Towards an Environment for Multiscale Applications
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 Cyfronet 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 present the preliminary solution for composing multiscale simulations from single scale models encapsulated as scientific software components and distributed in the various European e-Infrastructures. The presented environment is based on GridSpace Virtual Laboratory (GS) [GS2]. As an example we have used In-stent Restenosis application that simulate 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 application 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 formalism[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 environment [JADE].
The idea of the current approach is described in the Fig 1. It extends 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. Currently supported infrastructures include local distributed resource management system (on example of PBS) and grid resource management system (on example of QosCosGrid). In a future we plan to support also other grid access layers (Application Hosting Environment, gLite or others) according to user needs. The proposed environment includes also an adapted tool for visualization of available modules and connections. The support for MATLAB that is used for post-processing application data is also included. As mapping modules into available resources are performed transparently, this solution allows a user to concentrate only on the application specific details. Currently, we assume one module per node policy, but in the future we plan to build an advanced tool supporting more advanced modules distribution.
We plan to present a typical use case of GridSpace for ISR application. 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 choosen 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 European 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. Ciepiela, 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 pp. 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 Cellular Automata, Spinger Verlag, July 2010.
[ISR] Alfonso Caiazzo, David Evans, Jean-Luc Falcone, 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, pp. 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
