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solver_petsc.cc
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			/**
			* @file solver_petsc.cc
			*
			* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
			* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Tue May 13 2014
			* @date last modification: Tue Jan 19 2016
			*
			* @brief Solver class implementation for the petsc solver
			*
			* @section LICENSE
			*
			* Copyright (©) 2014, 2015 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 "solver_petsc.hh"
			#include "dof_manager_petsc.hh"
			#include "sparse_matrix_petsc.hh"
			#include "mpi_type_wrapper.hh"
			/* -------------------------------------------------------------------------- */
			#include <petscksp.h>
			//#include <petscsys.h>
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			SolverPETSc::SolverPETSc(DOFManagerPETSc & dof_manager, const ID & matrix_id,
			const ID & id, const MemoryID & memory_id)
			: SparseSolver(dof_manager, matrix_id, id, memory_id),
			dof_manager(dof_manager),
			matrix(dof_manager.getMatrix(matrix_id)),
			is_petsc_data_initialized(false) {
			PetscErrorCode ierr;

			/// create a solver context
			ierr = KSPCreate(PETSC_COMM_WORLD, &this->ksp);
			CHKERRXX(ierr);
			}

			/* -------------------------------------------------------------------------- */
			SolverPETSc::~SolverPETSc() {
			AKANTU_DEBUG_IN();

			this->destroyInternalData();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolverPETSc::destroyInternalData() {
			AKANTU_DEBUG_IN();

			if (this->is_petsc_data_initialized) {
			PetscErrorCode ierr;
			ierr = KSPDestroy(&(this->ksp));
			CHKERRXX(ierr);
			this->is_petsc_data_initialized = false;
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolverPETSc::initialize() {
			AKANTU_DEBUG_IN();

			this->is_petsc_data_initialized = true;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolverPETSc::solve() {
			AKANTU_DEBUG_IN();

			Vec & rhs = this->dof_manager.getResidual();
			Vec & solution = this->dof_manager.getGlobalSolution();

			PetscErrorCode ierr;
			ierr = KSPSolve(this->ksp, rhs, solution);
			CHKERRXX(ierr);

			AKANTU_DEBUG_OUT();
			}

			// /* -------------------------------------------------------------------------- */
			// void SolverPETSc::solve(Array<Real> & solution) {
			// AKANTU_DEBUG_IN();

			// this->solution = &solution;
			// this->solve();

			// PetscErrorCode ierr;
			// PETScMatrix * petsc_matrix = static_cast<PETScMatrix *>(this->matrix);

			// // ierr = VecGetOwnershipRange(this->petsc_solver_wrapper->solution,
			// // solution_begin, solution_end); CHKERRXX(ierr);
			// // ierr = VecGetArray(this->petsc_solver_wrapper->solution, PetscScalar
			// // **array); CHKERRXX(ierr);
			// UInt nb_component = solution.getNbComponent();
			// UInt size = solution.size();

			// for (UInt i = 0; i < size; ++i) {
			// for (UInt j = 0; j < nb_component; ++j) {
			// UInt i_local = i * nb_component + j;
			// if (this->matrix->getDOFSynchronizer().isLocalOrMasterDOF(i_local)) {
			// Int i_global =
			// this->matrix->getDOFSynchronizer().getDOFGlobalID(i_local);
			// ierr = AOApplicationToPetsc(petsc_matrix->getPETScMatrixWrapper()->ao,
			// 1, &(i_global));
			// CHKERRXX(ierr);
			// ierr = VecGetValues(this->petsc_solver_wrapper->solution, 1, &i_global,
			// &solution(i, j));
			// CHKERRXX(ierr);
			// }
			// }
			// }
			// synch_registry->synchronize(_gst_solver_solution);

			// AKANTU_DEBUG_OUT();
			// }

			/* -------------------------------------------------------------------------- */
			void SolverPETSc::setOperators() {
			AKANTU_DEBUG_IN();
			PetscErrorCode ierr;
			/// set the matrix that defines the linear system and the matrix for
			/// preconditioning (here they are the same)
			#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
			ierr = KSPSetOperators(this->ksp,
			this->matrix.getPETScMat(),
			this->matrix.getPETScMat());
			CHKERRXX(ierr);
			#else
			ierr = KSPSetOperators(this->ksp,
			this->matrix.getPETScMat(),
			this->matrix.getPETScMat(),
			SAME_NONZERO_PATTERN);
			CHKERRXX(ierr);
			#endif

			/// If this is not called the solution vector is zeroed in the call to
			/// KSPSolve().
			ierr = KSPSetInitialGuessNonzero(this->ksp, PETSC_TRUE);
			KSPSetFromOptions(this->ksp);

			AKANTU_DEBUG_OUT();
			}
			/* -------------------------------------------------------------------------- */
			// void finalize_petsc() {

