[kepler-dev] Can not open GUI with fresh Kepler check up .

Fri Sep 18 09:49:17 PDT 2009

A new fresh check out and update of existing one on my Mac machine still 
have the same problem. But they finally work when I restart the 
machine.  I think it may because some of my running processes also use 
kepler cache.

Jianwu Wang wrote:
> Hi Derik and Aaron,
>
>    Thanks for your info. New update on my window machine works now. 
> Haven't check it on my Mac machine.
>
> Best wishes
>
> Sincerely yours
>
> Jianwu Wang
> jianwu at sdsc.edu
> http://users.sdsc.edu/~jianwu/
>
> Scientific Workflow Automation Technologies (SWAT) Laboratory
> San Diego Supercomputer Center University of California, San Diego
> San Diego, CA, U.S.A.
>
>
> Aaron Schultz wrote:
>>
>> Seems to be better now.
>>
>> Aaron Schultz wrote:
>>>
>>> My fault, almost fixed...
>>>
>>>
>>> Derik Barseghian wrote:
>>>> Hi Jianwu,
>>>>
>>>> I just did a fresh checkout on linux (r20717) and the gui comes up 
>>>> for me.
>>>>
>>>> However I get a lot of warnings and then a number of errors to do 
>>>> with kar files, like:
>>>>
>>>>      [run] WARN  (org.kepler.kar.KARFile:populateCacheObjects:347) 
>>>> null KAREntry was not
>>>> recognized: PolygonDiagramsTransition.xml
>>>>      [run] WARN
>>>> (org.kepler.kar.KARCacheManager:synchronizeKARCacheWithLocalRepositories:153) 
>>>> Unable to
>>>> process kar file 
>>>> "/home/barseghian/dev3/new.kepler/actors/kar/actors-AddPointToSVG.kar". 
>>>>
>>>>      [run] org.kepler.objectmanager.cache.CacheException: Error 
>>>> creating KARCacheObject: null
>>>>      [run]     at 
>>>> org.kepler.kar.KARFile.populateCacheObjects(KARFile.java:364)
>>>>      [run]     at
>>>> org.kepler.kar.KARCacheManager.synchronizeKARCacheWithLocalRepositories(KARCacheManager.java:148) 
>>>>
>>>>      [run]     at
>>>> org.kepler.objectmanager.library.LibraryManager.buildLibrary(LibraryManager.java:904) 
>>>>
>>>>      [run]     at
>>>> org.kepler.objectmanager.library.LibraryManager.initialize(LibraryManager.java:1244) 
>>>>
>>>>
>>>>
>>>> Derik
>>>>
>>>>
>>>> On Sep 17, 2009, at 3:25 PM, Jianwu Wang wrote:
>>>>
>>>>> Hi guys,
>>>>>
>>>>>   I just did a fresh check-out with version 20717 and use 'ant 
>>>>> clean-cache run'. But I can not open the gui. Does anyone know 
>>>>> why? Thanks
>>>>>
>>>>> kepler:build-area jianwu$ ant clean-cache run
>>>>> Buildfile: build.xml
>>>>> Trying to override old definition of task patch
>>>>>
>>>>> clean-kar:
>>>>> [clean-kar] Deleting directory 
>>>>> /Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/r/kar 
>>>>>
>>>>> [clean-kar] Deleting directory 
>>>>> /Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/actors/kar 
>>>>>
>>>>> [clean-kar] Deleting directory 
>>>>> /Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/directors/kar 
>>>>>
>>>>>
>>>>> clean-cache:
>>>>>  [delete] Deleting directory /Users/jianwu/.kepler
>>>>>
>>>>> compile:
>>>>> [compile] Compiling module-manager...
>>>>> [compile] Getting Ptolemy paths from 
>>>>> /Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/ptolemy/.classpath.default 
>>>>>
>>>>> [compile] Compiling core...
>>>>> [compile] Compiling event-state...
>>>>> [compile] Compiling util...
>>>>> [compile] Compiling component-library...
>>>>> [compile] Compiling sms...
>>>>> [compile] Compiling data-handling...
>>>>> [compile] Compiling ssh...
>>>>> [compile] Compiling io...
>>>>> [compile] Compiling job...
>>>>> [compile] Compiling repository...
>>>>> [compile] Compiling authentication...
>>>>> [compile] Compiling gui...
>>>>> [compile] Compiling authentication-gui...
>>>>> [compile] Compiling ecogrid...
>>>>> [compile] Compiling opendap...
>>>>> [compile] Compiling actors...
>>>>> [compile] Compiling loader...
>>>>> [compile] Compiling r...
>>>>> [compile] Compiling apple-extensions...
>>>>>
>>>>> run:
>>>>>     [run] Getting Ptolemy paths from 
>>>>> /Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/ptolemy/.classpath.default 
>>>>>
