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From Florin Tatu <tatuflo...@gmail.com>
Subject Re: Error while trying to obtain the top elements.
Date Wed, 08 Jul 2015 09:22:06 GMT
Hi David, Gabriel,

Using Avros I get  org.apache.avro.UnresolvedUnionException: Not in union

The situation is similar to the crunch example from the hadoop book(first
make a clone:
git clone https://github.com/tomwhite/hadoop-book.git)
If you run on hadoop-book/ch18-crunch the following commands:

mvn package
hadoop jar target/ch18-crunch-4.0-job.jar
crunch.AvroGenericMaxTemperatureCrunch ncdc_data output

you obtain the following exception:

java.lang.Exception: org.apache.avro.UnresolvedUnionException: Not in union
[{"type":"record","name":"WeatherRecord","namespace":"org.apache.avro.mapred","doc":"A
weather
reading.","fields":[{"name":"year","type":"int"},{"name":"temperature","type":"int"},{"name":"stationId","type":"string"}]},"null"]:
{"year": 1928, "temperature": 28, "stationId": "011060-99999"}
at
org.apache.hadoop.mapred.LocalJobRunner$Job.runTasks(LocalJobRunner.java:462)
at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:522)
Caused by: org.apache.avro.UnresolvedUnionException: Not in union
[{"type":"record","name":"WeatherRecord","namespace":"org.apache.avro.mapred","doc":"A
weather
reading.","fields":[{"name":"year","type":"int"},{"name":"temperature","type":"int"},{"name":"stationId","type":"string"}]},"null"]:
{"year": 1928, "temperature": 28, "stationId": "011060-99999"}
at org.apache.avro.generic.GenericData.resolveUnion(GenericData.java:561)
at
org.apache.avro.generic.GenericDatumWriter.resolveUnion(GenericDatumWriter.java:144)
at
org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:71)
at
org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:58)
at
org.apache.crunch.types.avro.SafeAvroSerialization$AvroWrapperSerializer.serialize(SafeAvroSerialization.java:128)
at
org.apache.crunch.types.avro.SafeAvroSerialization$AvroWrapperSerializer.serialize(SafeAvroSerialization.java:113)
at
org.apache.hadoop.mapred.MapTask$MapOutputBuffer.collect(MapTask.java:1157)
at
org.apache.hadoop.mapred.MapTask$NewOutputCollector.write(MapTask.java:715)
at
org.apache.hadoop.mapreduce.task.TaskInputOutputContextImpl.write(TaskInputOutputContextImpl.java:89)
at
org.apache.hadoop.mapreduce.lib.map.WrappedMapper$Context.write(WrappedMapper.java:112)
at org.apache.crunch.impl.mr.emit.OutputEmitter.emit(OutputEmitter.java:41)
at org.apache.crunch.MapFn.process(MapFn.java:34)
at org.apache.crunch.impl.mr.run.RTNode.process(RTNode.java:98)
at
org.apache.crunch.impl.mr.emit.IntermediateEmitter.emit(IntermediateEmitter.java:56)
at
crunch.AvroGenericMaxTemperatureCrunch$2.process(AvroGenericMaxTemperatureCrunch.java:95)
at
crunch.AvroGenericMaxTemperatureCrunch$2.process(AvroGenericMaxTemperatureCrunch.java:82)
at org.apache.crunch.impl.mr.run.RTNode.process(RTNode.java:98)
at
org.apache.crunch.impl.mr.emit.IntermediateEmitter.emit(IntermediateEmitter.java:56)
at org.apache.crunch.MapFn.process(MapFn.java:34)
at org.apache.crunch.impl.mr.run.RTNode.process(RTNode.java:98)
at org.apache.crunch.impl.mr.run.RTNode.process(RTNode.java:109)
at org.apache.crunch.impl.mr.run.CrunchMapper.map(CrunchMapper.java:60)
at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:146)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:787)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
at
org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:243)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
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:745)

As far as I researched it seems to be related with:
https://issues.apache.org/jira/browse/CRUNCH-360
(but please correct me if I am wrong).

If this is a known issue, is there another alternative?

