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rAKA/src/solver/petsc_matrix.cc
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petsc_matrix.cc
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/**
* @file petsc_matrix.cc
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Mon Jul 21 17:40:41 2014
*
* @brief Implementation of PETSc matrix class
*
* @section LICENSE
*
* Copyright (©) 2010-2011 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 "petsc_matrix.hh"
#include "static_communicator.hh"
#include "static_communicator_mpi.hh"
#include "mpi_type_wrapper.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <cstring>
#include <mpi.h>
#include <petscmat.h>
#include <petscao.h>
#include <petscis.h>
#include <petscsys.h>
__BEGIN_AKANTU__
struct PETScWrapper {
Mat mat;
AO ao;
ISLocalToGlobalMapping mapping;
/// pointer to the MPI communicator for PETSc commands
MPI_Comm communicator;
};
/* -------------------------------------------------------------------------- */
PETScMatrix::PETScMatrix(UInt size,
const SparseMatrixType & sparse_matrix_type,
const ID & id,
const MemoryID & memory_id) :
SparseMatrix(size, sparse_matrix_type, id, memory_id),
petsc_wrapper(new PETScWrapper), d_nnz(0,1,"dnnz"), o_nnz(0,1,"onnz") {
AKANTU_DEBUG_IN();
this->init();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
PETScMatrix::PETScMatrix(const SparseMatrix & matrix,
const ID & id,
const MemoryID & memory_id) :
SparseMatrix(matrix, id, memory_id),
petsc_wrapper(new PETScWrapper), d_nnz(0,1,"dnnz"), o_nnz(0,1,"onnz") {
AKANTU_DEBUG_IN();
this->init();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
PETScMatrix::~PETScMatrix() {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
ierr = MatDestroy(&(this->petsc_wrapper->mat)); CHKERRXX(ierr);
delete petsc_wrapper;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PETScMatrix::init() {
AKANTU_DEBUG_IN();
#if defined(AKANTU_USE_MPI)
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
const StaticCommunicatorMPI & mpi_st_comm =
dynamic_cast<const StaticCommunicatorMPI &>(comm.getRealStaticCommunicator());
this->petsc_wrapper->communicator = mpi_st_comm.getMPITypeWrapper().getMPICommunicator();
#else
this->petsc_wrapper->communicator = PETSC_COMM_SELF;
#endif
PetscErrorCode ierr;
ierr = MatCreate(this->petsc_wrapper->communicator, &(this->petsc_wrapper->mat)); CHKERRXX(ierr);
/// set matrix type
ierr = MatSetType(this->petsc_wrapper->mat, MATAIJ); CHKERRXX(ierr);
if (this->sparse_matrix_type==_symmetric)
/// set flag for symmetry to enable ICC/Cholesky preconditioner
ierr = MatSetOption(this->petsc_wrapper->mat, MAT_SYMMETRIC, PETSC_TRUE); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PETScMatrix::resize(const DOFSynchronizer & dof_synchronizer) {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
/// find the number of dofs corresponding to master or local nodes
UInt nb_dofs = dof_synchronizer.getNbDOFs();
UInt nb_local_master_dofs = 0;
/// create array to store the global equation number of all local and master dofs
Array<Int> local_master_eq_nbs(nb_dofs);
Array<Int>::scalar_iterator it_eq_nb = local_master_eq_nbs.begin();
Array<Int> dof_types = dof_synchronizer.getDOFTypes();
Array<Int>::scalar_iterator it_dof_type = dof_types.begin();
/// get the pointer to the gloabl equation number array
Int * eq_nb_val = dof_synchronizer.getGlobalDOFEquationNumbers().storage();
for (UInt i = 0; i <nb_dofs; ++i, ++it_dof_type) {
if (*it_dof_type == -2 || *it_dof_type == -1 ) {
/// get for the local dof the global equation number
*it_eq_nb = eq_nb_val[i];
++it_eq_nb;
++nb_local_master_dofs;
}
}
local_master_eq_nbs.resize(nb_local_master_dofs);
/// set the local size
this->local_size = nb_local_master_dofs;
/// resize PETSc matrix
#if defined(AKANTU_USE_MPI)
