1 / 15

PyTrilinos: a Python Interface to Selected Trilinos Packages

PyTrilinos: a Python Interface to Selected Trilinos Packages. Bill Spotz Trilinos Users Group Meeting November 2, 2004. Outline. Python Why Python? Python basics Numeric demo PyTrilinos Packages currently wrapped PyTrilinos demo Epetra/Numeric integration Example

haig
Download Presentation

PyTrilinos: a Python Interface to Selected Trilinos Packages

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

  3. 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 Why Python? • string • symbol • sys • tarfile • thread • time • Tkinter • unicode • unittest • url • xml • Over 300 standard… • Numeric

  4. PythonObject Type: PyInt Value: 2004 RefCount: 1 a b PythonObject Type: PyString Value: "Sandia" RefCount: 1 1 2 Python Variables a = 2004 b = a a = "Sandia"

  5. Indexing: Get: val = container[i] Set: container[i] = val Slices: container[i:j:k] 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 = {key1:val1, key2:val2, …} Mutable Keys must be immutable Python Containers

  6. Python/Numeric Demo

  7. from PyTrilinos import … Epetra SerialComm BlockMap Map BLAS LAPACK MultiVector Vector IntVector CrsGraph MapColoring CrsMatrix SerialDense* EpetraExt Transform<Epetra_CrsGraph, Epetra_MapColoring> Transform<Epetra_CrsGraph, vector<Epetra_IntVector> > NOX Abstract Epetra Parameter Solver StatusTest PyInterface PyTrilinos

  8. 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) Epetra/Numeric Integration Result: Epetra.Vector is both Epetra_Vector and Numeric UserArray, and both base classes share same memory block for data.

  9. PyTrilinos Demo

  10. PhysicsModule 1 PhysicsModule r PhysicsModule P Example: Multiphysics Coupling Environment Solver … …

  11. SteadyState Implicit Transient Explicit BoundaryConditions Unknowns Knowns Functions Unstructured Structured Orthogonal Multiphysics Coupling Environment Objects MultiSolver Solver PhysicsModules Fields Grids Coordinates

  12. Example Problem: 1D Brusselator Governing Equations: Boundary Conditions: Initial Conditions: Data:

  13. #!/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) Brusselator Script

  14. # Create the Crank Nicolson solver, add the # Brusselators to it, and add the boundary # conditions to it cnSolver = CrankNicolson(0.5, endTime=20.0) 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() Brusselator Script, cont’d

  15. Concluding Remarks • Python should be a part of every programmer’s 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…

More Related