Jun031

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ACcESS Software System High Level Modelling
Languages

• by
• gross_at_access.edu.au

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Modeling the Earth

• Short medium-term processes
• Interactive faults, earthquakes
• Particle, FE methods, CA
• Long-term processes
• Mantel convection
• FEM PIC
• Mineralization, surface processes (FEM)
• Coupling

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ACcESS

• Major National Research Facility (MNRF)
• Hardware installation
• to provides sufficient compute power
• Software development
• to develop tools and models

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ACcESS (cont.)
ACcESS Science
ResearchCommuity
Terminal
Grid/XML
Scripting language algorithms models
ESyS Software System
Middleware data structures
Hardware 1-2Tflops OpenMPMPI
Kernels (BLAS) performance
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Users Profile

• Modelers mathematical background
• Development environment
• Fast Prototyping
• Debugging
• Unified access to software tools
• High-end users strong scope knowledge
• Using tested models
• set parameters via XML/GUI/web

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Components
Web Services
Interactive
GUI
Models High level algorithms
ESyS Python
Mesh/ParticleGeneration
Data bases
Visualization
Discretization
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ESyS Functionality

• Interactive modelling environment in Python
• platform and data structure independent
• Provides templates for implementations
• with lean interface
• to generic tools PDE solver, visualization
• specific functionality surface processes
• Coarse grain parallelization
• Facilitates the coupling of models
• Provides a Grid service(s)

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Discretization
ESyS
MOP
FEM
DEM
CA
PIC
ESyS-Finley Data structure array
ESyS-LSMEarth Data structure lists
ESyS-CA Data structure array
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ESyS-Finley

• Realizes a general PDE solver for ESyS
• 3D unstructured/structured grid FEM/PIC code
• in C
• parallelized optimized for SGI Altix
• Application
• long scale processes
• Interacting fault
• See also
• VECFEM general, 3D, unstructured, parallel
• FASTFLO

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A Simple Example
Domain
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Example

• import Finley
• import OpenDX
• from ESyS import
• get mesh
• mshFinley.Mesh(file.msh)
• identify faces
• topmsh.face(1)
• bottommsh.face(3)
• set values on the faces
• tmpTpScalar(top.nodes(),value20.)
• tmpBttmScalar(bottom.nodes(),value1820.)
• assemble and solve the PDE
• mat,rhsAssemble(A12.,ctmpTp,tmpBttm)
• Tmat.solve(rhs)
• visualization
• figOpenDX.Figure(msh)
• fig.addCarpet(T)

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assemble Method

• General interface
• Assemble(A,B,C,D,X,Y,a,b,c)
• A matrix or scalar (diag(A)) or not present
  (0)
• B,C,X vectors or not present (0)
• a,b,c scalars or not present (0)

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assemble (cont.)

• Coefficients can
• constant/piecewise constant
• or
• depending on location
• live on nodes or elements
• or
• equal zero/not present

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Some relevant Class
ESyS.Structure
ESyS.Domain
ESyS.Atoms
generic
inheritance
Region
Nodes
interfaces
Face
Finley.Mesh
instantiate
Elements
Points
access
implementation
libFinley.so
SciSL/BLAS
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Data
ESyS.Data
ESyS.assemble
inherits
Scalar
Tensor
Implemented by
Vector
Tensor4
Finley.assemble
numarray
access to coefficients
libFinley.so
libnumarray.so
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Another Example

• import Finley
• from ESyS import
• lam,mu,dt1.E12,0.1E5,0.1
• coeff
• mshFinley.Mesh(file.msh)
• dimmsh.getDim()
• topmsh.face(1)
• uAtTopVector(top.nodes(),value1,0)dt
• uAtBottomVector(bottom.nodes(),value-1,0)dt
• initialize stress,displacement,time
• sTensor(msh.elements(),Value0.)
• dVector(msh.nodes(),Value0.)
• t0
• while tlt1.
• mat,rhsAssemble(Acoeff,Xs,cuAtTop,uAtBotto
  m)
• ddmat.solve(rhs)
• ggradient(dd)
• dslam(gtranspose(g))/2mutrace(g)Id(dim)
• sds

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Operations on Data

• Binary operations
• arguments on the same Atoms or constant
• add ,sub ,mult, div, power
• in place ,-,
• Unitary operation
• abs, cos, sin, transpose, trace,
• Set get slices/items sv1, v2s
• In Finley implemented through numarray

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Substitutes for Finley

• Candidates
• SNARK for clusters, based of PETSc
• GeoFEM for the EarthSimulator
• no changes to the model codes
• has to pass the Finley test bed in Python.

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Beyond software integration

• Lazy evaluation of expressions
• Replaces partially numarray
• local evaluation gt improves efficiency
• Expression differentials non-linear problems
• Code generation
• Nicer interface for assemble