diff --git a/src/solver/sparse_matrix.cc b/src/solver/sparse_matrix.cc
index 0e2302a84..50cb10848 100644
--- a/src/solver/sparse_matrix.cc
+++ b/src/solver/sparse_matrix.cc
@@ -1,69 +1,69 @@
/**
* Copyright (©) 2010-2023 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This file is part of Akantu
*
* 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 <fstream>
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrix::SparseMatrix(DOFManager & dof_manager,
const MatrixType & matrix_type, const ID & id)
- : id(id), _dof_manager(dof_manager), matrix_type(matrix_type),
+ : id(id), dof_manager(dof_manager), matrix_type(matrix_type),
size_(dof_manager.getSystemSize()), nb_non_zero(0) {
AKANTU_DEBUG_IN();
- const auto & comm = _dof_manager.getCommunicator();
+ const auto & comm = dof_manager.getCommunicator();
this->nb_proc = comm.getNbProc();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrix::SparseMatrix(const SparseMatrix & matrix, const ID & id)
- : SparseMatrix(matrix._dof_manager, matrix.matrix_type, id) {
+ : SparseMatrix(matrix.dof_manager, matrix.matrix_type, id) {
nb_non_zero = matrix.nb_non_zero;
}
/* -------------------------------------------------------------------------- */
SparseMatrix::~SparseMatrix() = default;
// /* --------------------------------------------------------------------------
// */ Array<Real> & operator*=(SolverVector & vect, const SparseMatrix & mat) {
// Array<Real> tmp(vect.size(), vect.getNbComponent(), 0.);
// mat.matVecMul(vect, tmp);
// vect.copy(tmp);
// return vect;
// }
/* -------------------------------------------------------------------------- */
void SparseMatrix::add(const SparseMatrix & B, Real alpha) {
B.addMeTo(*this, alpha);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/solver/sparse_matrix.hh b/src/solver/sparse_matrix.hh
index 4881cf857..d46e6b7ed 100644
--- a/src/solver/sparse_matrix.hh
+++ b/src/solver/sparse_matrix.hh
@@ -1,158 +1,158 @@
/**
* Copyright (©) 2010-2023 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This file is part of Akantu
*
* 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 "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SPARSE_MATRIX_HH_
#define AKANTU_SPARSE_MATRIX_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManager;
class TermsToAssemble;
class SparseSolverVector;
} // namespace akantu
namespace akantu {
class SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrix(DOFManager & dof_manager, const MatrixType & matrix_type,
const ID & id = "sparse_matrix");
SparseMatrix(const SparseMatrix & matrix, const ID & id = "sparse_matrix");
virtual ~SparseMatrix();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// remove the existing profile
virtual void clearProfile();
/// set the matrix to 0
virtual void set(Real val) = 0;
virtual void zero() { this->set(0); }
/// add a non-zero element to the profile
virtual Idx add(Idx i, Idx j) = 0;
/// assemble a local matrix in the sparse one
virtual void add(Idx i, Idx j, Real value) = 0;
/// save the profil in a file using the MatrixMarket file format
virtual void saveProfile(const std::string & /* filename */) const {
AKANTU_TO_IMPLEMENT();
}
/// save the matrix in a file using the MatrixMarket file format
virtual void saveMatrix(const std::string & /* filename */) const {
AKANTU_TO_IMPLEMENT();
};
/// multiply the matrix by a coefficient
virtual void mul(Real alpha) = 0;
/// add matrices
virtual void add(const SparseMatrix & B, Real alpha = 1.);
/// Equivalent of *gemv in blas
virtual void matVecMul(const SparseSolverVector & x, SparseSolverVector & y,
Real alpha = 1., Real beta = 0.) const = 0;
/// modify the matrix to "remove" the blocked dof
virtual void applyBoundary(Real block_val = 1.) = 0;
/// copy the profile of another matrix
virtual void copyProfile(const SparseMatrix & other) = 0;
/// operator *=
SparseMatrix & operator*=(Real alpha) {
this->mul(alpha);
return *this;
}
/// Check if all entries are finite. The default implementation throws.
