Tpetra parallel linear algebra  Version of the Day
Tpetra Lesson 03: Power method

Use Tpetra sparse matrix and dense vector objects to implement a simple iteration (the power method)

# Lesson topics

This lesson demonstrates the following:

1. How to construct a Tpetra::CrsMatrix (a distributed sparse matrix)
2. How to modify the entries of a previously constructed CrsMatrix
3. How to use CrsMatrix and Vector to implement a simple iterative eigensolver (the power method)

This example is just like the Epetra power method example with which many users might be familiar, but uses Tpetra objects in place of Epetra objects.

# Relation to other lessons

Before starting this lesson, it helps to have learned Tpetra Lesson 01: Initialization (how to initialize Tpetra) and Tpetra::Vector (how to create distributions and distributed vectors). After completing this lesson, you might want to learn about more efficient ways to add or modify entries in a Tpetra sparse matrix.

# Creating and filling a sparse matrix

This is the first lesson in the usual sequence which covers adding entries to ("filling") a Tpetra sparse matrix, and modifying the values of those entries after creating the matrix. Creating and filling a Tpetra sparse matrix involves the following steps:

1. Create the CrsMatrix (by calling one of its constructors)
2. Call methods to add entries to the sparse matrix
3. Call the matrix's `fillComplete()` method

We will explain each of these steps in turn.

## Creating the CrsMatrix

Tpetra's sparse matrices are distributed over one or more parallel processes, just like vectors or other distributed objects. Also just like vectors, you have to tell the sparse matrix its distribution on construction. Unlike vectors, though, sparse matrices have two dimensions over which to be distributed: rows and columns.

Many users are perfectly happy ignoring the column distribution and just distributing the matrix in "one-dimensional" fashion over rows. In that case, you need only supply the "row Map" to the constructor. This implies that for any row which a process owns, that process may insert entries in any column in that row.

Some users want to use the full flexibility of distributing both the rows and columns of the matrix over processes. This "two-dimensional" distribution, if chosen optimally, can significantly reduce the amount of communication needed for distributed-memory parallel sparse matrix-vector multiply. Trilinos packages like Zoltan and Zoltan2 can help you compute this distribution. In that case, you may give both the "row Map" and the "column Map" to the constructor. This implies that for any row which a process owns, that process may insert entries in any column in that row which that process owns in its column Map.

Finally, other users already know the structure of the sparse matrix, and just want to fill in values. These users should first create the graph (a CrsGraph), call `fillComplete()` on the graph, and then give the graph to the constructor of CrsMatrix. The graph may have either a "1-D" or "2-D" distribution, as mentioned above.

## Adding entries to the sparse matrix

Methods of CrsMatrix that start with "insert" actually change the structure of the sparse matrix. Methods that start with "replace" or "sumInto" only modify existing values.

## Calling \c fillComplete()

Calling `fillComplete()` signals that you are done changing the structure (if allowed) or values of the sparse matrix. This is an expensive operation, because it both rearranges local data, and communicates in order to build reusable communication patterns for sparse matrix-vector multiply. You should try to amortize the cost of this operation whenever possible over many sparse matrix-vector multiplies.

`fillComplete()` takes two arguments:

• the domain Map (the distribution of the input vector x in a sparse matrix-vector multiply y = A*x)
• the range Map (the distribution of the output vector y in a sparse matrix-vector multiply y = A*x)

Both the domain and range Maps must be one-to-one: that is, each global index in the Map must be uniquely owned by one and only one process. You will need to supply these two arguments to `fillComplete()` under any of the following conditions:

• When the row Map is not the same as the range Map (it can't be if the row Map is not one to one)
• When the domain and range Maps are not equal (e.g., if the matrix is not square)
• When the domain or range Map as not the same as the row Map

If the domain and range Maps equal the row Map and the row Map is one-to-one, then you may call `fillComplete()` with no arguments.

The most significant difference between Epetra and Tpetra sparse matrices, is that in order to modify the entries of a Tpetra::CrsMatrix once you have called `fillComplete()`, you must first call `resumeFill()`. Epetra_CrsMatrix has no corresponding "resume fill" method, and you may modify the values of entries after `FillComplete()` has been called.

