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Cellular Automata
BIORemediation
system
M.C.Baracca P.Ornelli G.Clai
ENEA Italy
The Esprit HPCN Colombo Project consortium
• CRA Montecatini: a private
italian group involved in
polluted soil reclamation.
• Umweltschutz Nord: the
largest german soil remediation
company.
• Ironside Farrar: Scotlands
leading environmental
consultants.
• ENEA-HPCN: The High
Performance Computing group
of the Italian National Agency
for New Technologies, Energy
and Environment
• EPCC: the Edinburgh
University parallel computing
centre.
• ISI-CNR: The Computer
Science Institute of the Italian
National Research Centre.
• UNICAL: the Department of
Mathematics at Calabria
University in Italy.
• QSW: a European parallel
computers supplier.
The Colombo Project
CA Modelists
In situ bioremediation
CA based model
CAMELot
parallel environment
for CA based models
Bioremediation users
Cabior
graphical package
for bioremediation
intervention simulation
The Bioremediation Model
• Multiphase (water, air,pollutant) flow in a porous
saturated or unsaturated soil
• Solute transport, adsorption/desorption
• Chemical reactions
• Biomass growth and interaction with contaminants
and nutrients
The CA Bioremediation code
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•
•
•
•
3D automaton
each cell interacting with 8 neighbouring cells
185 general parameters
cell state defined by 86 substates
simulation evolution managed by a computational
steering mechanism
CAMELot environment
Edit
User Interface
Run
Compile
Build
Transition function
Master process
Process
Process
Process
.
.
.
.
CA Engine
Cabior system
CA Preprocessing
Simulation
Cabior Main
Window
Postprocessing
Optimization
Pilot Plant
Simulation
periodic
outcome
Real Field
Model Tuning
Cabior sw overview
• Based on AVS/Express 5.0
• built both connecting and customizing appropriate
AVS components and developing some new
modules
• developed on SGI Onyx2 platform
• ported on PC cluster running Linux and compiled
with LessTif freeware library
Preprocessing overview
• It assists the user allowing the visualization, while editing,
of the binary input files required by the bioremediation
simulation.
• It supports the definition of the automaton general
characteristic (dimensions, cell sizes, the real time to be
simulated ….).
• It permits to prepare all those files defining the state of
each cell ( substates), providing the modalities to represent
both homogeneous cell array and discontinuities like
surfaces and lateral walls, injection and extraction wells.
• It allows to import binary files coming from platforms with
incompatible binary formats.
Model parameters tuning
Optimization
methods
Cellular Automaton
Fitness evaluation
Soil
data
Pilot
plant
experiments
Best
Cellular
Automaton
Time
Target
t1
t2
t3
t4
…
tN
Y1
Y2
Y3
Y4
YN
FITNESS:
 reali  sim ulatedi 

f   
real
i 1 
i

N
2
Edit Experimental Data
Optimization Flow
Postprocessing overview
• To perform 3D visualization of the substates of the
automaton using different geometrical modalities;
• to show the substate value and the coordinates of a
single cell;
• to visualize the temporal evolution of a substate,
according to a chosen geometrical modality;
• to visualize vectorial fields.
Postprocessing application
• AVS/Express Single Window Application;
• the visualization window is composed of:
- the Visualization space
- the Application Modules space
• the data files to be visualized are retrieved by
means of specific descriptors produced together
with the simulation output.