dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Thu, Aug 21, 2008 at 11:14:09AM +0200, Niclas Jansson wrote:
> Anders Logg wrote:
> > On Thu, Aug 21, 2008 at 09:10:03AM +0200, Niclas Jansson wrote:
> >> Anders Logg wrote:
> >>> On Wed, Aug 20, 2008 at 06:17:30PM +0200, Niclas Jansson wrote:
> >>>
> >>>>>> Stage 2 seems to involve a lot of communication, with small messages.
> >>>>>> I think it would be more efficient if the stage were reorganized such
> >>>>>> that all messages could be exchanged "at once", in a couple of larger
> >>>>>> messages.
> >>>>> That would be nice. I'm very open to suggestions.
> >>>> If understand the {T, S, F} overlap correctly, a facet could be globally
> >>>> identified by the value of F(facet).
> >>> No, F(facet) would be the local number of the facet in subdomain S(facet).
> >>>
> >>>> If so, one suggestion is to buffer N_i and F(facet) in 0...p-1 buffers
> >>>> (one for each processor) and exchange these during stage 2.
> >>>>
> >>>> -- stage 1
> >>>>
> >>>>   for each facet  f \in T
> >>>>     j = S_i(f)
> >>>>     if j > i
> >>>>
> >>>>         -- calculate dof N_i
> >>>>
> >>>>         buffer[S_i(f)].add(N_i)
> >>>>         buffer[S_i(f)].add(F_i(f))
> >>>>     end
> >>>>   end
> >>>>
> >>>>
> >>>> -- stage 2
> >>>>
> >>>> -- Exchange shared dofs with fancy MPI_Allgatherv or a lookalike
> >>>> -- MPI_SendRecv loop.
> >>>>
> >>>>    for j = 1 to j = (num processors - 1)
> >>>>       src = (rank - j + num processors) % num processors
> >>>>       dest = (rank + j) % num processors
> >>>>
> >>>>       MPI_SendRecv(dest, buffer[dest], src, recv_buffer)
> >>>>
> >>>>       for i = 0 to sizeof(recv_buffer), i += 2
> >>>>          --update facet recv_buff(i+1) with dof value in  recv_buff(i)
> >>>>       end
> >>>>
> >>>>    end
> >>> I didn't look at this in detail (yet). Is it still valid with the
> >>> above interpretation of F(facet)?
> >>>
> >> Yes, I think so.
> > 
> > I think I understand your point, but I don't understand the details
> > of your code.
> 
> if j > i the processor is responsible for creating M_i for the shared 
> facet. The newly created M_i is placed in the send buffer for the 
> subdomain S_f(f), together with the local facet number in that subdomain.
> 
> So the send buffers contains tuples {M_i, F_i(f)}, since there is one 
> buffer for each subdomain, one could be sure that F_i(f) is valid on the 
> receiving processor.
> 
> Instead of iterating over all processors and facets in stage 2, each 
> processor receives a set of tuples (for all shared facets) from each 
> processor. These could then be used to identify the local facet (since 
> F_i(f) is the local facet number) and assign the dofs, which, if I 
> understand everything correctly is obtained from M_i.
>
> One modification to the above algorithm, I think it's easier if the 
> tuples are stored as {F_i(f), M_i}. Since M_i could be a long list of 
> dofs. So the update loop would be something similar to
> 
>   for i = 0 to size of recv_buff , i +=(number of dofs on each facet + 1)
>      local facet f = recv_buff(i)
>      for each facet on f, loop counter j
>         assign recv_buff( (i+1) + j) ) to facet dof j
>      end
>   end
> 
> > 
> > The mapping N_i is an auxiliary global-to-global mapping, which maps
> > the global dofs on a local mesh to global dofs on the global mesh. It
> > has a meaning only on each local mesh. What we want to communicate is
> > the stuff in M_i.
> 
> I see, then it should be M_i in the outlined code.
> 
> Niclas

Sounds very good.

Where do we start?

I guess one good place to start would be to get input/partitioning
working and you seem to have that working already. We should be able
to read in a mesh, partition it (with ParMetis for now) and construct
the MeshFunctions S_i and F_i.

Once that is in place, we can start hacking on DofMapBuilder::build().

Could you outline what you have in terms of input/partitioning and
then we can start applying those patches.

-- 
Anders

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