Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362017-05-11T23:38:59ZEcoinformatics Redmine
Redmine Bug #7189 (New): memory leak in Managerhttps://projects.ecoinformatics.org/ecoinfo/issues/71892017-05-11T23:38:59ZDaniel Crawldanielcrawl@gmail.com
<p>The Manager registers a shutdown thread with the JVM, but does not unregister it after execute() is finished, which prevents the Manager from being garbage collected. run() does unregister it.</p>
<p>It also seems odd that the thread is registered only once (in the constructors), but never registered again after it is unregistered. The purpose of the thread is to "gracefully stop the execution of a model if the JVM is shut down (by control-C, the user logging out, etc.)", so I would expect the thread to be registered every time execution takes place.</p> Bug #6893 (New): DateToken value inconsistenthttps://projects.ecoinformatics.org/ecoinfo/issues/68932015-12-03T00:33:05ZDaniel Crawldanielcrawl@gmail.com
<p>DateToken stores the date internally in _value and _calendar, but these fields are not kept consistent. For example, if you use ModifyDate to add 2 seconds, _value is not updated. See the attached test workflow.</p>
<p>Also, ModifyDate changes the state of the input token instead of creating a new one - I thought this was not allowed in actors.</p> Bug #5699 (New): Change the workflow scheduler server documentation link in the workflow-schedule...https://projects.ecoinformatics.org/ecoinfo/issues/56992012-08-28T00:15:15ZJing Taotao@nceas.ucsb.edu
<p>Currently the the workflow scheduler server documentation points to the svm trunk version. In the next workflow-scheduler-gui release, the documenation should be a branch or tag version.</p> Bug #5664 (New): Check for duplicate codehttps://projects.ecoinformatics.org/ecoinfo/issues/56642012-08-07T00:01:51ZChristopher Brookscxh@eecs.berkeley.edu
<p>See bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: Examine Kepler for duplicated Ptolemy code (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/4926">#4926</a> for how to check for duplicate code.</p>
<p>This bug is targeted to 2.5.0 so that we don't forget to do it.</p> Bug #5652 (New): Geon Scp and spa Ssh2Exec have duplicate code.https://projects.ecoinformatics.org/ecoinfo/issues/56522012-08-06T23:35:23ZChristopher Brookscxh@eecs.berkeley.edu
<p>Duplicate code detected with CPD. See</p>
<p>actors/src/org/geon/Scp.java line 295<br />actors/src/org/sdm/spa/Ssh2Exec.java line 361
# lines : 143</p> Bug #5590 (New): RExpression forces pdf if 'automatically show graphics' is checkedhttps://projects.ecoinformatics.org/ecoinfo/issues/55902012-04-26T01:34:05ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Look into this forced format change side-effect which is confusing to a user. If you select e.g. png, and 'auto show..', you get a pdf.</p> Bug #5444 (In Progress): Kepler can't run workflow if two instances exist at same timehttps://projects.ecoinformatics.org/ecoinfo/issues/54442011-07-30T00:21:27ZJing Taotao@nceas.ucsb.edu
<p>Both vanilla and reporting suites (2.3) have problems. But the behaviors are different:<br />1. Vanilla kepler:</p>
<p>Start a kepler then start antoher one. The second one runs a workflow. Then close the first kepler. Finally close the second one, it shows the error:<br />java.sql.SQLException: Connection is broken: java.io.EOFException<br />at org.hsqldb.jdbc.Util.sqlException(Unknown Source)<br />at org.hsqldb.jdbc.jdbcStatement.fetchResult(Unknown Source)<br />at org.hsqldb.jdbc.jdbcStatement.execute(Unknown Source)<br />at org.kepler.util.sql.DatabaseType._executeSQL(DatabaseType.java:930)<br />at org.kepler.util.sql.HSQL.disconnect(HSQL.java:79)<br />at org.kepler.objectmanager.lsid.LSIDGenerator.closeDatabase(LSIDGenerator.java:400)<br />at org.kepler.module.core.Shutdown.shutdownModule(Shutdown.java:48)<br />at org.kepler.Kepler._initializeModules(Kepler.java:572)<br />at org.kepler.Kepler.access$100(Kepler.java:81)<br />at org.kepler.Kepler$Shutdown.shutdown(Kepler.java:663)<br />at org.kepler.util.ShutdownNotifier.shutdown(ShutdownNotifier.java:48)<br />at org.kepler.gui.KeplerGraphFrame.dispose(KeplerGraphFrame.java:1146)</p>
<p>2. Reporting kepler.<br />Two kepers are running. One runs a workflow and get an error:<br /><jing> ptolemy.kernel.util.IllegalActionException: Error recording workflow structure: Error connecting or initializing database.
