[kepler-dev] Ptolemy & Kepler installation and quick workflow tests
Chad Berkley
berkley at nceas.ucsb.edu
Tue Feb 15 16:17:01 PST 2005
Hi again Carlos,
I also just noticed that you are using java 1.5 and ant 1.5.1. I
currently use java 1.4.2_04 and ant 1.6.1. I haven't tried the newest
java release on kepler so I can't vouch for it. I know for a fact that
the ant version is important though. You should probably upgrade it.
chad
Chad Berkley wrote:
> Hi Carlos,
>
> The best way to do this is to just use ant with kepler instead of
> running make for PTII. Here are the steps I use:
> $ wget
> http://ptolemy.eecs.berkeley.edu/ptolemyII/ptII4.0/ptII4.0.1.src.tar.gz
> $ tar -zxf ptII4.0.1.src.tar.gz
> $ cd ptII4.0.1
> $ export PTII=`pwd`
> $ cd ..
> $ cvs co kepler
> $ cd kepler
> $ export KEPLER=`pwd`
> $ ant ptolemy run-dev
>
> note that 'ant ptolemy' will compile the ptolemy release pointed to by
> PTII. run-dev runs kepler without creating the gigantic jar files (this
> just cuts down on your startup time for development). The reason you
> need to use ant from within kepler is that we have circumvented a major
> building block in the ptolemy system with the kepler code. if you just
> build ptolemy with make, the ant build system won't copy the needed
> files from the kepler source to the ptolemy source.
>
> let me know if this doesn't work for some reason.
>
> chad
>
> Carlos A. Rueda wrote:
>
>> Starting from scratch on a linux system, please find attached
>> a quick step-by-step tour you may find useful to trace the
>> possible causes of our unsuccessful kepler tests.
>>
>> Thanks much.
>>
>> carlos
>>
>>
>> ------------------------------------------------------------------------
>>
>> Ptolemy & Kepler installation and quick workflow tests
>> Carlos Rueda
>> 2/15/05
>>
>> ## My system:
>> $ uname -a
>> Linux px 2.4.24 #1 Mon May 17 04:48:14 PDT 2004 i686 unknown
>> unknown GNU/Linux
>>
>> $ java -version
>> java version "1.5.0_01"
>> Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_01-b08)
>> Java HotSpot(TM) Client VM (build 1.5.0_01-b08, mixed mode, sharing)
>>
>> $ ant -version
>> Apache Ant version 1.5.1 compiled on October 23 2002
>>
>>
>> ## PTII 4.0.1 installation
>> $ mkdir ptolemy
>> $ cd ptolemy
>> $ wget
>> http://ptolemy.eecs.berkeley.edu/ptolemyII/ptII4.0/ptII4.0.1.src.tar.gz
>> $ tar zxf ptII4.0.1.src.tar.gz
>> $ cd ptII4.0.1
>> $ export PTII=`pwd`
>> $ ./configure
>> $ make fast install
>> $ bin/vergil
>> # -> OK
>>
>>
>> ## Kepler installation
>> $ cvs -d:ext:rueda at cvs.ecoinformatics.org:/cvs -z9 co kepler
>> $ cd kepler
>> $ export KEPLER=`pwd`
>> $ ant usage # to see what's next...
>> $ ant install # Fails with many compile errors relate to
>> ptolemy packages
>> # Note that PTII is properly defined above.
>> $ ant vergil # copies a lot of stuff and the runs vergil
>> succesfully
>> $ ant install # now it works!
