Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-02-25T22:50:11ZEcoinformatics Redmine
Redmine Kepler - Bug #4846 (Resolved): error opening kar from local repositoryhttps://projects.ecoinformatics.org/ecoinfo/issues/48462010-02-25T22:50:11ZOliver Soongsoong@nceas.ucsb.edu
<p>This is with wrp at r23202. I deleted .kepler and KeplerData. I create a trivial workflow (default SDF and RExpression) and save it as a KAR in the default local repository. On restarting Kepler, the KAR and local repository are not listed in the components pane. If I go into Sources and manually trigger a re-build of the component library, I can see the KAR, but nothing happens when I attempt to open it (right-click menu) except an error in the console:</p>
<p>org.kepler.objectmanager.cache.CacheException: Exception occurred while deserializing object<br /> at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:529)<br /> at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.open(ActorMetadataKAREntryHandler.java:206)<br /> at org.kepler.kar.KARFile.open(KARFile.java:889)<br /> at org.kepler.kar.KARFile.openKARContents(KARFile.java:665)<br /> at org.kepler.gui.kar.OpenArchiveAction.openKAR(OpenArchiveAction.java:162)<br /> at org.kepler.gui.kar.OpenArchiveAction.actionPerformed(OpenArchiveAction.java:143)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:357)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> at java.awt.Component.processMouseEvent(Component.java:6263)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3255)<br /> at java.awt.Component.processEvent(Component.java:6028)<br /> at java.awt.Container.processEvent(Container.java:2041)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4630)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2099)<br /> at java.awt.Component.dispatchEvent(Component.java:4460)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2085)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2475)<br /> at java.awt.Component.dispatchEvent(Component.java:4460)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br />Caused by: java.io.IOException: Error in ActorCacheObject(ReadExternal): null<br /> at org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:250)<br /> at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1792)<br /> at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1751)<br /> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)<br /> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)<br /> at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:517)<br /> ... 32 more</p> Kepler - 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> Kepler - Bug #4764 (New): ProvenanceRecorder.changeExecuted slow after workflow runhttps://projects.ecoinformatics.org/ecoinfo/issues/47642010-02-06T02:19:48ZOliver Soongsoong@nceas.ucsb.edu
<p>If I run any of the tpc workflows (e.g., tpc09), any subsequent changes to Kepler (say changing workflow parameters) cause Java to peg one of my CPU cores. This includes canceling changes to RExpression. I've seen this behavior on Windows XP and 7. While I haven't seen it under linux or OS X, I haven't tested those as extensively. I have tried small test workflows, and haven't seen a particularly noticeable slowdown, so it may be related to the size of the workflow run. I have to restart Kepler to get things back up to speed, and it's bad enough that I'm actually restarting Kepler after every run.</p>
<p>I'm not sure it's a memory thing. java.exe is about maxed out on memory (~0.5 GB) in the Task Manager, but the Check System Settings window says I have 46% free. I was watching jstat, and changes don't seem to trigger a flurry of garbage collection.</p> Kepler - Bug #4655 (Resolved): data packages are suddenly unusablehttps://projects.ecoinformatics.org/ecoinfo/issues/46552010-01-08T02:23:01ZOliver Soongsoong@nceas.ucsb.edu
<p>For some reason, EML 2 Dataset actors are not outputting any tokens for most output formats. The data exists at .kepler/cache/cachedata, as expected. If I set the EML 2 Dataset Data Output Format to As ColumnBased Record, then I get an error message, "The data cloumn (sic) didn't match head column". If I set the EML 2 Dataset Data Output Format to "As All Cache File Names", then things seem to work as expected. All other output formats don't seem to work.</p>
<p>Things were definitely working as of Dec. 8 and possibly Dec. 10.</p> Kepler - 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> Kepler - Bug #4633 (Resolved): LSID conflictshttps://projects.ecoinformatics.org/ecoinfo/issues/46332009-12-15T01:04:31ZOliver Soongsoong@nceas.ucsb.edu
<p>Create a workflow and save a KAR (KAR1). Note the LSID. Change the workflow in some recognizable fashion and save a KAR (KAR2). The LSID bumps as expected. Close the workflow and open KAR1. Make a different change (so it's obviously not the workflow in KAR2) and save the KAR (KAR3). Notice that when the workflow reopens, it looks like KAR2 because it is KAR2 down to the MOML in KAR3.</p>
