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Message #17504
Re: [Fwd: [Branch ~dolfin-core/dolfin/main] Rev 4482: Add missing SCOTCH functions when SCOTCH is not available]
On Thu, Feb 11, 2010 at 07:24:51PM +0000, Garth N. Wells wrote:
>
>
> Anders Logg wrote:
> > I had to get things to compile so I could push a bug fix. I won't
> > touch it more.
> >
>
> Why are so many lines which are the same 'touched', e.g.
>
> - partition(local_graph, ghost_vertices, global_cell_indices,
> + partition(local_graph, ghost_vertices, global_cell_indices,
>
> Is it your editor?
>
> Garth
It's because of the following setting in my .emacs configuration file:
;; Remove trailing whitespaces before saving
(add-hook 'before-save-hook 'delete-trailing-whitespace)
This deletes whitespaces at the end of lines. So even if I change just
a single character, many lines will be cleaned up automatically. I
used to check this manually before but now I don't have to.
--
Anders
>
> >> Please don't touch the SCOCTH files just yet.
> >>
> >> Garth
> >>
> >> -------- Original Message --------
> >> Subject: [Branch ~dolfin-core/dolfin/main] Rev 4482: Add missing SCOTCH
> >> functions when SCOTCH is not available
> >> Date: Thu, 11 Feb 2010 18:11:17 -0000
> >> From: noreply@xxxxxxxxxxxxx
> >> Reply-To: noreply@xxxxxxxxxxxxx
> >> To: Garth Wells <gnw20@xxxxxxxxx>
> >>
> >> ------------------------------------------------------------
> >> revno: 4482
> >> committer: Anders Logg <logg@xxxxxxxxx>
> >> branch nick: dolfin-dev
> >> timestamp: Thu 2010-02-11 19:09:37 +0100
> >> message:
> >> Add missing SCOTCH functions when SCOTCH is not available
> >> modified:
> >> dolfin/graph/SCOTCH.cpp
> >>
> >>
> >
> >> === modified file 'dolfin/graph/SCOTCH.cpp'
> >> --- dolfin/graph/SCOTCH.cpp 2010-02-11 01:50:04 +0000
> >> +++ dolfin/graph/SCOTCH.cpp 2010-02-11 18:09:37 +0000
> >> @@ -2,7 +2,7 @@
> >> // Licensed under the GNU LGPL Version 2.1.
> >> //
> >> // First added: 2010-02-10
> >> -// Last changed:
> >> +// Last changed: 2010-02-11
> >>
> >> #include <algorithm>
> >> #include <numeric>
> >> @@ -40,7 +40,7 @@
> >>
> >> // Compute partitions
> >> cout << "Compute partitions" << endl;
> >> - partition(local_graph, ghost_vertices, global_cell_indices,
> >> + partition(local_graph, ghost_vertices, global_cell_indices,
> >> num_global_vertices, cell_partition);
> >> cout << "End compute parttions" << endl;
> >> }
> >> @@ -63,7 +63,7 @@
> >> for (vertices = cell_vertices.begin(); vertices != cell_vertices.end(); ++vertices)
> >> std::sort(vertices->begin(), vertices->end());
> >>
> >> - // Resize graph (cell are graph vertices, cell-cell connections are graph edges)
> >> + // Resize graph (cell are graph vertices, cell-cell connections are graph edges)
> >> local_graph.resize(num_local_cells);
> >>
> >> // Get number of cells on each process
> >> @@ -72,7 +72,7 @@
> >> // Compute offset for going from local to (internal) global numbering
> >> std::vector<uint> process_offsets(MPI::num_processes());
> >> for (uint i = 0; i < MPI::num_processes(); ++i)
> >> - process_offsets[i] = std::accumulate(cells_per_process.begin(), cells_per_process.begin() + i, 0);
> >> + process_offsets[i] = std::accumulate(cells_per_process.begin(), cells_per_process.begin() + i, 0);
> >> const uint process_offset = process_offsets[MPI::process_number()];
> >>
> >> // Compute local edges (cell-cell connections) using global (internal) numbering
