PyTrilinos: a Python Interface to Selected Trilinos Packages

1
PyTrilinos a Python Interface toSelected
Trilinos Packages

• Bill Spotz
• Trilinos Users Group Meeting
• November 2, 2004

2
Outline

• Python
• Why Python?
• Python basics
• Numeric demo
• PyTrilinos
• Packages currently wrapped
• PyTrilinos demo
• Epetra/Numeric integration
• Example
• Multi-physics coupling environment

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Why Python?

• Object-oriented scripting language
• Easy to learn
• Clean syntax
• Weakly typed
• Designed for rapid prototyping
• Designed to glue software packages together

• Module library
• calendar
• commands (Unix)
• curses
• datetime
• difflib
• distutils
• email
• ftplib
• getopt
• htmllib
• os
• random
• re

• string
• symbol
• sys
• tarfile
• thread
• time
• Tkinter
• unicode
• unittest
• url
• xml
• Over 300 standard
• Numeric

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Python Variables
a 2004
b a
a "Sandia"
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Python Containers

• Indexing
• Get val containeri
• Set containeri val
• Slices containerijk
• Strings
• string "Trilinos"
• Immutable
• Tuples
• tuple (1,3.14,string)
• Immutable

• Lists
• list 2,2.71,tuple
• Mutable
• Methods append, insert, pop, remove,
• Dictionaries
• dict key1val1, key2val2,
• Mutable
• Keys must be immutable

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Python/Numeric Demo
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PyTrilinos

• from PyTrilinos import
• Epetra
• SerialComm
• BlockMap
• Map
• BLAS
• LAPACK
• MultiVector
• Vector
• IntVector
• CrsGraph
• MapColoring
• CrsMatrix
• SerialDense

• EpetraExt
• TransformltEpetra_CrsGraph, Epetra_MapColoringgt
• TransformltEpetra_CrsGraph, vectorltEpetra_IntVector
  gt gt
• NOX
• Abstract
• Epetra
• Parameter
• Solver
• StatusTest
• PyInterface

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Epetra/Numeric Integration

• C
• class Epetra_NumPyVector
• public Epetra_Vector
• public
• Epetra_NumPyVector(Epetra_BlockMap )
• Epetra_NumPyVector(Epetra_BlockMap ,
• PyObject )
• Epetra_NumPyVector(PyObject )
• PyObject getArray()
• ...

• Python
• class Vector(UserArray,NumPyVector)
• def __init__(self, args)
• NumPyVector.__init__(self,args)
• UserArray.__init__(self,
• self.getArray(),
• 'd',0,1)
• def __str__(self)
• return str(self.array)

Result Epetra.Vector is both Epetra_Vector and
Numeric UserArray, and both base classes share
same memory block for data.
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PyTrilinos Demo
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Example Multiphysics Coupling Environment
Solver


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Multiphysics Coupling Environment Objects
MultiSolver
Solver
PhysicsModules
Fields
Grids
Coordinates
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Example Problem 1D Brusselator
Governing Equations
Boundary Conditions
Initial Conditions
Data
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Brusselator Script

• !/usr/bin/env python
• Local imports
• import setpath
• from BC.Dirichlet import
• from Brusselator import
• from CrankNicolson import
• from Grid import
• from Field import
• Define a 1D uniform grid
• n 11
• x Coordinate("x",n)
• grid OrthogonalGrid(x)
• Define the Unknowns
• speciesX Unknown("X", grid, "Species X")
• speciesY Unknown("Y", grid, "Species Y")

• Define parameters of Brusselator problem
• a 0.6
• b 2.0
• d1 0.025
• d2 0.025
• bParams BrusselatorParameters(a,b,d1,d2)
• Create the Brusselator modules
• brussX BrusselatorX("X-Brusselator",
• bParams, speciesX, speciesY)
• brussY BrusselatorY("Y-Brusselator",
• bParams, speciesX, speciesY)
• Define the boundary conditions
• bcx0 Dirichlet(speciesX 0, a )
• bcx1 Dirichlet(speciesX-1, a )
• bcy0 Dirichlet(speciesY 0, b/a)
• bcy1 Dirichlet(speciesY-1, b/a)

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Brusselator Script, contd

• Create the Crank Nicolson solver, add the
• Brusselators to it, and add the boundary
• conditions to it
• cnSolver CrankNicolson(0.5, endTime20.0)
• cnSolver.addPhysicsModule(brussX)
• cnSolver.addPhysicsModule(brussY)
• cnSolver.addPhysicsModule(bcx0)
• cnSolver.addPhysicsModule(bcx1)
• cnSolver.addPhysicsModule(bcy0)
• cnSolver.addPhysicsModule(bcy1)
• Create the state, residual and exact
• BlockArrays, and initialize all physics
• modules
• cnSolver.openIOFile("Brusselator1_cn.nc")
• cnSolver.initialize()
• print cnSolver

• Assign the initial conditions
• stateVector cnSolver.getBlockState()
• stateVector.setArrayToPoly(speciesX,a,
• 1.0,-1.0)
• stateVector.setArrayToPoly(speciesY,b/a,
• 10,-1.0)
• Execute the forward Euler problem
• cnSolver.execute()

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Concluding Remarks

• Python should be a part of every programmers
  toolkit
• Great alternative to shell or perl scripts
• Rapid prototyping (especially OO)
• To install PyTrilinos
• Check out developer branch
• Need python, Numeric, swig 1.3.19-21 (including
  shared libraries)
• Configure serial build
• Configure with --enable-pytrilinos
• Consider wrapping your own package