Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-08-18T02:44:23ZEcoinformatics Redmine
Redmine Bug #5689 (New): remove configs/.../configuration.xml overridehttps://projects.ecoinformatics.org/ecoinfo/issues/56892012-08-18T02:44:23ZDaniel Crawldanielcrawl@gmail.com
<p>The Ptolemy Configuration MoML for Kepler is in:</p>
<p>common/configs/ptolemy/configs/kepler/configuration.xml</p>
<p>This is overridden in several modules:</p>
<p>ddp-common/configs/ptolemy/configs/kepler/configuration.xml<br />fault-tolerance/configs/ptolemy/configs/kepler/configuration.xml<br />map-reduce/configs/ptolemy/configs/kepler/configuration.xml</p>
<p>As with other overrides, the problem is that when the master version changes, the copies need to be updated.</p>
<p>The difference is small:</p>
<p>diff common/configs/ptolemy/configs/kepler/configuration.xml fault-tolerance/configs/ptolemy/configs/kepler/configuration.xml <br />181a182</p>
<blockquote>
<p><input source="ptolemy/configs/kepler/contingencyTableauFactory.xml"/></p>
</blockquote>
<p>diff common/configs/ptolemy/configs/kepler/configuration.xml ddp-common/configs/ptolemy/configs/kepler/configuration.xml<br />181a182</p>
<blockquote>
<p><input source="ptolemy/configs/kepler/executionChoiceTableauFactory.xml"/></p>
</blockquote> 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 #5276 (New): component search performance is poorhttps://projects.ecoinformatics.org/ecoinfo/issues/52762011-01-24T22:21:07ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Searching for remote KARs through the Components pane is very slow -- search downloads and deals with karXML, each generally about twice as big as the kar it represents. During search the GUI is locked, and there is no progress indicator letting you know search is happening.</p>
<p>The query and related code probably need to be refactored to only download and utilize the bare minimum to show the results. This refactoring may necessitate some changes to what actions are possible on items in the results tree.</p>
<p>Jing and Matt will discuss this bug.</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 #5129 (In Progress): adding and removing configuration properties could be made easierhttps://projects.ecoinformatics.org/ecoinfo/issues/51292010-08-06T21:21:25ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Now that we've shipped 2.0, if a developer wants to add a new configuration property to a config file, they must first check if the user's config file has the property before accessing it, and add it if not. This is a minor hassle if your code tries to use this property in a number of places, each of which might be reached first during the user's kepler session...you have to do the check and possible add at each place. Instead, maybe the configuration manager could, during startup, run through all active modules config files and add properties if necessary to the user's copies in KeplerData. Handing removing properties would be harder -- if we remove a property, and then a user reverts to an older version of Kepler, this CM method would have to know to add the property back for that version.</p> Bug #5095 (In Progress): test kepler and wrp for memory leakshttps://projects.ecoinformatics.org/ecoinfo/issues/50952010-07-14T22:56:35ZMatt Jonesjones@nceas.ucsb.edu
<p>Oliver Soong reported having difficulties with memory leaks. There are two specific bugs about this, which I have set to block this testing bug. In addition, testing may reveal additional leaks, which should be fixed before 2.1 is released. Here's Oliver's synopsis of the issues:</p>
<p>I think this is limited to the wrp suite, but Kepler’s performance degrades significantly over time. Provenance recording can become prohibitively slow, and there is no native in-Kepler fix. There is a large memory leak somewhere, and many components are quite memory-intensive regardless. Given the intention to record executions and the large number of analyses scientists perform, I suspect any dedicated user of Kepler will quickly encounter data management problems. In my case, I stopped using local repositories and began closing Kepler after running any large workflows.</p> Bug #4953 (In Progress): Remote Components category sticks around sometimeshttps://projects.ecoinformatics.org/ecoinfo/issues/49532010-04-21T00:51:03ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If I search KeplerDevRepository for "run2", I currently get back one result: run2-mclaughlin_par,kar, inside the new category of Remote Components.<br />If I right-click on the kar and select Download, and then clear my search by, on the mac, hitting the little x button, or by hitting the Cancel button, the Remote Components category stills shows up in the tree. If you don't select download, the Remote Components category disappears, as I believe is intended.</p> Bug #4869 (In Progress): changes made to workflows during dialogs before committing (Edit Paramet...https://projects.ecoinformatics.org/ecoinfo/issues/48692010-03-04T19:04:24ZOliver Soongsoong@nceas.ucsb.edu
