Homec4science
Diffusion akantu (bugfixes/41-group-not-properly-updated-when-cohesive-elements-are-inserted) Browse

rAKA/src/model/dof_manager_petsc.cc
b8a8a46e2135bugfixes/41-group-not…

Last Change
Raw File

dof_manager_petsc.cc
View Options

/**
* @file dof_manager_petsc.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 07 2015
* @date last modification: Tue Feb 20 2018
*
* @brief DOFManaterPETSc is the PETSc implementation of the DOFManager
*
* @section LICENSE
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_petsc.hh"
#include "cppargparse.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_type_wrapper.hh"
#include "static_communicator.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <petscsys.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
#if not defined(PETSC_CLANGUAGE_CXX)
/// small hack to use the c binding of petsc when the cxx binding does notation
/// exists
int aka_PETScError(int ierr) {
CHKERRQ(ierr);
return 0;
}
#endif
UInt DOFManagerPETSc::petsc_dof_manager_instances = 0;
/// Error handler to make PETSc errors caught by Akantu
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
static PetscErrorCode PETScErrorHandler(MPI_Comm, int line, const char * dir,
const char * file,
PetscErrorCode number,
PetscErrorType type,
const char * message, void *) {
AKANTU_ERROR("An error occured in PETSc in file \""
<< file << ":" << line << "\" - PetscErrorCode " << number
<< " - \"" << message << "\"");
}
#else
static PetscErrorCode PETScErrorHandler(MPI_Comm, int line, const char * func,
const char * dir, const char * file,
PetscErrorCode number,
PetscErrorType type,
const char * message, void *) {
AKANTU_ERROR("An error occured in PETSc in file \""
<< file << ":" << line << "\" - PetscErrorCode " << number
<< " - \"" << message << "\"");
}
#endif
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFManagerPETSc(const ID & id, const MemoryID & memory_id)
: DOFManager(id, memory_id) {
// check if the akantu types and PETSc one are consistant
#if __cplusplus > 199711L
static_assert(sizeof(Int) == sizeof(PetscInt),
"The integer type of Akantu does not match the one from PETSc");
static_assert(sizeof(Real) == sizeof(PetscReal),
"The integer type of Akantu does not match the one from PETSc");
#else
AKANTU_DEBUG_ASSERT(
sizeof(Int) == sizeof(PetscInt),
"The integer type of Akantu does not match the one from PETSc");
AKANTU_DEBUG_ASSERT(
sizeof(Real) == sizeof(PetscReal),
"The integer type of Akantu does not match the one from PETSc");
#endif
if (this->petsc_dof_manager_instances == 0) {
#if defined(AKANTU_USE_MPI)
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
const StaticCommunicatorMPI & mpi_st_comm =
dynamic_cast<const StaticCommunicatorMPI &>(
comm.getRealStaticCommunicator());
this->mpi_communicator =
mpi_st_comm.getMPITypeWrapper().getMPICommunicator();
#else
this->mpi_communicator = PETSC_COMM_SELF;
#endif
cppargparse::ArgumentParser & argparser = getStaticArgumentParser();
int & argc = argparser.getArgC();
char **& argv = argparser.getArgV();
PetscErrorCode petsc_error = PetscInitialize(&argc, &argv, NULL, NULL);
if (petsc_error != 0) {
AKANTU_ERROR("An error occured while initializing Petsc (PetscErrorCode "
<< petsc_error << ")");
}
PetscPushErrorHandler(PETScErrorHandler, NULL);
this->petsc_dof_manager_instances++;
}
VecCreate(PETSC_COMM_WORLD, &this->residual);
VecCreate(PETSC_COMM_WORLD, &this->solution);
}
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::~DOFManagerPETSc() {
PetscErrorCode ierr;
ierr = VecDestroy(&(this->residual));
CHKERRXX(ierr);
ierr = VecDestroy(&(this->solution));
CHKERRXX(ierr);
this->petsc_dof_manager_instances--;
if (this->petsc_dof_manager_instances == 0) {
PetscFinalize();
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
DOFSupportType & support_type) {
DOFManager::registerDOFs(dof_id, dofs_array, support_type);
PetscErrorCode ierr;
PetscInt current_size;
ierr = VecGetSize(this->residual, &current_size);
CHKERRXX(ierr);
if (current_size == 0) { // first time vector is set
PetscInt local_size = this->pure_local_system_size;
ierr = VecSetSizes(this->residual, local_size, PETSC_DECIDE);
CHKERRXX(ierr);
ierr = VecSetFromOptions(this->residual);
CHKERRXX(ierr);
#ifndef AKANTU_NDEBUG
PetscInt global_size;
ierr = VecGetSize(this->residual, &global_size);
CHKERRXX(ierr);
AKANTU_DEBUG_ASSERT(this->system_size == UInt(global_size),
"The local value of the system size does not match the "
"one determined by PETSc");
#endif
PetscInt start_dof, end_dof;
VecGetOwnershipRange(this->residual, &start_dof, &end_dof);
PetscInt * global_indices = new PetscInt[local_size];
global_indices[0] = start_dof;
for (PetscInt d = 0; d < local_size; d++)
global_indices[d + 1] = global_indices[d] + 1;
// To be change if we switch to a block definition
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
ISLocalToGlobalMappingCreate(this->communicator, 1, local_size,
global_indices, PETSC_COPY_VALUES,
&this->is_ltog);
#else
ISLocalToGlobalMappingCreate(this->communicator, local_size, global_indices,
PETSC_COPY_VALUES, &this->is_ltog);
#endif
VecSetLocalToGlobalMapping(this->residual, this->is_ltog);
delete[] global_indices;