>>>>>     [run] Set environment variable: PATH = 
>>>>> /sw/bin:/sw/sbin:/opt/subversion/bin:/Applications/MATLAB_R2008b.app/bin:/Users/jianwu/Projects/hadoop/hadoop-0.20.0/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/kepler/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/apple-extensions/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/r/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/loader/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/actors/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/directors/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/opendap/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/ecogrid/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/authentication-gui/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/gui/lib:/Users/jianw 
>>>>>
> u
>>>>>
>> /Kepler/repository/kepler/kepler-trunk-0909/modules/authentication/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/repository/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/job/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/io/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/ssh/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/data-handling/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/sms/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/component-library/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/util/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/event-state/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/core/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/common/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/ptII/l 
>>
> i
>>
>> b:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/mo
>> d
>>>>>
>>> ule
>>>>>
>>>>> -manager/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/ptolemy/lib:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/ptolemy-lib/lib 
>>>>>
>>>>>     [run] Set environment variable: R_HOME = 
>>>>> /Library/Frameworks/R.framework/Resources
>>>>>     [run] 
>>>>> /Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules
>>>>>     [run] Found OS Extension file: 
>>>>> /Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/apple-extensions/module-info/osextension.txt 
>>>>>
>>>>>     [run] loading OS extensions for OS  Mac OS X with class 
>>>>> org.kepler.osx.KeplerOSXExtension
>>>>>     [run] Building Kars...
>>>>>     [run] Command failed
>>>>>     [run] Arguments: -kepler
>>>>>     [run]
>>>>>     [run] java.lang.Exception: Failed to parse "-kepler"
>>>>>     [run]     at 
>>>>> ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:635) 
>>>>>
>>>>>     [run]     at 
>>>>> ptolemy.actor.gui.ConfigurationApplication.<init>(ConfigurationApplication.java:292) 
>>>>>
>>>>>     [run]     at 
>>>>> ptolemy.actor.gui.MoMLApplication.<init>(MoMLApplication.java:81)
>>>>>     [run]     at 
>>>>> ptolemy.vergil.VergilApplication.<init>(VergilApplication.java:104)
>>>>>     [run]     at 
>>>>> ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:194)
>>>>>     [run]     at 
>>>>> java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>>>>>     [run]     at 
>>>>> java.awt.EventQueue.dispatchEvent(EventQueue.java:633)
>>>>>     [run]     at 
>>>>> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) 
>>>>>
>>>>>     [run]     at 
>>>>> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) 
>>>>>
>>>>>     [run]     at 
>>>>> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) 
>>>>>
>>>>>     [run]     at 
>>>>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
>>>>>     [run]     at 
>>>>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
>>>>>     [run]     at 
>>>>> java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
>>>>>     [run] Caused by: java.lang.Exception: Failed to read 
>>>>> configuration 
>>>>> 'file:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/common/configs/ptolemy/configs/kepler/configuration.xml' 
>>>>>
>>>>>     [run]     at 
>>>>> ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:286) 
