Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-08-07T18:07:33ZEcoinformatics Redmine
Redmine Kepler - Feature #5666 (New): Build system needs a target to build all common or blessed non-core...https://projects.ecoinformatics.org/ecoinfo/issues/56662012-08-07T18:07:33ZChristopher Brookscxh@eecs.berkeley.edu
<p>There should be a way to easily build all the common or "blessed" <br />non-core modules.<br />For example, "ant change-to -Dsuite=kepler" does not check out <br />reporting or tagging.</p>
<p>We should have notion of "blessed" modules, which I would say at a minumum<br />must meet two requirements:<br />1) There is someone on kepler-dev who is actively maintaining the module<br />2) There is at least one automatic test that at least does a smoke test<br />to ensure that the module works. More tests are better, but "ant test-blessed" <br />or something should do something with each module.</p>
<p>Having blessed modules would help in refactoring the tree because we<br />would have a better idea about what will break.</p> Kepler - Bug #5192 (New): Module Manager reacts badly to dot files in resources/configuration dir...https://projects.ecoinformatics.org/ecoinfo/issues/51922010-09-29T15:16:30ZChristopher Brookscxh@eecs.berkeley.edu
<p>I was trying to follow the 2.1 instructions at<br /><a class="external" href="https://kepler-project.org/developers/teams/build/kepler-2.1-release-roadmap/?searchterm=roadmap">https://kepler-project.org/developers/teams/build/kepler-2.1-release-roadmap/?searchterm=roadmap</a></p>
<p>and edited <br />kepler-2.1/module-manager-2.1/resources/configurations/configuration.xml<br />with Emacs, which created<br />kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml</p>
<p>Then ant clean-all run<br />failed:</p>
<p>run:<br /> [run] setting dock icon to -Xdock:icon=/Users/cxh/src/kepler-2.1/common-2.1/resources/icons/kepler-dock-icon.png<br /> [run] Set environment variable: PATH = /Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/opt/subversion/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/usr/local/texlive/2007/bin:/usr/local/git/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/opt/subversion/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/usr/local/texlive/2007/bin:/usr/texbin:/usr/local/texlive/2007/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/src/kepler-2.1/r-2.1/lib:/Users/cxh/src/kepler-2.1/common-2.1/lib/ptolemy/matlab:/Users/cxh/src/kepler-2.1/common-2.1/lib<br /> [run] Set environment variable: R_HOME = /Library/Frameworks/R.framework/Resources<br /> [run] /Users/cxh/src/kepler-2.1<br /> [run] java.io.FileNotFoundException: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at java.io.FileInputStream.open(Native Method)<br /> [run] at java.io.FileInputStream.<init>(FileInputStream.java:106)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfiguration(CommonsConfigurationReader.java:144)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:92)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:64)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:420)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] org.kepler.configuration.ConfigurationManagerException: Error loading configuration file: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfiguration(CommonsConfigurationReader.java:171)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:92)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:64)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:420)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] org.kepler.configuration.ConfigurationManagerException: Error loading configuration: Error loading configuration file: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:105)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:64)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:420)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] Exception in thread "main" java.lang.RuntimeException: Could not load configuration: Error loading configuration: Error loading configuration file: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:93)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)</p>
<p>BUILD FAILED<br />/Users/cxh/src/kepler-2.1/build-area/build.xml:36: Java returned: 1</p>
<p>Total time: 2 minutes 52 seconds<br />bash-3.2$ ls ~/src/kepler-2.1/module-manager-2.1/resources/configurations/<br />configuration.xml<br />bash-3.2$ ls -a ~/src/kepler-2.1/module-manager-2.1/resources/configurations/<br />. .. configuration.xml<br />.#configuration.xml .svn<br />bash-3.2$</p> Kepler - Bug #5155 (New): To exclude a file or directory requires updating at least four places, ...https://projects.ecoinformatics.org/ecoinfo/issues/51552010-08-18T22:53:13ZChristopher Brookscxh@eecs.berkeley.edu