PS: @Gabriel Reid: I saw you made a patch for the issue
https://issues.apache.org/jira/browse/CRUNCH-539
I am unfamiliar on how to apply it to the project, can you please provide
me some minimal guidance? :)


- Florin

On Tue, Jul 7, 2015 at 11:45 PM, Gabriel Reid <gabriel.reid@gmail.com>
wrote:

> Hi Florin,
>
> Thanks for the very detailed report. That appears to be a bug, brought on
> by the way that ObjectInputStream works with classloaders, together with
> how Hadoop manipulates classloaders.
>
> I've logged a JIRA ticket [1] for this. For now, like David I would
> recommend using Avros instead of Writables, as that should get around this
> issue without having any other consequences for now.
>
> - Gabriel
>
> 1. https://issues.apache.org/jira/browse/CRUNCH-539
>
>
> On Tue, Jul 7, 2015 at 3:27 PM David Ortiz <dpo5003@gmail.com> wrote:
>
>> That looks weird.  Can you try it using Avros in place of Writables and
>> see if it does the same thing?
>>
>> On Tue, Jul 7, 2015, 3:43 AM Florin Tatu <tatuflorin@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I am having a job that processes a set of files containing climatic
>>> data(more exactly data from this location:
>>> ftp://ftp.ncdc.noaa.gov/pub/data/noaa/)
>>>
>>> I downloaded and merged the data using a script so I will have one
>>> folder (ncdc_data) having a .gz archive for each year(eg: 1901.gz, 1902.gz
>>> etc)
>>> Each archive contains only one text file.
>>>
>>> My code is:
>>>
>>> import com.google.common.base.Charsets;
>>> import com.google.common.io.Files;
>>> import org.apache.crunch.*;
>>> import org.apache.crunch.fn.Aggregators;
>>> import org.apache.crunch.impl.mr.MRPipeline;
>>> import org.apache.crunch.io.To;
>>> import java.io.File;
>>> import static org.apache.crunch.types.writable.Writables.ints;
>>> import static org.apache.crunch.types.writable.Writables.strings;
>>> import static org.apache.crunch.types.writable.Writables.tableOf;
>>>
>>> public class MaxTemperatureCrunch {
>>>
>>>     public static void main(String[] args) throws Exception {
>>>         if (args.length != 2) {
>>>             System.err.println("Usage: MaxTemperatureCrunch <input path>
>>> <output path>");
>>>             System.exit(-1);
>>>         }
>>>
>>>         Pipeline pipeline = new MRPipeline(MaxTemperatureCrunch.class);
>>>
>>>         PCollection<String> records = pipeline.readTextFile(args[0]);
>>>
>>>         PTable<String, Integer> yearTemperatures = records
>>>                 .parallelDo(toYearTempPairsFn(), tableOf(strings(),
>>> ints()));
>>>
>>>         PTable<String, Integer> maxTemps = yearTemperatures
>>>                 .groupByKey()
>>>                 .combineValues(Aggregators.MAX_INTS())
>>>                 .top(1);   //LINE THAT CAUSES THE ERROR
>>>
>>>         maxTemps.write(To.textFile(args[1]));
>>>
>>>         PipelineResult result = pipeline.done();
>>>         String dot =
>>> pipeline.getConfiguration().get("crunch.planner.dotfile");
>>>         Files.write(dot, new File("pipeline.dot"), Charsets.UTF_8);
>>>         Runtime.getRuntime().exec("dot -Tpng -O pipeline.dot");
>>>         System.exit(result.succeeded() ? 0 : 1);
>>>     }
>>>
>>>     static DoFn<String, Pair<String, Integer>> toYearTempPairsFn()
{
>>>         return new DoFn<String, Pair<String, Integer>>() {
>>>             NcdcRecordParser parser = new NcdcRecordParser();
>>>             @Override
>>>             public void process(String input, Emitter<Pair<String,
>>> Integer>> emitter) {
>>>                 parser.parse(input);
>>>                 if (parser.isValidTemperature()) {
>>>                     emitter.emit(Pair.of(parser.getYear(),
>>> parser.getAirTemperature()));
>>>                 }
>>>             }
>>>         };
>>>     }
>>> }
>>>
>>>
>>> Hadoop runs locally in standalone mode.
>>> Hadoop version is: 2.7.0
>>> Crunch version is: 0.12.0  (maven dependency: 0.12.0-hadoop2)
>>>
>>> I build my application with: mvn package
