On 2014-01-14 16:24, Anders Logg wrote:
On Mon, Jan 13, 2014 at 07:16:01PM +0000, Garth N. Wells wrote:
On 2014-01-13 18:42, Anders Logg wrote:
>On Mon, Jan 13, 2014 at 12:45:11PM +0000, Garth N. Wells wrote:
>>I've just pushed some changes to master, which for
>>
>> from dolfin import *
>> mesh = UnitCubeMesh(128, 128, 128)
>> mesh.init(2)
>> mesh.init(2, 3)
>g>
>>give a factor 2 reduction in memory usage and a factor 2 speedup.
>>Change is at
>>https://bitbucket.org/fenics-project/dolfin/commits/8265008.
>>
>>The improvement is primarily due to d--d connectivity no being
>>computed. I'll submit a pull request to throw an error when d--d
>>connectivity is requested. The only remaining place where d--d is
>>(implicitly) computed is in the code for finding constrained mesh
>>entities (e.g., for periodic bcs). The code in question is
>>
>> for (MeshEntityIterator(facet, dim) e; . . . .)
>>
>>when dim is the same as the topological dimension if the facet. As
>>in other places, it would be consistent (and the original intention
>>of the programmer) if this just iterated over the facet itself
>>rather than all facets attached to it via a vertex.
>
>I don't see why an error message is needed. Could we not just add the
>possibility to specify what d -- d means? It might be useful for other
>algorithms to be able to compute that data.
>
I think it should be removed because it's (i) ad-hoc, (ii) is not
used/required in the library and (iii) is a memory monster.
Moreover, we have dimension-independent algorithms that work when
d--d connectivity is a connection from an entity to itself (for
which we don't need computation and memory eating). We shouldn't
have an unnecessary, memory monster d-0-d data structure being
created opaquely for no purpose, which is what what
for (MeshEntityIterator e(entity, dim); . . . .){....}
does at present when (dimension of entity) = dim. The excessive
memory usage is an issue for big problems.
If a user wants d-0-d it can be built explicitly, which makes both
the purpose and the intention clear.
How can it be built explicitly without calling mesh.init(d, d)?
Build d--0, then 0--d:
for (MeshEntityIterator e0(mesh, d); .....)
for (VertexIterator v(*e0); ....)
for (MeshEntityIterator e2(*v, d); .....)
Note that d--0--d is no longer used in DOLFIN (except by accident in
finding periodic bcs because of inconsistent behind-the-scenes
behaviour, and it should be changed because it's expensive and not
required for periodic bcs).
More generally, for d1--d0--d2
for (MeshEntityIterator e1(mesh, d1); .....)
for (MeshEntityIterator e0(*e1, d0); ....)
for (MeshEntityIterator e2(*e0, d2); .....)
Garth
--
Anders
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