PetscMatTools.cpp

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#include "PetscMatTools.hpp"
#include <algorithm>
#include <cassert>
 
 
// Implementation
 
void PetscMatTools::SetElement(Mat matrix, PetscInt row, PetscInt col, double value)
{
    PetscInt lo, hi;
    GetOwnershipRange(matrix, lo, hi);
 
    if (row >= lo && row < hi)
    {
        MatSetValue(matrix, row, col, value, INSERT_VALUES);
    }
}
 
void PetscMatTools::AddToElement(Mat matrix, PetscInt row, PetscInt col, double value)
{
    PetscInt lo, hi;
    GetOwnershipRange(matrix, lo, hi);
 
    if (row >= lo && row < hi)
    {
        MatSetValue(matrix, row, col, value, ADD_VALUES);
    }
}
 
void PetscMatTools::Finalise(Mat matrix)
{
    MatAssemblyBegin(matrix, MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(matrix, MAT_FINAL_ASSEMBLY);
}
 
void PetscMatTools::SwitchWriteMode(Mat matrix)
{
    MatAssemblyBegin(matrix, MAT_FLUSH_ASSEMBLY);
    MatAssemblyEnd(matrix, MAT_FLUSH_ASSEMBLY);
}
 
void PetscMatTools::Display(Mat matrix)
{
    //Give full precision, scientific notation
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 7) // PETSc 3.7+
    PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_MATLAB);
#else
    PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_MATLAB);
#endif
    MatView(matrix,PETSC_VIEWER_STDOUT_WORLD);
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 7) // PETSc 3.7+
    PetscViewerPopFormat(PETSC_VIEWER_STDOUT_WORLD);
#endif
}
 
void PetscMatTools::SetRow(Mat matrix, PetscInt row, double value)
{
    PetscInt lo, hi;
    GetOwnershipRange(matrix, lo, hi);
 
    if (row >= lo && row < hi)
    {
        PetscInt rows, cols;
        MatGetSize(matrix, &rows, &cols);
        for (PetscInt i=0; i<cols; i++)
        {
            SetElement(matrix, row, i, value);
        }
    }
}
 
void PetscMatTools::ZeroRowsWithValueOnDiagonal(Mat matrix, std::vector<unsigned>& rRows, double diagonalValue)
{
    Finalise(matrix);
 
    /*
     * Important! PETSc by default will destroy the sparsity structure for this row and deallocate memory
     * when the row is zeroed, and if there is a next timestep, the memory will have to reallocated when
     * assembly to done again. This can kill performance. The following makes sure the zeroed rows are kept.
     *
     * Note: if the following lines are called, then once MatZeroRows() is called below, there will be an
     * error if some rows have no entries at all. Hence for problems with dummy variables, Stokes flow for
     * example, the identity block needs to be added before dirichlet BCs.
     */
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 1) //PETSc 3.1 or later
    MatSetOption(matrix, MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE);
#elif (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR == 0) //PETSc 3.0
    MatSetOption(matrix, MAT_KEEP_ZEROED_ROWS, PETSC_TRUE);
#else //PETSc 2.x.x
    MatSetOption(matrix, MAT_KEEP_ZEROED_ROWS);
#endif
 
    PetscInt* rows = new PetscInt[rRows.size()];
    for (unsigned i=0; i<rRows.size(); i++)
    {
        rows[i] = rRows[i];
    }
#if (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 2) //PETSc 2.2
    IS is;
    ISCreateGeneral(PETSC_COMM_WORLD, rRows.size(), rows, &is);
    MatZeroRows(matrix, is, &diagonalValue);
    ISDestroy(PETSC_DESTROY_PARAM(is));
    /*
     *
[2]PETSC ERROR: MatMissingDiagonal_SeqAIJ() line 1011 in src/mat/impls/aij/seq/aij.c
[2]PETSC ERROR: PETSc has generated inconsistent data!
[2]PETSC ERROR: Matrix is missing diagonal number 15!
[2]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ() line 906 in src/mat/impls/aij/seq/aijfact.c
     *
     *
    // There appears to be a problem with MatZeroRows not setting diagonals correctly
    // While we are supporting PETSc 2.2, we have to do this the slow way
 
