Re: [Swarm-Modelling] Question about Distributed Simulations

[docgca]

Dr. Cleary,

Thanks for your email.  I'm a trauma surgeon in Chicago who's been 
doing cell-as-agent-level modeling of medical disease processes from a 
pathophysiological standpoint, with an emphasis on acute inflammation, 
for a few years.  We are dealing with some potentially pretty large 
scale simulations with respect to the number of agents and 
complicated-ness (I won't use the word "complexity!") of agent rule 
systems.  Thus far, working in Netlogo, I've been able to get 
qualitative behavior from reduced models, but getting to quantitative 
models will require (I think) a step up in scale.  Additionally, there 
are multi-scale issues as we try and build up cellular behaviors from 
molecular/enzymatic level ABMs, and further up to aggregated 
tissue/organ models in a multi-hierarchical framework.  I was actually 
approached by people from IBM who are looking for things to run on 
BlueGene.  Apparently there is a fair amount of interest in ABM at 
Watson, and the impetus for my posting the original question about 
distributed/parallel architecture was to see what had already been 
accomplished prior to my next discussion with them.  My hope (and 
expectation) is that a significant component of the CS/software 
development will come from within Watson; I'll be talking with them 
more over the next few weeks and you can be sure that I will pass on 
the things that I am allowed (!) to talk about.

Gary An

PS: I'm unfunded, but looking! :-)

-----Original Message-----
From: address@hidden
To: address@hidden
Sent: Tue, 22 Aug 2006 7:18 PM
Subject: [Swarm-Modelling] Question about Distributed Simulations

   Unfortunately, the work that I was doing that John mentions was a 
victim of the infathomable and maddening black art of "government 
funding" and did not get to a point where it could be used for these 
purposes, and the difficulty of trying to use a machine like BlueGene-L 
for an application person (that is: non-computer scientist) without a 
package to help you is probably insurmountable unless your simulations 
have some really, really nice properties (and most interesting 
simulations do not have these properties).

 I'm certainly interested in hearing what a surgeon is trying to model 
that requires BG/L; part of the reason for the loss of my funding was a 
question over the real-world need for ABM on such machines. The 
argument that there was clearly *going* to be a need for it and that to 
wait until that need knocked on your doorstep before beginning that 
work would mean a several year delay apparently wasn't very convincing, 
though it appears to be coming to pass. Perhaps you can partner with a 
CS team at one of the labs now and be that driver, though that will 
mean that you'll have a delay of several years waiting for the software 
to catch up, and by that time *you'll* probably lose your funding.

Cheers,
 Andy, who has no bitterness towards the government funding process at 
all... ok, maybe a *little*. ;-)

p.s. Syncer was neat stuff.

--
Dr Andrew J. Cleary
Director of Algorithms R&D
Visible Path Corporation
www.visiblepath.com

From: address@hidden
To: Agent-based modeling <address@hidden>
Date: Tue, 22 Aug 2006 09:51:40 -0400
Subject: Re: [Swarm-Modelling] Question about Distributed Simulations
As others will confirm, what you are asking to do is a hard computer
 science problem. We developed some Java code for doing what you want 
with
 Swarm called Syncer back in 2000. Unfortunately it was never updated 
with
 the newer releases of Swarm and the last time we checked it out, it 
would
not run with Swarm any longer. I would be willing to send you the paper
 describing the algorithm and the source code if you want to try and 
get it
to work with the current releases.

You can also check out a paper by Matthias Scheutz entitled, "Adaptive
Algorithms for the Dynamic Distribution and Parallel Execution of
Agent-Based Models". A copy can be found at:
 
http://www.nd.edu/~airolab/publications/scheutzschermerhorn06pardist.pdf 


 Finally, back in '02 I was in communication with Andy Cleary at 
Lawrence
Livermore who haunts these mailing lists on occasion. He was working on
 distributing Swarm over a 1000+ node tightly coupled architecture. He 
may
be able to help.

John A. Sauter
Business Unit Leader, Emerging Markets
ph: 734.302.4682 cell: 734.904.2313 fax: 734.302.5661
NewVectors, LLC (http://www.newvectors.net)
Innovative Solutions in Program Management, Analysis and Logistics
Street: Suite 250, 3520 Green Ct, Ann Arbor, MI 48105-1579



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Hello list,

I'm not sure which is the correct list for this question so my
apologies in advance. I am looking into the feasibility of running a
Swarm simulation on IBM's Blue Gene L, which has as its base rack a
1000 node cluster (2000 PPC 5 processors). The question is whether an
individual run could be done across the entire cluster, with groups of
agents distributed among all the nodes and communication across the
nodes. I recall threads having to with distributed simulations but
cannot remember if that was distribution for batch runs or for a single
run. If this has been extensively discussed perhaps someone could point
me towards that archived thread? Thanks in advance.

Gary An
Department of Surgery
Northwestern University
Chicago, IL
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