			// static bool finalized = false;
			// if (!finalized) {

			// cout<<"* INFO * PETSc is finalizing..."<<endl;
			// // finalize PETSc
			// PetscErrorCode ierr = PetscFinalize();CHKERRCONTINUE(ierr);
			// finalized = true;
			// }
			// }

			// SolverPETSc::sparse_vector_type
			// SolverPETSc::operator()(const SolverPETSc::sparse_matrix_type& AA,
			// const SolverPETSc::sparse_vector_type& bb) {

			// #ifdef CPPUTILS_VERBOSE
			// // parallel output stream
			// Output_stream out;
			// // timer
			// cpputils::ctimer timer;
			// out<<"Inside PETSc solver: "<<timer<<endl;
			// #endif

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Inside operator()(const sparse_matrix_type&, const
			// sparse_vector_type&)... "<<timer<<endl;
			// #endif

			// assert(AA.rows() == bb.size());

			// // KSP ksp; //!< linear solver context

			// Vec b; /* RHS */
			// PC pc; /* preconditioner context */
			// PetscErrorCode ierr;
			// PetscInt nlocal;
			// PetscInt n = bb.size();
			// VecScatter ctx;

			// /*
			// Create vectors. Note that we form 1 vector from scratch and
			// then duplicate as needed. For this simple case let PETSc decide how
			// many elements of the vector are stored on each processor. The second
			// argument to VecSetSizes() below causes PETSc to decide.
			// */
			// ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRCONTINUE(ierr);
			// ierr = VecSetSizes(b,PETSC_DECIDE,n);CHKERRCONTINUE(ierr);
			// ierr = VecSetFromOptions(b);CHKERRCONTINUE(ierr);
			// if (!allocated_) {
			// ierr = VecDuplicate(b,&x_);CHKERRCONTINUE(ierr);
			// } else
			// VecZeroEntries(x_);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Vectors created... "<<timer<<endl;
			// #endif

			// /* Set hight-hand-side vector */
			// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
			// bb.map_.end(); ++it) {
			// int row = it->first;
			// ierr = VecSetValues(b, 1, &row, &it->second, ADD_VALUES);
			// }

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Right hand side set... "<<timer<<endl;
			// #endif

			// /*
			// Assemble vector, using the 2-step process:
			// VecAssemblyBegin(), VecAssemblyEnd()
			// Computations can be done while messages are in transition
			// by placing code between these two statements.
			// */
			// ierr = VecAssemblyBegin(b);CHKERRCONTINUE(ierr);
			// ierr = VecAssemblyEnd(b);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Right-hand-side vector assembled... "<<timer<<endl;

			// ierr = VecView(b,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);

			// Vec b_all;
			// ierr = VecScatterCreateToAll(b, &ctx, &b_all);CHKERRCONTINUE(ierr);
			// ierr =
			// VecScatterBegin(ctx,b,b_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
			// ierr =
			// VecScatterEnd(ctx,b,b_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);

			// value_type nrm;
			// VecNorm(b_all,NORM_2,&nrm);
			// out<<" Norm of right hand side... "<<nrm<<endl;
			// #endif

			// /* Identify the starting and ending mesh points on each
			// processor for the interior part of the mesh. We let PETSc decide
			// above. */

			// // PetscInt rstart,rend;
			// // ierr = VecGetOwnershipRange(x_,&rstart,&rend);CHKERRCONTINUE(ierr);
			// ierr = VecGetLocalSize(x_,&nlocal);CHKERRCONTINUE(ierr);

			// /*
			// Create matrix. When using MatCreate(), the matrix format can
			// be specified at runtime.

			// Performance tuning note: For problems of substantial size,
			// preallocation of matrix memory is crucial for attaining good
			// performance. See the matrix chapter of the users manual for details.

			// We pass in nlocal as the "local" size of the matrix to force it
			// to have the same parallel layout as the vector created above.
			// */
			// if (!allocated_) {

			// ierr = MatCreate(PETSC_COMM_WORLD,&A_);CHKERRCONTINUE(ierr);
			// ierr = MatSetSizes(A_,nlocal,nlocal,n,n);CHKERRCONTINUE(ierr);
			// ierr = MatSetFromOptions(A_);CHKERRCONTINUE(ierr);
			// ierr = MatSetUp(A_);CHKERRCONTINUE(ierr);
			// } else {
			// // zero-out matrix
			// MatZeroEntries(A_);
			// }

			// /*
			// Assemble matrix.

