[petsc-dev] Seeking Advice on Petsc Preconditioners to Try
Dave Nystrom
dnystrom1 at comcast.net
Thu Dec 29 11:15:40 CST 2011
Hi Mark,
I have tried out -ksp_type cg -pc_type gamg -pc_gamg_type sa on my problem
and am encouraged enough with the results that I would like to try taking the
next step with using gamg. Could you provide some advice on how to do that?
I'm not sure how to provide the null space info you say is important.
Thanks,
Dave
Mark F. Adams writes:
>
> On Dec 20, 2011, at 10:33 AM, Dave Nystrom wrote:
>
> > Hi Mark,
> >
> > I would like to try GAMG on some of my linear solves. Could you suggest how
> > to get started? Is it more complicated than something like:
> >
> > -ksp_type cg -pc_type gamg
>
> This is a good start. for scalar SPD problems '-pc_gamg_type sa' is good (this might be the default, use -help to see.
>
> Mark
>
> >
> > I'm guessing I should first try it on one of my easier linear solves. I have
> > 5 of them that would have a block size of 1. Are the other GAMG option
> > defaults good to start with or should I be trying to configure them as well?
> > If so, I'm not familiar enough with multigrid to know off hand how to do
> > that.
> >
> > Thanks,
> >
> > Dave
> >
> > Mark F. Adams writes:
> >>
> >> On Dec 2, 2011, at 6:06 PM, Dave Nystrom wrote:
> >>
> >>> Mark F. Adams writes:
> >>>> It sounds like you have a symmetric positive definite systems like du/dt -
> >>>> div(alpha(x) grad)u. The du/dt term makes the systems easier to solve.
> >>>> I'm guessing your hard system does not have this mass term and so is
> >>>> purely elliptic. Multigrid is well suited for this type of problem, but
> >>>> the vector nature requires some thought. You could use PETSc AMG -pc_type
> >>>> gamg but you need to tell it that you have a system of two dof/vertex.
> >>>> You can do that with something like:
> >>>>
> >>>> ierr = MatSetBlockSize( mat, 2 ); CHKERRQ(ierr);
> >>>>
> >>>> For the best results from GAMG you need to give it null space information
> >>>> but we can worry about that later.
> >>>
> >>> Hi Mark,
> >>>
> >>> I have been interested in trying some of the multigrid capabilities in
> >>> petsc. I'm not sure I remember seeing GAMG so I guess I should go look for
> >>> that.
> >>
> >> GAMG is pretty new.
> >>
> >>> I have tried sacusp and sacusppoly but did not get good results on
> >>> this particular linear system.
> >>> In particular, sacusppoly seems broken. I
> >>> can't get it to work even with the petsc src/ksp/ksp/examples/tutorials/ex2.c
> >>> example. Thrust complains about an invalid device pointer I believe.
> >>> Anyway, I can get the other preconditioners to work just fine on this petsc
> >>> example problem. When I try sacusp on this matrix for the case of generating
> >>> a rhs from a known solution vector, the computed solution seems to diverge
> >>> from the exact solution. We also have an interface to an external agmg
> >>> package which is not able to solve this problem
> >>> but works well on the other 5
> >>> linear solves. So I'd like to try more from the multigrid toolbox but do not
> >>> know much about how to supply the extra stuff that these packages often need.
> >>>
> >>> So, it sounds like you are suggesting that I try gamg and that I could at
> >>> least try it out without having to initially supply lots of additional info.
> >>> So I will take a look at gamg.
> >>>
> >>
> >> There are many things that can break a solver but most probably want to know that its a system so if you can set the block size and try gamg then that would be a good start.
