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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