<p>I'm observing this at r22183 right now.</p> Kepler - Bug #4632 (Resolved): problems when loading a KAR, changing the workflow, then re-saving...https://projects.ecoinformatics.org/ecoinfo/issues/46322009-12-14T23:07:12ZOliver Soongsoong@nceas.ucsb.edu
<p>Create a workflow and report and save the KAR. Next, change the workflow (i.e., bump the MOML LSID), save the KAR (overwrite or not doesn't seem to matter), and run it. The report should be blank. Sometimes, the ROML still exists in the KAR, so closing and re-opening works fine. In this case, the run archive contains the correct workflow_ROML.xml entry and a different ROML.#.xml that doesn't match the workflow_ROML.xml entry. Other times, the ROML seems to be lost from the KAR, in which case the run archive has no workflow_ROML.xml entry and a blank ROML.#.xml.</p> Morpho - Bug #4625 (Resolved): authenticate against KNB, switch source to DEV, and still have accesshttps://projects.ecoinformatics.org/ecoinfo/issues/46252009-12-11T02:07:26ZOliver Soongsoong@nceas.ucsb.edu
<p>I have packages that exist on DEV but not KNB. I start Morpho r4682 with KNB set as the metacat source and authenticate. I can confirm my packages are not on KNB. I then switch the metacat source to dev and open the package list and can see my packages. I can export the packages and extract the data. There was no re-authentication.</p> Metacat - Bug #4612 (Rejected): EML file content out of sync with metacathttps://projects.ecoinformatics.org/ecoinfo/issues/46122009-12-09T00:46:47ZOliver Soongsoong@nceas.ucsb.edu
<p>This is on dev.nceas.ucsb.edu. Search for soong_test. There should be 2 entries for "soong_test 1". One has ID soong_test.3.2 and the other has ID doc.1260314433875.1. Open doc.1260314433875.1 and look at the EML, which should be for soong_test.3.3.</p>
<p>I was testing the ecogrid writer actor in Kepler. I may not have been doing things correctly.</p> Kepler - Bug #4608 (Resolved): ROML in KAR files not being shown at allhttps://projects.ecoinformatics.org/ecoinfo/issues/46082009-12-08T20:10:55ZOliver Soongsoong@nceas.ucsb.edu
<p>ROML in KAR files is not being loaded. This happens regardless of the LSID in the workflow and ROML matching the InstanceAuthNamespace. This happens regardless of opening from a local repository or not.</p>
<p>This is happening at 22117, but I think I also saw it at 22111. I'm guessing it has something to do with 22083, although I can't be sure.</p> Kepler - Bug #4559 (Resolved): local repositories not showing up in components treehttps://projects.ecoinformatics.org/ecoinfo/issues/45592009-11-19T22:25:52ZOliver Soongsoong@nceas.ucsb.edu
<p>Summary says it all. I'm at r21772, and the default workflows repository isn't in the components tree. Adding repositories doesn't do anything. I'm not even getting prompts to sign into KNB or DEV to cache data.</p> Kepler - Bug #4527 (Resolved): reports cannot be loaded when InstanceAuthNamespace changeshttps://projects.ecoinformatics.org/ecoinfo/issues/45272009-11-04T03:39:51ZOliver Soongsoong@nceas.ucsb.edu
<p>Generate a report and save the KAR. Close Kepler, clean-all, delete the configuration folder, LastObjectID, and .ptolemy-compiled (I think that's almost everything that Kepler generates). Run Kepler again, and open the KAR. The report layout should be there. Now close Kepler and delete only InstanceAuthNamespace. Run Kepler again and open the KAR. The report should not be there.</p>
<p>This makes it hard to transport a KAR file to another computer or even another build of Kepler.</p> Kepler - Bug #4521 (Resolved): KNB data error checking is overly aggressivehttps://projects.ecoinformatics.org/ecoinfo/issues/45212009-11-04T01:03:36ZOliver Soongsoong@nceas.ucsb.edu
<p>On r21314, I can no longer access the Kruger data. I believe this is due to some overly aggressive error checking on the data. The data packages (which are not directly under my control) have thrown errors on the console. I think this is due to negative numbers and zeroes in columns that are nominally whole numbers. In the past, there were non-fatal, but this is now major problem.</p>
<p>This change happened somewhere between r21218 and r21310.</p>
<p>The error message is specifically "Unable to parse the MetaData: Error parsing the eml package: Exception in DataTypeResolver"</p> Kepler - Bug #4507 (Resolved): report designer losing content when there are too many itemshttps://projects.ecoinformatics.org/ecoinfo/issues/45072009-10-27T23:25:05ZOliver Soongsoong@nceas.ucsb.edu
<p>If I have a lot of items in the report designer, the scroll bar seems to be too short for the content. Eventually, there are figures that are above and below the scrollable area and are not accessible. They still show up in reports, though.</p> Kepler - Bug #3801 (Resolved): open dialog, common places pane has white box instead of texthttps://projects.ecoinformatics.org/ecoinfo/issues/38012009-01-29T23:58:59ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11, Kepler 1.0.0 from kepler-project.org.</p>
<p>When I go to File->Open File..., the common places pane on the left has five icons and five white boxes where the icon labels are supposed to be.</p>
<p>Image at the URL.</p>