Hi Ilkay, Just yesterday, Antoon Goderis, Edward and I were looking over the Promoter Identification Workflow (PIW) workflow from https://www-casc.llnl.gov/sdm/download.php that Xiaowen created.
The PIW workflow is available via Webstart: https://www-casc.llnl.gov/sdm/downloads/spa-piw.jnlp That workflow is uses PN and basically takes advantage of a bug in older versions of PN where non-deterministic merges were easy to make. Now, to make a non-deterministic merge, one must use the NonDeterministicMerge actor. Where we saw this was in the Setup composite actor. The Setup is a little wacky, there is probably a better way. Edward might have more insight on this. The version of the PIW demo from webstart fails with: ptolemy.kernel.util.IllegalActionException: The length of the specified array is zero. at ptolemy.data.ArrayToken._initialize(ArrayToken.java:575) at ptolemy.data.ArrayToken.<init>(ArrayToken.java:68) at ptolemy.domains.sdf.lib.SequenceToArray.fire(SequenceToArray.java:139) at ptolemy.actor.process.ProcessThread.run(ProcessThread.java:181) The version of the PIW demo in Kepler (Start Kepler, Help -> Documentation -> Programmer Documentation -> Promotor Identification Workflow) fails with java.lang.OutOfMemoryError: unable to create new native thread at java.lang.Thread.start(Native Method) at org.apache.axis.wsdl.gen.Parser.run(Parser.java:306) at org.sdm.spa.WebService.fire(WebService.java:727) at ptolemy.actor.process.ProcessThread.run(ProcessThread.java:186) BTW - We are working on a short paper that discusses embedding domains and Antoon proposed working with the PIW example. If you can get it working under PN, then I'd like to see about converting it to DDF or ideally SDF. _Christopher -------- Hi Christopher, The workflows don't use the NondeterministicMerge actor but implement nondeterministic merge in the workflow. Until PTII 5.x, the PN director allowed this, but I'm trying to figure out why the workflow was implemented that way, and the workflow developer (Xiaowen--she left the project) insisted on keeping the old director. It was to avoid a race condition. I'll try to port the workflow to the current PTII version if I understand what the problem with using the new version of the PNDirector is. Thanks, -ilkay On Jun 22, 2006, at 3:23 PM, Christopher Brooks wrote: > Hi Ilkay, > > I'm not sure. Edward checked in a working nondeterministic merge > on 03 Oct 2004. > > I'm a little confused though, because the CVS head of Ptolemy has a > working nondeterministic merge actor (pn.kernel.NondeterministicMerge) > and a PN demo: pn/demo/NondeterministicMerge/NondeterministicMerge.xml > > _Christopher > -------- > > Hi, > > Does anyone know what exactly have changed between the version > of the > PNDirector that accepts nondeterministic merge and the current > one? > > There was an email thread on this but we couldn't find it. > > Nandita and I are trying to port older workflows that use > nondeterministic merge under PN domain to the newer version of PN. > > Thanks! > -ilkay > > > ---------------------------------------------------------------------- > ----- > - > Posted to the ptolemy-hackers mailing list. Please send > administrative > mail for this list to: ptolemy-hackers- > [EMAIL PROTECTED] > -------- -- Ilkay ALTINTAS Assistant Director, National Laboratory for Advanced Data Research (NLADR) Manager, Scientific Workflow Automation Technologies (SWAT) Lab San Diego Supercomputer Center(SDSC), UCSD 9500 Gilman Drive, MC: 0505 La Jolla, CA 92093-0505 phone: (858) 822-5453 fax: (858) 822-3693 web: http://users.sdsc.edu/~altintas --------------------------------------------------------------------------- - Posted to the ptolemy-hackers mailing list. Please send administrative mail for this list to: [EMAIL PROTECTED] -------- ---------------------------------------------------------------------------- Posted to the ptolemy-hackers mailing list. Please send administrative mail for this list to: [EMAIL PROTECTED]