//-----------------------------------------------------------------------------
void AssemblerBase::check(const Form& a)
{
dolfin_assert(a.ufc_form());
// Check the form
a.check();
// Extract mesh and coefficients
const Mesh& mesh = a.mesh();
const std::vector<std::shared_ptr<const GenericFunction>>
coefficients = a.coefficients();
// Check that we get the correct number of coefficients
if (coefficients.size() != a.num_coefficients())
{
dolfin_error("AssemblerBase.cpp",
"assemble form",
"Incorrect number of coefficients (got %d but expecting %d)",
coefficients.size(), a.num_coefficients());
}
// Check that all coefficients have valid value dimensions
for (std::size_t i = 0; i < coefficients.size(); ++i)
{
if (!coefficients[i])
{
dolfin_error("AssemblerBase.cpp",
"assemble form",
"Coefficient number %d (\"%s\") has not been set",
i, a.coefficient_name(i).c_str());
}
// unique_ptr deletes its object when it exits its scope
std::unique_ptr<ufc::finite_element>
fe(a.ufc_form()->create_finite_element(i + a.rank()));
// Checks out-commented since they only work for Functions, not
// Expressions
const std::size_t r = coefficients[i]->value_rank();
const std::size_t fe_r = fe->value_rank();
if (fe_r != r)
{
dolfin_error("AssemblerBase.cpp",
"assemble form",
"Invalid value rank for coefficient %d (got %d but expecting %d). \
You might have forgotten to specify the value rank correctly in an Expression subclass", i, r, fe_r);
}
for (std::size_t j = 0; j < r; ++j)
{
const std::size_t dim = coefficients[i]->value_dimension(j);
const std::size_t fe_dim = fe->value_dimension(j);
if (dim != fe_dim)
{
dolfin_error("AssemblerBase.cpp",
"assemble form",
"Invalid value dimension %d for coefficient %d (got %d but expecting %d). \
You might have forgotten to specify the value dimension correctly in an Expression subclass", j, i, dim, fe_dim);
}
}
//----------------------------------------------------------------------------
void OpenMpAssembler::assemble(GenericTensor& A, const Form& a)
{
// Get mesh
const Mesh& mesh = a.mesh();
if (MPI::size(mesh.mpi_comm()) > 1)
{
dolfin_error("OpenMPAssembler.cpp",
"perform multithreaded assembly using OpenMP assembler",
"The OpenMp assembler has not been tested in combination with MPI");
}
dolfin_assert(a.ufc_form());
// All assembler functions above end up calling this function, which
// in turn calls the assembler functions below to assemble over
// cells, exterior and interior facets. Note the importance of
// treating empty mesh functions as null pointers for the PyDOLFIN
// interface.
// Get cell domains
std::shared_ptr<const MeshFunction<std::size_t>> cell_domains
= a.cell_domains();
// Get exterior facet domains
std::shared_ptr<const MeshFunction<std::size_t>> exterior_facet_domains
= a.exterior_facet_domains();
// Get interior facet domains
std::shared_ptr<const MeshFunction<std::size_t>> interior_facet_domains
= a.interior_facet_domains();
// Check form
AssemblerBase::check(a);
// Create data structure for local assembly data
UFC ufc(a);
// Initialize global tensor
init_global_tensor(A, a);
// FIXME: The below selections should be made robust
if (a.ufc_form()->has_interior_facet_integrals())
assemble_interior_facets(A, a, ufc, interior_facet_domains, cell_domains, 0);
if (a.ufc_form()->has_exterior_facet_integrals())
{
assemble_cells_and_exterior_facets(A, a, ufc, cell_domains,
exterior_facet_domains, 0);
}
else
assemble_cells(A, a, ufc, cell_domains, 0);
// Finalize assembly of global tensor
if (finalize_tensor)
A.apply("add");
}
//-----------------------------------------------------------------------------
void AssemblerBase::init_global_tensor(GenericTensor& A, const Form& a)
{
dolfin_assert(a.ufc_form());
// Get dof maps
std::vector<const GenericDofMap*> dofmaps;
for (std::size_t i = 0; i < a.rank(); ++i)
dofmaps.push_back(a.function_space(i)->dofmap().get());
if (A.empty())
{
Timer t0("Build sparsity");
// Create layout for initialising tensor
std::shared_ptr<TensorLayout> tensor_layout;
tensor_layout = A.factory().create_layout(a.rank());
dolfin_assert(tensor_layout);
// Get dimensions and mapping across processes for each dimension
std::vector<std::shared_ptr<const IndexMap> > index_maps;
for (std::size_t i = 0; i < a.rank(); i++)
{
dolfin_assert(dofmaps[i]);
index_maps.push_back(dofmaps[i]->index_map());
}
// Initialise tensor layout
// FIXME: somewhere need to check block sizes are same on both axes
// NOTE: Jan: that will be done on the backend side; IndexMap will
// provide tabulate functions with arbitrary block size;
// moreover the functions will tabulate directly using a
// correct int type
tensor_layout->init(a.mesh().mpi_comm(), index_maps,
TensorLayout::Ghosts::UNGHOSTED);
// Build sparsity pattern if required
if (tensor_layout->sparsity_pattern())
{
GenericSparsityPattern& pattern = *tensor_layout->sparsity_pattern();
SparsityPatternBuilder::build(pattern,
a.mesh(), dofmaps,
a.ufc_form()->has_cell_integrals(),
a.ufc_form()->has_interior_facet_integrals(),
a.ufc_form()->has_exterior_facet_integrals(),
a.ufc_form()->has_vertex_integrals(),
keep_diagonal);
}
t0.stop();
// Initialize tensor
Timer t1("Init tensor");
A.init(*tensor_layout);
t1.stop();
// Insert zeros on the diagonal as diagonal entries may be
// prematurely optimised away by the linear algebra backend when
// calling GenericMatrix::apply, e.g. PETSc does this then errors
// when matrices have no diagonal entry inserted.