    AssembleFinal(matrix);
    PetscInt lo, hi;
    GetOwnershipRange(matrix, lo, hi);
    PetscInt size=GetSize(matrix);
    for (unsigned index=0; index<rRows.size(); index++)
    {
        PetscInt row = rRows[index];
        if (row >= lo && row < hi)
        {
            std::vector<unsigned> non_zero_cols;
            // This row is local, so zero it.
            for (PetscInt column = 0; column < size; column++)
            {
                if (GetElement(matrix, row, column) != 0.0)
                {
                    non_zero_cols.push_back(column);
                }
            }
            // Separate "gets" from "sets" so that we don't have to keep going into "assembled" mode
            for (unsigned i=0; i<non_zero_cols.size();i++)
            {
                SetElement(matrix, row, non_zero_cols[i], 0.0);
            }
            // Set the diagonal
            SetElement(matrix, row, row, diagonalValue);
        }
        // Everyone communicate after row is finished
        AssembleFinal(matrix);
    }
    */
#elif (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 2) //PETSc 3.2 or later
    MatZeroRows(matrix, rRows.size(), rows, diagonalValue , nullptr, nullptr);
#else
    MatZeroRows(matrix, rRows.size(), rows, diagonalValue);
#endif
    delete [] rows;
}
 
 
void PetscMatTools::ZeroRowsAndColumnsWithValueOnDiagonal(Mat matrix, std::vector<unsigned> rowColIndices, double diagonalValue)
{
    Finalise(matrix);
 
    // sort the vector as we will be repeatedly searching for entries in it
    std::sort(rowColIndices.begin(), rowColIndices.end());
 
    PetscInt lo, hi;
    GetOwnershipRange(matrix, lo, hi);
    unsigned size = hi-lo;
 
    std::vector<unsigned>* cols_to_zero_per_row = new std::vector<unsigned>[size];
 
    // collect the columns to be zeroed, for each row. We don't zero yet as we would
    // then have to repeatedly call Finalise before each MatGetRow
    for (PetscInt row = lo; row < hi; row++)
    {
        // get all the non-zero cols for this row
        PetscInt num_cols;
        const PetscInt* cols;
        MatGetRow(matrix, row, &num_cols, &cols, CHASTE_PETSC_NULLPTR);
 
        // see which of these cols are in the list of cols to be zeroed
        for (PetscInt i=0; i<num_cols; i++)
        {
            if (std::binary_search(rowColIndices.begin(), rowColIndices.end(), cols[i]))
            {
                cols_to_zero_per_row[row-lo].push_back(cols[i]);
            }
        }
 
        // this must be called for each MatGetRow
        MatRestoreRow(matrix, row, &num_cols, &cols, CHASTE_PETSC_NULLPTR);
    }
 
    // Now zero columns of each row
    for (PetscInt row = lo; row < hi; row++)
    {
        unsigned num_cols_to_zero_this_row = cols_to_zero_per_row[row-lo].size();
 
        if (num_cols_to_zero_this_row>0)
        {
            PetscInt* cols_to_zero = new PetscInt[num_cols_to_zero_this_row];
            double* zeros = new double[num_cols_to_zero_this_row];
            for (unsigned i=0; i<num_cols_to_zero_this_row; i++)
            {
                cols_to_zero[i] = cols_to_zero_per_row[row-lo][i];
                zeros[i] = 0.0;
            }
 
            PetscInt rows[1];
            rows[0] = row;
            MatSetValues(matrix, 1, rows, num_cols_to_zero_this_row, cols_to_zero, zeros, INSERT_VALUES);
            delete [] cols_to_zero;
            delete [] zeros;
        }
    }
 
    delete [] cols_to_zero_per_row;
 
    // Now zero the rows and add the diagonal entries
    ZeroRowsWithValueOnDiagonal(matrix, rowColIndices, diagonalValue);
}
 
void PetscMatTools::ZeroColumn(Mat matrix, PetscInt col)
{
    Finalise(matrix);
 
    PetscInt lo, hi;
    GetOwnershipRange(matrix, lo, hi);
 
    // Determine which rows in this column are non-zero (and therefore need to be zeroed)
    std::vector<unsigned> nonzero_rows;
    for (PetscInt row = lo; row < hi; row++)
    {
        if (GetElement(matrix, row, col) != 0.0)
        {
            nonzero_rows.push_back(row);
        }
    }
 
    // Set those rows to be zero by calling MatSetValues
    unsigned size = nonzero_rows.size();
    PetscInt* rows = new PetscInt[size];
    PetscInt cols[1];
    double* zeros = new double[size];
 
    cols[0] = col;
 
    for (unsigned i=0; i<size; i++)
    {
        rows[i] = nonzero_rows[i];
        zeros[i] = 0.0;
    }
 