ierr = MatSetSizes(this->petsc_wrapper->mat, this->size, this->size, this->local_size, this->local_size); CHKERRXX(ierr);
#else
ierr = MatSetSizes(this->petsc_wrapper->mat, this->local_size, this->local_size); CHKERRXX(ierr);
#endif
/// create mapping from akantu global numbering to petsc global numbering
this->createGlobalAkantuToPETScMap(local_master_eq_nbs.storage());
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PETScMatrix::createGlobalAkantuToPETScMap(Int* local_master_eq_nbs_ptr) {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt rank = comm.whoAmI();
//initialize vector to store the number of local and master nodes that are assigned to each processor
Vector<UInt> master_local_ndofs_per_proc(nb_proc);
/// store the nb of master and local dofs on each processor
master_local_ndofs_per_proc(rank) = this->local_size;
/// exchange the information among all processors
comm.allGather(master_local_ndofs_per_proc.storage(), 1);
/// each processor creates a map for his akantu global dofs to the corresponding petsc global dofs
/// determine the PETSc-index for the first dof on each processor
UInt petsc_start_index = 0;
for (UInt i = 0; i < rank; ++i) {
petsc_start_index += master_local_ndofs_per_proc(rank);
}
/// create array for petsc ordering
Array<Int> petsc_dofs(this->local_size);
Array<Int>::scalar_iterator it_petsc_dofs = petsc_dofs.begin();
for (UInt i = petsc_start_index; i < petsc_start_index + this->local_size; ++i, ++it_petsc_dofs) {
*it_petsc_dofs = i;
}
ierr = AOCreateBasic(this->petsc_wrapper->communicator, this->local_size, local_master_eq_nbs_ptr, petsc_dofs.storage(), &(this->petsc_wrapper->ao)); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
// void PETScMatrix::createLocalAkantuToPETScMap(const DOFSynchronizer & dof_synchronizer) {
// AKANTU_DEBUG_IN();
// AKANTU_DEBUG_ASSERT(this->petsc_wrapper->ao != NULL,
// "You should first create a mapping from the global"
// << " Akantu numbering to the global PETSc numbering");
// this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
// /// get the number of dofs
// Int nb_dofs = dof_synchronizer.getNbDOFs();
// /// get the global equation numbers for each node
// Array<Int> global_dof_equation_numbers = dof_synchronizer.getGlobalDOFEquationNumbers();
// /// map the global dof equation numbers to the corresponding PETSc ordering
// AOApplicationToPETSc(this->petsc_wrapper->ao, nb_dofs,
// global_dof_equation_numbers.storage());
// /// create the mapping from the local Akantu ordering to the global PETSc ordering
// ISLocalToGlobalMappingCreate(this->petsc_wrapper->communicator,
// 1, nb_dofs, global_dof_equation_numbers.storage(),
// PETSC_COPY_VALUES, mapping);
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void PETScMatrix::buildProfile(const Mesh & mesh, const DOFSynchronizer & dof_synchronizer, UInt nb_degree_of_freedom) {
AKANTU_DEBUG_IN();
//clearProfile();
PetscErrorCode ierr;
/// resize arrays to store the number of nonzeros in each row
this->d_nnz.resize(this->local_size);
this->o_nnz.resize(this->local_size);
/// set arrays to zero everywhere
this->d_nnz.set(0);
this->o_nnz.set(0);
this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
/// get the types for each local dof
const Array<Int> & dof_types = dof_synchronizer.getDOFTypes();
Int* dof_type_ptr = dof_types.storage();
// if(irn_jcn_to_k) delete irn_jcn_to_k;
// irn_jcn_to_k = new std::map<std::pair<UInt, UInt>, UInt>;
this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
coordinate_list_map::iterator irn_jcn_k_it;
Int * eq_nb_val = dof_synchronizer.getGlobalDOFEquationNumbers().storage();
/// Loop over all the ghost types
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
const GhostType & ghost_type = *gt;
/// Loop over all element types
