1. PyTrilinos: a Python Interface to Selected 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. 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

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

5. Python Containers 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

6. Python/Numeric Demo

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

8. 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.

9. PyTrilinos Demo

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

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

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

13. 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)

14. Brusselator Script, cont’d # 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()

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…