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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 15:49:38 GMT
Thanks that's super helpful.

J


On Tue, May 27, 2014 at 8:01 AM, Matt Massie <massie@berkeley.edu> wrote:

> I really should update that blog post. I created a gist (see
> https://gist.github.com/massie/7224868) which explains a cleaner, more
> efficient approach.
>
> --
> Matt <http://www.linkedin.com/in/mattmassie/> Massie<http://www.twitter.com/matt_massie>
> UC, Berkeley AMPLab <https://twitter.com/amplab>
>
>
> On Tue, May 27, 2014 at 7:18 AM, Jeremy Lewi <jeremy@lewi.us> wrote:
>
>> 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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