void linearSystemPETSc<scalar>::allocate(int nbRows)
{
int commSize;
MPI_Comm_size(_comm, &commSize);
int blockSize = _getBlockSizeFromParameters();
clear();
_try(MatCreate(_comm, &_a));
_try(MatSetSizes(_a, blockSize * nbRows, blockSize * nbRows, PETSC_DETERMINE, PETSC_DETERMINE));
if (blockSize > 1) {
if (commSize > 1) {
_try(MatSetType(_a, MATMPIBAIJ));
}
else {
_try(MatSetType(_a, MATSEQBAIJ));
}
}
// override the default options with the ones from the option
// database (if any)
if (this->_parameters.count("petscOptions"))
_try(PetscOptionsInsertString(this->_parameters["petscOptions"].c_str()));
if (this->_parameters.count("petscPrefix"))
_try(MatAppendOptionsPrefix(_a, this->_parameters["petscPrefix"].c_str()));
_try(MatSetFromOptions(_a));
//since PETSc 3.3 GetOwnershipRange and MatGetSize cannot be called before MatXXXSetPreallocation
_localSize = nbRows;
#ifdef HAVE_MPI
if (commSize>1){
_localRowStart = 0;
if (Msg::GetCommRank() != 0) {
MPI_Status status;
MPI_Recv((void*)&_localRowStart, 1, MPI_INT, Msg::GetCommRank() - 1, 1, MPI_COMM_WORLD, &status);
}
_localRowEnd = _localRowStart + nbRows;
if (Msg::GetCommRank() != Msg::GetCommSize() - 1) {
MPI_Send((void*)&_localRowEnd, 1, MPI_INT, Msg::GetCommRank() + 1, 1, MPI_COMM_WORLD);
}
MPI_Allreduce((void*)&_localSize, (void*)&_globalSize, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
}
else{
_localRowStart = 0;
_localRowEnd = nbRows;
_globalSize = _localSize;
}
#else
_localRowStart = 0;
_localRowEnd = nbRows;
_globalSize = _localSize;
#endif
// preallocation option must be set after other options
_try(VecCreate(_comm, &_x));
_try(VecSetSizes(_x, blockSize * nbRows, PETSC_DETERMINE));
// override the default options with the ones from the option
// database (if any)
if (this->_parameters.count("petscPrefix"))
_try(VecAppendOptionsPrefix(_x, this->_parameters["petscPrefix"].c_str()));
_try(VecSetFromOptions(_x));
_try(VecDuplicate(_x, &_b));
_isAllocated = true;
_entriesPreAllocated = false;
}
PetscErrorCode MatSetLocalToGlobalMapping_IS(Mat A,ISLocalToGlobalMapping rmapping,ISLocalToGlobalMapping cmapping)
{
PetscErrorCode ierr;
PetscInt n,bs;
Mat_IS *is = (Mat_IS*)A->data;
IS from,to;
Vec global;
PetscFunctionBegin;
PetscCheckSameComm(A,1,rmapping,2);
if (rmapping != cmapping) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_INCOMP,"MATIS requires the row and column mappings to be identical");
if (is->mapping) { /* Currenly destroys the objects that will be created by this routine. Is there anything else that should be checked? */
ierr = ISLocalToGlobalMappingDestroy(&is->mapping);CHKERRQ(ierr);
ierr = VecDestroy(&is->x);CHKERRQ(ierr);
ierr = VecDestroy(&is->y);CHKERRQ(ierr);
ierr = VecScatterDestroy(&is->ctx);CHKERRQ(ierr);
ierr = MatDestroy(&is->A);CHKERRQ(ierr);
}
ierr = PetscObjectReference((PetscObject)rmapping);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingDestroy(&is->mapping);CHKERRQ(ierr);
is->mapping = rmapping;
/*
ierr = PetscLayoutSetISLocalToGlobalMapping(A->rmap,rmapping);CHKERRQ(ierr);
ierr = PetscLayoutSetISLocalToGlobalMapping(A->cmap,cmapping);CHKERRQ(ierr);
*/
/* Create the local matrix A */
ierr = ISLocalToGlobalMappingGetSize(rmapping,&n);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetBlockSize(rmapping,&bs);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&is->A);CHKERRQ(ierr);
if (bs > 1) {
ierr = MatSetType(is->A,MATSEQBAIJ);CHKERRQ(ierr);
} else {
ierr = MatSetType(is->A,MATSEQAIJ);CHKERRQ(ierr);
}
ierr = MatSetSizes(is->A,n,n,n,n);CHKERRQ(ierr);
ierr = MatSetBlockSize(is->A,bs);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(is->A,((PetscObject)A)->prefix);CHKERRQ(ierr);
ierr = MatAppendOptionsPrefix(is->A,"is_");CHKERRQ(ierr);
ierr = MatSetFromOptions(is->A);CHKERRQ(ierr);
/* Create the local work vectors */
ierr = VecCreate(PETSC_COMM_SELF,&is->x);CHKERRQ(ierr);
ierr = VecSetBlockSize(is->x,bs);CHKERRQ(ierr);
ierr = VecSetSizes(is->x,n,n);CHKERRQ(ierr);
ierr = VecSetOptionsPrefix(is->x,((PetscObject)A)->prefix);CHKERRQ(ierr);
ierr = VecAppendOptionsPrefix(is->x,"is_");CHKERRQ(ierr);
ierr = VecSetFromOptions(is->x);CHKERRQ(ierr);
ierr = VecDuplicate(is->x,&is->y);CHKERRQ(ierr);
/* setup the global to local scatter */
ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&to);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApplyIS(rmapping,to,&from);CHKERRQ(ierr);
ierr = MatCreateVecs(A,&global,NULL);CHKERRQ(ierr);
ierr = VecScatterCreate(global,from,is->x,to,&is->ctx);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = ISDestroy(&to);CHKERRQ(ierr);
ierr = ISDestroy(&from);CHKERRQ(ierr);
PetscFunctionReturn(0);
}