[kepler-dev] Nondeterministic merge in PN domain
Christopher Brooks
cxh at eecs.berkeley.edu
Thu Jul 20 07:50:48 PDT 2006
Hi Bertram,
The Case demo can be found at
$PTII/ptolemy/actor/lib/hoc/demo/Case/Case.xml
in the CVS tree.
There is a link from the What's New page on the Ptolemy splash.
_Christopher
--------
>>> On Sat, 15 Jul 2006 10:06:53 -0700
>>> "Edward A. Lee" <eal at eecs.berkeley.edu> wrote:
EAL>
EAL> BooleanSelect reads from one of two input ports depending
EAL> on the value of the control input token. Thus, it is not
EAL> an SDF actor, since the number of tokens it consumes on each
EAL> input port is not fixed.
EAL>
EAL> The Case actor is a composite actor. If what you want is a
EAL> simple if-then-else, then the Case actor can do this and still
EAL> be SDF. The way it works is that it has two refinements instead
EAL> of the usual one for a composite actor (actually, it can have any
EAL> number), and it simply invokes one or the other depending on
EAL> the control token. If both refinements are SDF, then the overall
EAL> model is still SDF.
interesting, interesting.. does one of the Ptolemy demos make use of
the Case actor? (I guess I could do a grep on the corresponding moml
files.. )
Bertram
EAL>
EAL> Edward
EAL>
EAL> At 08:29 AM 7/15/2006, Bertram Ludaescher wrote:
EAL>
>> 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 ac
tor.
>> >>
>> >> We actually have a newer version of the workflow than the one that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/sd
m/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.l
lnl.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 domai
ns
>> >>> and Antoon proposed working with the PIW example. If
>> >>> you can get it working under PN, then I'd like to see about converti
ng
>> >>> it to DDF or ideally SDF.
>> >>>
>> >>> _Christopher
>> >>>
>> >>>
>> >>>
>> >>> --------
>> >>>
>> >>> Hi Christopher,
>> >>>
>> >>> The workflows don't use the NondeterministicMerge actor but implemen
t
>> >>> 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 wha
t
>> >>> 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.NondeterministicMer
ge)
>> >>>> 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 P
N.
>> >>>>
>> >>> 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 administrat
ive
>> >>> mail for this list to:
>> >>>
>> <mailto:ptolemy-hackers-request at ptolemy.eecs.berkeley.edu>ptolemy-hacker
s-request at ptolemy.eecs.berkeley.edu
>> >>> --------
>> >>
>> >>
>> >> --
>> >> Ilkay ALTINTAS
>> >> Assistant Director, National Laboratory for Advanced Data Research (N
LADR)
>> >> 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-d
ev
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
_______________________________________________
Kepler-dev mailing list
Kepler-dev at ecoinformatics.org
http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-dev
--------
More information about the Kepler-dev
mailing list