> >> @@ -92,12 +92,12 @@
> >> assert(i < local_graph.size());
> >> if (local_graph[i].size() != num_cell_facets)
> >> local_boundary_cells.push_back(i);
> >> - }
> >> - cout << "Number of possible boundary cells " << local_boundary_cells.size() << endl;
> >> + }
> >> + cout << "Number of possible boundary cells " << local_boundary_cells.size() << endl;
> >>
> >> // Get number of possible ghost cells coming from each process
> >> std::vector<uint> boundary_cells_per_process = MPI::gather(local_boundary_cells.size());
> >> -
> >> +
> >> // Pack local data for candidate ghost cells (global cell index and vertices)
> >> std::vector<uint> connected_cell_data;
> >> for (uint i = 0; i < local_boundary_cells.size(); ++i)
> >> @@ -108,8 +108,8 @@
> >> // Candidate cell vertices
> >> std::vector<uint>& vertices = cell_vertices[local_boundary_cells[i]];
> >> for (uint j = 0; j < num_cell_vertices; ++j)
> >> - connected_cell_data.push_back(vertices[j]);
> >> - }
> >> + connected_cell_data.push_back(vertices[j]);
> >> + }
> >>
> >> // Prepare package to send (do not send data belonging to this process)
> >> std::vector<uint> partition;
> >> @@ -118,7 +118,7 @@
> >> {
> >> if(i != MPI::process_number())
> >> {
> >> - transmit_data.insert(transmit_data.end(), connected_cell_data.begin(),
> >> + transmit_data.insert(transmit_data.end(), connected_cell_data.begin(),
> >> connected_cell_data.end());
> >> partition.insert(partition.end(), connected_cell_data.size(), i);
> >> }
> >> @@ -140,7 +140,7 @@
> >> uint _offset = 0;
> >> for (uint i = 0; i < MPI::num_processes()-1; ++i)
> >> {
> >> - const uint p = partition[_offset];
> >> + const uint p = partition[_offset];
> >> const uint data_length = (num_cell_vertices+1)*boundary_cells_per_process[p];
> >>
> >> std::vector<uint>& _global_cell_indices = candidate_ghost_cell_global_indices[p];
> >> @@ -158,9 +158,9 @@
> >> std::vector<uint> vertices;
> >> for (uint k = 0; k < num_cell_vertices; ++k)
> >> vertices.push_back(transmit_data[(j+1)+k]);
> >> - _cell_vertices.push_back(vertices);
> >> + _cell_vertices.push_back(vertices);
> >> }
> >> -
> >> +
> >> // Update offset
> >> _offset += data_length;
> >> }
> >> @@ -170,17 +170,17 @@
> >> std::set<uint> ghost_cell_global_indices;
> >> for (uint i = 0; i < candidate_ghost_cell_vertices.size(); ++i)
> >> {
> >> - compute_ghost_connectivity(cell_vertices, local_boundary_cells,
> >> - candidate_ghost_cell_vertices[i],
> >> - candidate_ghost_cell_global_indices[i],
> >> - num_cell_facets, num_facet_vertices,
> >> + compute_ghost_connectivity(cell_vertices, local_boundary_cells,
> >> + candidate_ghost_cell_vertices[i],
> >> + candidate_ghost_cell_global_indices[i],
> >> + num_cell_facets, num_facet_vertices,
> >> local_graph, ghost_cell_global_indices);
> >> }
> >> cout << "Finish compute graph ghost edges" << endl;
> >> }
> >> //-----------------------------------------------------------------------------
> >> void SCOTCH::compute_connectivity(const std::vector<std::vector<uint> >& cell_vertices,
> >> - uint num_cell_facets,
> >> + uint num_cell_facets,
> >> uint num_facet_vertices, uint offset,
> >> std::vector<std::set<uint> >& local_graph)
> >> {
> >> @@ -197,10 +197,10 @@
> >>
> >> // Find numer of vertices shared by cells i and j
> >> std::vector<uint> intersection(num_cell_facets);
> >> - it = std::set_intersection(cell_vertices[i].begin(), cell_vertices[i].end(),