>> $ ant run # process a bunch of .jar files and starts up
>>
>> ## A quick kepler tour
>> I'm starting kepler with ``ant run''
>>
>> # create a new graph: File -> New -> Graph Editor
>> Fails: the stacktrace starts as follows:
>>
>> [java] Exception in thread "AWT-EventQueue-0"
>> java.lang.NoSuchMethodError:
>> org.apache.log4j.Logger.log(Ljava/lang/String;Lorg/apache/log4j/Priority;Ljava/lang/Object;Ljava/lang/Throwable;)V
>>
>> [java] at
>> org.apache.commons.logging.impl.Log4JLogger.debug(Log4JLogger.java:137)
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.FBRuleInfGraph.addBRule(FBRuleInfGraph.java:225)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.impl.RETETerminal.fire(RETETerminal.java:144)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.impl.RETEClauseFilter.fire(RETEClauseFilter.java:222)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.impl.RETEEngine.runAll(RETEEngine.java:370)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.impl.RETEEngine.fastInit(RETEEngine.java:130)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.impl.RETEEngine.init(RETEEngine.java:103)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.FBRuleInfGraph.prepare(FBRuleInfGraph.java:434)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.GenericRuleReasoner.getPreload(GenericRuleReasoner.java:348)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.RDFSRuleReasoner.bind(RDFSRuleReasoner.java:141)
>>
>> [java] at
>> com.hp.hpl.jena.ontology.impl.OntModelImpl.generateGraph(OntModelImpl.java:2419)
>>
>> [java] at
>> com.hp.hpl.jena.ontology.impl.OntModelImpl.<init>(OntModelImpl.java:128)
>> [java] at
>> com.hp.hpl.jena.ontology.impl.OntModelImpl.<init>(OntModelImpl.java:116)
>> [java] at
>> com.hp.hpl.jena.rdf.model.ModelFactory.createOntologyModel(ModelFactory.java:375)
>>
>> [java] at
>> org.ecoinformatics.seek.sms.AnnotationEngine.initialize(AnnotationEngine.java:153)
>>
>> [java] at
>> org.ecoinformatics.seek.sms.AnnotationEngine.<init>(AnnotationEngine.java:119)
>>
>> [java] at
>> org.ecoinformatics.seek.sms.AnnotationEngine.instance(AnnotationEngine.java:129)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.TabbedLibraryPane.<init>(TabbedLibraryPane.java:107)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.TabbedLibraryPane$Factory.createLibraryPane(TabbedLibraryPane.java:243)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.LibraryPaneFactory.createLibraryPane(LibraryPaneFactory.java:119)
>>
>> [java] at
>> ptolemy.vergil.basic.BasicGraphFrame.<init>(BasicGraphFrame.java:352)
>> [java] at
>> ptolemy.vergil.basic.ExtendedGraphFrame.<init>(ExtendedGraphFrame.java:100)
>>
>> [java] at
>> ptolemy.vergil.actor.ActorGraphFrame.<init>(ActorGraphFrame.java:124)
>> [java] at
>> ptolemy.vergil.actor.ActorGraphTableau.<init>(ActorGraphTableau.java:105)
>> [java] at
>> ptolemy.vergil.actor.ActorGraphTableau$Factory.createTableau(ActorGraphTableau.java:162)
>>
>> [java] at
>> ptolemy.actor.gui.PtolemyTableauFactory.createTableau(PtolemyTableauFactory.java:98)
>>
>> [java] at
>> ptolemy.actor.gui.TableauFactory.createTableau(TableauFactory.java:122)
>> [java] at
>> ptolemy.actor.gui.Configuration.createPrimaryTableau(Configuration.java:193)
>>
>> [java] at
>> ptolemy.actor.gui.TableauFrame$1.actionPerformed(TableauFrame.java:349)
>> [java] at
>> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)
>>
>>
>> # test some of the offered workflows
>> * Click on Baseline 3-Actor GARP - Browser Display
>> Part of the stacktrace is as follows:
>>
>> [java] Exception in thread "AWT-EventQueue-0"
>> java.lang.NoSuchMethodError:
>> org.apache.log4j.Logger.log(Ljava/lang/String;Lorg/apache/log4j/Priority;Ljava/lang/Object;Ljava/lang/Throwable;)V
>>
>> [java] at
>> org.apache.commons.logging.impl.Log4JLogger.debug(Log4JLogger.java:137)
