Towards an Environment for Multiscale Applications

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Towards an Environment for

Multiscale A
pplications

Katarzyna Rycerz(1,2),
Eryk Ciepiela(2),
Joanna Kocot (2),
Marcin Nowak(1), Paweł Pierzchała(1),


Marian Bubak (1, 2)


(1) Institute of Computer Science AGH, Mickiewicza 30, 30
-
059 Kraków, Poland

(2) ACC Cy
fronet AGH, ul.
Nawojki 11, 30
-
950 Kraków, Poland

e
-
mail: kzajac
@agh.edu.pl


Multiscale
modeling

is one of the big challenges that science faces today. In this paper we prese
n
t the
preliminary solution
for composing multiscale simulations from single scale

models encapsulated as scientific
software components and distributed in the various European e
-
Infrastructures
.
T
he

prese
n
t
ed

environment is
based on GridSpace Virtual
Laboratory

(GS)

[GS2
]
.

As an example we have used
In
-
stent R
estenosis
application

tha
t simul
ate
biological response

of a cellular tissue for the treatment of atherosclerotic plague
[ISR]
.
The application

consists

of
the three
modules

of different scale
:
simulation of blood flow, simulation of
muscle
cells and drug diffusion. The applicatio
n includes also three
scale less

transformation modules

connecting

ones

with scale
.

The connections between ISR application
is defined by complex automata (CxA) formalism
[CxA]
and the communication is realized by MUSCLE library supporting that formalis
m
[MUSCLE]
.

MUSCLE
introduces concept of

configurable kernels communicating
using asynchronous message passing.

The
communication is either direct or by means of conduits (input/output converters). Current MUSCLE
implementation is based on JADE agent enviro
nment [JADE].

The
idea of
the
current
approach is described in the Fig 1. It
extend
s GS environment by
introducing

high level
interpreters

that transform CxA description
of multiscale software modules (implemented as MUSCLE kernels)
and their connections
into

specific
set of execution instructions

for local or grid infrastructures
.
Current
ly
supported

infrastructures include local distributed resource management system
(
on example of
PBS) and grid
resource
management system (
on example of
QosCosGrid
)
.

I
n a future we plan to support also other grid access
layers (A
pplication
H
osting
E
nvironment
, gLite or others) according to user needs.

The proposed environment
includes also

an adapted tool for visualization

of available modules and connections
. The suppo
rt for MATLAB
that is used for post
-
processing application data is also included
.

As mapping modules into available resources
are performed transparently, t
his solution allows a use
r to concentrate
only
on
the a
pplication
specific
details
.
Currently, we a
ssume one
module per node policy, but in the

future we plan to build a
n

advance
d tool supporting
more advanced
modules

distribution
.





Figure 1



GridSpace Experiment Workbench as a high level tool for MUSCLE
-
based multiscale simulation.



We plan t
o p
resent a typical use case of GridSpace for

ISR appli
cation
. First, the user will be able to create

or
load

CxA configuration of MUSCLE kernels and their connections and view it using the appropriate CxA
viewer. Next, he will
run the application on the choo
sen e
-
infrastructure. Finally, he will be able to interactively
explore output files with MATLAB tool integrated with GS environment.

Acknowledgements: The research presented in this paper has been partially supported by the European Union
within the Euro
pean Regional Development Fund program no. POIG.02.03.00
-
00
-
007/08
-
00 as part of the PL
-
Grid project (
www.plgrid.pl
) and within

MAPPER project

no.
261507

(http://www.mapper
-
project.eu) as well
as
ACC Cyfronet AGH grant 500
-
08.


References

[GS2
]

E. Ciepi
ela, D. Harezlak, J. Kocot, T. Bartynski, M. Kasztelnik, P. Nowakowski, T. Gubała,
M.Malawski, M. Bubak;
Exploratory Programming in the Virtual Laboratory
, in Proceedings of
the International Multiconference on Computer Science and Information Technology p
p. 621

628

[CxA
]

Alfons G. Hoekstra, Alfonso Caiazzo, Eric Lorenz, Jean
-
Luc Falcone, Bastien Chopard,
Complex Automata: multi
-
scale Modeling with coupled Cellular Automata, in A.G.Hoekstra, J.
Kroc, and P.M.A. Sloot (Eds) Modelling Complex Systems with Cel
lular Automata, Spinger
Verlag, July 2010.

[ISR
]


Alfonso Caiazzo, David Evans, Jean
-
Luc Fal
cone, Jan Hegewald, Eric Lorenz, Bernd Stahl
,
DinanWang, Jorg Bernsdorf, Bastien Chopard, Julian Gunn, Rod Hose, Manfred Krafczyk,
Patricia Lawford, Rod Smallwood, Dawn Walker, and Alfons G. Hoekstra. Towards a Complex
Automata Multiscale Model of In
-
Stent Restenosis; ICCS 2009, Part I, LNCS 5544, p
p. 705

714, 2009.
ICCS 2009

[MUSCLE]

Jan Hegewald, Manfred Krafczyk, Jonas Tölke, Alfons Hoekstra and Bastien Chopard, An
agent
-
based coupling platform for complex Automata c, M. Bubak et al. (Eds.): ICCS 2008, Part
II, LNCS 5102, pp. 227

233, 2008


[JADE]

JADE homepage
http://jade.tilab.com