Scientific computing in the Cloud
Romain Reuillon, Mathieu Leclaire,
Institut des Systèmes Complexes - Paris
{romain.reuillon,mathieu.leclaire}@openmole.org

In the complex-system community, the numerical modeling is a widespread tool for scientific investigations.




Most of the time the modeling process is really interresting when coupled with large scale experimentations on models.


Why large ?




Stochastic algorithms






Calibration algorithms





Genetic algorithms





Sensitivity analyzes





Exploration on a space of parameters





What does OpenMOLE do ?


1) it implements
complex-system sampling
algorithms

2) it delegates transparently the computation to massively parallel environments

OpenMOLE proposes a naturally parallel formalism to design experiments on the models



How to design my experiment ?





Embed your model as a black box :
launching command, inputs, outputs

How to design my experiment ?





Describe the way to explore your space of parameters

How to design my experiment ?





Connect the Tasks and build a Workflow

How to design my experiment ?





Assign execution environments to Tasks

How to design my experiment ?





Run and control the workflow execution

Scripted DSL

It's free and open-source !






Downloads : http://www.openmole.org


Scientific achievements : Chromosome structuring


C++ code

2 days of computation per simulation

1600 simulations

8.5 years of computation on a single machine!
Evaluating chromosome interactions according to their spatial structuration


> Publication Junier et al., CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus, Nucleic Acids Research, 2012.

Scientific achievements : Simpop project


Scala code

2.5 minutes computation per simulation

Model calibration using a multi-goal genetic algorithm

20 years of computation on a single machine !
Structuration of settlements hierarchy


> Publication Reuillon et al., Algorithmes évolutionnaires sur grille de calcul pour le calibrage de modéles géographiques, proceedings of France Grilles 2012.

Scientific achievements : SimTRAP project


NetLogo code

100000 replications

5 minutes per simulation

1 year of computation on a single machine !
Evalating the mean time of passenger exchange in a subway train

> PhD thesis of J. Figuel, Modélisation et simulation des comportements piétonniers dans les espaces de transport – Application aux échanges quai / train de voyageurs.