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
