[petsc-users] About DMDA (and extracting its ordering)

[Matthew Knepley]

On Thu, Feb 21, 2019 at 11:16 AM Thibaut Appel via petsc-users <
petsc-users at mcs.anl.gov> wrote:

> Dear PETSc developers/users,
>
> I’m solving linear PDEs on a regular grid with high-order finite
> differences, assembling an MPIAIJ matrix to solve linear systems or
> eigenvalue problems. I’ve been using vertex major, natural ordering for the
> parallelism with PetscSplitOwnership (yielding rectangular slices of the
> physical domain) and wanted to move to DMDA to have a more square-ish
> domain decomposition and minimize communication between processes.
>
> However, my application is memory critical, and I have finely-tuned matrix
> preallocation routines for allocating memory “optimally”. It seems the
> memory of a DMDA matrix is allocated along the value of the stencil width
> of DMDACreate and the manual says about it
>
> “These DMDA stencils have nothing directly to do with any finite
> difference stencils one might chose to use for a discretization”
>
> And despite reading the manual pages there must be something I do not
> understand in the DM topology, what is that "stencil width" for then? I
> will not use ghost values for my FD-method, right?
>

What this is saying is, "You might be using some stencil that is not STAR
or BOX, but we are preallocating according to one of those".
If you really care about how much memory is preallocated, which it seems
you do, then you might be able to use


https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMDA/DMDASetBlockFills.html

to tell use exactly how to preallocate.


> I was then wondering if I could just create a MPIAIJ matrix, and with a
> PETSc routine get the global indices of the domain for each process: in
> other words, an equivalent of PetscSplitOwnership that gives me the DMDA
> unknown ordering. So I can feed and loop on that in my preallocation and
> assembly routines.
>

You can make an MPIAIJ matrix yourself of course. It should have the same
division of rows as the DMDA division of dofs. Also, MatSetValuesStencil()
will not work for a custom matrix.

  Thanks,

     Matt


> Thanks very much,
>
> Thibaut
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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