Thanks that's super helpful. J
On Tue, May 27, 2014 at 8:01 AM, Matt Massie <mas...@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 <jer...@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 <jer...@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 <jmar...@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 <jer...@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) >>>>> >>>> >>> >> >
