[kepler-dev] Re: some Ready-to-run Workflows do not work

Dan Higgins higgins at nceas.ucsb.edu
Wed Feb 16 08:47:20 PST 2005


Hi Haiyan,

    The first several problem you mention are probably due to running 
under Linux. The 'Baseline 3-actor GARP' and the gisl workflows both use 
JNI to connect to C/C++ libraries, and were set up primarily for Windows 
users. So I think they would work for you under Windows, but the Linux 
shared object libraries are probably obsolete and non-functional. [The 
workflows that you say work are all pure Java.]

    In any case, these problem appear to be workflow specific and should 
not affect any workflows that you create.

    My apologies for the various problems you are coming across. Kepler 
is still 'under-construction' and continually changing. Your questions 
and comments are always helpful and appreciated.

Dan

---

Haiyan Yang wrote:

>Hi, Dan,
>
>I didn't export the PTII and KEPLER in the 'kepler.sh' file.  I did that at
>the prompt.  But I'm not sure whether this caused some problem.
>
>I tried to run all the 'Ready-to-run Workflows'.  Some worked well, such as
>'EML2 Simple Plot Example', 'Discrete Logistic', both 'LV prey model',
>'Biodiversity index calculator'.  But I got error messages for almost all
>the other half workflows.  Here are some examples:
>
>>From the ENM (GARP) Workflows link, I went to click the 'Baseline 3-Actor
>GARP - Browser Display" link, and run the flow, the error message says "no
>garp in java.library.path" or "null". The stack trace looks like this:
>
>
>java.lang.NoClassDefFoundError
>	at
>org.ecoinformatics.seek.garp.GarpPresampleLayers.fire(GarpPresampleLayers.java:149)
>	at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:283)
>	at
>ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:161)
>	at ptolemy.actor.CompositeActor.fire(CompositeActor.java:316)
>	at ptolemy.actor.Manager.iterate(Manager.java:519)
>	at ptolemy.actor.Manager.execute(Manager.java:295)
>	at ptolemy.actor.Manager.run(Manager.java:852)
>	at ptolemy.actor.Manager$2.run(Manager.java:901)
>
>
>If I run gisl.xml, the error says: "no gishull in java.library.path". And
>the Stack Trace looks like this:
>
>java.lang.UnsatisfiedLinkError: no gishull in java.library.path
>	at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1682)
>	at java.lang.Runtime.loadLibrary0(Runtime.java:822)
>	at java.lang.System.loadLibrary(System.java:992)
>	at org.ecoinformatics.seek.gis.grass.HullJniGlue.<clinit>(HullJniGlue.java:99)
>	at org.ecoinformatics.seek.gis.grass.GISHullActor.fire(GISHullActor.java:223)
>	at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:283)
>	at
>ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:161)
>	at ptolemy.actor.CompositeActor.fire(CompositeActor.java:316)
>	at ptolemy.actor.Manager.iterate(Manager.java:519)
>	at ptolemy.actor.Manager.execute(Manager.java:295)
>	at ptolemy.actor.Manager.run(Manager.java:852)
>	at ptolemy.actor.Manager$2.run(Manager.java:901)
>
>
>If I run GEON Mineral Classifier, an Exception window poped up:
>
>fire exception DB connection
>in .classifier.OpenDBConnection
>
>Because:
>IO Exception opening socket to server geon02.sdsc.edu on port 50000.  The
>DB2 Server may be down.
>
>
>There are other workflows that can't be run.  I'm listing them all here.
>
>So what could be the problem?  Will that affect building my own workflow?
>
>Thanks.
>
>
>Haiyan
>
>
>
>
>
>
>
>  
>
>>Hi Haiyan,
>>    It sounds like you have Kepler installed OK. To create a blank 
>>workspace, just go to the File menu in any of the windows and select 
>>'File/New/Graph Editor'. That should create an empty workflow window.
>>
>>    Kepler has its own copy of Ptolemy (You should find a directory 
>>called ptII4.0.0 inside the kepler dir). Note that you should not need 
>>to export the PTII and KEPLER environment variables in the 'kepler.sh' 
>>file. In fact, exporting the PTII variable there may be causing the 
>>problem with running Ptolemy. PTII should point to the independent 