> >> - cell_vertices[j].begin(), cell_vertices[j].end(),
> >> + it = std::set_intersection(cell_vertices[i].begin(), cell_vertices[i].end(),
> >> + cell_vertices[j].begin(), cell_vertices[j].end(),
> >> intersection.begin());
> >> - const uint num_shared_vertices = it - intersection.begin();
> >> + const uint num_shared_vertices = it - intersection.begin();
> >>
> >> // Insert edge if cells are neighbours
> >> if ( num_shared_vertices == num_facet_vertices )
> >> @@ -218,10 +218,10 @@
> >>
> >> // Find numer of vertices shared by cell0 and cell1
> >> std::vector<uint> intersection(num_cell_facets);
> >> - it = std::set_intersection(cell_vertices[i].begin(), cell_vertices[i].end(),
> >> - cell_vertices[j].begin(), cell_vertices[j].end(),
> >> + it = std::set_intersection(cell_vertices[i].begin(), cell_vertices[i].end(),
> >> + cell_vertices[j].begin(), cell_vertices[j].end(),
> >> intersection.begin());
> >> - const uint num_shared_vertices = it - intersection.begin();
> >> + const uint num_shared_vertices = it - intersection.begin();
> >>
> >> // Insert edge if cells are neighbours
> >> if ( num_shared_vertices == num_facet_vertices )
> >> @@ -229,7 +229,7 @@
> >> else if ( num_shared_vertices > num_facet_vertices)
> >> error("Too many shared vertices. Cannot construct dual graph.");
> >> }
> >> - }
> >> + }
> >> }
> >> //-----------------------------------------------------------------------------
> >> dolfin::uint SCOTCH::compute_ghost_connectivity(const std::vector<std::vector<uint> >& cell_vertices,
> >> @@ -241,7 +241,7 @@
> >> std::vector<std::set<uint> >& local_graph,
> >> std::set<uint>& ghost_cells)
> >> {
> >> - // FIXME: This function needs to be made more efficient.
> >> + // FIXME: This function needs to be made more efficient.
> >>
> >> const uint num_ghost_vertices_0 = ghost_cells.size();
> >>
> >> @@ -253,10 +253,10 @@
> >> {
> >> // Find numer of vertices shared by cells i and j
> >> std::vector<uint> intersection(num_cell_facets);
> >> - it = std::set_intersection(cell_vertices[local_cell_index].begin(), cell_vertices[local_cell_index].end(),
> >> - candidate_ghost_vertices[j].begin(), candidate_ghost_vertices[j].end(),
> >> + it = std::set_intersection(cell_vertices[local_cell_index].begin(), cell_vertices[local_cell_index].end(),
> >> + candidate_ghost_vertices[j].begin(), candidate_ghost_vertices[j].end(),
> >> intersection.begin());
> >> - const uint num_shared_vertices = it - intersection.begin();
> >> + const uint num_shared_vertices = it - intersection.begin();
> >>
> >> if ( num_shared_vertices == num_facet_vertices )
> >> {
> >> @@ -267,7 +267,7 @@
> >> error("Too many shared vertices. Cannot construct dual graph.");
> >> }
> >> }
> >> -
> >> +
> >> // Return number of newly added ghost vertices
> >> return ghost_cells.size() - num_ghost_vertices_0;
> >> }
> >> @@ -290,7 +290,7 @@
> >> //const uint vertgstnbr = local_graph.size() + ghost_vertices.size();
> >>
> >> // Number of local edges + edges connecting to ghost vertices
> >> - SCOTCH_Num edgelocnbr = 0;
> >> + SCOTCH_Num edgelocnbr = 0;
> >> std::vector<std::set<uint> >::const_iterator vertex;
> >> for(vertex = local_graph.begin(); vertex != local_graph.end(); ++vertex)
> >> edgelocnbr += vertex->size();
> >> @@ -323,8 +323,8 @@
> >> std::vector<SCOTCH_Num> proccnttab(MPI::num_processes());
> >> for (uint i = 0; i < MPI::num_processes(); ++i)
> >> proccnttab[i] = tmp[i];
> >> -
> >> - // Array containing . . . .
