[kepler-users] ERROR EXECUTING A .KAR FILE
ben leinfelder
leinfelder at nceas.ucsb.edu
Mon Mar 15 09:26:44 PDT 2010
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
>
>
> ------------------------------------------------------------------------
>
>
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>
>
>
> --
> Josep
> <05-LinearRegressionProvenance.kar>
>
>
>
>
> --
> Josep
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