Nondeterministic merge in PN domain

Nondeterministic merge in PN domain

Post by altinta » Fri, 23 Jun 2006 08:15:31


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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Nondeterministic merge in PN domain

Post by cxh » Sat, 24 Jun 2006 07:23:36

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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Nondeterministic merge in PN domain

Post by altinta » Sat, 24 Jun 2006 08:24:29

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





--
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://www.yqcomputer.com/ ~altintas



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Nondeterministic merge in PN domain

Post by cxh » Sun, 16 Jul 2006 08:27:02

i 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
>
 
 
 

Nondeterministic merge in PN domain

Post by altinta » Sun, 16 Jul 2006 09:03:47


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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:



--
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



<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Christopher,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>I'm aware of the problem with the problem with using onDeterministic merge in the workflow instead of using the actor.?/DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>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.?/DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Antoon will be here the?next couple of weeks.Maybe we can discuss this further.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>-ilkay</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On Jul 14, 2006, at 4:27 PM, Christopher Brooks wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi Ilkay,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Just yesterday, Antoon Goderis, Edward and I were looking over the</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Promoter Identification Workflow (PIW) workflow from</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="https://www-casc.llnl.gov/sdm/download.php">https://www-casc.llnl.gov/sdm/download.php</A> that Xiaowen created.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0p