It seems there is a problem with the maven class loading. I have created
the uberjar and then executed with traditional java -cp uberjar.jar args
and it worked with no problems. It could be interesting to investigate the
reason, as maven exec is very convenient. However, with the uberjar the
problems of classpath are eased, so I can live with it.
thanks a lot for your support.
saluti,
Stefano
2015-07-24 11:17 GMT+02:00 Stefano Bortoli <s.bort...@gmail.com>:
> HI Stephan,
>
> I think I may have found a possible root of the problem. I do not build
> the fat jar, I simply execute the main with maven exec:java with default
> install and compile. No uberjar created shading. I will try that and
> report. The fact that it runs in eclipse so easily makes it confusing
> somehow.
>
> saluti,
> Stefano
>
> 2015-07-24 11:09 GMT+02:00 Stephan Ewen <se...@apache.org>:
>
>> Hi!
>>
>> There is probably something going wrong in MongoOutputFormat or
>> MongoHadoop2OutputFormat.
>> Something fails, but Java swallows the problem during Serialization.
>>
>> It may be a classloading issue that gets not reported. Are the
>> MongoOutputFormat and the MongoHadoop2OutputFormat both in the fat jar?
>> If not, try putting them in there.
>>
>> The last check we could to (to validate the Flink Serialization
>> utilities) is the code pasted below. If that does not cause the error, it
>> is probably the issue described above.
>>
>> Greetings,
>> Stephan
>>
>>
>> ------------------------------
>>
>> UserCodeObjectWrapper<Object> userCode = new
>> UserCodeObjectWrapper<Object>(new MongoHadoop2OutputFormat<>(new
>> MongoOutputFormat<>(), Job.getInstance()));
>> Configuration cfg = new Configuration();
>> TaskConfig taskConfig = new TaskConfig(cfg);
>> taskConfig.setStubWrapper(userCode);
>> taskConfig.getStubWrapper(ClassLoader.getSystemClassLoader());
>>
>>
>>
>> On Fri, Jul 24, 2015 at 10:44 AM, Stefano Bortoli <s.bort...@gmail.com>
>> wrote:
>>
>>> I have implemented this test without any exception:
>>>
>>> package org.tagcloud.persistence.batch.test;
>>>
>>> import java.io.IOException;
>>>
>>> import org.apache.commons.lang.SerializationUtils;
>>> import org.apache.hadoop.mapreduce.Job;
>>> import org.tagcloud.persistence.batch.MongoHadoop2OutputFormat;
>>>
>>> import com.mongodb.hadoop.MongoOutputFormat;
>>>
>>> public class MongoHadoopSerializationTest {
>>>
>>> public static void main(String[] args) {
>>> Job job;
>>> try {
>>> job = Job.getInstance();
>>> SerializationUtils.clone(new MongoHadoop2OutputFormat<>(new
>>> MongoOutputFormat<>(), job));
>>> } catch (IOException e) {
>>> e.printStackTrace();
>>> }
>>>
>>> }
>>>
>>> }
>>>
>>> 2015-07-24 10:01 GMT+02:00 Stephan Ewen <se...@apache.org>:
>>>
>>>> Hi!
>>>>
>>>> The user code object (the output format here) has a corrupt
>>>> serialization routine.
>>>>
>>>> We use default Java Serialization for these objects. Either the
>>>> MongoHadoopOutputFormat
>>>> cannot be serialized and swallows an exception, or it overrides the
>>>> readObject() / writeObject() methods (from Java Serialization) in an
>>>> inconsistent way.
>>>>
>>>> To figure that out, can you try whether you can manually serialize the
>>>> MongoHadoopOutputFormat?
>>>>
>>>> Can you try and call "SerializationUtils.clone(new
>>>> MongoHadoopOutputFormat)", for example at the beginning of your main
>>>> method? The SerializationUtils are part of Apache Commons and are probably
>>>> in your class path anyways.
>>>>
>>>> Stephan
>>>>
>>>>
>>>> On Fri, Jul 24, 2015 at 9:51 AM, Stefano Bortoli <bort...@okkam.it>
>>>> wrote:
>>>>
>>>>> Hi guys!
>>>>>
>>>>> I could program a data maintenance job using Flink on MongoDB. The job
>>>>> runs smoothly if I start it from eclipse. However, when I try to run it
>>>>> using a bash script invoking a maven exec:java I have a serialization
>>>>> exception:
>>>>> org.apache.flink.runtime.client.JobExecutionException: Cannot
>>>>> initialize task 'DataSink
>>>>> (org.tagcloud.persistence.batch.MongoHadoopOutputFormat@19b88891)':
>>>>> Deserializing the OutputFormat
>>>>> (org.tagcloud.persistence.batch.MongoHadoopOutputFormat@19b88891)
>>>>> failed: Could not read the user code wrapper: unexpected block data
>>>>> at
>>>>> org.apache.flink.runtime.jobmanager.JobManager$$anonfun$org$apache$flink$runtime$jobmanager$JobManager$$submitJob$4.apply(JobManager.scala:523)
>>>>> at
>>>>> org.apache.flink.runtime.jobmanager.JobManager$$anonfun$org$apache$flink$runtime$jobmanager$JobManager$$submitJob$4.apply(JobManager.scala:507)
>>>>>
>>>>> attached the complete stack trace. I thought it was a matter of
>>>>> serializable classes, so I have made all my classes serializable.. still I
>>>>> have the same error. Perhaps it is not possible to do these things with
>>>>> Flink.
>>>>>
>>>>> any intuition? is it doable?
>>>>>
>>>>> thanks a lot for your support. :-)
>>>>>
>>>>> saluti,
>>>>>
>>>>> Stefano Bortoli, PhD
>>>>>
>>>>> *ENS Technical Director *
>>>>> _______________________________________________
>>>>> *OKKAM**Srl **- www.okkam.it <http://www.okkam.it/>*
>>>>>
>>>>> *Email:* bort...@okkam.it
>>>>>
>>>>> *Phone nr: +39 0461 1823912 <%2B39%200461%201823912> *
>>>>>
>>>>> *Headquarters:* Trento (Italy), Via Trener 8
>>>>> *Registered office:* Trento (Italy), via Segantini 23
>>>>>
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>>>>>
>>>>>
>>>>
>>>
>>
>
