[kepler-dev] Nondeterministic merge in PN domain

Edward A. Lee eal at eecs.berkeley.edu
Fri Jul 14 17:23:31 PDT 2006

Looking at the model, it looks like there is no need for NondeterministicMerge
in any form... A simple BoleanSelect actor would work just fine...
Even cleaner would be to use the Case actor, in which case everything could
be SDF, I think...


At 05:03 PM 7/14/2006, Ilkay Altintas wrote:
>Hi Christopher,
>I'm aware of the problem with the problem with 
>using  NonDeterministic merge in the workflow instead of using the actor.
>We actually have a newer version of the workflow than the one that 
>doesn't work under Kepler. A potential problem with switching to the 
>non-deterministic merge actor is that we don't know why Xiaowen 
>didn't use the actor and forced using the old version of the 
>director. We might recreate the error if we use the actor.
>Antoon will be here the  next couple of weeks.  Maybe we can discuss 
>this further.
>On Jul 14, 2006, at 4:27 PM, Christopher Brooks wrote:
>>Hi Ilkay,
>>Just yesterday, Antoon Goderis, Edward and I were looking over the
>>Promoter Identification Workflow (PIW) workflow from
>>that Xiaowen created.
>>The PIW workflow is available via Webstart:
>>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.
>>     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
>>>     Hi,
>>>     Does anyone know what exactly have changed between the version
>>>of the
>>>     PNDirector that accepts nondeterministic merge and the current
>>>     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
>>>     mail for this list to: ptolemy-hackers-
>>><mailto:request at ptolemy.eecs.berkeley.edu>request at ptolemy.eecs.berkeley.edu
>>     --
>>     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>http://users.sdsc.edu/~altintas
>>    -
>>     Posted to the ptolemy-hackers mailing list.  Please send administrative
>>     mail for this list to: 
>> <mailto:ptolemy-hackers-request at ptolemy.eecs.berkeley.edu>ptolemy-hackers-request at ptolemy.eecs.berkeley.edu
>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>http://users.sdsc.edu/~altintas
>Kepler-dev mailing list
>Kepler-dev at ecoinformatics.org

Edward A. Lee
Professor, Chair of EECS
231 Cory Hall, UC Berkeley, Berkeley, CA 94720-1770
phone: 510-642-0253 or 510-642-0455, fax: 510-642-2845
eal at eecs.Berkeley.EDU, http://ptolemy.eecs.berkeley.edu/~eal  

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