dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Fri, Aug 22, 2008 at 09:11:37AM +0200, Niclas Jansson wrote:
> Anders Logg wrote:
> > 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.
> > 
> 
> Parallel mesh parsing, the entire mesh is never represented on a single 
> processor. It's a two stage process, first the coordinates are loaded 
> and partitioned with a geometric partitioner. In the second stage each 
> processor loads the cells corresponding to the assigned coordinates, and 
> finally the mesh is partitioned with a graph partitioner.
> 
> Partitioning is done with the distributed geometric and mesh-to-dual 
> graph partitioner in parmetis.

How does this work? It seems as if you have already partitioned the
domain geometrically, then there's no need to make a partition based on
topology. Or is the geometric partitioning only a first approximation
and then vertices are exchanged between processors?

-- 
Anders


> Mesh distribution or more correctly redistribution (since the mesh is 
> always distributed) moves vertices between processors and construct a 
> new mesh with the MeshEditor. Since processors share vertices in the 
> overlap, I use the concept of ghosted vertices in order to decide which 
> processor should be responsible for redistributing a vertex.
> 
> 
> Niclas
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