On Mon, 19 Jan 2009, Tim Kroeger wrote:
Please find attached the first version of "my part". I haven't tested it
because I had no idea how to do that. Well, at least it compiles. Perhaps it
is best that you guys implement your part now and then run one of the
examples on it, and in the case that it doesn't work as expected, we will
have to somehow cooperate in finding the bugs.
I've found one of the bugs, but don't know the best way to fix it.
With the attached patch, ex9 (at least) fails because the PetscVector
operator= is capable of taking a ghosted vector and producing a
non-ghosted vector copy with a non-empty global_to_local_map, which
then fails in operator() when VecGhostGetLocalForm is called on it.
---
Roy
Index: include/numerics/petsc_vector.h
===================================================================
--- include/numerics/petsc_vector.h (revision 3225)
+++ include/numerics/petsc_vector.h (working copy)
@@ -654,6 +654,13 @@
int petsc_n=static_cast<int>(n);
int petsc_n_local=static_cast<int>(n_local);
int petsc_n_ghost=static_cast<int>(ghost.size());
+
+ // If the mesh is disjoint, the following assertion will fail.
+ // If the mesh is not disjoint, every processor will either have
+ // all the dofs, none of the dofs, or some non-zero dofs at the
+ // boundary between processors.
+ libmesh_assert(n_local == 0 || n_local == n || !ghost.empty());
+
int* petsc_ghost = ghost.empty() ? PETSC_NULL :
const_cast<int*>(reinterpret_cast<const int*>(&ghost[0]));
Index: include/base/dof_map.h
===================================================================
--- include/base/dof_map.h (revision 3225)
+++ include/base/dof_map.h (working copy)
@@ -582,7 +582,7 @@
* when projecting the solution onto the refined mesh, hence the parent's
* DOF indices need to be included in the \p _send_list.
*/
- void augment_send_list_for_projection(const MeshBase &);
+ // void augment_send_list_for_projection(const MeshBase &);
/**
* Fills the vector di with the global degree of freedom indices
@@ -681,12 +681,9 @@
* variable in the system.
* Starts at index next_free_dof, and increments it to
* the post-final index.
- * If build_send_list is true, builds the send list. If
- * false, clears and reserves the send list
*/
void distribute_local_dofs_var_major (unsigned int& next_free_dof,
- MeshBase& mesh,
- const bool build_send_list);
+ MeshBase& mesh);
/**
* Distributes the global degrees of freedom, for dofs on
@@ -701,8 +698,7 @@
* false, clears and reserves the send list
*/
void distribute_local_dofs_node_major (unsigned int& next_free_dof,
- MeshBase& mesh,
- const bool build_send_list);
+ MeshBase& mesh);
/**
* Adds entries to the \p _send_list vector corresponding to DoFs
Index: src/numerics/petsc_vector.C
===================================================================
--- src/numerics/petsc_vector.C (revision 3225)
+++ src/numerics/petsc_vector.C (working copy)
@@ -440,6 +440,7 @@
{
if (v.initialized())
{
+ // FIXME - we may need to init with a list of ghost indices!
this->init (v.size(), v.local_size());
this->_global_to_local_map = v._global_to_local_map;
this->_is_closed = v._is_closed;
@@ -514,7 +515,7 @@
PetscVector<T>* v_local = libmesh_cast_ptr<PetscVector<T>*>(&v_local_in);
libmesh_assert (v_local != NULL);
- libmesh_assert (v_local->local_size() == this->size());
+ libmesh_assert (v_local->size() == this->size());
int ierr = 0;
const int n = this->size();
@@ -573,19 +574,21 @@
PetscVector<T>* v_local = libmesh_cast_ptr<PetscVector<T>*>(&v_local_in);
libmesh_assert (v_local != NULL);
- libmesh_assert (v_local->local_size() == this->size());
+ libmesh_assert (v_local->size() == this->size());
libmesh_assert (send_list.size() <= v_local->size());
int ierr=0;
- const int n_sl = send_list.size();
+ const unsigned int n_sl = send_list.size();
IS is;
VecScatter scatter;
- std::vector<int> idx(n_sl);
+ std::vector<int> idx(n_sl + this->local_size());
- for (int i=0; i<n_sl; i++)
+ for (unsigned int i=0; i<n_sl; i++)
idx[i] = static_cast<int>(send_list[i]);
+ for (unsigned int i = 0; i != this->local_size(); ++i)
+ idx[n_sl+i] = i + this->first_local_index();
// Create the index set & scatter object
if (idx.empty())
Index: src/base/dof_map.C
===================================================================
--- src/base/dof_map.C (revision 3225)
+++ src/base/dof_map.C (working copy)
@@ -666,9 +666,9 @@
// Set temporary DOF indices on this processor
if (node_major_dofs)
- this->distribute_local_dofs_node_major (next_free_dof, mesh, false);
+ this->distribute_local_dofs_node_major (next_free_dof, mesh);
else
- this->distribute_local_dofs_var_major (next_free_dof, mesh, false);
+ this->distribute_local_dofs_var_major (next_free_dof, mesh);
// Get DOF counts on all processors
std::vector<unsigned int> dofs_on_proc(n_proc, 0);
@@ -692,9 +692,9 @@
// Set permanent DOF indices on this processor
if (node_major_dofs)
- this->distribute_local_dofs_node_major (next_free_dof, mesh, true);
+ this->distribute_local_dofs_node_major (next_free_dof, mesh);
else
- this->distribute_local_dofs_var_major (next_free_dof, mesh, true);
+ this->distribute_local_dofs_var_major (next_free_dof, mesh);
libmesh_assert(next_free_dof == _end_df[proc_id]);
@@ -723,6 +723,8 @@
STOP_LOG("distribute_dofs()", "DofMap");
+ _send_list.clear();
+
// Note that in the add_neighbors_to_send_list nodes on processor
// boundaries that are shared by multiple elements are added for
// each element.