>>>>>
>>>>>     [run]     at 
>>>>> ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:322) 
>>>>>
>>>>>     [run]     at 
>>>>> ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1109) 
>>>>>
>>>>>     [run]     at 
>>>>> ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:452) 
>>>>>
>>>>>     [run]     at 
>>>>> ptolemy.actor.gui.ConfigurationApplication.<init>(ConfigurationApplication.java:226) 
>>>>>
>>>>>     [run]     ... 11 more
>>>>>     [run] Caused by: java.lang.Exception: Failed to call 
>>>>> application initializer class "org.kepler.gui.KeplerInitializer".  
>>>>> Perhaps the configuration file 
>>>>> "file:/Users/jianwu/Kepler/repository/kepler/kepler-trunk-0909/modules/common/configs/ptolemy/configs/kepler/configuration.xml" 
>>>>> has a problem?
>>>>>     [run]     at 
>>>>> ptolemy.actor.gui.ConfigurationApplication.readConfiguration(ConfigurationApplication.java:448) 
>>>>>
>>>>>     [run]     at 
>>>>> ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:284) 
>>>>>
>>>>>     [run]     ... 15 more
>>>>>     [run] Caused by: java.sql.SQLException: Failed to connect to 
>>>>> url "jdbc:hsqldb:hsql://localhost/hsqldb" as user "sa. Perhaps 
>>>>> there was an error launching the db server. In addition, sometimes 
>>>>> the database cache can become corrupt, so another solution is to 
>>>>> remove the "/Users/jianwu/.kepler/cache/cachedata/hsqldb" directory.
>>>>>     [run]     at 
>>>>> org.kepler.util.DBConnectionFactory.getDBConnection(DBConnectionFactory.java:126) 
>>>>>
>>>>>     [run]     at 
>>>>> org.kepler.util.DBConnectionFactory.getDBConnection(DBConnectionFactory.java:99) 
>>>>>
>>>>>     [run]     at 
>>>>> org.kepler.gui.KeplerInitializer.initializeSystem(KeplerInitializer.java:156) 
>>>>>
>>>>>     [run]     at 
>>>>> org.kepler.gui.KeplerInitializer.<init>(KeplerInitializer.java:92)
>>>>>     [run]     at 
>>>>> sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>>>>     [run]     at 
>>>>> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) 
>>>>>
>>>>>     [run]     at 
>>>>> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) 
>>>>>
>>>>>     [run]     at 
>>>>> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>>>>>     [run]     at java.lang.Class.newInstance0(Class.java:355)
>>>>>     [run]     at java.lang.Class.newInstance(Class.java:308)
>>>>>     [run]     at 
>>>>> ptolemy.actor.gui.ConfigurationApplication.readConfiguration(ConfigurationApplication.java:446) 
>>>>>
>>>>>     [run]     ... 16 more
>>>>>
>>>>> BUILD SUCCESSFUL
>>>>> Total time: 15 seconds
>>>>>
>>>>> -- 
>>>>>
>>>>> Best wishes
>>>>>
>>>>> Sincerely yours
>>>>>
>>>>> Jianwu Wang
>>>>> wangjianwu at gmail.com
>>>>>
>>>>> Post-Doctor
>>>>> Scientific Workflow Automation Technologies (SWAT) Laboratory
>>>>> San Diego Supercomputer Center University of California, San Diego
>>>>> San Diego, U.S.A.
>>>>>
>>>>> _______________________________________________
>>>>> Kepler-dev mailing list
>>>>> Kepler-dev at kepler-project.org
>>>>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-dev
>>>>
>>>> _______________________________________________
>>>> Kepler-dev mailing list
>>>> Kepler-dev at kepler-project.org
>>>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-dev
>>>
>>>
>>> _______________________________________________
>>> Kepler-dev mailing list
>>> Kepler-dev at kepler-project.org
>>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-dev
>>
>>
>> _______________________________________________
>> Kepler-dev mailing list
>> Kepler-dev at kepler-project.org
>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-dev
>
> _______________________________________________
> Kepler-dev mailing list
> Kepler-dev at kepler-project.org
> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-dev

-- 

Best wishes

Sincerely yours

Jianwu Wang
wangjianwu at gmail.com

Post-Doctor
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center 
University of California, San Diego
San Diego, U.S.A. 