[kepler-users] ERROR EXECUTING A .KAR FILE
Josep Morer Muñoz
josep.morer at gmail.com
Tue Mar 16 01:20:06 PDT 2010
Thanks all for your efforts!
On 15 March 2010 19:55, Chad Berkley <berkley at nceas.ucsb.edu> wrote:
> I think we need more command line control for kar files. This won't be
> implemented for 2.0, but I'll make an enhancement request for 2.x in
> bugzilla. We should be able to specify a kar file, the workflow in the kar
> file to run and the output location on the command line. It really doesn't
> make sense to just have defaults. I think since we developed this
> capability for a specific purpose (SanParks) we were just trying to get it
> to work and didn't really look at the whole picture on what it should do.
> I'll add the bug now.
>
> chad
>
>
>
> ben leinfelder wrote:
>
>> Josep -
>> In the meantime, can you try removing the semantic type from your
>> workflow, resaving the KAR and then running it? I hope that will work until
>> we resolve this semantic type/cache issue.
>> Thanks,
>> -ben
>>
>> On Mar 13, 2010, at 2:21 AM, Josep Morer Muñoz wrote:
>>
>> Hello all,
>>>
>>> I have not executed any KAR yet. I always get the same error (executing
>>> the KAR with cache). Any idea?
>>>
>>> urops at urops-laptop:~/Kepler-2.0.0-beta1$ ./kepler.sh
>>> /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar -runwf
>>> -nogui
>>> [null] /home/urops/Kepler-2.0.0-beta1
>>> [null] Found OS Extension file:
>>> /home/urops/Kepler-2.0.0-beta1/apple-extensions/module-info/osextension.txt
>>> [null] Ran additional initialization for module gui from class
>>> org.kepler.module.gui.Initialize
>>> [null] Ran additional initialization for module tagging from class
>>> org.kepler.module.tagging.Initialize
>>> [null] Ran additional initialization for module provenance from class
>>> org.kepler.module.provenance.Initialize
>>> [null] common tabpane configuration overridden by reporting
>>> [null] Ran additional initialization for module reporting from class
>>> org.kepler.module.reporting.Initialize
>>> [null] loading: org.kepler.KeplerConfigurationApplication args:
>>> ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit
>>> /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar
>>> [null] invoking: org.kepler.KeplerConfigurationApplication.main
>>> [null] Kepler Initializing...
>>> [null] Extracting workflow from KAR
>>> [null] Cached KAR contents
>>> [null] Processing entry, LSID=urn:lsid:
>>> gamma.msi.ucsb.edu/OpenAuth/:8002:120:1,
>>> type=ptolemy.actor.TypedCompositeActor
>>> [null] Command failed
>>> [null] java.lang.Exception: Failed to parse
>>> "ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit
>>> /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar"
>>> [null] at
>>> ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:651)
>>>
>>> [null] at
>>> org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:289)
>>>
>>> [null] at
>>> org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:583)
>>>
>>> [null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
>>> Method)
>>> [null] at
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>
>>> [null] at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>
>>> [null] at java.lang.reflect.Method.invoke(Method.java:592)
>>> [null] at org.kepler.Kepler.load(Kepler.java:321)
>>> [null] at org.kepler.Kepler.load(Kepler.java:339)
>>> [null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)
>>> [null] at org.kepler.Kepler.main(Kepler.java:169)
>>> [null] Caused by: org.kepler.objectmanager.cache.CacheException:
>>> Exception occurred while deserializing object
>>> [null] at
>>> org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:531)
>>>
>>> [null] at
>>> org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:172)
>>>
>>> [null] ... 9 more
>>> [null] Caused by: java.io.IOException: Error in
>>> ActorCacheObject(ReadExternal): null
>>> [null] at
>>> org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:251)
>>>
>>> [null] at
>>> java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1756)
>>> [null] at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1717)
>>> [null] at
>>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1305)
>>> [null] at
>>> java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)
>>> [null] at
>>> org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:519)
>>>
>>> [null] ... 10 more
>>> [null] java.lang.Exception: Failed to parse
>>> "ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit
>>> /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar"
>>> [null] at
>>> ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:651)
>>>
>>> [null] at
>>> org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:289)
>>>
>>> [null] at
>>> org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:583)
>>>
>>> [null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
>>> Method)
>>> [null] at
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>
>>> [null] at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>
>>> [null] at java.lang.reflect.Method.invoke(Method.java:592)
>>> [null] at org.kepler.Kepler.load(Kepler.java:321)
>>> [null] at org.kepler.Kepler.load(Kepler.java:339)
>>> [null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)
>>> [null] at org.kepler.Kepler.main(Kepler.java:169)
>>> [null] Caused by: org.kepler.objectmanager.cache.CacheException:
>>> Exception occurred while deserializing object
>>> [null] at
>>> org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:531)
>>>
>>> [null] at
>>> org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:172)
>>>
>>> [null] ... 9 more
>>> [null] Caused by: java.io.IOException: Error in
>>> ActorCacheObject(ReadExternal): null
>>> [null] at
>>> org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:251)
>>>
>>> [null] at
>>> java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1756)
>>> [null] at
>>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1717)
>>> [null] at
>>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1305)
>>> [null] at
>>> java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)
>>> [null] at
>>> org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:519)
>>>
>>> [null] ... 10 more
>>> Exception in thread "main" Java returned: 1
>>> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:90)
>>> at org.kepler.build.runner.Kepler.main(Kepler.java:78)
>>> Caused by: Java returned: 1
>>> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)
>>> at org.kepler.build.Run.runSuite(Run.java:296)
>>> at org.kepler.build.Run.run(Run.java:201)
>>> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:86)
>>> ... 1 more
>>> --- Nested Exception ---
>>> Java returned: 1
>>> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)
>>> at org.kepler.build.Run.runSuite(Run.java:296)
>>> at org.kepler.build.Run.run(Run.java:201)
>>> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:86)
>>> at org.kepler.build.runner.Kepler.main(Kepler.java:78)
>>>
>>>
>>> 2010/3/10 ben leinfelder <leinfelder at nceas.ucsb.edu>
>>> My findings:
>>> -ran successfully with a clean-cache
>>> -second attempt to run (without cleaning the cache) failed due to an
>>> ObjectManager error relating to the semanticTypes.
