[kepler-dev] Re: kepler-dev digest, Vol 1 #387 - 4 msgs
Tim Wong
thwong at gmail.com
Tue Feb 15 13:46:41 PST 2005
Dear all,
I have been facing the similar problem trying to run the release
version of Kepler under Linux OS. When Kepler loads the composit
actor jar file, it just crashes and shows me the source code of the
jar file. The Windows Ver. works fine.
Also, I submitted a CVS read-only account request to thorugh the email
link on Kepler website last week, but I have received any response
yet. May I get an account for Kepler CVS as well? (user name:
thwong)
Thank you so much.
Tim Wong
UC Davis DBIS lab
On Tue, 15 Feb 2005 12:01:02 -0800 (PST),
kepler-dev-request at ecoinformatics.org
<kepler-dev-request at ecoinformatics.org> wrote:
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> Today's Topics:
>
> 1. Re: Re: Kepler installation problem (red hat) (Dan Higgins)
> 2. Re: Re: Kepler installation problem (red hat) (Shawn Bowers)
> 3. Re: Re: Kepler installation problem (red hat) (Haiyan Yang)
> 4. Re: Re: Kepler installation problem (red hat) (Dan Higgins)
>
> --__--__--
>
> Message: 1
> Date: Tue, 15 Feb 2005 10:34:51 -0800
> From: Dan Higgins <higgins at nceas.ucsb.edu>
> To: Shawn Bowers <sbowers at ucdavis.edu>
> Cc: "Carlos A. Rueda" <carueda at ucdavis.edu>,
> Chad Berkley <berkley at nceas.ucsb.edu>,
> Haiyan Yang <haiyan at ucdavis.edu>,
> Kepler-Dev <kepler-dev at ecoinformatics.org>
> Subject: Re: [kepler-dev] Re: Kepler installation problem (red hat)
>
> Shawn,
> There is no need to set the paths for the installer version; They
> KEPLER variable is set on the command line and the ptolemy code is in
> subdirectory
>
> Dan
>
> ----
>
> Shawn Bowers wrote:
>
> >
> > Another problem is that sometimes paths don't get setup correctly ...
> > Did you double check that this was done (i.e., that the Kepler and
> > Ptolemy paths are set)?
> >
> > Shawn
> >
> >
> >
> > Carlos A. Rueda wrote:
> >
> >> I guess the CVS co is the next step to try, and we understand
> >> we need to ask for a read-only account. Can we have two for:
> >> haiyan
> >> carueda
> >> ?
> >>
> >> Thanks
> >> carlos
> >>
> >>
> >> Chad Berkley wrote:
> >>
> >>> Hi,
> >>>
> >>> Are you running this from the release version or from a CVS
> >>> checkout? What OS are you running it under?
> >>>
> >>> chad
> >>>
> >>> Haiyan Yang wrote:
> >>>
> >>>> Hi, all,
> >>>>
> >>>> After I typed "./kepler.sh", I got one line:
> >>>> Opening user library /home/haiyan/.ptolemyII/UserLibrary.xml... Done
> >>>>
> >>>> A window poped up with title "Kepler: A System for Scientific
> >>>> Workflows".
> >>>> Nothing continued from there. If I click a link in the popup
> >>>> window, say,
> >>>> ENM(CARP) WORKFLOWS, another window poped up with title "Ecological
> >>>> Niche
> >>>> Modeling (GARP) Workflows". I then clicked the first link "Baseline
> >>>> 3-Actor GARP -Browser Display", a bunch of stuff were displayed at the
> >>>> shell prompt. Looks like this:
> >>>>
> >>>> [... kepler]$ ./kepler.sh
> >>>> Opening user library /home/haiyan/.ptolemyII/UserLibrary.xml... Done
> >>>> java.io.FileNotFoundException:
> >>>> /Applications/Kepler/configs/ptolemy/configs/kepler/ontology.owl
> >>>> (No such
> >>>> file or directory)
> >>>> at java.io.FileInputStream.open(Native Method)
> >>>> at java.io.FileInputStream.<init>(FileInputStream.java:106)
> >>>> at java.io.FileInputStream.<init>(FileInputStream.java:66)
> >>>> at
> >>>> sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:70)
> >>>>
> >>>> at
> >>>> sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:161)
> >>>>
> >>>> at
> >>>> com.hp.hpl.jena.ontology.impl.OntModelImpl.read(OntModelImpl.java:1894)
> >>>>
> >>>> at
> >>>> com.hp.hpl.jena.ontology.impl.OntModelImpl.read(OntModelImpl.java:1846)
> >>>>
> >>>>
> >>>>
> >>>> It's much longer.
> >>>>
> >>>> Also another window poped up. Looks like it is the file at
> >>>> ptolemy/actor/TypedCompositeActor.java
> >>>>
> >>>>
> >>>>
> >>>> What I should do now? Any help?
> >>>>
> >>>> Thanks.
> >>>>
> >>>>
> >>>> Haiyan
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> kepler-dev mailing list
> >>> kepler-dev at ecoinformatics.org
> >>> http://www.ecoinformatics.org/mailman/listinfo/kepler-dev
> >>>
> >> _______________________________________________
> >> 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
> *******************************************************************
>
> --__--__--
>
> Message: 2
> Date: Tue, 15 Feb 2005 10:45:53 -0800
> From: Shawn Bowers <sbowers at ucdavis.edu>
> To: Dan Higgins <higgins at nceas.ucsb.edu>
> Cc: "Carlos A. Rueda" <carueda at ucdavis.edu>,
> Chad Berkley <berkley at nceas.ucsb.edu>,
> Haiyan Yang <haiyan at ucdavis.edu>,
> Kepler-Dev <kepler-dev at ecoinformatics.org>
> Subject: Re: [kepler-dev] Re: Kepler installation problem (red hat)
>
> OK -- but sounds like it was fixed!