			// The linear system is distributed across the processors by
			// chunks of contiguous rows, which correspond to contiguous
			// sections of the mesh on which the problem is discretized.
			// For matrix assembly, each processor contributes entries for
			// the part that it owns locally.
			// */

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Zeroed-out sparse matrix entries... "<<timer<<endl;
			// #endif

			// for (sparse_matrix_type::const_hash_iterator it = AA.map_.begin(); it !=
			// AA.map_.end(); ++it) {

			// // get subscripts
			// std::pair<size_t,size_t> subs = AA.unhash(it->first);
			// PetscInt row = subs.first;
			// PetscInt col = subs.second;
			// ierr = MatSetValues(A_, 1, &row, 1, &col, &it->second,
			// ADD_VALUES);CHKERRCONTINUE(ierr);
			// }

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Filled sparse matrix... "<<timer<<endl;
			// #endif

			// /* Assemble the matrix */
			// ierr = MatAssemblyBegin(A_,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
			// ierr = MatAssemblyEnd(A_,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);

			// if (!allocated_) {
			// // set after the first MatAssemblyEnd
			// // ierr = MatSetOption(A_, MAT_NEW_NONZERO_LOCATIONS,
			// PETSC_FALSE);CHKERRCONTINUE(ierr);
			// ierr = MatSetOption(A_, MAT_NEW_NONZERO_ALLOCATION_ERR,
			// PETSC_FALSE);CHKERRCONTINUE(ierr);
			// }

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Sparse matrix assembled... "<<timer<<endl;
			// // view matrix
			// MatView(A_, PETSC_VIEWER_STDOUT_WORLD);

			// MatNorm(A_,NORM_FROBENIUS,&nrm);
			// out<<" Norm of stiffness matrix... "<<nrm<<endl;
			// #endif

			// /*
			// Set operators. Here the matrix that defines the linear system
			// also serves as the preconditioning matrix.
			// */
			// // ierr =
			// KSPSetOperators(ksp,A_,A_,DIFFERENT_NONZERO_PATTERN);CHKERRCONTINUE(ierr);
			// ierr =
			// KSPSetOperators(ksp_,A_,A_,SAME_NONZERO_PATTERN);CHKERRCONTINUE(ierr);

			// //
			// // /*
			// // Set runtime options, e.g.,
			// // -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
			// // These options will override those specified above as long as
			// // KSPSetFromOptions() is called _after_ any other customization
			// // routines.
			// // */
			// // ierr = KSPSetFromOptions(ksp);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Solving system... "<<timer<<endl;
			// #endif

			// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
			// Solve the linear system
			// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
			// /*
			// Solve linear system
			// */
			// ierr = KSPSolve(ksp_,b,x_);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE

			// /*
			// View solver info; we could instead use the option -ksp_view to
			// print this info to the screen at the conclusion of KSPSolve().
			// */
			// ierr = KSPView(ksp_,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);

			// int iter;
			// KSPGetIterationNumber(ksp_, &iter);
			// out<<" System solved in "<<iter<<" iterations... "<<timer<<endl;
			// KSPConvergedReason reason;
			// ierr = KSPGetConvergedReason(ksp_,&reason);CHKERRCONTINUE(ierr);
			// if (reason < 0)
			// out<<"* WARNING * PETSc solver diverged with flag ";
			// else
			// out<<"* INFO * PETSc solver converged with flag ";

			// if (reason == KSP_CONVERGED_RTOL)
			// out<<"KSP_CONVERGED_RTOL"<<endl;
			// else if (reason == KSP_CONVERGED_ATOL)
			// out<<"KSP_CONVERGED_ATOL"<<endl;
			// else if (reason == KSP_CONVERGED_ITS)
			// out<<"KSP_CONVERGED_ITS"<<endl;
			// else if (reason == KSP_CONVERGED_CG_NEG_CURVE)
			// out<<"KSP_CONVERGED_CG_NEG_CURVE"<<endl;
			// else if (reason == KSP_CONVERGED_CG_CONSTRAINED)
			// out<<"KSP_CONVERGED_CG_CONSTRAINED"<<endl;
			// else if (reason == KSP_CONVERGED_STEP_LENGTH)
			// out<<"KSP_CONVERGED_STEP_LENGTH"<<endl;
			// else if (reason == KSP_CONVERGED_HAPPY_BREAKDOWN)
			// out<<"KSP_CONVERGED_HAPPY_BREAKDOWN"<<endl;
			// else if (reason == KSP_DIVERGED_NULL)
			// out<<"KSP_DIVERGED_NULL"<<endl;
			// else if (reason == KSP_DIVERGED_ITS)
			// out<<"KSP_DIVERGED_ITS"<<endl;
			// else if (reason == KSP_DIVERGED_DTOL)
			// out<<"KSP_DIVERGED_DTOL"<<endl;
			// else if (reason == KSP_DIVERGED_BREAKDOWN)
			// out<<"KSP_DIVERGED_BREAKDOWN"<<endl;
			// else if (reason == KSP_DIVERGED_BREAKDOWN_BICG)
			// out<<"KSP_DIVERGED_BREAKDOWN_BICG"<<endl;
			// else if (reason == KSP_DIVERGED_NONSYMMETRIC)
			// out<<"KSP_DIVERGED_NONSYMMETRIC"<<endl;
			// else if (reason == KSP_DIVERGED_INDEFINITE_PC)
			// out<<"KSP_DIVERGED_INDEFINITE_PC"<<endl;
			// else if (reason == KSP_DIVERGED_NAN)
			// out<<"KSP_DIVERGED_NAN"<<endl;
			// else if (reason == KSP_DIVERGED_INDEFINITE_MAT)
			// out<<"KSP_DIVERGED_INDEFINITE_MAT"<<endl;
			// else if (reason == KSP_CONVERGED_ITERATING)
			// out<<"KSP_CONVERGED_ITERATING"<<endl;