    MatSetValues(matrix, size, rows, 1, cols, zeros, INSERT_VALUES);
    delete [] rows;
    delete [] zeros;
}
 
void PetscMatTools::Zero(Mat matrix)
{
    MatZeroEntries(matrix);
}
 
unsigned PetscMatTools::GetSize(Mat matrix)
{
    PetscInt rows, cols;
 
    MatGetSize(matrix, &rows, &cols);
    assert(rows == cols);
    return (unsigned) rows;
}
 
void PetscMatTools::GetOwnershipRange(Mat matrix, PetscInt& lo, PetscInt& hi)
{
    MatGetOwnershipRange(matrix, &lo, &hi);
}
 
double PetscMatTools::GetElement(Mat matrix, PetscInt row, PetscInt col)
{
    PetscInt lo, hi;
    GetOwnershipRange(matrix, lo, hi);
 
    assert(lo <= row && row < hi);
    PetscInt row_as_array[1];
    row_as_array[0] = row;
    PetscInt col_as_array[1];
    col_as_array[0] = col;
 
    double ret_array[1];
 
    MatGetValues(matrix, 1, row_as_array, 1, col_as_array, ret_array);
 
    return ret_array[0];
}
 
void PetscMatTools::SetOption(Mat matrix, MatOption option)
{
#if (PETSC_VERSION_MAJOR == 3) //PETSc 3.x.x
    MatSetOption(matrix, option, PETSC_TRUE);
#else
    MatSetOption(matrix, option);
#endif
}
 
Vec PetscMatTools::GetMatrixRowDistributed(Mat matrix, unsigned rowIndex)
{
    /*
     * We need to make sure that lhs_ith_row doesn't ignore off processor entries when assembling,
     * otherwise the VecSetValues call a few lines below will not work as expected.
     */
 
    PetscInt lo, hi;
    PetscMatTools::GetOwnershipRange(matrix, lo, hi);
    unsigned size = PetscMatTools::GetSize(matrix);
 
    Vec mat_ith_row = PetscTools::CreateVec(size, hi-lo, false);
 
    PetscInt num_entries;
    const PetscInt* column_indices;
    const PetscScalar* values;
 
    bool am_row_owner = (PetscInt)rowIndex >= lo && (PetscInt)rowIndex < hi;
 
    /*
     * Am I the owner of the row? If so get the non-zero entries and add them lhs_ith_row.
     * In parallel, VecAssembly{Begin,End} will send values to the rest of processors.
     */
    if (am_row_owner)
    {
        MatGetRow(matrix, rowIndex, &num_entries, &column_indices, &values);
        VecSetValues(mat_ith_row, num_entries, column_indices, values, INSERT_VALUES);
    }
 
    VecAssemblyBegin(mat_ith_row);
    VecAssemblyEnd(mat_ith_row);
 
    if (am_row_owner)
    {
        MatRestoreRow(matrix, rowIndex, &num_entries, &column_indices, &values);
    }
 
    return mat_ith_row;
}
 
 
bool PetscMatTools::CheckEquality(const Mat mat1, const Mat mat2, double tol)
{
    Mat y;
    MatDuplicate(mat2, MAT_COPY_VALUES, &y);
 
    double minus_one = -1.0;
#if (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 2) //PETSc 2.2
    // MatAYPX(*a, X, Y) does  Y = X + a*Y.
    MatAYPX(&minus_one, mat1, y);
#elif (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 3 && PETSC_VERSION_SUBMINOR == 1) //PETSc 2.3.1
    // MatAYPX( Y, a, X) does Y = a*Y + X.
    MatAYPX(y, minus_one, mat1);
#else
    // MatAYPX( Y, a, X, structure) does Y = a*Y + X.
    MatAYPX(y, minus_one, mat1, DIFFERENT_NONZERO_PATTERN);
#endif
    PetscReal norm;
    MatNorm(y, NORM_INFINITY, &norm);
    PetscTools::Destroy(y);
 
    return (norm < tol);
}
 
bool PetscMatTools::CheckSymmetry(const Mat matrix, double tol)
{
    Mat trans;
#if (PETSC_VERSION_MAJOR == 3) //PETSc 3.x.x
    MatTranspose(matrix, MAT_INITIAL_MATRIX, &trans);
#else
    MatTranspose(matrix, &trans);
#endif
    bool is_symmetric = PetscMatTools::CheckEquality(matrix, trans, tol);
    PetscTools::Destroy(trans);
    return is_symmetric;
}
 
void PetscMatTools::TurnOffVariableAllocationError(Mat matrix)
{
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 3) //PETSc 3.3 or later
    MatSetOption(matrix, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
#endif
}