virtual bool isFinite() const { AKANTU_TO_IMPLEMENT(); }
protected:
/// This is the revert of add \f[B += \alpha * *this\f];
virtual void addMeTo(SparseMatrix & B, Real alpha) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the values at potition i, j
virtual inline Real operator()(Idx /*i*/, Idx /*j*/) const {
AKANTU_TO_IMPLEMENT();
}
/// return the values at potition i, j
virtual inline Real & operator()(Idx /*i*/, Idx /*j*/) {
AKANTU_TO_IMPLEMENT();
}
AKANTU_GET_MACRO_AUTO(NbNonZero, nb_non_zero);
Int size() const { return size_; }
AKANTU_GET_MACRO_AUTO(MatrixType, matrix_type);
virtual Int getRelease() const = 0;
virtual Real min() = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ID id;
/// Underlying dof manager
- DOFManager & _dof_manager;
+ DOFManager & dof_manager;
/// sparce matrix type
MatrixType matrix_type;
/// Size of the matrix
Int size_;
/// number of processors
Int nb_proc;
/// number of non zero element
Int nb_non_zero;
};
// Array<Real> & operator*=(Array<Real> & vect, const SparseMatrix & mat);
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_inline_impl.hh"
#endif /* AKANTU_SPARSE_MATRIX_HH_ */
diff --git a/src/solver/sparse_matrix_petsc.cc b/src/solver/sparse_matrix_petsc.cc
index 60a1ce70b..1fd4b344a 100644
--- a/src/solver/sparse_matrix_petsc.cc
+++ b/src/solver/sparse_matrix_petsc.cc
@@ -1,284 +1,285 @@
/**
* Copyright (©) 2010-2023 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This file is part of Akantu
*
* 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 & matrix_type,
const ID & id)
- : SparseMatrix(dof_manager, matrix_type, id), dof_manager(dof_manager) {
+ : SparseMatrix(dof_manager, matrix_type, id) {
AKANTU_DEBUG_IN();
auto && mpi_comm = dof_manager.getMPIComm();
MatCreate(mpi_comm, &mat);
detail::PETScSetName(mat, id);
resize();
MatSetFromOptions(mat);
MatSetUp(mat);
MatSetOption(mat, MAT_ROW_ORIENTED, PETSC_TRUE);
MatSetOption(mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE);
if (matrix_type == _symmetric) {
MatSetOption(mat, MAT_SYMMETRIC, PETSC_TRUE);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::SparseMatrixPETSc(const SparseMatrixPETSc & matrix,
const ID & id)
- : SparseMatrix(matrix, id), dof_manager(matrix.dof_manager) {
+ : SparseMatrix(matrix, id) {
MatDuplicate(matrix.mat, MAT_COPY_VALUES, &mat);
detail::PETScSetName(mat, id);
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::~SparseMatrixPETSc() {
AKANTU_DEBUG_IN();
if (mat != nullptr) {
MatDestroy(&mat);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::resize() {
auto local_size = dof_manager.getPureLocalSystemSize();
MatSetSizes(mat, local_size, local_size, size_, size_);
- auto & is_ltog_mapping = dof_manager.getISLocalToGlobalMapping();
+ auto & is_ltog_mapping =
+ aka::as_type<DOFManagerPETSc>(dof_manager).getISLocalToGlobalMapping();
MatSetLocalToGlobalMapping(mat, is_ltog_mapping, is_ltog_mapping);
}
/* -------------------------------------------------------------------------- */
/**
* 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();
+ auto && mpi_comm = aka::as_type<DOFManagerPETSc>(dof_manager).getMPIComm();
/// create Petsc viewer
PetscViewer viewer;
PetscViewerASCIIOpen(mpi_comm, filename.c_str(), &viewer);
PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_MATRIXMARKET);
MatView(mat, viewer);
PetscViewerPopFormat(viewer);
PetscViewerDestroy(&viewer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// Equivalent of *gemv in blas
void SparseMatrixPETSc::matVecMul(const SparseSolverVector & _x,
SparseSolverVector & _y, Real alpha,
Real beta) const {
const auto & x = aka::as_type<SparseSolverVectorPETSc>(_x);
auto & y = aka::as_type<SparseSolverVectorPETSc>(_y);
// y = alpha A x + beta y
SparseSolverVectorPETSc w(x, this->id + ":tmp");
// w = A x
if (release == 0) {
VecZeroEntries(w);
} else {
MatMult(mat, x, w);
}
if (alpha != 1.) {
// w = alpha w
VecScale(w, alpha);
}
// y = w + beta y