			// PetscReal rnorm;
			// ierr = KSPGetResidualNorm(ksp_,&rnorm);CHKERRCONTINUE(ierr);

			// out<<"PETSc last residual norm computed: "<<rnorm<<endl;

			// ierr = VecView(x_,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);

			// VecNorm(x_,NORM_2,&nrm);
			// out<<" Norm of solution vector... "<<nrm<<endl;

			// #endif

			// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
			// Check solution and clean up
			// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

			// Vec x_all;

			// ierr = VecScatterCreateToAll(x_, &ctx, &x_all);CHKERRCONTINUE(ierr);
			// ierr =
			// VecScatterBegin(ctx,x_,x_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
			// ierr =
			// VecScatterEnd(ctx,x_,x_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Solution vector scattered... "<<timer<<endl;
			// VecNorm(x_all,NORM_2,&nrm);
			// out<<" Norm of scattered vector... "<<nrm<<endl;
			// // ierr = VecView(x_all,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
			// #endif

			// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
			// Get values from solution and store them in the object that will be
			// returned
			// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

			// sparse_vector_type xx(bb.size());

			// /* Set solution vector */
			// double zero = 0.;
			// double val;
			// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
			// bb.map_.end(); ++it) {
			// int row = it->first;
			// ierr = VecGetValues(x_all, 1, &row, &val);
			// if (val != zero)
			// xx[row] = val;
			// }

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Solution vector copied... "<<timer<<endl;
			// // out<<" Norm of copied solution vector... "<<norm(xx,
			// Insert_t)<<endl;
			// #endif

			// /*
			// Free work space. All PETSc objects should be destroyed when they
			// are no longer needed.
			// */
			// ierr = VecDestroy(&b);CHKERRCONTINUE(ierr);
			// // ierr = KSPDestroy(&ksp);CHKERRCONTINUE(ierr);

			// // set allocated flag
			// if (!allocated_) {
			// allocated_ = true;
			// }

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Temporary data structures destroyed... "<<timer<<endl;
			// #endif

			// return xx;
			// }

			// SolverPETSc::sparse_vector_type SolverPETSc::operator()(const
			// SolverPETSc::sparse_matrix_type& KKpf, const SolverPETSc::sparse_matrix_type&
			// KKpp, const SolverPETSc::sparse_vector_type& UUp) {

			// #ifdef CPPUTILS_VERBOSE
			// // parallel output stream
			// Output_stream out;
			// // timer
			// cpputils::ctimer timer;
			// out<<"Inside SolverPETSc::operator()(const sparse_matrix&, const
			// sparse_matrix&, const sparse_vector&). "<<timer<<endl;
			// #endif

			// Mat Kpf, Kpp;
			// Vec Up, Pf, Pp;

			// PetscErrorCode ierr =
			// MatCreate(PETSC_COMM_WORLD,&Kpf);CHKERRCONTINUE(ierr);
			// ierr = MatCreate(PETSC_COMM_WORLD,&Kpp);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Allocating memory... "<<timer<<endl;
			// #endif

			// ierr = MatSetFromOptions(Kpf);CHKERRCONTINUE(ierr);
			// ierr = MatSetFromOptions(Kpp);CHKERRCONTINUE(ierr);

			// ierr = MatSetSizes(Kpf,PETSC_DECIDE,PETSC_DECIDE, KKpf.rows(),
			// KKpf.columns());CHKERRCONTINUE(ierr);
			// ierr = MatSetSizes(Kpp,PETSC_DECIDE,PETSC_DECIDE, KKpp.rows(),
			// KKpp.columns());CHKERRCONTINUE(ierr);

			// // get number of non-zeros in both diagonal and non-diagonal portions of
			// the matrix

			// std::pair<size_t,size_t> Kpf_nz = KKpf.non_zero_off_diagonal();
			// std::pair<size_t,size_t> Kpp_nz = KKpp.non_zero_off_diagonal();

			// ierr = MatMPIAIJSetPreallocation(Kpf, Kpf_nz.first, PETSC_NULL,
			// Kpf_nz.second, PETSC_NULL); CHKERRCONTINUE(ierr);
			// ierr = MatMPIAIJSetPreallocation(Kpp, Kpp_nz.first, PETSC_NULL,
			// Kpp_nz.second, PETSC_NULL); CHKERRCONTINUE(ierr);
			// ierr = MatSeqAIJSetPreallocation(Kpf, Kpf_nz.first, PETSC_NULL);
			// CHKERRCONTINUE(ierr);
			// ierr = MatSeqAIJSetPreallocation(Kpp, Kpp_nz.first, PETSC_NULL);
			// CHKERRCONTINUE(ierr);

