EpetraExt Development
I/O Operations for Epetra Objects

Epetra supports I/O operations for Epetra objects based on

  1. Matlab triplet (i,j,value) format for writing and reading of Epetra RowMatrix and Operator objects.
  2. Matrix Market format: Support writing and reading of Epetra BlockMap, Map, MultiVector, Vector, RowMatrix and Operator objects.
  3. HDF5 format: Support writing and reading of Epetra BlockMap, Map, MultiVector, Vector, RowMatrix and Operator objects. Available when EpetraExt is configured with --enable-epetraext-hdf5.
  4. An XML-compatible reader and writer is available when Teuchos is configures with --enable-teuchos-expat.

The simplest of the input function is EpetraExt::MatlabFileToCrsMatrix. This function requires only a valid ASCII file containing 1 or more lines where each row is of the form: (row_index, col_index, value) and a valid Epetra_Comm object. The matrix domain and range maps are assumed to have a size of the maximum row and column index present in the file, respectively, and will be constructed as uniform distributed maps. The row map will be identical to the range map and the column map will be determined by which columns are present for the rows on a given processor.

The simplest output functions are EpetraExt::RowMatrixToMatlabFile and EpetraExt:OperatorToMatlabFile, which write out any Epetra_RowMatrix or Epetra_Operator object, respectively. Epetra_Operator coefficients are generated by multiplying the operator with the canonical vectors, several at a time for performance reasons.

The I/O function are summarized below:

  1. BlockMap and Map I/O:
    1. EpetraExt::MatrixMarketFileToBlockMap
    2. EpetraExt::BlockMapToMatrixMarketFile
    3. EpetraExt::MatrixMarketFileToMap
  2. CrsMatrix Input:
    1. EpetraExt::MatlabFileToCrsMatrix
    2. EpetraExt::MatrixMarketFileToCrsMatrix
  3. RowMatrix output (includes all Epetra matrix classes):
    1. EpetraExt::RowMatrixToMatrixMarketFile
    2. EpetraExt::RowMatrixToMatlabFile
  4. Operator output (includes all Epetra matrix and operator classes):
    1. EpetraExt::RowMatrixToMatrixMarketFile
    2. EpetraExt::RowMatrixToMatlabFile
  5. MultiVector and Vector I/O:
  6. MultiVector and Vector I/O:
    1. EpetraExt::MatrixMarketFileToMultiVector
    2. EpetraExt::MatrixMarketFileToVector
    3. EpetraExt::MultiVectorToMatrixMarketFile
    4. EpetraExt::VectorToMatrixMarketFile
  7. HDF5 class: EpetraExt::HDF5
  8. XML classes: EpetraExt::XMLReader and EpetraExt::XMLWriter.

The following example (from Trilinos/packages/aztecoo/example/AztecOO_Matlab_Input) shows an interesting use of these classes, illustrating how to use these classes in conjunction with AztecOO to write out the coefficients of the inverse of a matrix:

// ***********************************************************************
//     AztecOO: An Object-Oriented Aztec Linear Solver Package
//                 Copyright (2002) Sandia Corporation
// Under terms of Contract DE-AC04-94AL85000, there is a non-exclusive
// license for use of this work by or on behalf of the U.S. Government.
// This library is free software; you can redistribute it and/or modify
// it under the terms of the GNU Lesser General Public License as
// published by the Free Software Foundation; either version 2.1 of the
// License, or (at your option) any later version.
// This library is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of
// Lesser General Public License for more details.
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
// USA
// Questions? Contact Michael A. Heroux (maherou@sandia.gov) 
// ***********************************************************************
#include "AztecOO_config.h"
#ifdef HAVE_MPI
#include "mpi.h"
#include "Epetra_MpiComm.h"
#include "Epetra_SerialComm.h"
#include "Epetra_Map.h"
#include "Epetra_Vector.h"
#include "Epetra_CrsMatrix.h"
#include "EpetraExt_OperatorOut.h"
#include "EpetraExt_CrsMatrixIn.h"
#include "AztecOO_Operator.h"
#include "Epetra_InvOperator.h"
#include <string>
// prototypes

int checkValues( double x, double y, string message = "", bool verbose = false) { 
  if (fabs((x-y)/x) > 0.01) {
    if (verbose) cout << "********** " << message << " check failed.********** " << endl;
  else {
    if (verbose) cout << message << " check OK." << endl;    

int main(int argc, char *argv[]) {

#ifdef HAVE_MPI
  Epetra_MpiComm comm (MPI_COMM_WORLD);
  Epetra_SerialComm comm;

  int MyPID = comm.MyPID();

  bool verbose = false;
  bool verbose1 = false; 
  // Check if we should print results to standard out
  if (argc > 1) {
    if ((argv[1][0] == '-') && (argv[1][1] == 'v')) {
      verbose1 = true;
      if (MyPID==0) verbose = true;

  if (verbose1) cout << comm << endl;

  // Uncomment the next three lines to debug in mpi mode
  //int tmp;
  //if (MyPID==0) cin >> tmp;

  Epetra_CrsMatrix * A; 
  EPETRA_CHK_ERR(EpetraExt::MatlabFileToCrsMatrix("A.dat", comm, A));

  Epetra_Vector  x(A->OperatorDomainMap()); 
  Epetra_Vector  b(A->OperatorRangeMap());
  A->Apply(x,b); // Generate RHS from x
  Epetra_Vector xx(x); // Copy x to xx for later use

  Epetra_LinearProblem problem(A, &x, &b);
  // Construct a solver object for this problem

  AztecOO solver(problem);
  solver.SetAztecOption(AZ_precond, AZ_none);
  if (!verbose1) solver.SetAztecOption(AZ_output, AZ_none);
  solver.SetAztecOption(AZ_kspace, A->NumGlobalRows());
  AztecOO_Operator AOpInv(&solver, A->NumGlobalRows());
  Epetra_InvOperator AInvOp(&AOpInv);

  EPETRA_CHK_ERR(EpetraExt::OperatorToMatlabFile("Ainv.dat", AInvOp));


  Epetra_CrsMatrix * AInv; 
  EPETRA_CHK_ERR(EpetraExt::MatlabFileToCrsMatrix("Ainv.dat", comm, AInv));


  EPETRA_CHK_ERR(x.Update(1.0, xx, -1.0));
  double residual = 0.0;
  if (verbose) cout << "Norm of difference between computed x and exact x = " << residual << endl;
  int ierr = checkValues(residual,0.0,"Norm of difference between computed A1x1 and A1x1 from file", verbose);

  delete A;
  delete AInv;

  #ifdef HAVE_MPI
  MPI_Finalize() ;

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