Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-09-19T18:36:47ZEcoinformatics Redmine
Redmine Bug #5715 (New): Actor Reference documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/57152012-09-19T18:36:47Zjianwu jianwujianwu@sdsc.edu
<p>this doc hasn't changed since 2.0, but in 2.4, many actors are visible for the first time. So we might need to update this doc.</p>
<p>435 pages.</p> Feature #5626 (New): interacting with kepler.sh to know the status and other information in batch...https://projects.ecoinformatics.org/ecoinfo/issues/56262012-06-15T19:43:39Zjianwu jianwujianwu@sdsc.edu
<p>When we run kepler in batch mode, it's good to know its status and other information.</p>
<p>CAMERA has done something for it. Jianwu will check it.</p> Bug #5357 (New): invocation problems with Distributed Composite Actor Options dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/53572011-03-24T02:06:19ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Sometimes the Distributed Composite Actor Options (DCAO) dialog doesn't come up when it should, and sometimes it appears when it shouldn't. Also, I'm not clear on if the text in the alert that appears when it refuses to come up (shown below) is correct.</p>
<p>In master-slave, drag out a DistributedCompositeActor.<br />If you right-click on the DistributedCompositeActor, and select Distribute this actor, you get an Alert:<br />---<br />'Distribute this actor' is not available for actors of type: org.kepler.distributed.DistributedCompositeActor. Only TypedCompositeActor and CompositeActor can be distributed<br />---<br />Yet if you double-click on it, you're able to bring up the DCAO dialog.</p>
<p>Also, if you drag out a CompositeActor, and double-click on it, you get the usual Edit Parameters dialog. If you right-click 'Distribute this actor', you get the DCAO dialog. A subsequent double-click on the actor and now instead of the Edit Parameters dialog, the DCAO dialog appears. A subsequent right-click 'Distribute this actor' and now you get the Alert message saying you can't.</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 #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 #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 #4783 (New): Standardize workflow parsing to get parametershttps://projects.ecoinformatics.org/ecoinfo/issues/47832010-02-09T23:56:23ZIlkay Altintasaltintas@sdsc.edu
<p>There are a few different approaches (SciencePipes, CAMERA, UCGrid, Hydrant, etc.) to get workflow parameters from an existing workflow description, i.e., MoML file. Analyze the similarities and differences in these approaches and at the minimum come up with a consolidated best practice solution and a general API for it. If a generic implementation is feasible, also publish as a module.</p> Bug #4706 (New): support provenance in master-slave 2.0https://projects.ecoinformatics.org/ecoinfo/issues/47062010-01-28T18:49:46Zjianwu jianwujianwu@sdsc.edu
<p>provenance should be supported in Master-Slave 2.0. There should be an option on whether to firstly save provenance info at slave side or not before integrated back to Master.</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 #4040 (New): make a new module called globus to host globus actors and needed packages.https://projects.ecoinformatics.org/ecoinfo/issues/40402009-04-30T17:04:17Zjianwu jianwujianwu@sdsc.edu
<p>we have duplicate globus libs in current build system: common\etc\cog\, util\lib\jar\globus\lib, util\lib\jar\globus\lib-gt4_0_0</p>
<p>Also globus related actors need to be updated to support new version of globus.</p>
<p>I'll try to make it ready to be shipped with Kepler 2.0.</p> Bug #4003 (New): Support for non-GUI Kepler installer.https://projects.ecoinformatics.org/ecoinfo/issues/40032009-04-21T16:12:59Zjianwu jianwujianwu@sdsc.edu
<p>Many users need to install Kepler on a cluster or other distributed environments where they do not have a GUI. So it would be nice if we support Kepler no-GUI installation. An ideal way is to provide a Kepler rpm package.</p>