The reason for this difference is that Tpetra's `fillComplete()` has the right to rearrange the matrix's data in ways that violate user expectations. For example, it may give the data to a third-party library that rearranges them in an opaque way, or even copy them into a different memory space (for example, into GPU memory). Calling `resumeFill()` signals Tpetra that you want to change either the values or the structure.

# Code example

The following code example shows how to fill and compute with a Tpetra sparse matrix, using the procedure discussed in the text above.

// ***********************************************************************
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// Tpetra: Templated Linear Algebra Services Package
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// this software without specific prior written permission.
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// Questions? Contact Michael A. Heroux (maherou@sandia.gov)
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// ************************************************************************
#include <Tpetra_Core.hpp>
#include <Tpetra_CrsMatrix.hpp>
#include <Tpetra_Map.hpp>
#include <Tpetra_MultiVector.hpp>
#include <Tpetra_Vector.hpp>
#include <Tpetra_Version.hpp>
#include <Teuchos_Array.hpp>
#include <Teuchos_ScalarTraits.hpp>
#include <Teuchos_RCP.hpp>
// Power method for estimating the eigenvalue of maximum magnitude of
// a matrix. This function returns the eigenvalue estimate.
//
// We don't intend for you to write your own eigensolvers; the Anasazi
// package provides them. You should instead see this class as a
// surrogate for a Tpetra interface to a Trilinos package.
//
// TpetraOperatorType: the type of the Tpetra::Operator specialization
// used to represent the sparse matrix or operator A.
//
// Tpetra::Operator implements a function from one
// Tpetra::(Multi)Vector to another Tpetra::(Multi)Vector.
// Tpetra::CrsMatrix implements Tpetra::Operator; its apply() method
// computes a sparse matrix-(multi)vector multiply. It's typical for
// numerical algorithms that use Tpetra objects to be templated on the
// type of the Tpetra::Operator specialization. We do so here, and
// thus demonstrate how you can use the public typedefs in Tpetra
// classes to write generic code.
//
// One could use a templated function here instead of a templated
// class with a static (class) method. I prefer the class approach
// because one can lift typedefs out of the function into the class.
// It tends to makes the function declaration easier to read.
template <class TpetraOperatorType>
class PowerMethod {
public:
typedef typename TpetraOperatorType::scalar_type scalar_type;
typedef typename TpetraOperatorType::local_ordinal_type local_ordinal_type;
typedef typename TpetraOperatorType::global_ordinal_type global_ordinal_type;
typedef typename TpetraOperatorType::node_type node_type;
// The type of a Tpetra vector with the same template parameters as
// those of TpetraOperatorType.
typedef Tpetra::Vector<scalar_type, local_ordinal_type,
global_ordinal_type, node_type> vec_type;
// The type of the norm of the above Tpetra::Vector specialization.
typedef typename vec_type::mag_type magnitude_type;
// Run the power method and return the eigenvalue estimate.
//
// Input arguments:
//
// A: The sparse matrix or operator, as a Tpetra::Operator.
// niters: Maximum number of iterations of the power method.
// tolerance: If the 2-norm of the residual A*x-lambda*x (for the
// current eigenvalue estimate lambda) is less than this, stop
// iterating. The complicated expression for the type ensures that
// if the type of entries in the matrix A (scalar_type) is complex,
// then we'll be using a real-valued type ("magnitude") for the
// tolerance. (You can't compare complex numbers using less than,
// so you can't test for convergence using a complex number.)
// out: output stream to which to print the current status of the
// power method.
static scalar_type
run (const TpetraOperatorType& A,
const int niters,
const magnitude_type tolerance,
std::ostream& out)
{
using std::endl;
typedef Teuchos::ScalarTraits<scalar_type> STS;
typedef Teuchos::ScalarTraits<magnitude_type> STM;
const int myRank = A.getMap ()->getComm ()->getRank ();
// Create three vectors for iterating the power method. Since the
