[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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