Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362009-07-21T00:47:32ZEcoinformatics Redmine
Redmine 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> Bug #3539 (New): wierd behaviors of port parameterhttps://projects.ecoinformatics.org/ecoinfo/issues/35392008-10-16T21:32:13Zjianwu jianwujianwu@sdsc.edu
<p>when put a port parameter in a composite actor, there are some wierd behaviors:<br />I put DDF/PN in top level and have an actor whose firingCountLimit is 2.<br />1) If DDF is set in composite actor, firingCountLimit of the first actor in the composite actor is set 1 or other number, the actor is only fired once.<br />2) If DDF is set in composite actor, firingCountLimit of the first actor in the composite actor is set NONE, the actor is fired for infinite times.<br />3) If no director is set in composite actor, firingCountLimit of the first actor in the composite actor is set NONE, the actor is only fired once. Also its value from the port parameter may be wrong.</p>
<p>I will attach the worflow later.</p>