Hello all,<br><br>I have not executed any KAR yet. I always get the same error (executing the KAR with cache). Any idea?<br><br>urops@urops-laptop:~/Kepler-2.0.0-beta1$ ./kepler.sh /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar -runwf -nogui <br>
[null] /home/urops/Kepler-2.0.0-beta1<br> [null] Found OS Extension file: /home/urops/Kepler-2.0.0-beta1/apple-extensions/module-info/osextension.txt<br> [null] Ran additional initialization for module gui from class org.kepler.module.gui.Initialize<br>
[null] Ran additional initialization for module tagging from class org.kepler.module.tagging.Initialize<br> [null] Ran additional initialization for module provenance from class org.kepler.module.provenance.Initialize<br>
[null] common tabpane configuration overridden by reporting<br> [null] Ran additional initialization for module reporting from class org.kepler.module.reporting.Initialize<br> [null] loading: org.kepler.KeplerConfigurationApplication args: ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar <br>
[null] invoking: org.kepler.KeplerConfigurationApplication.main<br> [null] Kepler Initializing...<br> [null] Extracting workflow from KAR<br> [null] Cached KAR contents<br> [null] Processing entry, LSID=urn:lsid:<a href="http://gamma.msi.ucsb.edu/OpenAuth/:8002:120:1">gamma.msi.ucsb.edu/OpenAuth/:8002:120:1</a>, type=ptolemy.actor.TypedCompositeActor<br>
[null] Command failed<br> [null] java.lang.Exception: Failed to parse "ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar"<br>
[null] at ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:651)<br> [null] at org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:289)<br>
[null] at org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:583)<br> [null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br> [null] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)<br>
[null] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br> [null] at java.lang.reflect.Method.invoke(Method.java:592)<br> [null] at org.kepler.Kepler.load(Kepler.java:321)<br>
[null] at org.kepler.Kepler.load(Kepler.java:339)<br> [null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)<br> [null] at org.kepler.Kepler.main(Kepler.java:169)<br> [null] Caused by: org.kepler.objectmanager.cache.CacheException: Exception occurred while deserializing object<br>
[null] at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:531)<br> [null] at org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:172)<br> [null] ... 9 more<br>
[null] Caused by: java.io.IOException: Error in ActorCacheObject(ReadExternal): null<br> [null] at org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:251)<br> [null] at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1756)<br>
[null] at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1717)<br> [null] at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1305)<br> [null] at java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)<br>
[null] at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:519)<br> [null] ... 10 more<br> [null] java.lang.Exception: Failed to parse "ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar"<br>
[null] at ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:651)<br> [null] at org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:289)<br>
[null] at org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:583)<br> [null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br> [null] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)<br>
[null] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br> [null] at java.lang.reflect.Method.invoke(Method.java:592)<br> [null] at org.kepler.Kepler.load(Kepler.java:321)<br>
[null] at org.kepler.Kepler.load(Kepler.java:339)<br> [null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)<br> [null] at org.kepler.Kepler.main(Kepler.java:169)<br> [null] Caused by: org.kepler.objectmanager.cache.CacheException: Exception occurred while deserializing object<br>
[null] at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:531)<br> [null] at org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:172)<br> [null] ... 9 more<br>
[null] Caused by: java.io.IOException: Error in ActorCacheObject(ReadExternal): null<br> [null] at org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:251)<br> [null] at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1756)<br>
[null] at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1717)<br> [null] at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1305)<br> [null] at java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)<br>
[null] at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:519)<br> [null] ... 10 more<br>Exception in thread "main" Java returned: 1<br> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:90)<br>