ierr = VecDuplicate(this->residual, &this->solution);
CHKERRXX(ierr);
} else { // this is an update of the object already created
AKANTU_TO_IMPLEMENT();
}
/// set the solution to zero
// ierr = VecZeroEntries(this->solution);
// CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
/**
* This function creates the non-zero pattern of the PETSc matrix. In
* PETSc the parallel matrix is partitioned across processors such
* that the first m0 rows belong to process 0, the next m1 rows belong
* to process 1, the next m2 rows belong to process 2 etc.. where
* m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores
* values corresponding to [m x N] submatrix
* (http://www.mcs.anl.gov/petsc/).
* @param mesh mesh discretizing the domain we want to analyze
* @param dof_synchronizer dof synchronizer that maps the local
* dofs to the global dofs and the equation numbers, i.e., the
* position at which the dof is assembled in the matrix
*/
// void SparseMatrixPETSc::buildProfile(const Mesh & mesh,
// const DOFSynchronizer &
// dof_synchronizer,
// UInt nb_degree_of_freedom) {
// AKANTU_DEBUG_IN();
// // clearProfile();
// this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
// this->setSize();
// 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);
// // if(irn_jcn_to_k) delete irn_jcn_to_k;
// // irn_jcn_to_k = new std::map<std::pair<UInt, UInt>, UInt>;
// coordinate_list_map::iterator irn_jcn_k_it;
// Int * eq_nb_val = dof_synchronizer.getGlobalDOFEquationNumbers().storage();
// UInt nb_global_dofs = dof_synchronizer.getNbGlobalDOFs();
// Array<Int> index_pair(2);
// /// 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;
// 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, ghost_type);
// 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, ghost_type).storage();
// 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_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) {
// /**
// * !!!!!!Careful!!!!!! This is a ugly fix. @todo this is a
// * very ugly fix, because the offset for the global
// * equation number, where the dof will be assembled, is
// * hardcoded. In the future a class dof manager has to be
// * added to Akantu to handle the mapping between the dofs
// * and the equation numbers
// *
// */
// *tmp_local_eq_nb_val++ =
// eq_nb_val[n * nb_degree_of_freedom + d] -
// (dof_synchronizer.isPureGhostDOF(n * nb_degree_of_freedom +
// d)
// ? nb_global_dofs
// : 0);
// }
// }
// for (UInt i = 0; i < size_mat; ++i) {
// Int c_irn = local_eq_nb_val[i];
// UInt j_start = 0;
// for (UInt j = j_start; j < size_mat; ++j) {
// Int c_jcn = local_eq_nb_val[j];
// index_pair(0) = c_irn;
// index_pair(1) = c_jcn;
// AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, 2,
// index_pair.storage());
// if (index_pair(0) >= first_global_index &&
// index_pair(0) < first_global_index + this->local_size) {
// KeyCOO irn_jcn = keyPETSc(c_irn, c_jcn);
// 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;
// // check if node is slave node
// if (index_pair(1) >= first_global_index &&
// index_pair(1) < first_global_index + this->local_size)
// this->d_nnz(index_pair(0) - first_global_index) += 1;
// else
// this->o_nnz(index_pair(0) - first_global_index) += 1;
// nb_non_zero++;
// }
// }
// }
// }
// conn_val += nb_nodes_per_element;
// }
// 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++;
// // }
// // }
// // }
// // 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_matrix_wrapper->mat, &type);
// /// std::cout << "the matrix type is: " << type << std::endl;
// /**
// * PETSc will use only one of the following preallocation commands
// * depending on the matrix type and ignore the rest. Note that for
// * the block matrix format a block size of 1 is used. This might
// * result in bad performance. @todo For better results implement
// * buildProfile() with larger block size.
// *
// */
// /// build profile:
// if (strcmp(type, MATSEQAIJ) == 0) {
// ierr = MatSeqAIJSetPreallocation(this->petsc_matrix_wrapper->mat, 0,
// d_nnz.storage());
// CHKERRXX(ierr);
// } else if ((strcmp(type, MATMPIAIJ) == 0)) {
// ierr = MatMPIAIJSetPreallocation(this->petsc_matrix_wrapper->mat, 0,
// d_nnz.storage(), 0, o_nnz.storage());
// CHKERRXX(ierr);
// } else {
// AKANTU_ERROR("The type " << type
// << " of PETSc matrix is not handled by"
// << " akantu in the preallocation step");
// }
// // ierr = MatSeqSBAIJSetPreallocation(this->petsc_matrix_wrapper->mat, 1,
// // 0, d_nnz.storage()); CHKERRXX(ierr);
// if (this->sparse_matrix_type == _symmetric) {
// /// set flag for symmetry to enable ICC/Cholesky preconditioner
// ierr = MatSetOption(this->petsc_matrix_wrapper->mat, MAT_SYMMETRIC,
// PETSC_TRUE);
// CHKERRXX(ierr);
// /// set flag for symmetric positive definite
// ierr = MatSetOption(this->petsc_matrix_wrapper->mat, MAT_SPD,
// PETSC_TRUE);
// CHKERRXX(ierr);
// }
// /// once the profile has been build ignore any new nonzero locations
// ierr = MatSetOption(this->petsc_matrix_wrapper->mat,
// MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE);
// CHKERRXX(ierr);
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
} // akantu
c4science · Help