[kepler-dev] Nondeterministic merge in PN domain

Sat Jul 15 10:06:53 PDT 2006

BooleanSelect reads from one of two input ports depending
on the value of the control input token.  Thus, it is not
an SDF actor, since the number of tokens it consumes on each
input port is not fixed.

The Case actor is a composite actor.  If what you want is a
simple if-then-else, then the Case actor can do this and still
be SDF.  The way it works is that it has two refinements instead
of the usual one for a composite actor (actually, it can have any
number), and it simply invokes one or the other depending on
the control token.  If both refinements are SDF, then the overall
model is still SDF.

Edward

At 08:29 AM 7/15/2006, Bertram Ludaescher wrote:

>Hi everybody -- too bad we don't have Xiaowen listening in; not sure
>why she didn't use the BooleanSelect or Case.
>
>Edward:
>Since we had recently discussions here about BooleanSelect and SDF,
>can you explain (or provide a pointer) why SDF might have problems
>with BooleanSelect, but apparently not with Case?
>
>thanks, cheers
>
>Bertram
>
> >>> On Fri, 14 Jul 2006 17:23:31 -0700
> >>> "Edward A. Lee" <eal at eecs.berkeley.edu> wrote:
>EAL>
>EAL> Looking at the model, it looks like there is no need for 
>NondeterministicMerge
>EAL> in any form... A simple BoleanSelect actor would work just fine...
>EAL> Even cleaner would be to use the Case actor, in which case 
>everything could
>EAL> be SDF, I think...
>EAL>
>EAL> Edward
>EAL>
>EAL> 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 We actually have a newer version of the workflow than the one that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.
> >>
> >> -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>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>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-
> >>>> 
> <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
> >>> --------
> >>
> >>
> >> --
> >> 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
> >>
> >>
> >> _______________________________________________
> >> Kepler-dev mailing list
> >> Kepler-dev at ecoinformatics.org
> >> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-dev
>EAL>
>EAL> ------------
>EAL> Edward A. Lee
>EAL> Professor, Chair of EECS
>EAL> 231 Cory Hall, UC Berkeley, Berkeley, CA 94720-1770
>EAL> phone: 510-642-0253 or 510-642-0455, fax: 510-642-2845
>EAL> eal at eecs.Berkeley.EDU, http://ptolemy.eecs.berkeley.edu/~eal
>EAL>
>EAL> _______________________________________________
>EAL> Kepler-dev mailing list
>EAL> Kepler-dev at ecoinformatics.org
>EAL> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-dev

------------
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  