dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Friday 13 June 2008 10:57:00 Anders Logg wrote:
> On Fri, Jun 13, 2008 at 10:43:12AM +0200, Johan Hake wrote:
> > On Friday 13 June 2008 10:17:20 Anders Logg wrote:
> > > On Fri, Jun 13, 2008 at 10:08:31AM +0200, Johan Hake wrote:
> > > > On Thursday 12 June 2008 22:05:43 Anders Logg wrote:
> > > > > On Wed, Jun 11, 2008 at 08:27:14AM +0200, Johan Hake wrote:
> > > > > > On Tuesday 10 June 2008 14:52:52 Anders Logg wrote:
> > > > > > > On Tue, Jun 10, 2008 at 02:28:51PM +0200, Johan Hake wrote:
> > > > > > > > On Tuesday 10 June 2008 13:23:45 Anders Logg wrote:
> > > > > > > > > On Tue, Jun 10, 2008 at 09:55:51AM +0200, Martin Sandve
> > > > > > > > > Alnæs
> >
> > wrote:
> > > > > > > > > > 2008/6/9 DOLFIN <dolfin@xxxxxxxxxx>:
> > > > > > > > > > > One or more new changesets pushed to the primary dolfin
> > > > > > > > > > > repository. A short summary of the last three
> > > > > > > > > > > changesets is included below.
> > > > > > > > > > >
> > > > > > > > > > > changeset:  
> > > > > > > > > > > 4282:5f6759a7460d81435abf4d67911667e3e628e164 tag:     
> > > > > > > > > > >    tip
> > > > > > > > > > > user:        Anders Logg <logg@xxxxxxxxx>
> > > > > > > > > > > date:        Mon Jun 09 23:06:51 2008 +0200
> > > > > > > > > > > files:       dolfin/fem/Assembler.cpp
> > > > > > > > > > > dolfin/fem/UFC.cpp dolfin/fem/UFC.h description:
> > > > > > > > > > > Reset local tensor A^K before call to tabulate_tensor()
> > > > > > > > > >
> > > > > > > > > > Why? This is the job of tabulate_tensor, which can do it
> > > > > > > > > > much more efficiently?
> > > > > > > > >
> > > > > > > > > I added this for convenience. It is used when assembling
> > > > > > > > > forms over subdomains and the form compiler needs to
> > > > > > > > > generate code for zero contributions from other domains,
> > > > > > > > > for example when integrating
> > > > > > > > >
> > > > > > > > >   M = f*ds(5)
> > > > > > > > >
> > > > > > > > > Then the compiler needs to add zero integrals for
> > > > > > > > > ds([0-4]). Then this code just needs to be empty.
> > > > > > > >
> > > > > > > > It would be great to be able to integrate the above mentioned
> > > > > > > > form. It took me some time to realise that you could only
> > > > > > > > assemble subdomains that was contiguously numbered from 0 and
> > > > > > > > up.
> > > > > > >
> > > > > > > That's not needed anymore. It should be possible now to
> > > > > > > integrate the form above without adding any additional terms.
> > > > > >
> > > > > > Nice!
> > > > > >
> > > > > > > > But is this implementation the most logical? What if I think
> > > > > > > > it is natural to mark a subdomain with "100"? Then 100 empty
> > > > > > > > integrals would be created? Is it possible to store the
> > > > > > > > integrals in a map, with markers as keys. Or store the
> > > > > > > > integrals in a contiguous array, and then map these to
> > > > > > > > markers?
> > > > > > >
> > > > > > > Yes, this can be done. It's related to building a mapping from
> > > > > > > subdomains to cells that's been discussed before. Now we only
> > > > > > > have the inverse, the mapping from cells to subdomains. I don't
> > > > > > > know when this will happen. It's something I'd like to have but
> > > > > > > it's not critical.
> > > > > >
> > > > > > OK
> > > > > >
> > > > > > > > This would add flexibility for assigning a form integral an
> > > > > > > > arbitrary number, but it also introduce a map lookup overhead
> > > > > > > > that would slow down the assembly. The latter could be solved
> > > > > > > > with an inverse MeshFunction, which map values to
> > > > > > > > cells/facets.
> > > > > > >
> > > > > > > Don't think it needs to slow down assembly.
> > > > > >
> > > > > > OK
> > > > > >
> > > > > > > > It would also be nice to separate a facet MeshFunction in one
> > > > > > > > only for interior facets and one only for the exterior ones.
> > > > > > > > This would fit nicely in to the above mentioned procedure. I
> > > > > > > > do not know how to do this nicely though...
> > > > > > >
> > > > > > > Yes.
> > > > > > >