>
> Shawn
>
> Dan Higgins wrote:
> > Shawn,
> > There is no need to set the paths for the installer version; They
> > KEPLER variable is set on the command line and the ptolemy code is in
> > subdirectory
> >
> > Dan
> >
> > ----
> >
> > Shawn Bowers wrote:
> >
> >>
> >> Another problem is that sometimes paths don't get setup correctly ...
> >> Did you double check that this was done (i.e., that the Kepler and
> >> Ptolemy paths are set)?
> >>
> >> Shawn
> >>
> >>
> >>
> >> Carlos A. Rueda wrote:
> >>
> >>> I guess the CVS co is the next step to try, and we understand
> >>> we need to ask for a read-only account. Can we have two for:
> >>> haiyan
> >>> carueda
> >>> ?
> >>>
> >>> Thanks
> >>> carlos
> >>>
> >>>
> >>> Chad Berkley wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> Are you running this from the release version or from a CVS
> >>>> checkout? What OS are you running it under?
> >>>>
> >>>> chad
> >>>>
> >>>> Haiyan Yang wrote:
> >>>>
> >>>>> Hi, all,
> >>>>>
> >>>>> After I typed "./kepler.sh", I got one line:
> >>>>> Opening user library /home/haiyan/.ptolemyII/UserLibrary.xml... Done
> >>>>>
> >>>>> A window poped up with title "Kepler: A System for Scientific
> >>>>> Workflows".
> >>>>> Nothing continued from there. If I click a link in the popup
> >>>>> window, say,
> >>>>> ENM(CARP) WORKFLOWS, another window poped up with title "Ecological
> >>>>> Niche
> >>>>> Modeling (GARP) Workflows". I then clicked the first link "Baseline
> >>>>> 3-Actor GARP -Browser Display", a bunch of stuff were displayed at the
> >>>>> shell prompt. Looks like this:
> >>>>>
> >>>>> [... kepler]$ ./kepler.sh
> >>>>> Opening user library /home/haiyan/.ptolemyII/UserLibrary.xml... Done
> >>>>> java.io.FileNotFoundException:
> >>>>> /Applications/Kepler/configs/ptolemy/configs/kepler/ontology.owl
> >>>>> (No such
> >>>>> file or directory)
> >>>>> at java.io.FileInputStream.open(Native Method)
> >>>>> at java.io.FileInputStream.<init>(FileInputStream.java:106)
> >>>>> at java.io.FileInputStream.<init>(FileInputStream.java:66)
> >>>>> at
> >>>>> sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:70)
> >>>>>
> >>>>> at
> >>>>> sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:161)
> >>>>>
> >>>>> at
> >>>>> com.hp.hpl.jena.ontology.impl.OntModelImpl.read(OntModelImpl.java:1894)
> >>>>>
> >>>>> at
> >>>>> com.hp.hpl.jena.ontology.impl.OntModelImpl.read(OntModelImpl.java:1846)
> >>>>>
> >>>>>
> >>>>>
> >>>>> It's much longer.
> >>>>>
> >>>>> Also another window poped up. Looks like it is the file at
> >>>>> ptolemy/actor/TypedCompositeActor.java
> >>>>>
> >>>>>
> >>>>>
> >>>>> What I should do now? Any help?
> >>>>>
> >>>>> Thanks.
> >>>>>
> >>>>>
> >>>>> Haiyan
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> kepler-dev mailing list
> >>>> kepler-dev at ecoinformatics.org
> >>>> http://www.ecoinformatics.org/mailman/listinfo/kepler-dev
> >>>>
> >>> _______________________________________________
> >>> kepler-dev mailing list
> >>> kepler-dev at ecoinformatics.org
> >>> http://www.ecoinformatics.org/mailman/listinfo/kepler-dev
> >>
> >>
> >
> >
>
> --__--__--
>
> Message: 3
> Date: Tue, 15 Feb 2005 11:15:46 -0800 (PST)
> To: Dan Higgins <higgins at nceas.ucsb.edu>,
> "Carlos A. Rueda" <carueda at ucdavis.edu>
> Subject: Re: [kepler-dev] Re: Kepler installation problem (red hat)
> From: "Haiyan Yang" <haiyan at ucdavis.edu>
> Cc: Chad Berkley <berkley at nceas.ucsb.edu>,
> Kepler-Dev <kepler-dev at ecoinformatics.org>
>
> 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
> >
>
> --__--__--
>
> Message: 4
> Date: Tue, 15 Feb 2005 11:28:24 -0800
> From: Dan Higgins <higgins at nceas.ucsb.edu>
> To: Haiyan Yang <haiyan at ucdavis.edu>
> Cc: "Carlos A. Rueda" <carueda at ucdavis.edu>,
> Chad Berkley <berkley at nceas.ucsb.edu>,
> Kepler-Dev <kepler-dev at ecoinformatics.org>
> Subject: Re: [kepler-dev] Re: Kepler installation problem (red hat)
>
> 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
>
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