if (A.rank() == 2 && keep_diagonal)
{
// Down cast to GenericMatrix
GenericMatrix& _matA = A.down_cast<GenericMatrix>();
// Loop over rows and insert 0.0 on the diagonal
const double block = 0.0;
const std::pair<std::size_t, std::size_t> row_range = A.local_range(0);
const std::size_t range = std::min(row_range.second, A.size(1));
for (std::size_t i = row_range.first; i < range; i++)
{
dolfin::la_index _i = i;
_matA.set(&block, 1, &_i, 1, &_i);
}
A.apply("flush");
}
// Delete sparsity pattern
Timer t2("Delete sparsity");
t2.stop();
}
else
{
// If tensor is not reset, check that dimensions are correct
for (std::size_t i = 0; i < a.rank(); ++i)
{
if (A.size(i) != dofmaps[i]->global_dimension())
{
dolfin_error("AssemblerBase.cpp",
"assemble form",
"Dim %d of tensor does not match form", i);
}
}
}
if (!add_values)
A.zero();
}
//-----------------------------------------------------------------------------
void AssemblerBase::init_global_tensor(GenericTensor& A, const Form& a)
{
dolfin_assert(a.ufc_form());
// Get dof maps
std::vector<const GenericDofMap*> dofmaps;
for (std::size_t i = 0; i < a.rank(); ++i)
dofmaps.push_back(a.function_space(i)->dofmap().get());
if (A.size(0) == 0)
{
Timer t0("Build sparsity");
// Create layout for initialising tensor
std::shared_ptr<TensorLayout> tensor_layout;
tensor_layout = A.factory().create_layout(a.rank());
dolfin_assert(tensor_layout);
// Get dimensions
std::vector<std::size_t> global_dimensions;
std::vector<std::pair<std::size_t, std::size_t> > local_range;
std::vector<std::size_t> block_sizes;
for (std::size_t i = 0; i < a.rank(); i++)
{
dolfin_assert(dofmaps[i]);
global_dimensions.push_back(dofmaps[i]->global_dimension());
local_range.push_back(dofmaps[i]->ownership_range());
block_sizes.push_back(dofmaps[i]->block_size);
}
// Set block size for sparsity graphs
std::size_t block_size = 1;
if (a.rank() == 2)
{
const std::vector<std::size_t> _bs(a.rank(), dofmaps[0]->block_size);
block_size = (block_sizes == _bs) ? dofmaps[0]->block_size : 1;
}
// Initialise tensor layout
tensor_layout->init(a.mesh().mpi_comm(), global_dimensions, block_size,
local_range);
// Build sparsity pattern if required
if (tensor_layout->sparsity_pattern())
{
GenericSparsityPattern& pattern = *tensor_layout->sparsity_pattern();
SparsityPatternBuilder::build(pattern,
a.mesh(), dofmaps,
a.ufc_form()->has_cell_integrals(),
a.ufc_form()->has_interior_facet_integrals(),
a.ufc_form()->has_exterior_facet_integrals(),
keep_diagonal);
}
t0.stop();
// Initialize tensor
Timer t1("Init tensor");
A.init(*tensor_layout);
t1.stop();
// Insert zeros on the diagonal as diagonal entries may be prematurely
// optimised away by the linear algebra backend when calling
// GenericMatrix::apply, e.g. PETSc does this then errors when matrices
// have no diagonal entry inserted.
if (A.rank() == 2 && keep_diagonal)
{
// Down cast to GenericMatrix
GenericMatrix& _A = A.down_cast<GenericMatrix>();
// Loop over rows and insert 0.0 on the diagonal
const double block = 0.0;
const std::pair<std::size_t, std::size_t> row_range = A.local_range(0);
const std::size_t range = std::min(row_range.second, A.size(1));
for (std::size_t i = row_range.first; i < range; i++)
{
dolfin::la_index _i = i;
_A.set(&block, 1, &_i, 1, &_i);
}
A.apply("flush");
}
// Delete sparsity pattern
Timer t2("Delete sparsity");
t2.stop();
}
else
{
// If tensor is not reset, check that dimensions are correct
for (std::size_t i = 0; i < a.rank(); ++i)
{
if (A.size(i) != dofmaps[i]->global_dimension())
{
dolfin_error("AssemblerBase.cpp",
"assemble form",
"Reset of tensor in assembly not requested, but dim %d of tensor does not match form", i);
}
}
}
if (!add_values)
A.zero();
}