// power method computes z = A*q, q should be in the domain of A and
// z should be in the range. (Obviously the power method requires
// that the domain and the range are equal, but it's a good idea to
// get into the habit of thinking whether a particular vector
// "belongs" in the domain or range of the matrix.) The residual
// vector "resid" is of course in the range of A.
vec_type q (A.getDomainMap ());
vec_type z (A.getRangeMap ());
vec_type resid (A.getRangeMap ());
// Fill the iteration vector z with random numbers to start.
// Don't have grand expectations about the quality of our
// pseudorandom number generator, but it is usually good enough
// for eigensolvers.
z.randomize ();
// lambda: Current approximation of the eigenvalue of maximum magnitude.
// normz: 2-norm of the current iteration vector z.
// residual: 2-norm of the current residual vector 'resid'.
//
// Teuchos::ScalarTraits defines what zero and one means for any
// type. Most number types T know how to turn a 0 or a 1 (int)
// into a T. I have encountered some number types in C++ that do
// not. These tend to be extended-precision types that define
// number operators and know how to convert from a float or
// double, but don't have conversion operators for int. Thus,
// using Teuchos::ScalarTraits makes this code maximally general.
scalar_type lambda = STS::zero ();
magnitude_type normz = STM::zero ();
magnitude_type residual = STM::zero ();
const scalar_type one = STS::one ();
const scalar_type zero = STS::zero ();
// How often to report progress in the power method. Reporting
// progress requires computing a residual, which can be expensive.
// However, if you don't compute the residual often enough, you
// might keep iterating even after you've converged.
const int reportFrequency = 10;
// Do the power method, until the method has converged or the
// maximum iteration count has been reached.
for (int iter = 0; iter < niters; ++iter) {
normz = z.norm2 (); // Compute the 2-norm of z
q.scale (one / normz, z); // q := z / normz
A.apply (q, z); // z := A * q
lambda = q.dot (z); // Approx. max eigenvalue
// Compute and report the residual norm every reportFrequency
// iterations, or if we've reached the maximum iteration count.
if (iter % reportFrequency == 0 || iter + 1 == niters) {
resid.update (one, z, -lambda, q, zero); // z := A*q - lambda*q
residual = resid.norm2 (); // 2-norm of the residual vector
if (myRank == 0) {
out << "Iteration " << iter << ":" << endl
<< "- lambda = " << lambda << endl
<< "- ||A*q - lambda*q||_2 = " << residual << endl;
}
}
if (residual < tolerance) {
if (myRank == 0) {
out << "Converged after " << iter << " iterations" << endl;
}
break;
}
else if (iter+1 == niters) {
if (myRank == 0) {
out << "Failed to converge after " << niters
<< " iterations" << endl;
}
break;
}
}
return lambda;
}
};
int
main (int argc, char *argv[])
{
using Teuchos::Array;
using Teuchos::ArrayView;
using Teuchos::ArrayRCP;
using Teuchos::arcp;
using Teuchos::RCP;
using Teuchos::rcp;
using Teuchos::tuple;
using std::cout;
using std::endl;
typedef Tpetra::Map<> map_type;
typedef Tpetra::Vector<>::scalar_type scalar_type;
typedef Tpetra::Vector<>::global_ordinal_type global_ordinal_type;
typedef Tpetra::Vector<>::mag_type magnitude_type;
typedef Tpetra::CrsMatrix<> crs_matrix_type;
typedef typename crs_matrix_type::nonconst_global_inds_host_view_type gids_type;
typedef typename crs_matrix_type::nonconst_values_host_view_type vals_type;
Tpetra::ScopeGuard tpetraScope (&argc, &argv);
{
// Never create Tpetra objects at main() scope.
// Never allow them to persist past ScopeGuard's destructor.
auto comm = Tpetra::getDefaultComm ();
const size_t myRank = comm->getRank();
//const size_t numProcs = comm->getSize();
if (myRank == 0) {
cout << Tpetra::version () << endl << endl;
}
// The number of rows and columns in the matrix.
const Tpetra::global_size_t numGblIndices = 50;
// Construct a Map that puts approximately the same number of
// equations on each processor.
const global_ordinal_type indexBase = 0;
RCP<const map_type> map =
rcp (new map_type (numGblIndices, indexBase, comm));
const size_t numMyElements = map->getLocalNumElements ();
// If you like, you may get the list of global indices that the
// calling process owns. This is unnecessary if you don't mind