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.FBRuleInfGraph.addBRule(FBRuleInfGraph.java:225)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.impl.RETETerminal.fire(RETETerminal.java:144)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.impl.RETEClauseFilter.fire(RETEClauseFilter.java:222)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.impl.RETEEngine.runAll(RETEEngine.java:370)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.impl.RETEEngine.fastInit(RETEEngine.java:130)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.impl.RETEEngine.init(RETEEngine.java:103)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.FBRuleInfGraph.prepare(FBRuleInfGraph.java:434)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.GenericRuleReasoner.getPreload(GenericRuleReasoner.java:348)
>>
>> [java] at
>> com.hp.hpl.jena.reasoner.rulesys.RDFSRuleReasoner.bind(RDFSRuleReasoner.java:141)
>>
>> [java] at
>> com.hp.hpl.jena.ontology.impl.OntModelImpl.generateGraph(OntModelImpl.java:2419)
>>
>> [java] at
>> com.hp.hpl.jena.ontology.impl.OntModelImpl.<init>(OntModelImpl.java:128)
>> [java] at
>> com.hp.hpl.jena.ontology.impl.OntModelImpl.<init>(OntModelImpl.java:116)
>> [java] at
>> com.hp.hpl.jena.rdf.model.ModelFactory.createOntologyModel(ModelFactory.java:375)
>>
>> [java] at
>> org.ecoinformatics.seek.sms.AnnotationEngine.initialize(AnnotationEngine.java:153)
>>
>> [java] at
>> org.ecoinformatics.seek.sms.AnnotationEngine.<init>(AnnotationEngine.java:119)
>>
>> [java] at
>> org.ecoinformatics.seek.sms.AnnotationEngine.instance(AnnotationEngine.java:129)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.TabbedLibraryPane.<init>(TabbedLibraryPane.java:107)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.TabbedLibraryPane$Factory.createLibraryPane(TabbedLibraryPane.java:243)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.LibraryPaneFactory.createLibraryPane(LibraryPaneFactory.java:119)
>>
>> [java] at
>> ptolemy.vergil.basic.BasicGraphFrame.<init>(BasicGraphFrame.java:352)
>>
>> * Click on Baseline 3-Actor GARP - ImageJ Display
>> It opens the source of .../ptolemy/actor/TypedCompositeActor.java
>> and prints the following stacktrace:
>> [java] java.lang.NullPointerException
>> [java] at
>> org.ecoinformatics.seek.sms.AnnotationEngine.buildDefaultActorLibrary(AnnotationEngine.java:324)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.TabbedLibraryPane.<init>(TabbedLibraryPane.java:109)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.TabbedLibraryPane$Factory.createLibraryPane(TabbedLibraryPane.java:243)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.LibraryPaneFactory.createLibraryPane(LibraryPaneFactory.java:119)
>>
>> [java] at
>> ptolemy.vergil.basic.BasicGraphFrame.<init>(BasicGraphFrame.java:352)
>> [java] at
>> ptolemy.vergil.basic.ExtendedGraphFrame.<init>(ExtendedGraphFrame.java:100)
>>
>> [java] at
>> ptolemy.vergil.actor.ActorGraphFrame.<init>(ActorGraphFrame.java:124)
>> [java] at
>> ptolemy.vergil.actor.ActorGraphTableau.<init>(ActorGraphTableau.java:105)
>> [java] at
>> ptolemy.vergil.actor.ActorGraphTableau$Factory.createTableau(ActorGraphTableau.java:162)
>>
>> [java] at
>> ptolemy.actor.gui.PtolemyTableauFactory.createTableau(PtolemyTableauFactory.java:98)
>>
>> [java] at
>> ptolemy.actor.gui.TableauFactory.createTableau(TableauFactory.java:122)
>> [java] at
>> ptolemy.actor.gui.Configuration.createPrimaryTableau(Configuration.java:193)
>>
>> [java] at
>> ptolemy.actor.gui.Configuration.openModel(Configuration.java:391)
>> [java] at
>> ptolemy.actor.gui.Configuration.openModel(Configuration.java:317)
>> [java] at
>> ptolemy.actor.gui.HTMLViewer.hyperlinkUpdate(HTMLViewer.java:214)
>> [java] at
>> javax.swing.JEditorPane.fireHyperlinkUpdate(JEditorPane.java:320)
>> ...
