[kepler-dev] Ptolemy & Kepler installation and quick workflow tests
Chad Berkley
berkley at nceas.ucsb.edu
Tue Feb 15 16:11:40 PST 2005
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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