VecAYPX(y, beta, w);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addMeToImpl(SparseMatrixPETSc & B, Real alpha) const {
// std::cout << "addMeTo" << std::endl;
// PETSc_call(MatView, B.mat, PETSC_VIEWER_STDOUT_WORLD);
MatAXPY(B.mat, alpha, mat, SAME_NONZERO_PATTERN);
// PETSc_call(MatView, B.mat, PETSC_VIEWER_STDOUT_WORLD);
B.release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addMeTo(SparseMatrix & B, Real alpha) const {
if (aka::is_of_type<SparseMatrixPETSc>(B)) {
auto & B_petsc = aka::as_type<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::applyModifications() {
this->beginAssembly();
this->endAssembly();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::beginAssembly() {
MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::endAssembly() {
MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);
MatSetOption(mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::copyProfile(const SparseMatrix & other) {
const auto & A = aka::as_type<SparseMatrixPETSc>(other);
MatDestroy(&mat);
MatDuplicate(A.mat, MAT_DO_NOT_COPY_VALUES, &mat);
detail::PETScSetName(mat, id);
this->zero();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::applyBoundary(Real block_val) {
AKANTU_DEBUG_IN();
const auto & blocked_dofs = this->dof_manager.getGlobalBlockedDOFsIndexes();
// std::vector<PetscInt> rows;
// for (auto && data : enumerate(blocked)) {
// if (std::get<1>(data)) {
// rows.push_back(std::get<0>(data));
// }
// }
// applyModifications();
// static int c = 0;
// saveMatrix("before_blocked_" + std::to_string(c) + ".mtx");
MatZeroRowsColumnsLocal(mat, blocked_dofs.size(), blocked_dofs.data(),
block_val, nullptr, nullptr);
// saveMatrix("after_blocked_" + std::to_string(c) + ".mtx");
// ++c;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::mul(Real alpha) {
MatScale(mat, alpha);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::zero() {
MatZeroEntries(mat);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::clearProfile() {
SparseMatrix::clearProfile();
MatResetPreallocation(mat);
MatSetOption(mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE);
// MatSetOption( MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE);
// MatSetOption( MAT_NEW_NONZERO_ALLOCATIONS, PETSC_TRUE);
// MatSetOption( MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
this->zero();
}
/* -------------------------------------------------------------------------- */
Idx SparseMatrixPETSc::add(Idx i, Idx j) {
MatSetValue(mat, i, j, 0, ADD_VALUES);
return 0;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::add(Idx i, Idx j, Real val) {
MatSetValue(mat, i, j, val, ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(Idx i, Idx j) {
MatSetValueLocal(mat, i, j, 0, ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(Idx i, Idx j, Real val) {
MatSetValueLocal(mat, i, j, val, ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(const Vector<Int> & rows,
const Vector<Int> & cols,
const Matrix<Real> & values) {
MatSetValuesLocal(mat, rows.size(), rows.data(), cols.size(), cols.data(),
values.data(), ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addValues(const Vector<Int> & rows,
const Vector<Int> & cols,
const Matrix<Real> & values,
MatrixType values_type) {
if (values_type == _unsymmetric and matrix_type == _symmetric) {
MatSetOption(mat, MAT_SYMMETRIC, PETSC_FALSE);
MatSetOption(mat, MAT_STRUCTURALLY_SYMMETRIC, PETSC_FALSE);
}
MatSetValues(mat, rows.size(), rows.data(), cols.size(), cols.data(),
values.data(), ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/solver/sparse_matrix_petsc.hh b/src/solver/sparse_matrix_petsc.hh
index 8be6a4901..9d3971baf 100644
--- a/src/solver/sparse_matrix_petsc.hh
+++ b/src/solver/sparse_matrix_petsc.hh
@@ -1,151 +1,148 @@
/**
* Copyright (©) 2010-2023 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* This file is part of Akantu
*
* 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/>.