>> * Click on EML2 Simple Plot Example
>> Similarly: opens the same source file as the previous and prints:
>>
>> [java] java.lang.NullPointerException
>> [java] at
>> org.ecoinformatics.seek.sms.AnnotationEngine.buildDefaultActorLibrary(AnnotationEngine.java:324)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.TabbedLibraryPane.<init>(TabbedLibraryPane.java:109)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.TabbedLibraryPane$Factory.createLibraryPane(TabbedLibraryPane.java:243)
>>
>> [java] at
>> org.ecoinformatics.seek.ecogrid.LibraryPaneFactory.createLibraryPane(LibraryPaneFactory.java:119)
>>
>> [java] at
>> ptolemy.vergil.basic.BasicGraphFrame.<init>(BasicGraphFrame.java:352)
>> [java] at
>> ptolemy.vergil.basic.ExtendedGraphFrame.<init>(ExtendedGraphFrame.java:100)
>>
>> [java] at
>> ptolemy.vergil.actor.ActorGraphFrame.<init>(ActorGraphFrame.java:124)
>> [java] at
>> ptolemy.vergil.actor.ActorGraphTableau.<init>(ActorGraphTableau.java:105)
>> [java] at
>> ptolemy.vergil.actor.ActorGraphTableau$Factory.createTableau(ActorGraphTableau.java:162)
>>
>> [java] at
>> ptolemy.actor.gui.PtolemyTableauFactory.createTableau(PtolemyTableauFactory.java:98)
>>
>> [java] at
>> ptolemy.actor.gui.TableauFactory.createTableau(TableauFactory.java:122)
>> [java] at
>> ptolemy.actor.gui.Configuration.createPrimaryTableau(Configuration.java:193)
>>
>> [java] at
>> ptolemy.actor.gui.Configuration.openModel(Configuration.java:391)
>> [java] at
>> ptolemy.actor.gui.Configuration.openModel(Configuration.java:317)
>> [java] at
>> ptolemy.actor.gui.HTMLViewer.hyperlinkUpdate(HTMLViewer.java:214)
>> [java] at
>> javax.swing.JEditorPane.fireHyperlinkUpdate(JEditorPane.java:320)
>>
>> * Click on Promotor Identification Workflow
>> Fails with a message window. The stacktrace starts as follows:
>>
>> ptolemy.kernel.util.IllegalActionException: Cannot find class:
>> ptolemy.actor.lib.hoc.IterateOverArray
>> Because:
>> Could not find 'ptolemy/actor/lib/hoc/IterateOverArray.xml' or
>> 'ptolemy/actor/lib/hoc/IterateOverArray.moml' using base
>> 'jar:file:/home/carueda/prg/kepler/build/kepler-configs.jar!/ptolemy/configs/kepler/workflows/bio/PIW.xml':
>> in
>> jar:file:/home/carueda/prg/kepler/build/kepler-configs.jar!/ptolemy/configs/kepler/workflows/bio/PIW.xml
>> at line 729 and column 85
>> Caused by:
>> com.microstar.xml.XmlException: -- JAR entry
>> ptolemy/configs/kepler/workflows/bio/ptolemy/actor/lib/hoc/IterateOverArray.xml
>> not found in /home/carueda/prg/kepler/build/kepler-configs.jar
>> -- XML file not found relative to classpath.
