“Possibly, but if you are doing FD, then there is built-in topology in DMDA
that is not present in Plex, so
finding the neighbors in the right order is harder (possible, but harder, we
address this in some new work that is not yet merged). There is also structured
adaptive support with DMForest, but this also does not preserve the stencil.
“
I’m using an FEM which doesn’t utilize such neighbor info, so perhaps Plex or
DMForest could be easier to use then
“The efficiency of active set VI solvers in PETSc demonstrates to me that
solving reduced systems can be done efficiently with geometric multigrid using
a structured grid so I would not suggest giving up on what you started.
You can do it in two steps
1) Use PCREDISTRIBUTE but hack the code in redistribute.c to not move dof
between MPI ranks, just have it remove the locked rows/columns (to start just
run on one MPI rank since then nothing is moved) Then in your code you just
need to pull out the appropriate rows and columns of the interpolation that
correspond to the dof you have kept and pass this smaller interpolation to the
inner KSP PCMG. This is straightforward and like what is in DMSetVI. The MG
convergence should be just as good as on the full system.
2) the only problem with 1 is it is likely to be poorly load balanced (but you
can make some runs to see how imbalanced it is, that will depend exactly on
what parts are locked and what MPI processes they are on). So if it is poorly
balanced then you would need to get out of redistribute.c a mapping for each
kept dof to what MPI rank it is moved to and use that to move the entries in
the reduced interpolation you have created.
If you do succeed it would actually be useful code that we could add to
PCREDISTRIBUTE for more general use by others.
Barry
“
Thanks, that seems doable, if not super easy. I might try that
Kind regards
/Carl-Johan
From: Barry Smith <bsm...@petsc.dev>
Sent: Friday, June 30, 2023 5:21 PM
To: Matthew Knepley <knep...@gmail.com>
Cc: Carl-Johan Thore <carl-johan.th...@liu.se>; petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] PCMG with PCREDISTRIBUTE
On Jun 30, 2023, at 10:22 AM, Matthew Knepley
<knep...@gmail.com<mailto:knep...@gmail.com>> wrote:
On Fri, Jun 30, 2023 at 10:16 AM Carl-Johan Thore via petsc-users
<petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> wrote:
Thanks for the quick reply and the suggestions!
“ … you should first check that the PCMG works quite well “
Yes, the PCMG works very well for the full system.
“I am guessing that your code is slightly different than ex42.c because you
take the interpolation matrix provided by the DM
and give it to the inner KSP PCMG?. So you solve problem 2 but not problem 1.”
Yes, it’s slightly different so problem 2 should be solved.
It looked somewhat complicated to get PCMG to work with redistribute, so I’ll
try with PCGAMG first
(it ran immediately with redistribute, but was slower than PCMG on my, very
small, test problem. I’ll try
to tune the settings).
A related question: I’m here using a DMDA for a structured grid but I’m locking
so many DOFs that for many of the elements
all DOFs are locked. In such a case could it make sense to switch/convert the
DMDA to a DMPlex containing only those
elements that actually have DOFs?
Possibly, but if you are doing FD, then there is built-in topology in DMDA that
is not present in Plex, so
finding the neighbors in the right order is harder (possible, but harder, we
address this in some new work that is not yet merged). There is also structured
adaptive support with DMForest, but this also does not preserve the stencil.
The efficiency of active set VI solvers in PETSc demonstrates to me that
solving reduced systems can be done efficiently with geometric multigrid using
a structured grid so I would not suggest giving up on what you started.
You can do it in two steps
1) Use PCREDISTRIBUTE but hack the code in redistribute.c to not move dof
between MPI ranks, just have it remove the locked rows/columns (to start just
run on one MPI rank since then nothing is moved) Then in your code you just
need to pull out the appropriate rows and columns of the interpolation that
correspond to the dof you have kept and pass this smaller interpolation to the
inner KSP PCMG. This is straightforward and like what is in DMSetVI. The MG
convergence should be just as good as on the full system.