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PETSC_MATRIX_HH_
#define AKANTU_PETSC_MATRIX_HH_
/* -------------------------------------------------------------------------- */
#include "aka_types.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <petscmat.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManagerPETSc;
}
namespace akantu {
class SparseMatrixPETSc : public SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrixPETSc(DOFManagerPETSc & dof_manager,
const MatrixType & matrix_type,
const ID & id = "sparse_matrix_petsc");
SparseMatrixPETSc(const SparseMatrixPETSc & matrix,
const ID & id = "sparse_matrix_petsc");
~SparseMatrixPETSc() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set the matrix to 0
void zero() override;
void set(Real /*val*/) override { AKANTU_TO_IMPLEMENT(); }
void clearProfile() override;
/// add a non-zero element to the profile
Idx add(Idx i, Idx j) override;
/// assemble a local matrix in the sparse one
void add(Idx i, Idx j, Real value) override;
void addLocal(Idx i, Idx j);
void addLocal(Idx i, Idx j, Real val);
void addLocal(const Vector<Int> & rows, const Vector<Int> & cols,
const Matrix<Real> & values);
/// add a block of values
void addValues(const Vector<Int> & rows, const Vector<Int> & cols,
const Matrix<Real> & values, MatrixType values_type);
/// save the profil in a file using the MatrixMarket file format
// void saveProfile(__attribute__((unused)) const std::string &) const
// override {
// AKANTU_DEBUG_TO_IMPLEMENT();
// }
/// save the matrix in a file using the MatrixMarket file format
void saveMatrix(const std::string & filename) const override;
/// multiply the matrix by a coefficient
void mul(Real alpha) override;
/// Equivalent of *gemv in blas
void matVecMul(const SparseSolverVector & x, SparseSolverVector & y,
Real alpha = 1., Real beta = 0.) const override;
/// modify the matrix to "remove" the blocked dof
void applyBoundary(Real block_val = 1.) override;
/// copy the profile of a matrix
void copyProfile(const SparseMatrix & other) override;
void applyModifications();
void resize();
Real min() override { AKANTU_TO_IMPLEMENT(); }
protected:
void addMeTo(SparseMatrix & B, Real alpha) const override;
/// This is the specific implementation
void addMeToImpl(SparseMatrixPETSc & B, Real alpha) const;
void beginAssembly();
void endAssembly();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the values at potition i, j
inline Real operator()(Idx /*i*/, Idx /*j*/) const override {
AKANTU_TO_IMPLEMENT();
}
/// return the values at potition i, j
inline Real & operator()(Idx /*i*/, Idx /*j*/) override {
AKANTU_TO_IMPLEMENT();
}
Int getRelease() const override { return release; };
operator Mat &() { return mat; }
operator const Mat &() const { return mat; }
AKANTU_GET_MACRO(Mat, mat, const Mat &);
AKANTU_GET_MACRO_NOT_CONST(Mat, mat, Mat &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
- // DOFManagerPETSc that contains the numbering for petsc
- DOFManagerPETSc & dof_manager;
-
/// store the PETSc matrix
Mat mat;
/// matrix release
Int release{0};
};
} // namespace akantu
#endif /* AKANTU_PETSC_MATRIX_HH_ */