Hi Matthew,
Is your first part of your answer (using DMDASetBlockFills) valid only
in the case I create a DMDA object?
Yes I think that is the kind of stencil I am using. I could know how the
stencil looks like exactly, but I preallocate looping, for each process
on all the elements of the stencil, grid node by grid node (which is not
that costly, and "exact")
If I do NOT use a DMDA object and create my MPIAIJ matrix myself, how do
I get the global row indices owned by the process (the "DMDA-like" ones
you mentioned)? The problem is that MatGetOwnershipRange cannot be
called if the matrix hasn't been preallocated, and I need the global
indices to preallocate.
Thibaut
On 21/02/2019 17:49, Matthew Knepley wrote:
On Thu, Feb 21, 2019 at 11:16 AM Thibaut Appel via petsc-users
<[email protected] <mailto:[email protected]>> 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/>