>>> I run it with: hadoop jar target/crunch-demo-1.0-SNAPSHOT-job.jar
>>> ncdc_data/ output
>>>
>>> If I do not call .top(1) (see comment:  //LINE THAT CAUSES THE ERROR)
>>> everything works fine, but I obtain the maximum temperatures for each year
>>> only and I want to obtain the overall maximum temperature or the top N
>>> temperatures for the whole data set.
>>>
>>> If I call .top(1) I obtain the following error:
>>>
>>> java.lang.Exception: org.apache.crunch.CrunchRuntimeException: Error
>>> reloading writable comparable codes
>>> at
>>> org.apache.hadoop.mapred.LocalJobRunner$Job.runTasks(LocalJobRunner.java:462)
>>> at
>>> org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:522)
>>> Caused by: org.apache.crunch.CrunchRuntimeException: Error reloading
>>> writable comparable codes
>>> at
>>> org.apache.crunch.types.writable.TupleWritable.setConf(TupleWritable.java:71)
>>> at
>>> org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:76)
>>> at
>>> org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:136)
>>> at
>>> org.apache.hadoop.io.serializer.WritableSerialization$WritableDeserializer.deserialize(WritableSerialization.java:66)
>>> at
>>> org.apache.hadoop.io.serializer.WritableSerialization$WritableDeserializer.deserialize(WritableSerialization.java:42)
>>> at
>>> org.apache.hadoop.io.SequenceFile$Reader.deserializeValue(SequenceFile.java:2247)
>>> at
>>> org.apache.hadoop.io.SequenceFile$Reader.getCurrentValue(SequenceFile.java:2220)
>>> at
>>> org.apache.hadoop.mapreduce.lib.input.SequenceFileRecordReader.nextKeyValue(SequenceFileRecordReader.java:78)
>>> at
>>> org.apache.crunch.impl.mr.run.CrunchRecordReader.nextKeyValue(CrunchRecordReader.java:157)
>>> at
>>> org.apache.hadoop.mapred.MapTask$NewTrackingRecordReader.nextKeyValue(MapTask.java:556)
>>> at
>>> org.apache.hadoop.mapreduce.task.MapContextImpl.nextKeyValue(MapContextImpl.java:80)
>>> at
>>> org.apache.hadoop.mapreduce.lib.map.WrappedMapper$Context.nextKeyValue(WrappedMapper.java:91)
>>> at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:145)
>>> at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:787)
>>> at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
>>> at
>>> org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:243)
>>> at
>>> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
>>> at java.util.concurrent.FutureTask.run(FutureTask.java:262)
>>> at
>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>> at
>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>> at java.lang.Thread.run(Thread.java:745)
>>> Caused by: java.lang.ClassNotFoundException:
>>> org.apache.crunch.types.writable.TupleWritable
>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>>> at java.security.AccessController.doPrivileged(Native Method)
>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
>>> at java.lang.Class.forName0(Native Method)
>>> at java.lang.Class.forName(Class.java:274)
>>> at java.io.ObjectInputStream.resolveClass(ObjectInputStream.java:625)
>>> at
>>> java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1612)
>>> at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1517)
>>> at java.io.ObjectInputStream.readClass(ObjectInputStream.java:1483)
>>> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1333)
>>> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)
>>> at
>>> com.google.common.collect.Serialization.populateMap(Serialization.java:91)
>>> at com.google.common.collect.HashBiMap.readObject(HashBiMap.java:109)
>>> 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.readObject(ObjectInputStream.java:370)
>>> at
>>> org.apache.crunch.types.writable.Writables.reloadWritableComparableCodes(Writables.java:145)
>>> at
>>> org.apache.crunch.types.writable.TupleWritable.setConf(TupleWritable.java:69)
>>> ... 20 more
>>>
>>>
>>> Did anyone encountered this issue?
>>> If you need any other details please ask me.
>>>
>>> Thank you,
>>> Florin
>>>
>>

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