> > > > > > > > A note related to this issue:
> > > > > > > > A typical small mesh I generate have 23K vertices, and 86K
> > > > > > > > tetrahedrons, it takes ~0.3 s to load. The boundary mesh have
> > > > > > > > 35K facets but the whole mesh have 190K facets, including the
> > > > > > > > interior facets. This takes ~5s to load, almost 20 times more
> > > > > > > > time than the mesh, and it loads information about 160K
> > > > > > > > facets that is not needed.
> > > > > > >
> > > > > > > I guess you need this for boundary conditions? If that is the
> > > > > > > case, then the internal facets never need to be generated if
> > > > > > > you use the new mesh file format (which VTK uses) where all the
> > > > > > > boundary information is included in the mesh file.
> > > > > >
> > > > > > ?
> > > > > >
> > > > > > Maybee I was unclear? I need a MeshFunction to define my boundary
> > > > > > subdomains, to send to assemble. Do you say that I can store this
> > > > > > subdomain meshfunction in the new mesh format, by only storing
> > > > > > the information of the exterior facets? I thought a Meshfunction
> > > > > > was tied to the same entities in the mesh, and needed to be of
> > > > > > the same length, i.e., a facet meshfunction need to include
> > > > > > information of all facets in the mesh.
> > > > >
> > > > > Yes, that's true, but in the "new" (extended) mesh format, we store
> > > > > Arrays, not MeshFunctions. These don't have to have the same
> > > > > length.
> > > > >
> > > > > Take a look at data/meshes/aneurysm.xml.gz.
> > > > >
> > > > > Only DirichletBC can currently handle this data. Assembler still
> > > > > relies on a MeshFunction for the subdomains.
> > > >
> > > > Ok, this MeshData can take an arbitrary number of MeshFunctions and
> > > > Arrays. But three arrays with name "boundary facet cells", "boundary
> > > > facet numbers" and "boundary indicators" are treated specially in the
> > > > function DirichleBC().
> > >
> > > Correct.
> > >
> > > > I do not really understand what these name stand for. Shouldn't it be
> > > > enough to use two arrays? One for the global facet number of the
> > > > facets laying on the boundary, and one for the markers?
> > >
> > > No, it's not enough. It would be enough if everyone numbered the
> > > facets in the same way as DOLFIN, but that is not the case, in
> > > particular since the way DOLFIN numbers the facets depends on the
> > > particular algorithm implemented in DOLFIN for generating the facets
> > > for a mesh. So we need to store the markers based on the *cells*
> > > rather than the *facets*. So we basically store a list of the cells
> > > adjacent to the facets on the boundary, the local numbering of the
> > > facets relative to those cells, and the markers for the facets.
> >
> > OK!
> >
> > > > I still can't figure out why a mesh takes ~20 times logner to load?
> > > > First I thought that a MeshFunction stores more information, but 20
> > > > times, and the file is actually much smaller than the mesh file.
> > > > Could the implementation of XMLMeshFunction be to blame?
> > >
> > > I think the problem is that when you load markers on the facets of a
> > > mesh, then DOLFIN first needs to compute the facets and that may take
> > > some time. (Only the vertices and cells are present in the XML file.)
> >
> > Jepp, you are correct here!
> >
> > mesh.init(2) took 55 s and loading the mesh function after this took
> > 2s... :P
>
> Good. (But actually not that good. Looks like we might need to do
> something to improve the speed of mesh.init().)

Yes it takes quite a while...

I timed the TopologyComputation::computeEntities() function:
Start initializing mesh:
  ComputeConnectivity: 25.60s
  Initializing local arrays: 0.00s
  Counting entities: 5.94s
  Initialising entities and connections: 0.04s
  Adding entities: 23.60s
  Deleting data: 0.00s
Initializing mesh took 55.35s

One could probably get a better view with a propper profiling. But I just made 
a quick timing of the different parts of the function. Looks like most of the 
time is spent in initalising the connectivities and creating and add the 
actuall entities.

Johan