[petsc-dev] [pflotran-dev: 976] Re: [pflotran-users: 998] Distorted structured grid

[Paolo Orsini]

Hi Jed,

I am back to work on this now...

Thanks for explaining how I can do this. it makes perfectly sense:

A. Assign entries values = 1, when forming the Adj matrix,

B. Convert the Adj matrix to AIJ matrix, so I can use MatMatTransposeMult
(or form AIJ directly): can I preallocate AIJ before calling MatConvert? To
avoid slow performance? Is there any conflict between the preallocoation
functions and MatConvert?

C. Filter AIJ, to remove entries with values <3 (for 3d problems). What
function shall I use to do this operation?

Thank you

Paolo



On Sun, Nov 3, 2013 at 1:34 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:

> Paolo Orsini <paolo.orsini at gmail.com> writes:
>
> > The computation of the dual graph of the mesh is a bit more complicated
> > than multiplying the adjacency matrix by its transpose, but not far off.
> > With this operation, also the cells that share only one node are
> connected
> > in the dual graph.
> > Instead, the minimum number of common nodes is >1 (2 in 2D probelms, 3 in
> > 3D problems). In fact, this is an input of MatMeshToCellGraph, I should
> > have understood this before.
> >
> > This can be computed doing the transpose adjacency matrix (Adj_T), then
> > doing the multiplication line by line of Adj time Adj_T, and discard the
> > non zero entries coming from to elements that share a number of nodes
> less
> > than  the minimum number of common nodes imposed. I have not implement
> this
> > yet, any suggestion is welcome.
>
>
> You can just put in weights of 1.0, call MatMatTransposeMult, and filter
> the resulting matrix.  It'll take a bit more memory, but probably not
> prohibitively much.
>
> > I also found out that Schotch has a facility to compute a dual graph
> from a
> > mesh, but not PTScotch.
> > Once the graph is computed, PTSchotch can load the central dual graph,
> and
> > distribute it into several processors during the loading.
> > Am i right to say that PETSC is interfaced only with PTSchotch and not
> with
> > Scotch?
>
> Scotch is serial so even if we had a specialized Scotch interface, it
> would not be scalable (memory or time).
>
> > To check if the PTSchotch partition works (within PFLOTRAN ), I am
> > computing a DualMat with parmetis, saving it into a file. Then I
> recompile
> > the code (using a petsc compiled with ptscotch), an load the DualMat
> from a
> > file rather then forming a new one. I did a successful test when running
> on
> > one processor. but I am having trouble when try on more.
>
> Make sure you load on the same communicator with the same sizes set (so
> that the distribution matches what you expect).  You'll have to be more
> specific if you want more help.
>
> > I though the the dual graph was computed only once, even during the mpi
> > process, instead it seems to be recomputed more than once. Not sure
> why....
> > sure i am missing something ???
>
> That seems like a question about your program logic.  Should be easy to
> figure out if you set a breakpoint in the debugger.
>
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