With ParallelMesh you can add nodes out of order by setting the id
before the add_node() call. You could probably get the same
functionality out of SerialMesh easily enough by first appending a
bunch of NULLs to the nodes vector to make sure the indexing matches
up.
---
Roy
On Thu, 14 Nov 2013, John Peterson wrote:
Hi,
(Ben and Roy, since you guys wrote most of the Parallel communication stuff I
hope you can comment on this...)
Cubit 14 has apparently started doing something new when writing Exodus files:
it uses the node_num_map and elem_num_map data
fields to define a node and element numbering which is different from the order
in which the x,y,z coordinates and element
connectivities are actually written to the file.
I patched the Exodus reader to try and respect these element and node numbering
mappings in c4a7cd1a71 and e669b64e17. This
is important for users who assign nodesets to specific nodes using the Cubit
GUI, or who have to interface with different
codes using the same mesh file, and would like to maintain a consistent node
numbering in both.
Cubit is also more than happy to use non-contiguous numberings in these maps...
in one example mesh I have, there are 61,794
nodes, but the node IDs range from 1 to 108,878, meaning there are around 47,000
"unused" node IDs. This is a little
annoying, but keeping NULL pointers in the _nodes and _elements vectors of
SerialMesh seems to work OK when running in serial.
In parallel, things are working fine until we hit the call to
MeshCommunication::broadcast(), as shown in the stack trace
below. The issue is that we create a packed range from
mesh.nodes_begin()/end(), which automatically skips over all the NULL
entries. When you unpack this range, you end up trying to append a Node in the
wrong place (by calling add_node()) and get an
assert:
Assertion `!n->valid_id() || n->id() == _nodes.size()' failed.
[1] ../src/mesh/serial_mesh.C, line 478, compiled Nov 13 2013 at 09:56:49
The same thing would most likely happen with the elements as well.
Would it be possible to have the mesh_inserter_iterator do something other than
call mesh.add_node(n)? I think if it did
something with logic more similar to Mesh::add_point(), which inserts a node
with a valid ID in the appropriate location of
the _nodes vector, MeshCommunication::broadcast() might actually just work...
Thoughts?
0: 0 libmesh_dbg.0.dylib 0x00000001091dabb5
libMesh::print_trace(std::ostream&) + 39
1: 1 libmesh_dbg.0.dylib 0x00000001091dadaf
libMesh::write_traceout() + 226
2: 2 libmesh_dbg.0.dylib 0x00000001091d6de2
libMesh::MacroFunctions::report_error(char const*, int, char
const*, char const*) + 61
3: 3 libmesh_dbg.0.dylib 0x0000000109644168
libMesh::SerialMesh::add_node(libMesh::Node*) + 294
4: 4 libmesh_dbg.0.dylib 0x000000010953c05e
libMesh::mesh_inserter_iterator<libMesh::Node>::operator=(libMesh::Node*) + 54
5: 5 libmesh_dbg.0.dylib 0x00000001095373df void
libMesh::Parallel::unpack_range<libMesh::MeshBase, unsigned
long long, libMesh::mesh_inserter_iterator<libMesh::Node> >(std::vector<unsigned long
long, std::allocator<unsigned long long>
> const&, libMesh::MeshBase*, libMesh::mesh_inserter_iterator<libMesh::Node>) +
288
6: 6 libmesh_dbg.0.dylib 0x0000000109532a68 void
libMesh::Parallel::Communicator::broadcast_packed_range<libMesh::MeshBase,
libMesh::MeshBase,
libMesh::MeshBase::node_iterator, libMesh::mesh_inserter_iterator<libMesh::Node>
>(libMesh::MeshBase const*,
libMesh::MeshBase::node_iterator, libMesh::MeshBase::node_iterator,
libMesh::MeshBase*,
libMesh::mesh_inserter_iterator<libMesh::Node>, unsigned int) const + 332
7: 7 libmesh_dbg.0.dylib 0x0000000109528674
libMesh::MeshCommunication::broadcast(libMesh::MeshBase&) const
+ 1134
8: 8 libmesh_dbg.0.dylib 0x000000010967569a
libMesh::UnstructuredMesh::read(std::string const&,
libMesh::MeshData*, bool) +
...
--
John
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