@@ -734,14 +736,13 @@
void DofMap::distribute_local_dofs_node_major(unsigned int &next_free_dof,
- MeshBase& mesh,
- const bool build_send_list)
+ MeshBase& mesh)
{
const unsigned int sys_num = this->sys_number();
const unsigned int n_vars = this->n_variables();
- // Number of elements to add to send_list
- unsigned int send_list_size = 0;
+ // We now only add remote dofs to the _send_list
+ // unsigned int send_list_size = 0;
// _var_first_local_df does not work with node_major dofs
_var_first_local_df.resize(n_vars+1);
@@ -781,17 +782,6 @@
0,
next_free_dof);
next_free_dof += node->n_comp(sys_num,var);
-
- // If we've been requested to, add local dofs to the
- // _send_list
- if (build_send_list)
- for (unsigned int index=0;
index<node->n_comp(sys_num,var);
- index++)
- _send_list.push_back(node->dof_number(sys_num,
- var,
- index));
- else
- send_list_size += node->n_comp(sys_num,var);
}
}
}
@@ -810,17 +800,6 @@
next_free_dof);
next_free_dof += elem->n_comp(sys_num,var);
-
- // If we've been requested to, add local dofs to the
- // _send_list
- if (build_send_list)
- for (unsigned int index=0; index<elem->n_comp(sys_num,var);
- index++)
- _send_list.push_back(elem->dof_number(sys_num,
- var,
- index));
- else
- send_list_size += elem->n_comp(sys_num,var);
}
} // done looping over elements
@@ -845,25 +824,18 @@
}
}
#endif // DEBUG
-
- if (!build_send_list)
- {
- _send_list.clear();
- _send_list.reserve(send_list_size);
- }
}
void DofMap::distribute_local_dofs_var_major(unsigned int &next_free_dof,
- MeshBase& mesh,
- const bool build_send_list)
+ MeshBase& mesh)
{
const unsigned int sys_num = this->sys_number();
const unsigned int n_vars = this->n_variables();
- // Number of elements to add to send_list
- unsigned int send_list_size = 0;
+ // We now only add remote dofs to the _send_list
+ // unsigned int send_list_size = 0;
// We will cache the first local index for each variable
_var_first_local_df.clear();
@@ -909,17 +881,6 @@
0,
next_free_dof);
next_free_dof += node->n_comp(sys_num,var);
-
- // If we've been requested to, add local dofs to the
- // _send_list
- if (build_send_list)
- for (unsigned int index=0; index<node->n_comp(sys_num,var);
- index++)
- _send_list.push_back(node->dof_number(sys_num,
- var,
- index));
- else
- send_list_size += node->n_comp(sys_num,var);
}
}
@@ -935,17 +896,6 @@
next_free_dof);
next_free_dof += elem->n_comp(sys_num,var);
-
- // If we've been requested to, add local dofs to the
- // _send_list
- if (build_send_list)
- for (unsigned int index=0; index<elem->n_comp(sys_num,var);
- index++)
- _send_list.push_back(elem->dof_number(sys_num,
- var,
- index));
- else
- send_list_size += elem->n_comp(sys_num,var);
}
} // end loop on elements
_var_first_local_df.push_back(next_free_dof);
@@ -972,12 +922,6 @@
}
}
#endif // DEBUG
-
- if (!build_send_list)
- {
- _send_list.clear();
- _send_list.reserve(send_list_size);
- }
}
@@ -987,7 +931,6 @@
START_LOG("add_neighbors_to_send_list()", "DofMap");
//-------------------------------------------------------------------------
- // The _send_list now only contains entries from the local processor.