{DB User Name=sa, Password=, DB Host=, DB Name=provenanceDB, DB Type=HSQL, DB Port=9002, DB Table Prefix=, JDBC URL=}<br />The database is already in use by another process: lockFile: org.hsqldb.persist.LockFile@aef9f24b[file =/home/tao/KeplerData/modules/provenance/db-2.3/provenanceDB.lck, exists=true, locked=false, valid=false, ] method: checkHeartbeat read: 2011-07-28 13:32:04.979 heartbeat - read: -8463 ms.<br />in .testWithReport.TOP Provenance Recorder<br />Because:<br />Error connecting or initializing database.
{DB User Name=sa, Password=, DB Host=, DB Name=provenanceDB, DB Type=HSQL, DB Port=9002, DB Table Prefix=, JDBC URL=}<br />The database is already in use by another process: lockFile: org.hsqldb.persist.LockFile@aef9f24b[file =/home/tao/KeplerData/modules/provenance/db-2.3/provenanceDB.lck, exists=true, locked=false, valid=false, ] method: checkHeartbeat read: 2011-07-28 13:32:04.979 heartbeat - read: -8463 ms.<br />at org.kepler.provenance.ProvenanceRecorder._recordWorkflowContents(ProvenanceRecorder.java:2618)<br />at org.kepler.provenance.ProvenanceRecorder.preinitialize(ProvenanceRecorder.java:583)<br />at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1682)<br />at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:930)<br />at ptolemy.actor.Manager.initialize(Manager.java:636)<br />at ptolemy.actor.Manager.execute(Manager.java:340)<br />at ptolemy.actor.Manager.run(Manager.java:1111)<br />at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1641)</p> Bug #5333 (New): 2.2 rc3: getenv("") doesn't work for mac installation.https://projects.ecoinformatics.org/ecoinfo/issues/53332011-03-01T23:46:41Zjianwu jianwujianwu@sdsc.edu
<p>getenv is to get environment variable value in Kepler. It works for me in my installation on windows. On mac, it doesn't work if I start Kepler using Kepler.app. It only works if I start using Kepler.app/Contents/Resources/Java/kepler.sh.</p> Bug #5290 (New): originModule not always sethttps://projects.ecoinformatics.org/ecoinfo/issues/52902011-02-02T19:34:54ZDaniel Crawldanielcrawl@gmail.com
<p>The <originModule> property is added to configuration files so that properties will be ignored when their originating module is not loaded. However, sometimes <originModule> is not set. For example:</p>
<p>ant change-to -Dsuite=reporting<br />ant run<br />ant change-to -Dsuite=fault-tolerance<br />ant run<br />ant change-to -Dsuite=kepler<br />ant run</p>
<p>Results in:</p>
<p>[run] java.lang.ClassNotFoundException: org.kepler.reporting.gui.ItemsOfInterestPanel$Factory</p>
<p>In ~/KeplerData/modules/gui/configuration/configuration.xml, the <tabPane> for Items Of Interest does not have <originModule>.</p> Bug #5249 (In Progress): test kepler for memory leakshttps://projects.ecoinformatics.org/ecoinfo/issues/52492010-11-30T22:50:17Zjianwu jianwujianwu@sdsc.edu
<p>a separate bug only for memory leak fixing for Kepler suite. bug 5095 depends on it.</p> Bug #5153 (New): Save As... closes all windows associated with a workflowhttps://projects.ecoinformatics.org/ecoinfo/issues/51532010-08-17T18:04:51ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you're working on a complex workflow, it's not uncommon to have multiple windows open for the one workflow -- windows for different contained composites. When you Save Archive, a new KAR is written, all windows for the workflow are closed, and the new KAR is opened. This process is slow, and also does not open all your windows in the state they were at before save, only the top level window is opened, requiring you navigate through your workflow re-opening everything as you had it.</p> Bug #4978 (In Progress): Create additional 'module' property for any menu entries that are insert...https://projects.ecoinformatics.org/ecoinfo/issues/49782010-05-05T00:21:51ZSean Riddleswriddle@gmail.com
<p>As of revision r24221 and r24222-3 on the branch, there's a way to avoid those errors that look like:</p>
<pre><code>[run] ERROR (org.kepler.gui.MenuMapper:getActionFor:271) Exception trying to create an Action for classname: &lt;org.kepler.tagging.TagManagerAction&gt;:<br /> [run] null (java.lang.ClassNotFoundException: org.kepler.tagging.TagManagerAction)</code></pre>