2) the only problem with 1 is it is likely to be poorly load balanced (but you
can make some runs to see how imbalanced it is, that will depend exactly on
what parts are locked and what MPI processes they are on). So if it is poorly
balanced then you would need to get out of redistribute.c a mapping for each
kept dof to what MPI rank it is moved to and use that to move the entries in
the reduced interpolation you have created.
If you do succeed it would actually be useful code that we could add to
PCREDISTRIBUTE for more general use by others.
Barry
Thanks,
Matt
From: Barry Smith <bsm...@petsc.dev<mailto:bsm...@petsc.dev>>
Sent: Friday, June 30, 2023 3:57 PM
To: Carl-Johan Thore <carl-johan.th...@liu.se<mailto:carl-johan.th...@liu.se>>
Cc: petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>
Subject: Re: [petsc-users] PCMG with PCREDISTRIBUTE
Oh, I forgot to mention you should first check that the PCMG works quite
well for the full system (without the PCREDISTRIBUTE); the convergence
on the redistributed system (assuming you did all the work to get PCMG to work
for you) should be very similar to (but not measurably better) than the
convergence on the full system.
On Jun 30, 2023, at 9:17 AM, Barry Smith
<bsm...@petsc.dev<mailto:bsm...@petsc.dev>> wrote:
ex42.c provides directly the interpolation/restriction needed to move
between levels in the loop
for (k = 1; k < nlevels; k++) {
PetscCall(DMCreateInterpolation(da_list[k - 1], da_list[k], &R, NULL));
PetscCall(PCMGSetInterpolation(pc, k, R));
PetscCall(MatDestroy(&R));
}
The more standard alternative to this is to call KSPSetDM() and have the PCMG
setup use the DM
to construct the interpolations (I don't know why ex42.c does this construction
itself instead of having the KSPSetDM() process handle it but that doesn't
matter). The end result is the same in both cases.
Since PCREDISTRIBUTE builds its own new matrix (by using only certain rows
and columns of the original matrix) the original interpolation
cannot be used for two reasons
1) (since it is for the full system) It is for the wrong problem.
2) In addition, if you ran with ex42.c the inner KSP does not have access to
the interpolation that was constructed so you could not get PCMG to to work as
indicated below.
I am guessing that your code is slightly different than ex42.c because you take
the interpolation matrix provided by the DM
and give it to the inner KSP PCMG?. So you solve problem 2 but not problem 1.
So the short answer is that there is no "canned" way to use the PCMG process
trivially with PCDISTRIBUTE.
To do what you want requires two additional steps
1) after you construct the full interpolation matrix (by using the DM) you
need to remove the rows associated with the dof that have been removed by the
"locked" variables (and the columns that are associated with coarse grid points
that live on the removed points) so that the interpolation is the correct
"size" for the smaller problem
2) since PCREDISTRIBUTE actually moves dof of freedom between MPI processes for
load balancing after it has removed the locked variables you would need to do
the exact same movement for the rows of the interpolation matrix that you have
constructed (after you have removed the "locked" rows of the interpolation.
Lots of bookkeeping to acheive 1 and 2 but conceptually simple.
As an experiment you can try using PCGAMG on the redistributed matrix
-redistribute_pc_type gamg to use algebraic multigrid just to see the time and
convergence rates. Since GAMG creates its own interpolation based on the matrix
and it will be built on the smaller redistributed matrix there will no issue
with the wrong "sized" interpolation. Of course you have the overhead of
algebraic multigrid and cannot take advantage of geometric multigrid. The GAMG
approach may be satisfactory to your needs.
If you are game for looking more closely at using redistribute with geometric
multigrid and PETSc (which will require digging into PETSc source code and
using internal information in the PETSc source code) you can start by looking
at how we solve variational problems with SNES using reduced space active set
methods. SNESVINEWTONRSLS /src/snes/impls/vi/rs/virs.c This code solves problem
1 see() it builds the entire interpolation and then pulls out the required
non-locked part. Reduced space active set methods essentially lock the
constrained dof and solve a smaller system without those dof at each iteration.