			// for (sparse_matrix_type::const_hash_iterator it = KKpf.map_.begin(); it !=
			// KKpf.map_.end(); ++it) {

			// // get subscripts
			// std::pair<size_t,size_t> subs = KKpf.unhash(it->first);
			// int row = subs.first;
			// int col = subs.second;
			// ierr = MatSetValues(Kpf, 1, &row, 1, &col, &it->second,
			// ADD_VALUES);CHKERRCONTINUE(ierr);
			// }

			// for (sparse_matrix_type::const_hash_iterator it = KKpp.map_.begin(); it !=
			// KKpp.map_.end(); ++it) {

			// // get subscripts
			// std::pair<size_t,size_t> subs = KKpp.unhash(it->first);
			// int row = subs.first;
			// int col = subs.second;
			// ierr = MatSetValues(Kpf, 1, &row, 1, &col, &it->second,
			// ADD_VALUES);CHKERRCONTINUE(ierr);
			// }

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Filled sparse matrices... "<<timer<<endl;
			// #endif

			// /*
			// Assemble matrix, using the 2-step process:
			// MatAssemblyBegin(), MatAssemblyEnd()
			// Computations can be done while messages are in transition
			// by placing code between these two statements.
			// */
			// ierr = MatAssemblyBegin(Kpf,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
			// ierr = MatAssemblyBegin(Kpp,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
			// ierr = MatAssemblyEnd(Kpf,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
			// ierr = MatAssemblyEnd(Kpp,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Sparse matrices assembled... "<<timer<<endl;
			// #endif

			// ierr = VecCreate(PETSC_COMM_WORLD,&Up);CHKERRCONTINUE(ierr);
			// ierr = VecSetSizes(Up,PETSC_DECIDE, UUp.size());CHKERRCONTINUE(ierr);
			// ierr = VecSetFromOptions(Up);CHKERRCONTINUE(ierr);

			// ierr = VecCreate(PETSC_COMM_WORLD,&Pf);CHKERRCONTINUE(ierr);
			// ierr = VecSetSizes(Pf,PETSC_DECIDE, KKpf.rows());CHKERRCONTINUE(ierr);
			// ierr = VecSetFromOptions(Pf);CHKERRCONTINUE(ierr);
			// ierr = VecDuplicate(Pf,&Pp);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Vectors created... "<<timer<<endl;
			// #endif

			// /* Set hight-hand-side vector */
			// for (sparse_vector_type::const_hash_iterator it = UUp.map_.begin(); it !=
			// UUp.map_.end(); ++it) {
			// int row = it->first;
			// ierr = VecSetValues(Up, 1, &row, &it->second, ADD_VALUES);
			// }

			// /*
			// Assemble vector, using the 2-step process:
			// VecAssemblyBegin(), VecAssemblyEnd()
			// Computations can be done while messages are in transition
			// by placing code between these two statements.
			// */
			// ierr = VecAssemblyBegin(Up);CHKERRCONTINUE(ierr);
			// ierr = VecAssemblyEnd(Up);CHKERRCONTINUE(ierr);

			// // add Kpf*Uf
			// ierr = MatMult(Kpf, x_, Pf);

			// // add Kpp*Up
			// ierr = MatMultAdd(Kpp, Up, Pf, Pp);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Matrices multiplied... "<<timer<<endl;
			// #endif

			// VecScatter ctx;
			// Vec Pp_all;

			// ierr = VecScatterCreateToAll(Pp, &ctx, &Pp_all);CHKERRCONTINUE(ierr);
			// ierr =
			// VecScatterBegin(ctx,Pp,Pp_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
			// ierr =
			// VecScatterEnd(ctx,Pp,Pp_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Vector scattered... "<<timer<<endl;
			// #endif

			// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
			// Get values from solution and store them in the object that will be
			// returned
			// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

			// sparse_vector_type pp(KKpf.rows());

			// // get reaction vector
			// for (int i=0; i<KKpf.rows(); ++i) {

			// PetscScalar v;
			// ierr = VecGetValues(Pp_all, 1, &i, &v);
			// if (v != PetscScalar())
			// pp[i] = v;
			// }

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Vector copied... "<<timer<<endl;
			// #endif

			// ierr = MatDestroy(&Kpf);CHKERRCONTINUE(ierr);
			// ierr = MatDestroy(&Kpp);CHKERRCONTINUE(ierr);
			// ierr = VecDestroy(&Up);CHKERRCONTINUE(ierr);
			// ierr = VecDestroy(&Pf);CHKERRCONTINUE(ierr);
			// ierr = VecDestroy(&Pp);CHKERRCONTINUE(ierr);
			// ierr = VecDestroy(&Pp_all);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Temporary data structures destroyed... "<<timer<<endl;
			// #endif

