[kepler-dev] Nondeterministic merge in PN domain

[Ilkay Altintas]

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We actually have a newer version of the workflow than the one that  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.

-ilkay


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
> 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
>>
>>
>> --------------------------------------------------------------------- 
>> -
>> -----
>>    -
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>> --------
>
>
>     --
>     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: ptolemy-hackers- 
> 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


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