>> -- /home/carueda/prg/kepler:ptolemy/actor/lib/hoc/IterateOverArray.xml
>> /home/carueda/prg/ptolemy/actor/lib/hoc/IterateOverArray.xml (No such
>> file or directory)
>> in
>> jar:file:/home/carueda/prg/kepler/build/kepler-configs.jar!/ptolemy/configs/kepler/workflows/bio/PIW.xml
>> at line 729 and column 85
>> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3144)
>> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2027)
>> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:945)
>> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1125)
>> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:947)
>> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1125)
>> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:947)
>> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1125)
>> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:947)
>> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1125)
>> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:947)
>> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:496)
>> at com.microstar.xml.XmlParser.doParse(XmlParser.java:176)
>> at com.microstar.xml.XmlParser.parse(XmlParser.java:146)
>> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1212)
>> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1174)
>> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1151)
>> at
>> ptolemy.actor.gui.PtolemyEffigy$Factory.createEffigy(PtolemyEffigy.java:350)
>>
>> at
>> ptolemy.actor.gui.EffigyFactory.createEffigy(EffigyFactory.java:137)
>> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:356)
>> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:317)
>> at ptolemy.actor.gui.HTMLViewer.hyperlinkUpdate(HTMLViewer.java:214)
>> at javax.swing.JEditorPane.fireHyperlinkUpdate(JEditorPane.java:320)
>> at
>> javax.swing.text.html.HTMLEditorKit$LinkController.activateLink(HTMLEditorKit.java:827)
>>
>> at
>> javax.swing.text.html.HTMLEditorKit$LinkController.mouseClicked(HTMLEditorKit.java:637)
>>
>> at
>> java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:212)
>> at java.awt.Component.processMouseEvent(Component.java:5491)
>> at javax.swing.JComponent.processMouseEvent(JComponent.java:3093)
>> at java.awt.Component.processEvent(Component.java:5253)
>> at java.awt.Container.processEvent(Container.java:1966)
>> at java.awt.Component.dispatchEventImpl(Component.java:3955)
>> at java.awt.Container.dispatchEventImpl(Container.java:2024)
>> at java.awt.Component.dispatchEvent(Component.java:3803)
>> at
>> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)
>> at
>> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3901)
>> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
>> at java.awt.Container.dispatchEventImpl(Container.java:2010)
>> at java.awt.Window.dispatchEventImpl(Window.java:1766)
>> at java.awt.Component.dispatchEvent(Component.java:3803)
>> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>> at
>> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:234)
>>
>> at
>> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
>>
>> at
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
>> at
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
>> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>> Caused by: com.microstar.xml.XmlException: Could not find
>> 'ptolemy/actor/lib/hoc/IterateOverArray.xml' or
>> 'ptolemy/actor/lib/hoc/IterateOverArray.moml' using base
>> 'jar:file:/home/carueda/prg/kepler/build/kepler-configs.jar!/ptolemy/configs/kepler/workflows/bio/PIW.xml':
>> in
>> jar:file:/home/carueda/prg/kepler/build/kepler-configs.jar!/ptolemy/configs/kepler/workflows/bio/PIW.xml
>> at line 729 and column 85
>> Caused by:
>> com.microstar.xml.XmlException: -- JAR entry
>> ptolemy/configs/kepler/workflows/bio/ptolemy/actor/lib/hoc/IterateOverArray.xml
>> not found in /home/carueda/prg/kepler/build/kepler-configs.jar
>> -- XML file not found relative to classpath.
>> -- /home/carueda/prg/kepler:ptolemy/actor/lib/hoc/IterateOverArray.xml
>> /home/carueda/prg/ptolemy/actor/lib/hoc/IterateOverArray.xml (No such
>> file or directory)
>> in
>> jar:file:/home/carueda/prg/kepler/build/kepler-configs.jar!/ptolemy/configs/kepler/workflows/bio/PIW.xml
>> at line 729 and column 85
>> at
>> ptolemy.moml.MoMLParser._attemptToFindMoMLClass(MoMLParser.java:3001)
>> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3139)
>> ... 44 more
>>
>>
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