<p>jianwu <<a class="email" href="mailto:jianwu@sdsc.edu">jianwu@sdsc.edu</a>> writes:</p>
<blockquote>
<p>If excluding those from building system, please make sure it's also updated for<br />eclipse building. To update it, just modify the PtolemyClasspathStart file at<br />build-area/resources/eclipse.</p>
<p>We probably also need to update corresponding files at<br />build-area/resources/netbeans and build-area/resources/idea.</p>
</blockquote>
<p>I'm mystified as to why a human has to update four locations with<br />the same data. Isn't this why we have computers?<br />I should update one master file, the Netbeans, Eclipse and Idea <br />files should be automatically updated.</p> Kepler - Bug #5081 (New): A system for adding and removing GUI menus.https://projects.ecoinformatics.org/ecoinfo/issues/50812010-07-07T17:25:27ZChristopher Brookscxh@eecs.berkeley.edu
<p>The existing system needs documentation.</p>
<p>Also, refactoring to use RCP would help here</p> Kepler - Bug #5027 (New): Users should be able to build installers for the Kepler-2.0 branchhttps://projects.ecoinformatics.org/ecoinfo/issues/50272010-05-24T17:32:46ZChristopher Brookscxh@eecs.berkeley.edu
<p>Kepler users should be able to build installers so that they may deploy<br />a shrinkwrapped installation to other users. Currently, "ant installer" <br />works in the Kepler devel trunk, but fails in the 2.0 branch.</p>
<p>[installer] Writing installer file to /Users/cxh/src/kepler-2.0/build-area/installer/install.xml<br /> [izpack] ERROR: 'The content of elements must consist of well-formed character data or markup.'<br /> [izpack] ERROR: 'com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: The content of elements must consist of well-formed character data or markup.'<br /> [izpack] javax.xml.transform.TransformerException: javax.xml.transform.TransformerException: com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: The content of elements must consist of well-formed character data or markup.<br /> [izpack] at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:673)<br /> [izpack] at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:300)<br /> [izpack] at com.izforge.izpack.adaptator.impl.XMLParser.parseLineNrFromInputSource(Unknown Source)</p>
<p>We are not currently exposing the "ant installer" command to users, so<br />this is an RFE, not a bug.</p>
<p>See bug 4994 at<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4994">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4994</a></p> Kepler - Bug #4909 (New): Actor documentation: updates ignored, duplicate info, how to refer to o...https://projects.ecoinformatics.org/ecoinfo/issues/49092010-03-29T21:15:59ZChristopher Brookscxh@eecs.berkeley.edu
<p>A few comments about the Kepler Actor Documentation system</p>
<p>1. If I update the .xml file for a Director, then preexisting models<br />do not get the updates. I think this is wrong. For example,<br />I added text to PNDirector.xml. If a user has a preexisting model<br />that uses PNDirector, then to see the new text, they would need<br />to drag in a new PNDirector.</p>
<p>2. The model files contain copies of the documentation. This is<br />related to point 1 above. This will be an issue for large systems<br />because parsing a large file with redundant info takes time and<br />possibly consumes lots of memory</p>
<p>3. In a documentation .xml file, how do I refer to another actor<br />or director? For example in<br />kepler/directors/resources/kar/CoreDirectors/PNDirector.xml<br />I want to refer to the Ramp actor so that if the user<br />clicks on the link, then they are shown the Ramp actor documentation<br />How do I do that?</p>
<p>4. In a documentation .xml file, how do I refer to a model?<br />For example, in<br />kepler/directors/resources/kar/CoreDirectors/PNDirector.xml<br />I want to refer to<br />ptolemy/domains/pn/demo/RemoveNilTokens/RemoveNilTokens.xml<br />How do I do that?</p> Kepler - Bug #4908 (New): actor/director/attribute .xml file documentation needs to be updatedhttps://projects.ecoinformatics.org/ecoinfo/issues/49082010-03-29T21:05:36ZChristopher Brookscxh@eecs.berkeley.edu
<p>The kar files include documentation for actors, directors and attributes.</p>
<p>These files need to be checked against the corresponding Ptolemy<br />actors, directors and attributes and updated accordingly.</p>
<p>For example, the directors/resources/kar/CoreDirectors/PNDirector.xml<br />file did not include information from June, 2008 about how to stop<br />a PN model.</p>
<p>To fix this bug, all of the .kar files should be reviewed and compared<br />with the original class comments in the .java files.</p> Kepler - Bug #4887 (New): If a module is added to a configuration, the error message should inclu...https://projects.ecoinformatics.org/ecoinfo/issues/48872010-03-17T22:15:04ZChristopher Brookscxh@eecs.berkeley.edu