			// return pp;
			// }

			// SolverPETSc::sparse_vector_type SolverPETSc::operator()(const
			// SolverPETSc::sparse_vector_type& aa, const SolverPETSc::sparse_vector_type&
			// bb) {

			// assert(aa.size() == bb.size());

			// #ifdef CPPUTILS_VERBOSE
			// // parallel output stream
			// Output_stream out;
			// // timer
			// cpputils::ctimer timer;
			// out<<"Inside SolverPETSc::operator()(const sparse_vector&, const
			// sparse_vector&). "<<timer<<endl;
			// #endif

			// Vec r;

			// PetscErrorCode ierr = VecCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
			// ierr = VecSetSizes(r,PETSC_DECIDE, aa.size());CHKERRCONTINUE(ierr);
			// ierr = VecSetFromOptions(r);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Vectors created... "<<timer<<endl;
			// #endif

			// // set values
			// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
			// aa.map_.end(); ++it) {
			// int row = it->first;
			// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
			// }
			// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
			// bb.map_.end(); ++it) {
			// int row = it->first;
			// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
			// }

			// /*
			// Assemble vector, using the 2-step process:
			// VecAssemblyBegin(), VecAssemblyEnd()
			// Computations can be done while messages are in transition
			// by placing code between these two statements.
			// */
			// ierr = VecAssemblyBegin(r);CHKERRCONTINUE(ierr);
			// ierr = VecAssemblyEnd(r);CHKERRCONTINUE(ierr);

			// sparse_vector_type rr(aa.size());

			// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
			// aa.map_.end(); ++it) {
			// int row = it->first;
			// ierr = VecGetValues(r, 1, &row, &rr[row]);
			// }
			// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
			// bb.map_.end(); ++it) {
			// int row = it->first;
			// ierr = VecGetValues(r, 1, &row, &rr[row]);
			// }

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Vector copied... "<<timer<<endl;
			// #endif

			// ierr = VecDestroy(&r);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Temporary data structures destroyed... "<<timer<<endl;
			// #endif

			// return rr;
			// }

			// SolverPETSc::value_type SolverPETSc::norm(const
			// SolverPETSc::sparse_matrix_type& aa, Element_insertion_type flag) {

			// #ifdef CPPUTILS_VERBOSE
			// // parallel output stream
			// Output_stream out;
			// // timer
			// cpputils::ctimer timer;
			// out<<"Inside SolverPETSc::norm(const sparse_matrix&). "<<timer<<endl;
			// #endif

			// Mat r;

			// PetscErrorCode ierr = MatCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
			// ierr = MatSetSizes(r,PETSC_DECIDE,PETSC_DECIDE, aa.rows(),
			// aa.columns());CHKERRCONTINUE(ierr);
			// ierr = MatSetFromOptions(r);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Matrix created... "<<timer<<endl;
			// #endif

			// // set values
			// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
			// aa.map_.end(); ++it) {
			// // get subscripts
			// std::pair<size_t,size_t> subs = aa.unhash(it->first);
			// int row = subs.first;
			// int col = subs.second;

			// if (flag == Add_t)
			// ierr = MatSetValues(r, 1, &row, 1, &col, &it->second, ADD_VALUES);
			// else if (flag == Insert_t)
			// ierr = MatSetValues(r, 1, &row, 1, &col, &it->second, INSERT_VALUES);
			// CHKERRCONTINUE(ierr);
			// }

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Matrix filled..."<<timer<<endl;
			// #endif

			// /*
			// Assemble vector, using the 2-step process:
			// VecAssemblyBegin(), VecAssemblyEnd()
			// Computations can be done while messages are in transition
			// by placing code between these two statements.
			// */
			// ierr = MatAssemblyBegin(r,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
			// ierr = MatAssemblyEnd(r,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);

			// value_type nrm;

			// MatNorm(r,NORM_FROBENIUS,&nrm);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Norm computed... "<<timer<<endl;
			// #endif

			// ierr = MatDestroy(&r);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Temporary data structures destroyed... "<<timer<<endl;
			// #endif

			// return nrm;
			// }

			// SolverPETSc::value_type SolverPETSc::norm(const
			// SolverPETSc::sparse_vector_type& aa, Element_insertion_type flag) {

			// #ifdef CPPUTILS_VERBOSE
			// // parallel output stream
			// Output_stream out;
			// // timer
			// cpputils::ctimer timer;
			// out<<"Inside SolverPETSc::norm(const sparse_vector&). "<<timer<<endl;
			// #endif

			// Vec r;

			// PetscErrorCode ierr = VecCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
			// ierr = VecSetSizes(r,PETSC_DECIDE, aa.size());CHKERRCONTINUE(ierr);
			// ierr = VecSetFromOptions(r);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Vector created... "<<timer<<endl;
			// #endif

