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sparse_matrix_petsc.cc
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sparse_matrix_petsc.cc
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/**
* @file sparse_matrix_petsc.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Sat Feb 03 2018
*
* @brief Implementation of PETSc matrix class
*
* @section LICENSE
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu 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 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_communicator_data.hh"
#include "solver_vector_petsc.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::SparseMatrixPETSc(DOFManagerPETSc & dof_manager,
const MatrixType & sparse_matrix_type,
const ID & id)
: SparseMatrix(dof_manager, matrix_type, id), dof_manager(dof_manager) {
AKANTU_DEBUG_IN();
auto mpi_comm = dof_manager.getMPIComm();
PETSc_call(MatCreate, mpi_comm, &mat);
if (sparse_matrix_type == _symmetric)
PETSc_call(MatSetOption, mat, MAT_SYMMETRIC, PETSC_TRUE);
PETSc_call(MatSetOption, mat, MAT_ROW_ORIENTED, PETSC_TRUE);
auto local_size = dof_manager.getPureLocalSystemSize();
PETSc_call(MatSetSizes, mat, local_size, local_size, size_, size_);
auto & is_ltog_mapping = dof_manager.getISLocalToGlobalMapping();
PETSc_call(MatSetUp, mat);
PETSc_call(MatSetLocalToGlobalMapping, mat, is_ltog_mapping, is_ltog_mapping);
PETSc_call(PetscObjectSetName, reinterpret_cast<PetscObject>(mat),
id.c_str());
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::SparseMatrixPETSc(const SparseMatrixPETSc & matrix,
const ID & id)
: SparseMatrix(matrix, id), dof_manager(matrix.dof_manager) {
PETSc_call(MatDuplicate, matrix.mat, MAT_COPY_VALUES, &mat);
PETSc_call(PetscObjectSetName, reinterpret_cast<PetscObject>(mat),
id.c_str());
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::~SparseMatrixPETSc() {
AKANTU_DEBUG_IN();
if (mat)
PETSc_call(MatDestroy, &mat);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Method to save the nonzero pattern and the values stored at each position
* @param filename name of the file in which the information will be stored
*/
void SparseMatrixPETSc::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
auto mpi_comm = dof_manager.getMPIComm();
/// create Petsc viewer
PetscViewer viewer;
PETSc_call(PetscViewerASCIIOpen, mpi_comm, filename.c_str(), &viewer);
PETSc_call(PetscViewerPushFormat, viewer, PETSC_VIEWER_ASCII_MATRIXMARKET);
PETSc_call(MatView, mat, viewer);
PETSc_call(PetscViewerPopFormat, viewer);
PETSc_call(PetscViewerDestroy, &viewer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// Equivalent of *gemv in blas
void SparseMatrixPETSc::matVecMul(const SolverVector & _x, SolverVector & _y,
Real alpha, Real beta) const {
auto & x = dynamic_cast<const SolverVectorPETSc &>(_x).getVector();
auto & y = dynamic_cast<SolverVectorPETSc &>(_y).getVector();
// y = alpha A x + beta y
SolverVectorPETSc w(x);
// w = A x
PETSc_call(MatMult, mat, x, w);
if (alpha != 1.) {
// w = alpha w
PETSc_call(VecScale, w, alpha);
}
// y = w + beta y
PETSc_call(VecAYPX, y, beta, w);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addMeToImpl(SparseMatrixPETSc & B, Real alpha) const {
PETSc_call(MatAXPY, B.mat, alpha, mat, SAME_NONZERO_PATTERN);
B.release++;
}
/* -------------------------------------------------------------------------- */
/**
* Method to add another PETSc matrix to this PETSc matrix
* @param matrix PETSc matrix to be added
* @param alpha the factor specifying how many times the matrix should be added
*/
void SparseMatrixPETSc::addMeTo(SparseMatrix & B, Real alpha) const {
if (auto * B_petsc = dynamic_cast<SparseMatrixPETSc *>(&B)) {
this->addMeToImpl(*B_petsc, alpha);
} else {
AKANTU_TO_IMPLEMENT();
// this->addMeToTemplated<SparseMatrix>(*this, alpha);
}
}
/* -------------------------------------------------------------------------- */
/**
* MatSetValues() generally caches the values. The matrix is ready to
* use only after MatAssemblyBegin() and MatAssemblyEnd() have been
* called. (http://www.mcs.anl.gov/petsc/)
*/
void SparseMatrixPETSc::performAssembly() {
this->beginAssembly();
this->endAssembly();
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::beginAssembly() {
PETSc_call(MatAssemblyBegin, mat, MAT_FINAL_ASSEMBLY);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::endAssembly() {
PETSc_call(MatAssemblyEnd, mat, MAT_FINAL_ASSEMBLY);
PETSc_call(MatSetOption, mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_FALSE);
// PETSc_call(MatSetOption, mat, MAT_NEW_NONZERO_ALLOCATIONS, PETSC_TRUE);
// PETSc_call(MatSetOption, mat, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::applyBoundary(Real block_val) {
AKANTU_DEBUG_IN();
const auto & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
std::vector<PetscInt> rows;
for (auto && data : enumerate(blocked)) {
if (std::get<1>(data)) {
rows.push_back(std::get<0>(data));
}
}
PETSc_call(MatZeroRowsColumnsLocal, mat, roew.size(),
rows.storage(), block_val, nullptr, nullptr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::mul(Real alpha) {
PETSc_call(MatScale, mat, alpha);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::clear() {
PETSc_call(MatZeroEntries, mat);
this->release++;
}
/* -------------------------------------------------------------------------- */
// void SparseMatrixPETSc::clearProfile() {
// SparseMatrix::clearProfile();
// PETSc_call(MatSetOption, MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE);
// PETSc_call(MatSetOption, MAT_NEW_NONZERO_ALLOCATIONS, PETSC_TRUE);
// PETSc_call(MatSetOption, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
// PETSc_call(MatZeroEntries, mat);
// //this->value_release++;
// }
/* -------------------------------------------------------------------------- */
UInt SparseMatrixPETSc::add(UInt i, UInt j) {
PETSc_call(MatSetValue, mat, i, j, 0, ADD_VALUES);
this->release++;
return 0;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::add(UInt i, UInt j, Real val) {
PETSc_call(MatSetValue, mat, i, j, val, ADD_VALUES);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(UInt i, UInt j) {
PETSc_call(MatSetValueLocal, mat, i, j, 0, ADD_VALUES);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(UInt i, UInt j, Real val) {
PETSc_call(MatSetValueLocal, mat, i, j, val, ADD_VALUES);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(Vector<Int> & rows, Vector<Int> & cols,
Matrix<Real> & vals) {
PETSc_call(MatSetValuesLocal, mat, rows.size(), rows.storage(), cols.size(),
cols.storage(), vals.storage(), ADD_VALUES);
this->release++;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu

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