Mesh::type_iterator it = mesh.firstType(mesh.getSpatialDimension(), ghost_type, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType (mesh.getSpatialDimension(), ghost_type, _ek_not_defined);
for(; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom;
UInt * conn_val = mesh.getConnectivity(*it, _not_ghost).storage();
Int * global_eq_nb_val = new Int[nb_degree_of_freedom * nb_nodes_per_element];
Int * local_eq_nb_val = new Int[nb_degree_of_freedom * nb_nodes_per_element];
for (UInt e = 0; e < nb_element; ++e) {
Int * tmp_global_eq_nb_val = global_eq_nb_val;
Int * tmp_local_eq_nb_val = local_eq_nb_val;
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
UInt n = conn_val[i];
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
*tmp_global_eq_nb_val++ = eq_nb_val[n * nb_degree_of_freedom + d];
*tmp_local_eq_nb_val++ = n * nb_degree_of_freedom + d;
}
// memcpy(tmp_global_eq_nb_val, eq_nb_val + n * nb_degree_of_freedom, nb_degree_of_freedom * sizeof(Int));
// tmp_global_eq_nb_val += nb_degree_of_freedom;
}
for (UInt i = 0; i < size_mat; ++i) {
if (dof_type_ptr[local_eq_nb_val[i]] == -2 || dof_type_ptr[local_eq_nb_val[i]] == -1 ) {
UInt c_irn = global_eq_nb_val[i];
if(c_irn < size ) {
//UInt j_start = (sparse_matrix_type == _symmetric) ? i : 0;
for (UInt j = 0; j < size_mat; ++j) {
UInt c_jcn = global_eq_nb_val[j];
if(c_jcn < size) {
KeyCOO irn_jcn = key(c_irn, c_jcn);
irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
if (irn_jcn_k_it == irn_jcn_k.end()) {
if (dof_type_ptr[local_eq_nb_val[j]] == -2 || dof_type_ptr[local_eq_nb_val[j]] == -1 )
this->d_nnz(local_eq_nb_val[i]) += 1;
else
this->o_nnz(local_eq_nb_val[i]) += 1;
}
}
}
}
}
}
conn_val += nb_nodes_per_element;
}
delete [] global_eq_nb_val;
delete [] local_eq_nb_val;
}
// /// for pbc @todo correct it for parallel
// if(StaticCommunicator::getStaticCommunicator().getNbProc() == 1) {
// for (UInt i = 0; i < size; ++i) {
// KeyCOO irn_jcn = key(i, i);
// irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
// if(irn_jcn_k_it == irn_jcn_k.end()) {
// irn_jcn_k[irn_jcn] = nb_non_zero;
// irn.push_back(i + 1);
// jcn.push_back(i + 1);
// nb_non_zero++;
// }
// }
// }
}
/// map arrays of nonzeros per row from akantu global to petsc global numbering
ierr = AOApplicationToPetsc(this->petsc_wrapper->ao,
local_size, d_nnz.storage()); CHKERRXX(ierr);
ierr = AOApplicationToPetsc(this->petsc_wrapper->ao,
local_size, o_nnz.storage()); CHKERRXX(ierr);
// std::string mat_type;
// mat_type.resize(20, 'a');
// std::cout << "MatType: " << mat_type << std::endl;
// const char * mat_type_ptr = mat_type.c_str();
MatType type;
MatGetType(this->petsc_wrapper->mat, &type);
// PetscTypeCompare((PetscObject)(this->petsc_wrapper->mat),MATSEQAIJ,&sametype);
//ierr = PetscTypeCompare(pet, MATSEQAIJ, &sametype); CHKERRXX(ierr);
/// build profile:
if (strcmp(type, MATSEQAIJ) == 0) {
ierr = MatSeqAIJSetPreallocation(this->petsc_wrapper->mat,
0, d_nnz.storage()); CHKERRXX(ierr);
} else if ((strcmp(type, MATMPIAIJ) == 0)) {
ierr = MatMPIAIJSetPreallocation(this->petsc_wrapper->mat,
0, d_nnz.storage(), 0,
o_nnz.storage()); CHKERRXX(ierr);
} else {
AKANTU_DEBUG_ERROR("The type " << type << " of PETSc matrix is not handled by"
<< " akantu in the preallocation step");
}
/// assemble matrix
MatAssemblyBegin(this->petsc_wrapper->mat, MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(this->petsc_wrapper->mat, MAT_FINAL_ASSEMBLY);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PETScMatrix::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
/// create Petsc viewer
PetscViewer viewer;
ierr = PetscViewerASCIIOpen(this->petsc_wrapper->communicator, filename.c_str(), &viewer); CHKERRXX(ierr);
/// save the matrix
ierr = MatView(this->petsc_wrapper->mat, viewer); CHKERRXX(ierr);