<p>Those come from modules inserting menu entry information into the persistent gui module configuration and then the user removing that module from their active configuration. The system still tries to create that entry, which references a class that is no longer available. If a property named 'module' is created as a peer to 'name' and 'value', then the menu entry will only be generated if a module by that name is in the active configuration. See org.kepler.module.tagging.Initialize from the tagging module for an example of how to do this without hardwiring the module name.</p>
<p>So in order to eliminate error messages like the above, these additional properties need to be created when the menu entry is added to the gui configuration.</p> Bug #4801 (In Progress): out of memoryhttps://projects.ecoinformatics.org/ecoinfo/issues/48012010-02-17T22:13:10ZOliver Soongsoong@nceas.ucsb.edu
<p>ERROR: RecordingException: Unable to query data table: out of memory</p>
<p>I opened tpc01, ran it, closed it, opened tpc03-herbs, ran it, closed it, opened tpc03-large-herbivores, ran it, closed it, opened tpc03-woody, ran it, closed it, opened tpc09, ran it, and hit the above out of memory error. I have 68 runs in the wrm, but 63 of them are various iterations of the small test workflow for bug 4789. I also have those 5 Kruger KARs in a local repository and all the data for them is cached. I can start Kepler and run any of those workflows by themselves. I started Kepler with an ant run, so the jvm should have a 512MB memory max.</p>
<p>Kruger workflows: <a class="external" href="https://code.ecoinformatics.org/code/kruger/trunk/workflows">https://code.ecoinformatics.org/code/kruger/trunk/workflows</a><br />Kruger: r439<br />Kepler: wrp r23080</p>
<p>It may be worth looking at bug 4642.</p> Bug #4642 (New): memory usage & slowdownshttps://projects.ecoinformatics.org/ecoinfo/issues/46422009-12-19T03:45:53ZOliver Soongsoong@nceas.ucsb.edu
<p>I just hit a big slowdown caused by OOM problems. This bug is mostly a place to put down some of the stuff I found out. I used jmap to produce histograms when Kepler was crawling and immediately after a fresh restart. When Kepler was slow, there was a single workflow open with 4 actors and the Check System Settings window. The fresh Kepler retained the wrm and cache content, but discarded the 4 actors and all the accumulated memory leaking cruft.</p>
<p>A few things jump out at me, and I'd say I'm pretty uninformed. I've formatted as Object: stale #, fresh #.</p>
<p>org.kepler.util.WorkflowRun: 39206, 29<br />javax.swing.JMenuItem: 3411, 96<br />java.util.HashMap: 689643, 22885<br />org.kepler.objectmanager.lsid.KeplerLSID: 120115, 1339<br />java.util.LinkedList: 95565, 4468<br />ptolemy.kernel.util.Location: 1837, 45</p>
<p>Interestingly enough, I have 28 wrm entries. I think something's up with the wrm, but also a lot of GUI objects seem to be hanging around as well, so there may be other things going on as well.</p>
<p>And on a side note, jps -> jmap -> jhat produces some pretty cool results.</p> Bug #4281 (In Progress): ant update produces message about running svn cleanuphttps://projects.ecoinformatics.org/ecoinfo/issues/42812009-08-05T20:21:19ZChristopher Brookscxh@eecs.berkeley.edu
<p>Under Windows 2003 Server, running "ant update" produces a message<br />about a file being locked and suggesting running "svn cleanup".</p>
<p>If I do:</p>
<p>svn co <a class="external" href="https://code.kepler-project.org/code/kepler/trunk/modules/build-area">https://code.kepler-project.org/code/kepler/trunk/modules/build-area</a><br />cd build-area<br />ant change-to -Dsuite=kepler<br />ant update</p>
<p>Then I get:</p>
<p>[update-modules] Updating ptolemy-lib...<br />[update-modules] svn -r head update c:\tmp\cxh\src\kepler\ptolemy-lib <br />[update-modules] At revision 20190.<br />[update-modules] <br />[update-modules] svn -r head update c:\tmp\cxh\src\kepler\build-area <br />[update-modules] svn: Working copy 'c:\tmp\cxh\src\kepler\build-area' locked<br />[update-modules] svn: run 'svn cleanup' to remove locks (type 'svn help cleanup' for details)<br />[update-modules] <br />[update-modules] WARNING: It appears that the command did not execute properly and exited with an exit code of: 1</p>
<p>Running "ant cleanup" does not change the results.</p>
<p>This should probably be addressed before 2.0 as Windows users will find it<br />confusing.</p>
<p>I believe that the problem is likely that a file in build-area is being<br />changed and Windows is not able to deal with this.</p>
<p>I think this is a new failure, it may have started only in the last few weeks.</p>