dolfin team mailing list archive

[Niclas Jansson <njansson@xxxxxx>]

Niclas Jansson wrote:
> Anders Logg wrote:
>   
> > On Thu, Aug 14, 2008 at 01:23:26PM +0200, Johan Hoffman wrote:
> >
> >     
> > > > On Thu, Aug 14, 2008 at 11:48:14AM +0200, Johan Hoffman wrote:
> > > >
> > > >         
> > > > > > On Wed, Aug 13, 2008 at 2:57 PM, Johan Hoffman <jhoffman@xxxxxxxxxx>
> > > > > > wrote:
> > > > > >
> > > > > >
> > > > > >             
> > > > > > > > Johan Hoffman wrote:
> > > > > > > >
> > > > > > > >                 
> > > > > > > > > > Anders Logg wrote:
> > > > > > > > > >
> > > > > > > > > >                     
> > > > > > > > > > > On Tue, Jun 17, 2008 at 02:45:41PM +0100, Garth N. Wells wrote:
> > > > > > > > > > >
> > > > > > > > > > >                       
> > > > > > > > > > > > It would be useful to lay out a plan for tackling DofMaps.
> > > > > > > > > > > >
> > > > > > > > > > > >                         
> > > > > Getting
> > > > >
> > > > >           
> > > > > > > > > > > > this
> > > > > > > > > > > > right is the key to parallel assembly, assembly optimisations
> > > > > > > > > > > >
> > > > > > > > > > > >                         
> > > > > and
> > > > >
> > > > >           
> > > > > > > > > > > > applying Dirichlet boundary conditions by eliminating Dirichlet
> > > > > > > > > > > >
> > > > > > > > > > > >                         
> > > > > > > dofs
> > > > > > >
> > > > > > >               
> > > > > > > > > > > > from the global system.
> > > > > > > > > > > >
> > > > > > > > > > > > I'm happy to take a look, but I'll need some time because I've
> > > > > > > > > > > >
> > > > > > > > > > > >                         
> > > > > > > lost
> > > > > > >
> > > > > > >               
> > > > > > > > > > > > my
> > > > > > > > > > > > overview of DofMaps. If someone else is already on top of it,
> > > > > > > > > > > >
> > > > > > > > > > > >                         
> > > > > I'd
> > > > >
> > > > >           
> > > > > > > be
> > > > > > >
> > > > > > >               
> > > > > > > > > > > > happy to provide feedback.
> > > > > > > > > > > >
> > > > > > > > > > > > Garth
> > > > > > > > > > > >
> > > > > > > > > > > >                         
> > > > > > > > > > > I won't have time to look at it until after the summer and I
> > > > > > > > > > >
> > > > > > > > > > >                       
> > > > > > > haven't
> > > > > > >
> > > > > > >               
> > > > > > > > > > > started.
> > > > > > > > > > >
> > > > > > > > > > > Anyway, I think we should wait until after the next release
> > > > > > > > > > >
> > > > > > > > > > >                       
> > > > > until
> > > > >
> > > > >           
> > > > > > > we
> > > > > > >
> > > > > > >               
> > > > > > > > > > > start messing with the dof maps.
> > > > > > > > > > >
> > > > > > > > > > > Are there any issues we need to sort out before releasing 0.8?
> > > > > > > > > > >
> > > > > > > > > > >                       
> > > > > I'm
> > > > >
> > > > >           
> > > > > > > > > > > thinking about a new release some time this or next week.
> > > > > > > > > > >
> > > > > > > > > > > One is to fix the bug in DirichletBC, but other than that?
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >                       
> > > > > > > > > > Now would be a good time for a release so I can start messing
> > > > > > > > > >
> > > > > > > > > >                     
> > > > > with
> > > > >
> > > > >           
> > > > > > > > > > DofMaps.
> > > > > > > > > >
> > > > > > > > > > Garth
> > > > > > > > > >
> > > > > > > > > >                     
> > > > > > > > > Has anything more been done about the DofMap design? During the
> > > > > > > > >
> > > > > > > > >                   
> > > > > > > summer
> > > > > > >
> > > > > > >               
> > > > > > > > > Niclas has extended to general elements his adaptive algorithm for
> > > > > > > > > distributed parallel computing, so we are now ready to start
> > > > > > > > >
> > > > > > > > >                   
> > > > > messing
> > > > >
> > > > >           
> > > > > > > > > with
> > > > > > > > > the DofMaps in order to implement his algorithm in DOLFIN.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >                   
> > > > > > > > It has been given some thought, but no changes have been made in
> > > > > > > >
> > > > > > > >                 
> > > > > the
> > > > >
> > > > >           
> > > > > > > > code yet.
> > > > > > > >
> > > > > > > >                 
> > > > > > > Ok. Any threads on the list to point to where this is discussed?
> > > > > > >