>>Ptolemy installation.
>>
>>Dan
>>
>>Haiyan Yang wrote:
>>
>>    
>>
>>>Hi, 
>>>
>>>I edited the "kepler.sh" file as you said.  (BTW, I'm using linux red hat).
>>>
>>>I also did something like this:
>>>export PTII=/home/haiyan/289F/Proj/ptII4.0.1
>>>export KEPLER=/home/haiyan/289F/Proj/kepler
>>>
>>>
>>>Now after typed "./kepler.sh", first, I go the same line:
>>>
>>>Opening user library /home/haiyan/.ptolemyII/UserLibrary.xml... Done
>>>
>>>The window "Kepler: A System for Scienfific Workflows" poped up.  I then
>>>clicked the "ENM (GARP) Workflows" link, then click the "Baseline 3-Actor
>>>GARP - Browser Display" link, another window poped up with some work flow,
>>>looks like it's opening the "garpModel.xml" file.  I can see SDF Director
>>>and other actors on this window.  
>>>
>>>Does this mean it's installed correctly?  If yes, how do I open an
>>>interface (something like vergil) to create my own workflow later?  
>>>
>>>
>>>Another problem: I had installed Ptolemy before and it worked perfect. 
>>>After I tried to install Kepler yesterday and failed, I can't open vergil
>>>any more.  It gave me an error like this:
>>>
>>>[...bin]$ vergil
>>>"/opt/java/jdk1.5.0_01/bin/java" -Xmx256M "-Dptolemy.ptII.dir=" -classpath
>>>      
>>>
>>":/lib/diva.jar:/home/haiyan/289F/Proj/ptII4.0.1/lib/ptCal.jar:/home/haiyan/289F/Proj/ptII4.0.1/lib/java_cup.jar:/home/haiyan/289F/Proj/ptII4.0.1/lib/sootclasses.jar:/home/haiyan/289F/Proj/ptII4.0.1/lib/jasminclasses.jar:/opt/java/jdk1.5.0_01/jre/lib/rt.jar:/home/haiyan/289F/Proj/ptII4.0.1/lib/ptjacl.jar:/home/haiyan/289F/Proj/ptII4.0.1/lib/jython.jar::/home/haiyan/289F/Proj/ptII4.0.1/lib/mapss.jar:/lib/saxon7.jar:"
>>    
>>
>>>ptolemy.vergil.VergilApplication
>>>Exception in thread "main" java.lang.NoClassDefFoundError:
>>>ptolemy/vergil/VergilApplication
>>>
>>>
>>>What's wrong with this?  Should I have Ptolemy work properly in order for
>>>Kepler to work?
>>>
>>>
>>>Thanks.
>>>
>>>
>>>Haiyan
>>>
>>>
>>>
>>> 
>>>
>>>      
>>>
>>>>Hi,
>>>>   I reproduced the described problem running ./kepler.sh on Mac and 
>>>>discovered that the problem was due to a mistake in the path of some 
>>>>command line parameters. Please check the 'kepler.sh' file. The line for 
>>>>launching kepler is
>>>>
>>>>java -Xmx512m -Xss5m -DKEPLER=/Applications/Kepler -DDBGPRN=0  
>>>>-Djava.endorsed.dirs=/Applications/Kepler/lib/jar/apache 
>>>>ptolemy.vergil.VergilApplication -kepler
>>>>
>>>>The -DKEPLER parameter should point to the directory where kepler is 
>>>>installed. In my case, it should have been
>>>>-DKEPLER=/Applications/kepler-1.0.0alpha4. Similarly, the 
>>>>-Djava.endorsed.dirs should start with the actual path to the kepler 
>>>>dir. These 2 parameters are apparently not getting set correctly. Please 
>>>>check on your Linux system and see if the setting are incorrect. If so, 
>>>>please try correcting and let me know if that solves your problem
>>>>
>>>>Dan Higgins
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>-- 
>>*******************************************************************
>>Dan Higgins                                  higgins at nceas.ucsb.edu
>>http://www.nceas.ucsb.edu/    Ph: 805-893-5127
>>National Center for Ecological Analysis and Synthesis (NCEAS) 
>>Marine Science Building - Room 3405
>>Santa Barbara, CA 93195
>>*******************************************************************
>>
>>_______________________________________________
>>kepler-dev mailing list
>>kepler-dev at ecoinformatics.org
>>http://www.ecoinformatics.org/mailman/listinfo/kepler-dev
>>
>>    
>>


-- 
*******************************************************************
Dan Higgins                                  higgins at nceas.ucsb.edu
http://www.nceas.ucsb.edu/    Ph: 805-893-5127
National Center for Ecological Analysis and Synthesis (NCEAS) 
Marine Science Building - Room 3405
Santa Barbara, CA 93195
*******************************************************************




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