			// // set values
			// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
			// aa.map_.end(); ++it) {
			// int row = it->first;
			// if (flag == Add_t)
			// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
			// else if (flag == Insert_t)
			// ierr = VecSetValues(r, 1, &row, &it->second, INSERT_VALUES);
			// CHKERRCONTINUE(ierr);
			// }

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Vector filled..."<<timer<<endl;
			// #endif

			// /*
			// Assemble vector, using the 2-step process:
			// VecAssemblyBegin(), VecAssemblyEnd()
			// Computations can be done while messages are in transition
			// by placing code between these two statements.
			// */
			// ierr = VecAssemblyBegin(r);CHKERRCONTINUE(ierr);
			// ierr = VecAssemblyEnd(r);CHKERRCONTINUE(ierr);

			// value_type nrm;

			// VecNorm(r,NORM_2,&nrm);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Norm computed... "<<timer<<endl;
			// #endif

			// ierr = VecDestroy(&r);CHKERRCONTINUE(ierr);

			// #ifdef CPPUTILS_VERBOSE
			// out<<" Temporary data structures destroyed... "<<timer<<endl;
			// #endif

			// return nrm;

			// }

			// //
			// ///*
			// -------------------------------------------------------------------------- */
			// //SolverMumps::SolverMumps(SparseMatrix & matrix,
			// // const ID & id,
			// // const MemoryID & memory_id) :
			// //Solver(matrix, id, memory_id), is_mumps_data_initialized(false),
			// rhs_is_local(true) {
			// // AKANTU_DEBUG_IN();
			// //
			// //#ifdef AKANTU_USE_MPI
			// // parallel_method = SolverMumpsOptions::_fully_distributed;
			// //#else //AKANTU_USE_MPI
			// // parallel_method = SolverMumpsOptions::_master_slave_distributed;
			// //#endif //AKANTU_USE_MPI
			// //
			// // CommunicatorEventHandler & comm_event_handler = *this;
			// //
			// // communicator.registerEventHandler(comm_event_handler);
			// //
			// // AKANTU_DEBUG_OUT();
			// //}
			// //
			// ///*
			// -------------------------------------------------------------------------- */
			// //SolverMumps::~SolverMumps() {
			// // AKANTU_DEBUG_IN();
			// //
			// // AKANTU_DEBUG_OUT();
			// //}
			// //
			// ///*
			// -------------------------------------------------------------------------- */
			// //void SolverMumps::destroyMumpsData() {
			// // AKANTU_DEBUG_IN();
			// //
			// // if(is_mumps_data_initialized) {
			// // mumps_data.job = _smj_destroy; // destroy
			// // dmumps_c(&mumps_data);
			// // is_mumps_data_initialized = false;
			// // }
			// //
			// // AKANTU_DEBUG_OUT();
			// //}
			// //
			// ///*
			// -------------------------------------------------------------------------- */
			// //void SolverMumps::onCommunicatorFinalize(const StaticCommunicator & comm) {
			// // AKANTU_DEBUG_IN();
			// //
			// // try{
			// // const StaticCommunicatorMPI & comm_mpi =
			// // dynamic_cast<const StaticCommunicatorMPI
			// &>(comm.getRealStaticCommunicator());
			// // if(mumps_data.comm_fortran ==
			// MPI_Comm_c2f(comm_mpi.getMPICommunicator()))
			// // destroyMumpsData();
			// // } catch(...) {}
			// //
			// // AKANTU_DEBUG_OUT();
			// //}
			// //
			// ///*
			// -------------------------------------------------------------------------- */
			// //void SolverMumps::initMumpsData(SolverMumpsOptions::ParallelMethod
			// parallel_method) {
			// // switch(parallel_method) {
			// // case SolverMumpsOptions::_fully_distributed:
			// // icntl(18) = 3; //fully distributed
			// // icntl(28) = 0; //automatic choice
			// //
			// // mumps_data.nz_loc = matrix->getNbNonZero();
			// // mumps_data.irn_loc = matrix->getIRN().values;
			// // mumps_data.jcn_loc = matrix->getJCN().values;
			// // break;
			// // case SolverMumpsOptions::_master_slave_distributed:
			// // if(prank == 0) {
			// // mumps_data.nz = matrix->getNbNonZero();
			// // mumps_data.irn = matrix->getIRN().values;
			// // mumps_data.jcn = matrix->getJCN().values;
			// // } else {
			// // mumps_data.nz = 0;
			// // mumps_data.irn = NULL;
			// // mumps_data.jcn = NULL;
			// //
			// // icntl(18) = 0; //centralized
			// // icntl(28) = 0; //sequential analysis
			// // }
			// // break;
			// // }
			// //}
			// //
			// ///*
			// -------------------------------------------------------------------------- */