> > > > > > > If you have something already, I would suggest making it
> > > > > > >
> > > > > > >               
> > > > > > > > publicly available somewhere for feedback before starting work on
> > > > > > > >
> > > > > > > >                 
> > > > > > > DOLFIN.
> > > > > > >
> > > > > > > It is a refinement and generalization of the thesis work of Niclas
> > > > > > > Jansson
> > > > > > > which was discussed on the list before the summer. Is is outlined in
> > > > > > >
> > > > > > >               
> > > > > his
> > > > >
> > > > >           
> > > > > > > report:
> > > > > > >
> > > > > > > http://www.nada.kth.se/utbildning/grukth/exjobb/rapportlistor/2008/rapporter08/jansson_niclas_08051.pdf
> > > > > > >
> > > > > > > My announcement here was to initiate a discussion of the detailed
> > > > > > > implementation, and to check if other DOLFIN-people were working on
> > > > > > > similar stuff to avoid double/conflicting development.
> > > > > > >
> > > > > > > /Johan
> > > > > > >
> > > > > > >
> > > > > > >               
> > > > > > Very good. We were about to start on this task, so now a good point in
> > > > > > time
> > > > > > to join forces.
> > > > > > As a starting point, it would be nice to agreeing on what data is
> > > > > >
> > > > > >             
> > > > > needed
> > > > >
> > > > >           
> > > > > > in
> > > > > > addition to the partitioned meshes to construct the global dofmap.
> > > > > >
> > > > > >             
> > > > > I.e.
> > > > >
> > > > >           
> > > > > > which MeshFunctions to construct during the mesh paritioning process.
> > > > > >
> > > > > >             
> > > > > Are
> > > > >
> > > > >           
> > > > > > you people using the same {T,S,F} input as Anders describes in
> > > > > >
> > > > > >             
> > > > > Algorithm 5
> > > > >
> > > > >           
> > > > > > in his paper?
> > > > > >
> > > > > >             
> > > > > We have discussed this, and it seems that for our adaptive algorithms we
> > > > > need some more info. Basically, we have two aims:
> > > > >
> > > > > 1. Fully distributed computing (no collection of data on one processor)
> > > > > 2. Possibility for dynamic load balancing
> > > > >
> > > > > To realize 1-2 we need information on the processor ownership of
> > > > > entities,
> > > > > and for resdistributing the mesh we need global vertex numbering. That
> > > > > is,
> > > > > we would need something like: {T,S,F,V,O}, where V is global vertex
> > > > > number
> > > > > and O is information whether boundary (between processors) vertices are
> > > > > own by the processor or if they are ghost nodes.
> > > > >
> > > > >           
> > > > How do you deal with global edge or face numbers?
> > > >
> > > >         
> > > I believe this is rebuilt from global vertex numbers.
> > >
> > >       
> > The mesh will number the edges and faces, and then the generated UFC
> > code will compute a dof map from those edge and face numbers. The
> > local dof map will look different for different elements and the
> > global must be based on the local.
> >
> >
> >     
> > > > My suggestion is to start without a global numbering and then build it
> > > > (in parallel).
> > > >
> > > >         
> > > I am not sure how from only local info you can construct information on
> > > which boundary vertices are owned by which processes?
> > >
> > >       
> > Each processor knows which facets are shared and with which other
> > process.
> >
> >
> >     
> > > > >  Possibly this is too much information, since for example S,F can be
> > > > > computed from V,O, but by storing all info faster algorithms can be
> > > > > constructed, so there is a trad-off between speed and memory.
> > > > >
> > > > > What do you say?
> > > > >
> > > > >           
> > > > If you have something that works, just send us a patch so we can try it.
> > > >
> > > >         
> > > Niclas can send you his code.
> > >
> > >       
> > Send it to the list, and even better as a patch for DofMapBuilder::build().
> > If it works we can just use it.
> >
> > --
> > Anders
> >
> >     
> I send the code to the list.  It's not suitable as a patch due to the
> modification done to the Mesh class.
>
> Niclas
> _______________________________________________
>
>   



The code could be fetched from

http://www.csc.kth.se/~njansson/dolfin-2008-08-14.tar.bz2

Requires PETSc and parmetis, (customLinkFlags = '-lmetis -lparmetis')

DofMap::build don't construct a global dofmap. It reorders the map in 
order to minimize communication during assembly.
The global dofmap is obtained from the ordinary tabulate_dofs call.

Niclas