> >> +
> >> + // Array containing . . . .
> >> std::vector<SCOTCH_Num> procvrttab(MPI::num_processes() + 1);
> >> for (uint i = 0; i < MPI::num_processes(); ++i)
> >> procvrttab[i] = std::accumulate(proccnttab.begin(), proccnttab.begin() + i, 0);
> >> @@ -383,7 +383,7 @@
> >> //if (err != 0)
> >> // error("Error buidling SCOTCH ghost points.");
> >>
> >> - // Check graph
> >> + // Check graph
> >> if (SCOTCH_dgraphCheck(&dgrafdat))
> >> error("Consistency error in SCOTCH graph.");
> >>
> >> @@ -409,6 +409,49 @@
> >> cell_partition[i] = partloctab[i];
> >> }
> >> //-----------------------------------------------------------------------------
> >> +#else
> >> +//-----------------------------------------------------------------------------
> >> +void SCOTCH::compute_partition(std::vector<uint>& cell_partition,
> >> + const LocalMeshData& mesh_data)
> >> +{
> >> + error("This function requires SCOTCH.");
> >> +}
> >> +//-----------------------------------------------------------------------------
> >> +void SCOTCH::compute_dual_graph(const LocalMeshData& mesh_data,
> >> + std::vector<std::set<uint> >& local_graph,
> >> + std::set<uint>& ghost_vertices)
> >> +{
> >> + error("This function requires SCOTCH.");
> >> +}
> >> +//-----------------------------------------------------------------------------
> >> +void SCOTCH::compute_connectivity(const std::vector<std::vector<uint> >& cell_vertices,
> >> + uint num_cell_facets, uint num_facet_vertices,
> >> + uint offset,
> >> + std::vector<std::set<uint> >& graph)
> >> +{
> >> + error("This function requires SCOTCH.");
> >> +}
> >> +//-----------------------------------------------------------------------------
> >> +dolfin::uint SCOTCH::compute_ghost_connectivity(const std::vector<std::vector<uint> >& cell_vertices,
> >> + const std::vector<uint>& local_boundary_cells,
> >> + const std::vector<std::vector<uint> >& candidate_ghost_vertices,
> >> + const std::vector<uint>& candidate_ghost_global_indices,
> >> + uint num_cell_facets, uint num_facet_vertices,
> >> + std::vector<std::set<uint> >& ghost_graph_edges,
> >> + std::set<uint>& ghost_cells)
> >> +{
> >> + error("This function requires SCOTCH.");
> >> + return 0;
> >> +}
> >> +//-----------------------------------------------------------------------------
> >> +void SCOTCH::partition(const std::vector<std::set<uint> >& local_graph,
> >> + const std::set<uint>& ghost_vertices,
> >> + const std::vector<uint>& global_cell_indices,
> >> + uint num_global_vertices,
> >> + std::vector<uint>& cell_partition)
> >> +{
> >> + error("This function requires SCOTCH.");
> >> +}
> >> +//-----------------------------------------------------------------------------
> >>
> >> #endif
> >> -
> >>
> >>
> >
> >> _______________________________________________
> >> Mailing list: https://launchpad.net/~dolfin
> >> Post to : dolfin@xxxxxxxxxxxxxxxxxxx
> >> Unsubscribe : https://launchpad.net/~dolfin
> >> More help : https://help.launchpad.net/ListHelp
> >
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