1 The Mapper project receives funding from the EC's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° RI-261507. Towards Environment.

1The Mapper project receives funding from the EC's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° RI-261507.

Towards Environment for Multiscale Applications

Katarzyna Rycerz, Eryk Ciepiela, Joanna Kocot, Marcin Nowak, Pawel Pierzchała, Marian Bubak

KUKDM, Zakopane,

9-11.03 2011

2

Overview

• Multiscale simulations - overview• Tools for multiscale simulations• MUSCLE-based multiscale application in

GridSpace• Example demo with In-stent restenosis

application• Summary and future work

3

Multiscale Simulations• Consists of modules of

different scale

• Examples – e.g. modelling:• virtual physiological

human initiative• reacting gas flows• capillary growth • colloidal dynamics• stellar systems • and many more ...

virtual physiological humanvirtual physiological human fusionfusion hydrologyhydrology

nano material sciencenano material science computational biologycomputational biology

the reoccurrence of stenosis, a

narrowing of a blood vessel, leading to

restricted blood flow

4

Tools for multiscale simulations

• Model Couling Toolkit

• Applies a message passing (MPI) style of communication between simulation models.

• Oriented towards domain data decomposition of the simulated problem

• Provides a support for advanced data transformations between different models

• J. Larson, R. Jacob, E. Ong ”The Model Coupling Toolkit: A New Fortran90 Toolkit for Building Multiphysics Parallel Coupled Models.” 2005: Int. J. High Perf. Comp. App.,19(3), 277-292.

• Astrophysical Multi-Scale Environment (AMUSE)

• Scripting approach (Python) is used to couple models together., MPI used to distribute modules

• Astrophysical models : stellar evolution, hydrodynamics, stellar dynamics and radiative transfer

• S. Portegies Zwart, S. McMillan, at al. A Multiphysics and Multiscale Software Environment for Modeling Astrophysical Systems, New Astronomy, volume 14, issue 4, year 2009, pp. 369 - 378

• High Level Architecture components:• Application components run concurrently and communicate using HLA mechanisms

• Coponents are steerable from outside during runtime using script interface

• Support for synchronisation between multiscale modules - time stamps, advanced time management

• K. Rycerz, M. Bubak, P. M. A. Sloot: HLA Component Based Environment For Distributed Multiscale Simulations In: T. Priol and M. Vanneschi (Eds.), From Grids to Service and Pervasive Computing, Springer, 2008, pp. 229-239

5

Goals

• Support composition of simulation models.• scripting approach to programmatically access

simulation components to build multi-disciplinary and multi-scale “in silico” experiments

• Support execution of such experiments and achieve their reusability

• Integrate solutions designed for multiscale simulations’ development with possibilities given by:• tools for multiscale simulations• environments for application composition• computational e-Infrastructures

6

• Experiment workbench• Constructing experiment plans

from code snippets• Interactively run experiments

• Experiment Execution Environment• Multiple interpreters• Access to libraries, programs and

services (gems)• Access to computing infrastructure:

Cluster, grid, cloud• Experience

• Virolab project• PL-Grid NGI

• 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.

GridSpace

7

Multiscale Coupling Library and Environment (MUSCLE)

• Provides a software framework to build simulations according to the complex automata theory

• Introduces concept of kernels that communicate by unidirectional pipelines dedicated to pass a specific kind of data from/to a kernel (asynchronous communication)

• J. Hegewald, M. Krafczyk, J. Tlke, A. G. Hoekstra, and B. Chopard. An agent-based coupling platform for complex automata. ICCS, volume 5102 of Lecture Notes in Computer Science, pages 227233. Springer, 2008.

# CxA configuration of sample application# configure cxa propertiescxa = Cxa.LAST

cxa.env["max_timesteps"] = 2cxa.env["cxa_path"] = File.dirname(__FILE__)

# declare kernelscxa.add_kernel('w', 'examples.simplejava.Sender')cxa.add_kernel('r', 'examples.simplejava.ConsoleWriter')

# configure connection schemecs = cxa.cs

cs.attach('w' => 'r') {tie('data', 'data')

}

SenderModule

Console Module

Sample application

MUSCLE communication

8

GridSpace for MUSCLE application

• Integrated environment for:• Configuring modules connections and

parameters in cxa file• Visualizing modules connections• Running application on a chosen

e-infrastructure• Interactive post-processing the output using

various tools (e.g. MATLAB)

9

MUSCLE application in GridSpace

GridSpace Experiment host:• Interpreters and libraries accessing PBS• User files

GridSpace Experiment Workbench

QCG Grid Resource ManagementSystem

BFModule

SMC Module

DDModule

otherModules

QCG infrastructure


BFModule

SMC Module

DDModule

otherModules

Local DRMS (PBS)


MUSCLE CxA Graphical Viewer

- Models connections

Various scripts editorsGeneral (Python, Ruby, Perl ..)Specific (Matlab, Mathematica,

CxA interpreter)

Infrastructure access layer

User file management-simulation output view

clustercluster

10

Tool for automatic MUSCLE application distribution

• Main features• Accessible from GridSpace

level• Automatically distributes

MUSCLE applications in GRID environment

• Live stdout/stderr streaming• Based on Distributed Ruby

(DRb) and PBS

11

Demo – Instent restenosis in GridSpace

• http://www.youtube.com/watch?v=3S9-kljyXIw

12

Summary and Future Work• GridSpace can be used as a high level tool for setting up and

running MUSCLE-based multiscale applications • We plan to extend our solution to a set of tools supporting

programming and execution of multiscale applications in general

• To control and test behaviour of such applications we plan to support creation of their skeletons • parametrised „empty” multiscale application of the same structure

and requirements as the real one.

• We plan support for various European e-infrastructures and cloud resources

See: http://dice.cyfronet.pl

1 The Mapper project receives funding from the EC's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° RI-261507. Towards Environment.

Documents