>>>
>>> I noticed there is a tag on the workflow which is likely the source of
>>> the problem. We should fix whatever issue is causing this error when the
>>> MOML is parsed:
>>> Caused by: ptolemy.kernel.util.NameDuplicationException: Attempt to
>>> insert object named "semanticType" into a container that already contains an
>>> object with that name.
>>> ....the problems seem to begin around here:
>>> at
>>> org.kepler.objectmanager.ActorMetadata.getActorAsNamedObj(ActorMetadata.java:790)
>>>
>>>
>>> Aaron - can you take a look at this?
>>>
>>> Thanks,
>>> -ben
>>>
>>> On Mar 8, 2010, at 2:06 PM, Josep Morer Muñoz wrote:
>>>
>>> Thanks for your help Chad. Attached the file.
>>>
>>> 2010/3/8 Chad Berkley <berkley at nceas.ucsb.edu>
>>> Hi Josep,
>>>
>>> Could you send me the kar file so I can take a look? You can create the
>>> kar from the workflow by opening the workflow in kepler, then choosing
>>> File/Save Archive.
>>>
>>> I just tried the command:
>>> ./kepler.sh test.kar -runwf -nogui
>>> which worked for me with a kar that I generated the way I said above. I
>>> don't think the -nocache option will work with a kar file because the kar
>>> needs to be cached to be processed. Ben, do you know if this is true?
>>>
>>> thanks,
>>> chad
>>>
>>>
>>> Josep Morer Muñoz wrote:
>>> Hi all,
>>>
>>> I am getting this error when I try to execute a .KAR that contains the
>>> Regression Workflow (included in the examples) and another XML that
>>> cointains the report's layout. When I execute it using kepler.sh I get this
>>> following exception. Any idea? I do not know if I have generated the .KAR
>>> correctly since I do not know what a sematic type means in Kepler.
>>>
>>> urops at urops-laptop:~/KeplerLast$ ./kepler.sh
>>> /home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar -runwf
>>> -nogui -nocache
>>> [null] /home/urops/KeplerLast
>>> [null] Found OS Extension file:
>>> /home/urops/KeplerLast/apple-extensions/module-info/osextension.txt
>>> [null] Ran additional initialization for module gui from class
>>> org.kepler.module.gui.Initialize
>>> [null] Ran additional initialization for module tagging from class
>>> org.kepler.module.tagging.Initialize
>>> [null] Ran additional initialization for module provenance from class
>>> org.kepler.module.provenance.Initialize
>>> [null] common tabpane configuration overridden by reporting
>>> [null] Ran additional initialization for module reporting from class
>>> org.kepler.module.reporting.Initialize
>>> [null] loading: ptolemy.moml.MoMLCommandLineApplication args:
>>> /home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar
>>> [null] invoking: ptolemy.moml.MoMLCommandLineApplication.main
>>> [null] Command failed: com.microstar.xml.XmlException: expected
>>> character (found "P") (expected "<") in
>>> file:/home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar at
>>> line 1 and column 5
>>> * [null] com.microstar.xml.XmlException: expected character (found
>>> "P") (expected "<") in
>>> file:/home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar at
>>> line 1 and column 5*
>>> [null] at ptolemy.moml.MoMLParser.error(MoMLParser.java:1057)
>>> [null] at com.microstar.xml.XmlParser.error(XmlParser.java:448)
>>> [null] at com.microstar.xml.XmlParser.error(XmlParser.java:459)
>>> [null] at com.microstar.xml.XmlParser.require(XmlParser.java:2335)
>>> [null] at
>>> com.microstar.xml.XmlParser.parseDocument(XmlParser.java:480)
>>> [null] at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)
>>> [null] at com.microstar.xml.XmlParser.parse(XmlParser.java:132)
>>> [null] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1402)
>>> [null] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1354)
>>> [null] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1298)
>>> [null] at
>>> ptolemy.moml.MoMLCommandLineApplication.<init>(MoMLCommandLineApplication.java:128)
>>>
>>> [null] at
>>> ptolemy.moml.MoMLCommandLineApplication.main(MoMLCommandLineApplication.java:214)
>>>
>>> [null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
>>> Method)
>>> [null] at
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>
>>> [null] at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>
>>> [null] at java.lang.reflect.Method.invoke(Method.java:592)
>>> [null] at org.kepler.Kepler.load(Kepler.java:321)
>>> [null] at org.kepler.Kepler.load(Kepler.java:339)
>>> [null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)
>>> [null] at org.kepler.Kepler.main(Kepler.java:169)
>>>
>>>
>>> Thanks in advance
>>> --
>>> Josep
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>>
>>> _______________________________________________
>>> Kepler-users mailing list
>>> Kepler-users at kepler-project.org
>>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>
>>>
>>>
>>> --
>>> Josep
>>> <05-LinearRegressionProvenance.kar>
>>>
>>>
>>>
>>>
>>> --
>>> Josep
>>>
>>
>>
--
Josep
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