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 Mu?oz 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 Mu?oz 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 Mu?oz 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 -------------- next part -------------- An HTML attachment was scrubbed... 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