// converting local indices to global indices.
//
// ArrayView<const global_ordinal_type> myGlobalElements =
// map->getLocalElementList ();
if (myRank == 0) {
cout << endl << "Creating the sparse matrix" << endl;
}
// Create a Tpetra sparse matrix whose rows have distribution
// given by the Map. We expect at most three entries per row.
RCP<crs_matrix_type> A (new crs_matrix_type (map, 3));
// Fill the sparse matrix, one row at a time.
const scalar_type two = static_cast<scalar_type> (2.0);
const scalar_type negOne = static_cast<scalar_type> (-1.0);
for (local_ordinal_type lclRow = 0;
lclRow < static_cast<local_ordinal_type> (numMyElements);
++lclRow) {
const global_ordinal_type gblRow = map->getGlobalElement (lclRow);
// A(0, 0:1) = [2, -1]
if (gblRow == 0) {
A->insertGlobalValues (gblRow,
tuple<global_ordinal_type> (gblRow, gblRow + 1),
tuple<scalar_type> (two, negOne));
}
// A(N-1, N-2:N-1) = [-1, 2]
else if (static_cast<Tpetra::global_size_t> (gblRow) == numGblIndices - 1) {
A->insertGlobalValues (gblRow,
tuple<global_ordinal_type> (gblRow - 1, gblRow),
tuple<scalar_type> (negOne, two));
}
// A(i, i-1:i+1) = [-1, 2, -1]
else {
A->insertGlobalValues (gblRow,
tuple<global_ordinal_type> (gblRow - 1, gblRow, gblRow + 1),
tuple<scalar_type> (negOne, two, negOne));
}
}
// Tell the sparse matrix that we are done adding entries to it.
A->fillComplete ();
// Number of iterations
const int niters = 500;
// Desired (absolute) residual tolerance
const magnitude_type tolerance = 1.0e-2;
// Run the power method and report the result.
scalar_type lambda =
PowerMethod<crs_matrix_type>::run (*A, niters, tolerance, cout);
if (myRank == 0) {
cout << endl << "Estimated max eigenvalue: " << lambda << endl;
}
//
// Now we will change values in the sparse matrix and run the
// power method again. In Tpetra, if fillComplete() has been
// called on a matrix, you must call resumeFill() on that matrix
// before you may change it.
//
//
// Increase diagonal dominance
//
if (myRank == 0) {
cout << endl << "Increasing magnitude of A(0,0), "
"solving again" << endl;
}
// Must call resumeFill() before changing the matrix.
A->resumeFill ();
if (A->getRowMap ()->isNodeGlobalElement (0)) {
// Get a copy of the row with with global index 0. Modify the
// diagonal entry of that row. Submit the modified values to
// the matrix.
const global_ordinal_type idOfFirstRow = 0;
size_t numEntriesInRow = A->getNumEntriesInGlobalRow (idOfFirstRow);
vals_type rowvals ("vals",numEntriesInRow);
gids_type rowinds ("gids",numEntriesInRow);
// Fill rowvals and rowinds with the values resp. (global)
// column indices of the sparse matrix entries owned by the
// calling process.
//
// Note that it's legal (though we don't exercise it in this
// example) for the row Map of the sparse matrix not to be one
// to one. This means that more than one process might own
// entries in the first row. In general, multiple processes
// might own the (0,0) entry, so that the global A(0,0) value is
// really the sum of all processes' values for that entry.
// However, scaling the entry by a constant factor distributes
// across that sum, so it's OK to do so.
//
// The parentheses after rowinds and rowvalues indicate "a view
// of the Array's data." Array::operator() returns an
// ArrayView.
A->getGlobalRowCopy (idOfFirstRow, rowinds, rowvals, numEntriesInRow);
for (size_t i = 0; i < numEntriesInRow; i++) {
if (rowinds[i] == idOfFirstRow) {
// We have found the diagonal entry; modify it.
rowvals[i] *= 10.0;
}
}
// "Replace global values" means modify the values, but not the
// structure of the sparse matrix. If the specified columns
// aren't already populated in this row on this process, then this
// method throws an exception. If you want to modify the
// structure (by adding new entries), you'll need to call
// insertGlobalValues().
A->replaceGlobalValues (idOfFirstRow, rowinds, rowvals);
}
// Call fillComplete() again to signal that we are done changing the
// matrix.
A->fillComplete ();
// Run the power method again.
lambda = PowerMethod<crs_matrix_type>::run (*A, niters, tolerance,
cout);
if (myRank == 0) {
cout << endl << "Estimated max eigenvalue: " << lambda << endl;
}
// This tells the Trilinos test framework that the test passed.
if (myRank == 0) {
cout << "End Result: TEST PASSED" << endl;
}
}
return 0;
}