at org.kepler.build.runner.Kepler.main(Kepler.java:78)<br>Caused by: Java returned: 1<br> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br> at org.kepler.build.Run.runSuite(Run.java:296)<br> at org.kepler.build.Run.run(Run.java:201)<br>
at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:86)<br> ... 1 more<br>--- Nested Exception ---<br>Java returned: 1<br> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br> at org.kepler.build.Run.runSuite(Run.java:296)<br>
at org.kepler.build.Run.run(Run.java:201)<br> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:86)<br> at org.kepler.build.runner.Kepler.main(Kepler.java:78)<br><br><br><div class="gmail_quote">2010/3/10 ben leinfelder <span dir="ltr"><<a href="mailto:leinfelder@nceas.ucsb.edu">leinfelder@nceas.ucsb.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">My findings:<br>
-ran successfully with a clean-cache<br>
-second attempt to run (without cleaning the cache) failed due to an ObjectManager error relating to the semanticTypes.<br>
<br>
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:<br>
Caused by: ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "semanticType" into a container that already contains an object with that name.<br>
....the problems seem to begin around here:<br>
at org.kepler.objectmanager.ActorMetadata.getActorAsNamedObj(ActorMetadata.java:790)<br>
<br>
Aaron - can you take a look at this?<br>
<br>
Thanks,<br>
-ben<br>
<br></div><div><div></div><div class="h5">
On Mar 8, 2010, at 2:06 PM, Josep Morer Muñoz wrote:<br>
<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
Thanks for your help Chad. Attached the file.<br>
<br>
2010/3/8 Chad Berkley <<a href="mailto:berkley@nceas.ucsb.edu" target="_blank">berkley@nceas.ucsb.edu</a>><br>
Hi Josep,<br>
<br>
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.<br>
<br>
I just tried the command:<br>
./kepler.sh test.kar -runwf -nogui<br>
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?<br>
<br>
thanks,<br>
chad<br>
<br>
<br>
Josep Morer Muñoz wrote:<br>
Hi all,<br>
<br>
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.<br>
<br>
urops@urops-laptop:~/KeplerLast$ ./kepler.sh /home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar -runwf -nogui -nocache<br>
[null] /home/urops/KeplerLast<br>
[null] Found OS Extension file: /home/urops/KeplerLast/apple-extensions/module-info/osextension.txt<br>
[null] Ran additional initialization for module gui from class org.kepler.module.gui.Initialize<br>
[null] Ran additional initialization for module tagging from class org.kepler.module.tagging.Initialize<br>
[null] Ran additional initialization for module provenance from class org.kepler.module.provenance.Initialize<br>
[null] common tabpane configuration overridden by reporting<br>
[null] Ran additional initialization for module reporting from class org.kepler.module.reporting.Initialize<br>
[null] loading: ptolemy.moml.MoMLCommandLineApplication args: /home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar<br>
[null] invoking: ptolemy.moml.MoMLCommandLineApplication.main<br>
[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<br>
* [null] com.microstar.xml.XmlException: expected character (found "P") (expected "<") in file:/home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar at line 1 and column 5*<br>
[null] at ptolemy.moml.MoMLParser.error(MoMLParser.java:1057)<br>
[null] at com.microstar.xml.XmlParser.error(XmlParser.java:448)<br>
[null] at com.microstar.xml.XmlParser.error(XmlParser.java:459)<br>
[null] at com.microstar.xml.XmlParser.require(XmlParser.java:2335)<br>
[null] at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:480)<br>
[null] at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)<br>
[null] at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br>
[null] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1402)<br>
[null] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1354)<br>
[null] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1298)<br>
[null] at ptolemy.moml.MoMLCommandLineApplication.<init>(MoMLCommandLineApplication.java:128)<br>
[null] at ptolemy.moml.MoMLCommandLineApplication.main(MoMLCommandLineApplication.java:214)<br>
[null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
[null] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)<br>
[null] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br>
[null] at java.lang.reflect.Method.invoke(Method.java:592)<br>
[null] at org.kepler.Kepler.load(Kepler.java:321)<br>
[null] at org.kepler.Kepler.load(Kepler.java:339)<br>
[null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)<br>
[null] at org.kepler.Kepler.main(Kepler.java:169)<br>
<br>
<br>
Thanks in advance<br>
-- <br>
Josep<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
<br>
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<br>
<br>
-- <br>
Josep<br></div></div>
<05-LinearRegressionProvenance.kar><br>
</blockquote>
<br>
</blockquote></div><br><br clear="all"><br>-- <br>Josep<br>