.spark.executor.Executor$TaskRunner$$anonfun$run$1.apply$mcV$sp(Executor.scala:193)
>>> at
>>> org.apache.spark.deploy.SparkHadoopUtil$$anon$1.run(SparkHadoopUtil.scala:42)
>>>  at
>>> org.apache.spark.deploy.SparkHadoopUtil$$anon$1.run(SparkHadoopUtil.scala:41)
>>> at java.security.AccessController.doPrivileged(Native Method)
>>>  at javax.security.auth.Subject.doAs(Subject.java:415)
>>> at
>>> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1121)
>>>  at
>>> org.apache.spark.deploy.SparkHadoopUtil.runAsUser(SparkHadoopUtil.scala:41)
>>> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:176)
>>>  at
>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>> at
>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>>  at java.lang.Thread.run(Thread.java:744)
>>> 14/05/24 02:00:48 WARN TaskSetManager: Lost TID 2 (task 0.0:2)
>>> 14/05/24 02:00:48 INFO TaskSetManager: Loss was due to
>>> java.lang.ClassNotFoundException:
>>> $line16.$read$$iwC$$iwC$$iwC$$iwC$$anonfun$1 [duplicate 1]
>>> 14/05/24 02:00:48 WARN TaskSetManager: Lost TID 4 (task 0.0:4)
>>> 14/05/24 02:00:48 INFO TaskSetManager: Loss was due to
>>> java.lang.ClassNotFoundException:
>>> $line16.$read$$iwC$$iwC$$iwC$$iwC$$anonfun$1 [duplicate 2]
>>> 14/05/24 02:00:48 WARN TaskSetManager: Lost TID 3 (task 0.0:3)
>>> 14/05/24 02:00:48 INFO TaskSetManager: Loss was due to
>>> java.lang.ClassNotFoundException:
>>> $line16.$read$$iwC$$iwC$$iwC$$iwC$$anonfun$1 [duplicate 3]
>>> 14/05/24 02:00:48 INFO TaskSetManager: Starting task 0.0:3 as TID 12 on
>>> executor 0: spark-slave00.c.biocloudops.internal (PROCESS_LOCAL)
>>> 14/05/24 02:00:48 INFO TaskSetManager: Serialized task 0.0:3 as 1703
>>> bytes in 1 ms
>>> 14/05/24 02:00:48 INFO TaskSetManager: Starting task 0.0:4 as TID 13 on
>>> executor 0: spark-slave00.c.biocloudops.internal (PROCESS_LOCAL)
>>> 14/05/24 02:00:48 INFO TaskSetManager: Serialized task 0.0:4 as 1703
>>> bytes in 1 ms
>>> 14/05/24 02:00:48 INFO TaskSetManager: Starting task 0.0:2 as TID 14 on
>>> executor 0: spark-slave00.c.biocloudops.internal (PROCESS_LOCAL)
>>> 14/05/24 02:00:48 INFO TaskSetManager: Serialized task 0.0:2 as 1703
>>> bytes in 0 ms
>>> 14/05/24 02:00:48 WARN TaskSetManager: Lost TID 7 (task 0.0:7)
>>> 14/05/24 02:00:48 INFO TaskSetManager: Loss was due to
>>> java.lang.ClassNotFoundException:
>>> $line16.$read$$iwC$$iwC$$iwC$$iwC$$anonfun$1 [duplicate 4]
>>> 14/05/24 02:00:48 WARN TaskSetManager: Lost TID 6 (task 0.0:6)
>>>
>>
>

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