<p>Apparently, the dataturbine module was added to the kepler trunk.</p>
<p>After doing<br />ant update<br />ant run</p>
<p>I got:<br />run:<br /> [run] Error: The following modules are missing: <br /> [run] dataturbine</p>
<p>The fix is to do <br />ant change-to -Dsuite=kepler<br />ant run</p>
<p>It would be nice if the error message would tell the user to do an<br />ant change-to</p>
<p>Even better, it would be nice if the system would get the module.</p> Kepler - Bug #4254 (New): wrapping up, never ending workflow! (PN inside PN)https://projects.ecoinformatics.org/ecoinfo/issues/42542009-07-21T00:47:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>[I'm going through my email logs looking for bugs that have<br />not really been solved.]</p>
<p>The problem is that a trivial example of PN inside PN<br />results in a "wrapping up" message and never terminates.</p>
<p>In January, 2009, Edward responded to email from Josep Maria Campanera.</p>
<p>Edward wrote:</p>
<blockquote>
<p>In theory, PN inside PN should behave exactly as if the inside PN director<br />were not present. Why not just delete it?</p>
<p>It is arguably a bug that the PN director doesn't tolerate<br />PN opaque actors. I think I tried to fix that once, but never<br />got it fixed...</p>
<p>Edward</p>
</blockquote>
<p>Josep Maria Campanera Alsina wrote:</p>
<blockquote>
<p>Dear all,<br />I've found out that the error comes from the fact of using a PN<br />director as an opaque director inside a worflow managed by another PN<br />director! Somehow this problem is related to "Director compatibility" <br />issue.</p>
<p>So I've decided to simplify the workflow and use a model workflow just<br />in order someone can find a trick to run it succesfully. The main idea<br />is ¿How can we can continue the execution of a workflow after the<br />execution of an opaque composite actors with PN director inside when<br />the overall director is an PN one?</p>
<p>In the attached example (exampleCompositeActors.xml), I cannot get a<br />"Execution finished" but the Kepler shows the "wrapping up" signal or<br />alternatively a permament "executing" signal although apparently<br />nothing is running (only finished partly). No error message is<br />displayed!</p>
<p>Which worflow design I should adopt? What Am I doing wrong? How Can I<br />pursue my aim to execute PN composite actors sequentially?</p>
<p>All help appreciated!</p>
<p>Josep Maria Campanera,</p>
<p>PS1: I use Kepler Release 1.0.0 (May 2008) under Linux<br />PS2: Thanks Edward for your comments,</p>
<p>2009/1/14 Edward A. Lee <<a class="email" href="mailto:eal@eecs.berkeley.edu">eal@eecs.berkeley.edu</a>>:</p>
<blockquote>
<p>This is not a situation where it is refusing to terminate because of<br />unconsumed tokens. Typically, this is called by a deadlock. If you<br />are running on a Windows machine from the command line, you can get<br />a stack trace of all the executing threads by typing control-break.<br />If you forward that to this list, we can (maybe) identify<br />the culprit...</p>
<p>Edward</p>
<p>Josep Maria Campanera Alsina wrote:</p>
<blockquote>
<p>Dear all,<br />I get a "wrapping up" message from an execution of a workflow that<br />coordinates the submission of computational chemistry jobs in a<br />cluster queue system. The workflow is based on the<br />TestJobFullCycle-SGE.xml provided by kepler itself, with some<br />variations. Find attached the mentioned workflows.</p>
<p>My workflow is a composite one. I'd like to execute sequentially<br />several tasks: 1st) submit jobs to a cluster, 2nd) collect all outputs<br />and save them locally and then 3rd) convert output files to other<br />formats. Since some tasks are designed for PN director and some for<br />SDF director the overall director is a PN director.</p>
<p>However, the task under the PN director (in charge of job submission)<br />never finishes tough the task is already completed and early shows the<br />message "wrapping up", so the execution never finish step 1st and 2nd<br />so the 3rd is never executed. Why PN director doesn't finish the task?<br />How Can I stop the director and allow the workflow to continue?</p>
<p>I think the problem is related to the PN director that as said in the<br />user manual "may refuse to automatically terminate because tokens are<br />always generated and available to downstream actors"! Here it comments<br />that "One can correct the problem by changing the firingCountLimit<br />parameter of the Constant actor to some finite value". If done that<br />but it continues with the same problem.</p>
<p>How can I overcome this? all comment will be appreciated!</p>