/// destroy the viewer
ierr = PetscViewerDestroy(&viewer); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
// /* -------------------------------------------------------------------------- */
// Array<Real> & operator*=(Array<Real> & vect, const PETScMatrix & mat) {
// AKANTU_DEBUG_IN();
// Array<Real> result
// MatMult(this->mat, vect, )
// // AKANTU_DEBUG_ASSERT((vect.getSize()*vect.getNbComponent() == mat.getSize()) &&
// // (vect.getNbComponent() == mat.getNbDegreOfFreedom()),
// // "The size of the matrix and the vector do not match");
// const PETScMatrixType & sparse_matrix_type = mat.getPETScMatrixType();
// DOFSynchronizer * dof_synchronizer = mat.getDOFSynchronizerPointer();
// UInt nb_non_zero = mat.getNbNonZero();
// Real * tmp = new Real [vect.getNbComponent() * vect.getSize()];
// std::fill_n(tmp, vect.getNbComponent() * vect.getSize(), 0);
// Int * i_val = mat.getIRN().storage();
// Int * j_val = mat.getJCN().storage();
// Real * a_val = mat.getA().storage();
// Real * vect_val = vect.storage();
// for (UInt k = 0; k < nb_non_zero; ++k) {
// UInt i = *(i_val++);
// UInt j = *(j_val++);
// Real a = *(a_val++);
// UInt local_i = i - 1;
// UInt local_j = j - 1;
// if(dof_synchronizer) {
// local_i = dof_synchronizer->getDOFLocalID(local_i);
// local_j = dof_synchronizer->getDOFLocalID(local_j);
// }
// tmp[local_i] += a * vect_val[local_j];
// if((sparse_matrix_type == _symmetric) && (local_i != local_j))
// tmp[local_j] += a * vect_val[local_i];
// }
// memcpy(vect_val, tmp, vect.getNbComponent() * vect.getSize() * sizeof(Real));
// delete [] tmp;
// if(dof_synchronizer)
// dof_synchronizer->reduceSynchronize<AddOperation>(vect);
// AKANTU_DEBUG_OUT();
// return vect;
// }
// /* -------------------------------------------------------------------------- */
// void PETScMatrix::copyContent(const PETScMatrix & matrix) {
// AKANTU_DEBUG_IN();
// AKANTU_DEBUG_ASSERT(nb_non_zero == matrix.getNbNonZero(),
// "The two matrices don't have the same profiles");
// MatCopy(this->mat, matrix->mat, SAME_NONZERO_PATTERN);
// AKANTU_DEBUG_OUT();
// }
// ///* -------------------------------------------------------------------------- */
// //void PETScMatrix::copyProfile(const PETScMatrix & matrix) {
// // AKANTU_DEBUG_IN();
// // irn = matrix.irn;
// // jcn = matrix.jcn;
// // nb_non_zero = matrix.nb_non_zero;
// // irn_jcn_k = matrix.irn_jcn_k;
// // a.resize(nb_non_zero);
// // AKANTU_DEBUG_OUT();
// //}
/* -------------------------------------------------------------------------- */
void PETScMatrix::add(const SparseMatrix & matrix, Real alpha) {
PetscErrorCode ierr;
AKANTU_DEBUG_ASSERT(nb_non_zero == matrix.getNbNonZero(),
"The two matrix don't have the same profiles");
const Array<Real> matrix_a = matrix.getA();
Array<Int> matrix_irn = matrix.getIRN();
Array<Int> matrix_jcn = matrix.getJCN();
UInt matrix_nb_non_zero = matrix.getNbNonZero();
/// map global akantu to global petsc
ierr = AOApplicationToPetsc(this->petsc_wrapper->ao, matrix_nb_non_zero,matrix_irn.storage()); CHKERRXX(ierr);
ierr = AOApplicationToPetsc(this->petsc_wrapper->ao, matrix_nb_non_zero,matrix_jcn.storage()); CHKERRXX(ierr);
Real val_to_add = 0;
for (UInt n = 0; n < matrix_nb_non_zero; ++n) {
val_to_add = alpha * matrix_a(n);
ierr = MatSetValue(this->petsc_wrapper->mat, matrix_irn(n), matrix_jcn(n), val_to_add,INSERT_VALUES); CHKERRXX(ierr);
}
}
/* -------------------------------------------------------------------------- */
void PETScMatrix::performAssembly() {
PetscErrorCode ierr;
ierr = MatAssemblyBegin(this->petsc_wrapper->mat, MAT_FINAL_ASSEMBLY); CHKERRXX(ierr);
ierr = MatAssemblyEnd(this->petsc_wrapper->mat, MAT_FINAL_ASSEMBLY); CHKERRXX(ierr);
}
__END_AKANTU__
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