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stochastic simulations & multi-cpu environment [message #30524] Sun, 17 June 2007 14:09 Go to next message
Eclipse User
Originally posted by: vega42.gmail.com

Hi,

since I got this thing running meanwhile I do have some more specific
questions I would like to address here. I did have a look in the docs
and code but I do undestand that you guys are still quite deep in the
development phase, so I will ask you directly.

1. How far are the stochastic models actually implemented? I find a
basic framework in stem.diseaesemodel but have the impresion, that those
haven't been implemented yet. Is this correct?

2. What about multiprocesser-environments? Is there an easy way to
instruct Eclipse to thread over multiple cores of one engine? What about
clusters?

thx

Vincent
Re: stochastic simulations & multi-cpu environment [message #30664 is a reply to message #30524] Mon, 18 June 2007 14:45 Go to previous message
Daniel Ford is currently offline Daniel Ford
Messages: 138
Registered: July 2009
Location: New York
Senior Member
Vincent,
here's the long story.....the Eclipse version of STEM is the 2nd
implementation of STEM. The first version was released on alphaWorks about
two years ago. That version had both deterministic and stochastic
implementations for SI, SIR and SEIR models. The implementations in the new
Eclipse code base are the same mathematics as in the first.

I've been very careful with testing the implementations of the disease model
mathematics. I created simple scenarios and worked out all the computations
by hand to make sure that they were correct (otherwise, what is the point?)
I only had enough cycles to complete those calculations for deterministic
calculations, not for stochastic. So, because they were not tested, they
were not exposed in this first milestone release.

We have a number of different kinds of disease models in plan that will be
considerably more sophisticated than what currently exists in the code base.
Some are models we're working on internally and some are ones we've funded
others to develop (e.g.,
http://web.mit.edu/newsoffice/2007/influenza-0531.html). We should probably
start up a thread on the topic.

As for multiprocessor environments, I think Eclipse is at the mercy of the
JVM and its ability to influence threading (not much). STEM uses the
Eclipse Jobs api for threading and is completely at the mercy of Eclipse's
scheduling of threads to Jobs. In the current implementation, there is a
single thread to compute the next state of the canonical graph. I'm
skeptical that this could change easily as there is a specified order for
execution of the Decorators defined in the tree that defines the Model of
the Scenario. The graphics for the Map view delegate the rendering of the
image to a background job and all of the I/O to retrieve lat/long data is
parallelized by multiple Jobs, one for each country.

Dan

"Vincent David" <vega42@gmail.com> wrote in message
news:f53tca$81d$1@build.eclipse.org...
> Hi,
>
> since I got this thing running meanwhile I do have some more specific
> questions I would like to address here. I did have a look in the docs and
> code but I do undestand that you guys are still quite deep in the
> development phase, so I will ask you directly.
>
> 1. How far are the stochastic models actually implemented? I find a basic
> framework in stem.diseaesemodel but have the impresion, that those haven't
> been implemented yet. Is this correct?
>
> 2. What about multiprocesser-environments? Is there an easy way to
> instruct Eclipse to thread over multiple cores of one engine? What about
> clusters?
>
> thx
>
> Vincent
Re: stochastic simulations & multi-cpu environment [message #579285 is a reply to message #30524] Mon, 18 June 2007 14:45 Go to previous message
Daniel Ford is currently offline Daniel Ford
Messages: 138
Registered: July 2009
Location: New York
Senior Member
Vincent,
here's the long story.....the Eclipse version of STEM is the 2nd
implementation of STEM. The first version was released on alphaWorks about
two years ago. That version had both deterministic and stochastic
implementations for SI, SIR and SEIR models. The implementations in the new
Eclipse code base are the same mathematics as in the first.

I've been very careful with testing the implementations of the disease model
mathematics. I created simple scenarios and worked out all the computations
by hand to make sure that they were correct (otherwise, what is the point?)
I only had enough cycles to complete those calculations for deterministic
calculations, not for stochastic. So, because they were not tested, they
were not exposed in this first milestone release.

We have a number of different kinds of disease models in plan that will be
considerably more sophisticated than what currently exists in the code base.
Some are models we're working on internally and some are ones we've funded
others to develop (e.g.,
http://web.mit.edu/newsoffice/2007/influenza-0531.html). We should probably
start up a thread on the topic.

As for multiprocessor environments, I think Eclipse is at the mercy of the
JVM and its ability to influence threading (not much). STEM uses the
Eclipse Jobs api for threading and is completely at the mercy of Eclipse's
scheduling of threads to Jobs. In the current implementation, there is a
single thread to compute the next state of the canonical graph. I'm
skeptical that this could change easily as there is a specified order for
execution of the Decorators defined in the tree that defines the Model of
the Scenario. The graphics for the Map view delegate the rendering of the
image to a background job and all of the I/O to retrieve lat/long data is
parallelized by multiple Jobs, one for each country.

Dan

"Vincent David" <vega42@gmail.com> wrote in message
news:f53tca$81d$1@build.eclipse.org...
> Hi,
>
> since I got this thing running meanwhile I do have some more specific
> questions I would like to address here. I did have a look in the docs and
> code but I do undestand that you guys are still quite deep in the
> development phase, so I will ask you directly.
>
> 1. How far are the stochastic models actually implemented? I find a basic
> framework in stem.diseaesemodel but have the impresion, that those haven't
> been implemented yet. Is this correct?
>
> 2. What about multiprocesser-environments? Is there an easy way to
> instruct Eclipse to thread over multiple cores of one engine? What about
> clusters?
>
> thx
>
> Vincent
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