			// //void SolverMumps::initialize(SolverOptions & options) {
			// // AKANTU_DEBUG_IN();
			// //
			// // mumps_data.par = 1;
			// //
			// // if(SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions
			// *>(&options)) {
			// // if(opt->parallel_method ==
			// SolverMumpsOptions::_master_slave_distributed) {
			// // mumps_data.par = 0;
			// // }
			// // }
			// //
			// // mumps_data.sym = 2 * (matrix->getSparseMatrixType() == _symmetric);
			// // prank = communicator.whoAmI();
			// //#ifdef AKANTU_USE_MPI
			// // mumps_data.comm_fortran = MPI_Comm_c2f(dynamic_cast<const
			// StaticCommunicatorMPI
			// &>(communicator.getRealStaticCommunicator()).getMPICommunicator());
			// //#endif
			// //
			// // if(AKANTU_DEBUG_TEST(dblTrace)) {
			// // icntl(1) = 2;
			// // icntl(2) = 2;
			// // icntl(3) = 2;
			// // icntl(4) = 4;
			// // }
			// //
			// // mumps_data.job = _smj_initialize; //initialize
			// // dmumps_c(&mumps_data);
			// // is_mumps_data_initialized = true;
			// //
			// // /*
			// ------------------------------------------------------------------------ */
			// // UInt size = matrix->size();
			// //
			// // if(prank == 0) {
			// // std::stringstream sstr_rhs; sstr_rhs << id << ":rhs";
			// // rhs = &(alloc<Real>(sstr_rhs.str(), size, 1, REAL_INIT_VALUE));
			// // } else {
			// // rhs = NULL;
			// // }
			// //
			// // /// No outputs
			// // icntl(1) = 0;
			// // icntl(2) = 0;
			// // icntl(3) = 0;
			// // icntl(4) = 0;
			// // mumps_data.nz_alloc = 0;
			// //
			// // if (AKANTU_DEBUG_TEST(dblDump)) icntl(4) = 4;
			// //
			// // mumps_data.n = size;
			// //
			// // if(AKANTU_DEBUG_TEST(dblDump)) {
			// // strcpy(mumps_data.write_problem, "mumps_matrix.mtx");
			// // }
			// //
			// // /*
			// ------------------------------------------------------------------------ */
			// // // Default Scaling
			// // icntl(8) = 77;
			// //
			// // icntl(5) = 0; // Assembled matrix
			// //
			// // SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions *>(&options);
			// // if(opt)
			// // parallel_method = opt->parallel_method;
			// //
			// // initMumpsData(parallel_method);
			// //
			// // mumps_data.job = _smj_analyze; //analyze
			// // dmumps_c(&mumps_data);
			// //
			// // AKANTU_DEBUG_OUT();
			// //}
			// //
			// ///*
			// -------------------------------------------------------------------------- */
			// //void SolverMumps::setRHS(Array<Real> & rhs) {
			// // if(prank == 0) {
			// // matrix->getDOFSynchronizer().gather(rhs, 0, this->rhs);
			// // } else {
			// // matrix->getDOFSynchronizer().gather(rhs, 0);
			// // }
			// //}
			// //
			// ///*
			// -------------------------------------------------------------------------- */
			// //void SolverMumps::solve() {
			// // AKANTU_DEBUG_IN();
			// //
			// // if(parallel_method == SolverMumpsOptions::_fully_distributed)
			// // mumps_data.a_loc = matrix->getA().values;
			// // else
			// // if(prank == 0) {
			// // mumps_data.a = matrix->getA().values;
			// // }
			// //
			// // if(prank == 0) {
			// // mumps_data.rhs = rhs->values;
			// // }
			// //
			// // /// Default centralized dense second member
			// // icntl(20) = 0;
			// // icntl(21) = 0;
			// //
			// // mumps_data.job = _smj_factorize_solve; //solve
			// // dmumps_c(&mumps_data);
			// //
			// // AKANTU_DEBUG_ASSERT(info(1) != -10, "Singular matrix");
			// // AKANTU_DEBUG_ASSERT(info(1) == 0,
			// // "Error in mumps during solve process, check mumps
			// user guide INFO(1) ="
			// // << info(1));
			// //
			// // AKANTU_DEBUG_OUT();
			// //}
			// //
			// ///*
			// -------------------------------------------------------------------------- */
			// //void SolverMumps::solve(Array<Real> & solution) {
			// // AKANTU_DEBUG_IN();
			// //
			// // solve();
			// //
			// // if(prank == 0) {
			// // matrix->getDOFSynchronizer().scatter(solution, 0, this->rhs);
			// // } else {
			// // matrix->getDOFSynchronizer().scatter(solution, 0);
			// // }
			// //
			// // AKANTU_DEBUG_OUT();
			// //}

			} // akantu

rAKA/src/solver/solver_petsc.cc1fcfbf02b9bdbugfixes/41-group-not…

solver_petsc.ccView Options

rAKA/src/solver/solver_petsc.cc
1fcfbf02b9bdbugfixes/41-group-not…

solver_petsc.cc
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