// We need to add the DOFs from elements that live on neighboring processors
// that are neighbors of the elements on the local processor
//-------------------------------------------------------------------------
@@ -1032,10 +975,12 @@
// Get the DOF indices for this neighboring element
this->dof_indices (family[i], di);
- // Insert the DOF indices into the send list
- _send_list.insert (_send_list.end(),
- di.begin(), di.end());
- }
+ // Insert the remote DOF indices into the send list
+ for (unsigned int j=0; j != di.size(); ++j)
+ if (di[j] < this->first_dof() ||
+ di[j] >= this->end_dof())
+ _send_list.push_back(di[j]);
+ }
}
}
@@ -1070,9 +1015,11 @@
// Get the DOF indices for this neighboring element
this->dof_indices (elem, di);
- // Insert the DOF indices into the send list
- _send_list.insert (_send_list.end(),
- di.begin(), di.end());
+ // Insert the remote DOF indices into the send list
+ for (unsigned int j=0; j != di.size(); ++j)
+ if (di[j] < this->first_dof() &&
+ di[j] >= this->end_dof())
+ _send_list.push_back(di[j]);
}
}
@@ -1559,6 +1506,7 @@
+/*
void DofMap::augment_send_list_for_projection(const MeshBase& mesh)
{
// Loop over the active local elements in the mesh.
@@ -1610,6 +1558,7 @@
// The send-list might need to be sorted again.
if (needs_sorting) this->sort_send_list ();
}
+*/
#endif // LIBMESH_ENABLE_AMR
Index: src/solvers/transient_system.C
===================================================================
--- src/solvers/transient_system.C (revision 3225)
+++ src/solvers/transient_system.C (working copy)
@@ -98,8 +98,10 @@
Base::init_data();
// Initialize the old & older solutions
- old_local_solution->init (this->n_dofs());
- older_local_solution->init (this->n_dofs());
+ old_local_solution->init (this->n_dofs(), this->n_local_dofs(),
+ this->get_dof_map().get_send_list());
+ older_local_solution->init (this->n_dofs(), this->n_local_dofs(),
+ this->get_dof_map().get_send_list());
}
Index: src/solvers/system.C
===================================================================
--- src/solvers/system.C (revision 3225)
+++ src/solvers/system.C (working copy)
@@ -185,7 +185,8 @@
solution->init (this->n_dofs(), this->n_local_dofs());
// Resize the current_local_solution for the current mesh
- current_local_solution->init (this->n_dofs());
+ current_local_solution->init (this->n_dofs(), this->n_local_dofs(),
+ _dof_map->get_send_list());
// from now on, no chance to add additional vectors
_can_add_vectors = false;
@@ -211,19 +212,22 @@
v->init (this->n_dofs(), this->n_local_dofs());
}
+ const std::vector<unsigned int>& send_list = _dof_map->get_send_list ();
+
// Restrict the solution on the coarsened cells
if (_solution_projection)
{
this->project_vector (*solution);
current_local_solution->clear();
- current_local_solution->init(this->n_dofs());
- const std::vector<unsigned int>& send_list = _dof_map->get_send_list ();
+ current_local_solution->init(this->n_dofs(),
+ this->n_local_dofs(), send_list);
solution->localize (*current_local_solution, send_list);
}
else
{
current_local_solution->clear();
- current_local_solution->init(this->n_dofs());
+ current_local_solution->init(this->n_dofs(),
+ this->n_local_dofs(), send_list);
}
#endif
}
@@ -257,7 +261,8 @@
solution->init (this->n_dofs(), this->n_local_dofs());
libmesh_assert (solution->size() == current_local_solution->size());
- libmesh_assert (solution->size() == current_local_solution->local_size());
+ // Not true with ghosted vectors
+ // libmesh_assert (solution->size() == current_local_solution->local_size());
const unsigned int first_local_dof = solution->first_local_index();
const unsigned int local_size = solution->local_size();
@@ -275,7 +280,7 @@
const std::vector<unsigned int>& send_list = _dof_map->get_send_list ();
// Check sizes
- libmesh_assert (current_local_solution->local_size() == solution->size());
+ libmesh_assert (current_local_solution->size() == solution->size());
// More processors than elements => empty send_list
// libmesh_assert (!send_list.empty());
libmesh_assert (send_list.size() <= solution->size());
@@ -298,8 +303,9 @@
Utility::iota (send_list.begin(), send_list.end(), 0);
// Check sizes
- libmesh_assert (current_local_solution->local_size() == solution->size());
libmesh_assert (current_local_solution->size() == solution->size());
+ // Not true with ghosted vectors
+ // libmesh_assert (current_local_solution->local_size() == solution->size());
libmesh_assert (!send_list.empty());
libmesh_assert (send_list.size() <= solution->size());
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