<p>Thanks in advance,</p>
<p>Josep Maria,</p>
</blockquote></blockquote></blockquote> Kepler - Bug #4056 (New): create developer documentation for svn configuration.https://projects.ecoinformatics.org/ecoinfo/issues/40562009-05-06T01:00:34ZChristopher Brookscxh@eecs.berkeley.edu
<p>When svn checks in files, it checks them in using a binary mode.<br />This is a problem when files are checked in using windows and checked<br />out under Linux or Mac OS X. Usually, things just work, but<br />not always. When they don't work, the failure is mysterious because<br />the file looks the same, but has the wrong end of line characters.</p>
<p>In addition, svn needs to be configured to properly set the svn keywords<br />such as Id and Version.</p>
<p>For details, see "Keyword Substition and end of line issues" <br /><a class="external" href="http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Subversion#toc22">http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Subversion#toc22</a><br />and</p>
<p><a class="external" href="http://chess.eecs.berkeley.edu/ptexternal/nightly/doc/coding/eclipse.htm#Subversive">http://chess.eecs.berkeley.edu/ptexternal/nightly/doc/coding/eclipse.htm#Subversive</a></p>
<p>One quick way to check is:</p>
<p>find . -name "*.java" | grep -v .svn > /tmp/kj<br />cat /tmp/kj | xargs ptolemy/adm/bin/svnpropcheck</p>
<p>another way is:<br />cat /tmp/kj | xargs ptolemy/util/testsuite/controlm</p>
<p>which yields:<br />./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./util/src/org/camera/service/AverageGenomeSizeParserV2.java has controlms<br />./util/src/org/camera/service/CAMERARESTService.java has controlms<br />./util/src/org/camera/service/CAMERAURLProcessor.java has controlms<br />./util/src/org/camera/service/IdSizeMapForSeqFile.java has controlms<br />./util/src/org/camera/service/NameValuePair.java has controlms<br />./util/src/org/camera/service/ServiceUtils.java has controlms<br />./util/src/org/kepler/ssh/SftpExec.java has controlms<br />./util/src/org/sdm/spa/actors/transport/BbcpCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/FileCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/FileCopierFactory.java has controlms<br />./util/src/org/sdm/spa/actors/transport/GenericFileCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/LocalFileCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/ScpCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/SftpCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/SrmliteCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/vo/ConnectionDetails.java has controlms<br />./util/tests/src/org/sdm/spa/actors/transport/GenericFileCopierTest.java has controlms<br />./util/tests/src/org/sdm/spa/actors/transport/RunGenericFileCopierTests.java has controlms</p>
<p>./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms</p>
<p>I also checked the .xml files, and<br />common/etc/bundle_build.xml has control-ms<br />To fix these, run:</p>
<p>svn propset svn:eol-style native filename</p>
<p>To set the keywords on an alredy checked in file, run:</p>
<p>svn propset svn:keywords "Author Date Id Revision" filename</p>
<p>Then run:</p>
<p>svn commit</p>
<p>to commit the change.</p> Kepler - Bug #3903 (New): Use Java logging utilities instead of Apache commons logging facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/39032009-03-18T19:21:30ZChristopher Brookscxh@eecs.berkeley.edu
<p>ersonally, I'd like to switch to the logging utilities that<br />now ship with Java, see<br /><a class="external" href="http://java.sun.com/j2se/1.4.2/docs/guide/util/logging/">http://java.sun.com/j2se/1.4.2/docs/guide/util/logging/</a><br />The advantage is that it would be one less jar file to ship.<br />A quick search finds 144 files that use the apache logging facility.<br />Most of these changes could be handled automatically by a script.</p>
<p>Notes about the logging system can be found at<br /><a class="external" href="https://kepler-project.org/developers/reference/using-commons-logging">https://kepler-project.org/developers/reference/using-commons-logging</a></p> Kepler - Bug #3204 (New): Kepler should have FSM exampleshttps://projects.ecoinformatics.org/ecoinfo/issues/32042008-04-02T21:15:37ZChristopher Brookscxh@eecs.berkeley.edu
<p>Finite State Machines are very powerful, there should<br />be a Kepler-specific scientific workflow that <br />illustrates FSMs.</p> Kepler - Bug #3106 (New): Out of memory while opening all demos, is -Xss5m or SVG the problem?https://projects.ecoinformatics.org/ecoinfo/issues/31062008-01-29T04:54:18ZChristopher Brookscxh@eecs.berkeley.edu
<p>I'm marking this as having a target milestone of 1.0.0rc1 because<br />I suspect we should remove -Xss5m from build.xml because it means<br />we cannot open up very many models. Once that is addressed, the<br />milestone should be changed to something later.</p>