But it does not solve problem 2. Moving the rows of the "smaller" interpolation
to the correct MPI process based on where PCREDISTRIBUTE moved rows. To do this
would requring looking at the PCREDISTRUBUTE code and extracting the
information of where each row was moving and performing the process for the
interpolation matrix.
src/ksp/pc/impls/redistribute/redistribute.c
Barry
On Jun 30, 2023, at 8:21 AM, Carl-Johan Thore via petsc-users
<petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> wrote:
Hi,
I'm trying to run an iterative solver (FGMRES for example) with PCMG as
preconditioner. The setup of PCMG
is done roughly as in ex42 of the PETSc-tutorials
(https://petsc.org/main/src/ksp/ksp/tutorials/ex42.c.html).
Since I have many locked degrees-of-freedom I would like to use
PCREDISTRIBUTE. However, this
results in (30039 is the number of DOFs after redistribute and 55539 the number
before):
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Nonconforming object sizes
[0]PETSC ERROR: Matrix dimensions of A and P are incompatible for
MatProductType PtAP: A 30039x30039, P 55539x7803
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.19.0-238-g512d1ae6db4 GIT
Date: 2023-04-24 16:37:00 +0200
[0]PETSC ERROR: topopt on a arch-linux-c-opt Fri Jun 30 13:28:41 2023
[0]PETSC ERROR: Configure options COPTFLAGS="-O3 -march=native"
CXXOPTFLAGS="-O3 -march=native" FOPTFLAGS="-O3 -march=native" CUDAOPTFLAGS=-O3
--with-cuda --with-cusp --with-debugging=0 --download-scalapack --download-hdf5
--download-zlib --download-mumps --download-parmetis --download-metis
--download-ptscotch --download-hypre --download-spai
[0]PETSC ERROR: #1 MatProductSetFromOptions_Private() at
/mnt/c/mathware/petsc/src/mat/interface/matproduct.c:420
[0]PETSC ERROR: #2 MatProductSetFromOptions() at
/mnt/c/mathware/petsc/src/mat/interface/matproduct.c:541
[0]PETSC ERROR: #3 MatPtAP() at
/mnt/c/mathware/petsc/src/mat/interface/matrix.c:9868
[0]PETSC ERROR: #4 MatGalerkin() at
/mnt/c/mathware/petsc/src/mat/interface/matrix.c:10899
[0]PETSC ERROR: #5 PCSetUp_MG() at
/mnt/c/mathware/petsc/src/ksp/pc/impls/mg/mg.c:1029
[0]PETSC ERROR: #6 PCSetUp() at
/mnt/c/mathware/petsc/src/ksp/pc/interface/precon.c:994
[0]PETSC ERROR: #7 KSPSetUp() at
/mnt/c/mathware/petsc/src/ksp/ksp/interface/itfunc.c:406
[0]PETSC ERROR: #8 PCSetUp_Redistribute() at
/mnt/c/mathware/petsc/src/ksp/pc/impls/redistribute/redistribute.c:327
[0]PETSC ERROR: #9 PCSetUp() at
/mnt/c/mathware/petsc/src/ksp/pc/interface/precon.c:994
[0]PETSC ERROR: #10 KSPSetUp() at
/mnt/c/mathware/petsc/src/ksp/ksp/interface/itfunc.c:406
[0]PETSC ERROR: #11 KSPSolve_Private() at
/mnt/c/mathware/petsc/src/ksp/ksp/interface/itfunc.c:824
[0]PETSC ERROR: #12 KSPSolve() at
/mnt/c/mathware/petsc/src/ksp/ksp/interface/itfunc.c:1070
It’s clear what happens I think, and it kind of make since not all levels are
redistributed as they should (?).
Is it possible to use PCMG with PCREDISTRIBUTE in an easy way?
Kind regards,
Carl-Johan
--
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/>