<p>When I make changes to an actor through the dialog, it seems like the changes are made to the workflow immediately, before the "Commit" button is clicked.</p>
<p>For example, create a workflow with an EML 2 Dataset actor. Make sure Kepler has not already authenticated with KNB. Now edit the EML 2 Dataset actor to reference a data package that requires authentication. The KNB login window will immediately pop up, even though no changes have been committed. Dismiss the window in some way. Now click the Help button and close the help window. The dialog will have disappeared. Open the actor dialog again, and the change will be there.</p>
<p>I should point out that the "Cancel" button does seem to work, but I suspect (based on debugging comments and comments in code) that this acts by reverting the changes already made.</p>
<p>I've seen this for sure on EML 2 Dataset and RExpression, since changes to one trigger visual feedback and I've mucked around in the code of the other. I suspect this is a general problem, though, and it may be a result of the underlying ptolemy design.</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 #4139 (In Progress): port names are displayed twicehttps://projects.ecoinformatics.org/ecoinfo/issues/41392009-06-09T02:20:31ZOliver Soongsoong@nceas.ucsb.edu
<p>When I choose to show port names, they are displayed once next to the port as expected and once in the upper left corner of the actor in a bold-looking font. This appears in both XP and linux.</p> Bug #3552 (In Progress): Annotation elements in trace file do not appear in details pane of prove...https://projects.ecoinformatics.org/ecoinfo/issues/35522008-10-22T20:07:51ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>The provenance browser shows the details for the selected data or collection element of a trace in the lower left-hand panel. When the element selected has been annotated with one or more Metadata elements, these appear as name-value pairs under the heading "Annotations" in that panel. However, if an <strong>Annotation</strong> element has been applied to the selected element, it is not displayed.</p>
<p>Annotation and Metadata elements should both appear in the details panel, probably under two distinct headings, 'Metadata' and 'Annotations'.</p>
<p>(Note that the distinction between metadata and annotations in COMAD is that the former are reserved for things that have always been true about the item it is associated with, while the former can be used for any purpose. Consequently, Metadata elements cannot be deleted or replaced during a COMAD workflow run, while Annotation elements can be.)</p> Bug #3361 (In Progress): parameters lose their Display Name when copy and pastedhttps://projects.ecoinformatics.org/ecoinfo/issues/33612008-06-04T00:23:06ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>It may be this is the 'proper' behavior, but it doesn't seem so to me (cxh?).</p>
<p>steps to reproduce:<br />- Drag Parameter to canvas<br />- Right click, Customize Name<br />- type in a New Name: new_name, and a Display Name: display_name<br />- Commit<br />- copy and paste the Parameter</p>
<pre><code>The second Parameter has New name: new_name2, and Display name: new_name2, but I think Display name should be: display_name2.</code></pre>
<p>This affects:</p>
<p>GriddlesParameter<br />ColorParameter<br />FileParameter<br />Parameter<br />PortParameter<br />RequireVersion<br />SemanticTypeParameter <br />StringParameter</p> Bug #3266 (In Progress): ENM/GARP_MultipleSpecies-V.xml problemshttps://projects.ecoinformatics.org/ecoinfo/issues/32662008-05-02T18:02:43ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>ENM/GARP_MultipleSpecies-V.xml crashes Ubuntu Kepler. <br />On mac execution completes but just gives ImageJ "Unrecognized comand: ASC TextReader" messages.</p> Bug #1914 (In Progress): Implement the 'most recently used' concept for workflows and actorshttps://projects.ecoinformatics.org/ecoinfo/issues/19142005-01-24T18:45:25ZDan Higginshiggins@nceas.ucsb.edu