<p>Under Windows XP with Java 1.5.0_11, Kepler runs out of memory when opening all the demos whereas Ptolemy does not.</p>
<p>It could be that SVG is the issue, or it could be because Kepler<br />does not do lazy evaluation and thus loads in everything.</p>
<p>To replicate<br />1) Start Kepler with "ant run-dev", which uses -Xmx512m<br />2) Help -> Documentation -> Ptolemy Documentation -> Acknowledgements<br />3) Click on the copyright link at the bottom<br />4) Click on copyrights in<br />"Other copyrights about this configuration (may take a moment to run)." <br />5) Click on about in<br />"Other information about this configuration." <br />6) In the "ptolemy/configs/doc/completeDemosPtinyKepler.htm" line, click on<br /> "Open the .htm, .html, .xml and .pdf "</p>
<p>Roughly 25 windows will open and eventually, we get:</p>
<p>Caused by: java.lang.OutOfMemoryError: unable to create new native thread<br /> at java.lang.Thread.start0(Native Method)</p>
<p>Under Windows, the task manager says we are using 330Mb of memory,</p>
<p>Editing the run-dev entry in build.xml and removing:<br /><jvmarg value="-Xss5m"/><br />means we get to 580Mb in the task manager and then Kepler hangs with the<br />CPU Usage at 99%</p>
<p>java -X says that -Xss<br />-Xss<size> set java thread stack size</p>
<p>Perhaps -Xss should be removed from build.xml?</p>
<p>If I increase the Xmx from 512 to 1024, then the show all demos works,<br />At the end the amount of memory reported by the Task Manager is <br />258Mb, with a max of 608Mb<br />Running the last demo (sr/demo/TrafficLight/TrafficLight.xml) shows<br />this memory usage under Kepler:<br /> [java] 14471 ms. Memory: 968096K Free: 211261K (22%)</p>
<p>In contrast, doing the same thing with Ptolemy (no SVG), the task<br />manager reports 142Mb with a max of 142Mb. Running the same demo<br />reports:<br />6780 ms. Memory: 117172K Free: 24710K (21%)</p> Kepler - Bug #2414 (New): Opening a preexisting model should open in a blank viewerhttps://projects.ecoinformatics.org/ecoinfo/issues/24142006-04-13T21:42:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>In "add welcome screen for release 1.0" at<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343</a></p>
<p>Matthew wrote:</p>
<blockquote>
<p>Now this has been added, here is a very common use case, which seems incorrect<br />(reported by Kevin):</p>
<p>1) User starts kepler - gets blank graph frame, with new welcome screen in front</p>
<p>2) User dismisses welcome screen, and is left with blank graph frame</p>
<p>3) User then does "File->Open" and opens an existing workflow</p>
<p>4) The workflow then opens in a <strong>new</strong> graph frame, leaving the original, empty <br />graph frame on the screen.</p>
<p>Proposed resolution:</p>
<p>BEST: at startup, if user does the above, then the workflow gets opened in the<br /><strong>existing</strong> blank graph frame. Subsequently-opened workflows open up in <strong>new</strong><br />graph frames, as before</p>
</blockquote>
<blockquote>
<p>INTERIM: if we don't have time to implement the above for this release, then<br />check to see if we are in the above use-case, and if so, close the blank graph<br />frame after the first workflow has been opened</p>
<p>Any other thoughts/comments/ideas?</p>
</blockquote>
<p>I wrote:</p>
<blockquote>
<p>Probably File Open should be smart enough to realize that the current window<br />is mostly blank and a candidate for replacement. I'm not sure if<br />this will be very easy. For example, when one does File -> Save As, and<br />uses a new name, a new window appears. We need to handle "Unnamed" models<br />specially. I can take a look at this at some point, but probably not before<br />early March.</p>
</blockquote>
<p>I won't have time before Kepler 1.0, so I'm opening this as a separate <br />enhancement. This new bug has to do with the blank or Unnamed models,<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343</a><br />has to do with the welcome window.</p> Kepler - Bug #2349 (New): Actors should have preconditions to test for long runshttps://projects.ecoinformatics.org/ecoinfo/issues/23492006-02-07T18:19:21ZChristopher Brookscxh@eecs.berkeley.edu
<p>It would be nice if there was an easy way to for a model to test for<br />trivial problems before getting far down a long run.</p>
<p>One idea would be to have such actors implement an interface that included a<br />method that the director would run.</p>
<p>We should think about why having actors do more testing in preinitialize()<br />will not work here. For example, if we have an FSM model, do all<br />the actors get preinitialize() called right away? What about the Case actor.</p>