> >>
> >> Mark
> >>
> >>> Thanks,
> >>>
> >>> Dave
> >>>
> >>>> Mark
> >>>>
> >>>> On Nov 30, 2011, at 8:15 AM, Matthew Knepley wrote:
> >>>>
> >>>>> On Wed, Nov 30, 2011 at 12:41 AM, Dave Nystrom <dnystrom1 at comcast.net> wrote:
> >>>>> I have a linear system in a code that I have interfaced to petsc that is
> >>>>> taking about 80 percent of the run time per timestep. This linear system is
> >>>>> a symmetric block banded matrix where the blocks are 2x2. The matrix looks
> >>>>> as follows:
> >>>>>
> >>>>> 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0
> >>>>> 1X X Y Y Y
> >>>>> 2X X X Y Y Y
> >>>>> 3 X X X Y Y Y
> >>>>> 4 X X X Y Y Y
> >>>>> 5 X X X Y Y Y
> >>>>> 6 X X X Y Y Y
> >>>>> 7 X X X Y Y Y
> >>>>> 8 X X X Y Y Y
> >>>>> 9 X X X Y Y Y
> >>>>> 0 X X X Y Y Y
> >>>>> 1 X X X Y Y Y
> >>>>> 2 X X X Y Y Y
> >>>>> 3Z X X X Y Y Y
> >>>>> 4Z Z X X X Y Y Y
> >>>>> 5Z Z Z X X X Y Y Y
> >>>>> 6 Z Z Z X X X Y Y Y
> >>>>> 7 Z Z Z X X X Y Y Y
> >>>>> 8 Z Z Z X X X Y Y Y
> >>>>> 9 Z Z Z X X X Y Y Y
> >>>>> 0 Z Z Z X X X Y Y Y
> >>>>>
> >>>>> So in my diagram above, X, Y and Z are 2x2 blocks. The symmetry of the
> >>>>> matrix requires that X_ij = transpose(X_ji) and Y_ij = transpose(Z_ji). So
> >>>>> far, I have just input this matrix to petsc without indicating that it was
> >>>>> block banded with 2x2 blocks. I have also not told petsc that the matrix is
> >>>>> symmetric. And I have allowed petsc to decide the best way to store the
> >>>>> matrix.
> >>>>>
> >>>>> I can solve this linear system over the course of a run using -ksp_type
> >>>>> preonly -pc_type lu. But that will not scale very well to larger problems
> >>>>> that I want to solve. I can also solve this system over the course of a run
> >>>>> using -ksp_type cg -pc_type jacobi -vec_type cusp -mat_type aijcusp.
> >>>>> However, over the course of a run, the iteration count ranges from 771 to
> >>>>> 47300. I have also tried sacusp, ainvcusp, sacusppoly, ilu(k) and icc(k)
> >>>>> with k=0. The sacusppoly preconditioner fails because of a thrust error
> >>>>> related to an invalid device pointer, if I am remembering correctly. I
> >>>>> reported this problem to petsc-maint a while back and have also reported it
> >>>>> for the cusp bugtracker. But it does not appear that anyone has really
> >>>>> looked into the bug. For the other preconditioners of sacusp, ilu(k) and
> >>>>> icc(k), they do not result in convergence to a solution and the runs fail.
> >>>>>
> >>>>> All preconditioners are custom. Have you done a literature search for PCs
> >>>>> known to work for this problem? Can yu say anything about the spectrum of the
> >>>>> operator? conditioning? what is the principal symbol (if its a PDE)? The pattern
> >>>>> is not enough to recommend a PC.
> >>>>>
> >>>>> Matt
> >>>>>
> >>>>> I'm wondering if there are suggestions of other preconditioners in petsc that
> >>>>> I should try. The only third party package that I have tried is the
> >>>>> txpetscgpu package. I have not tried hypre or any of the multigrid
> >>>>> preconditioners yet. I'm not sure how difficult it is to try those
> >>>>> packages. Anyway, so far I have not found a preconditioner available in
> >>>>> petsc that provides a robust solution to this problem and would be interested
> >>>>> in any suggestions that anyone might have of things to try.
> >>>>>
> >>>>> I'd be happy to provide additional info and am planning on packaging up a
> >>>>> couple of examples of the matrix and rhs for people I am interacting with at
> >>>>> Tech-X and EMPhotonics. So I'd be happy to provide the matrix examples for
> >>>>> this forum as well if anyone wants a copy.
> >>>>>
> >>>>> Thanks,
> >>>>>
> >>>>> Dave
> >>>>>
> >>>>> --
> >>>>> Dave Nystrom
> >>>>>
> >>>>> phone: 505-661-9943 (home office)
> >>>>> 505-662-6893 (home)
> >>>>> skype: dave.nystrom76
> >>>>> email: dnystrom1 at comcast.net
> >>>>> smail: 219 Loma del Escolar
> >>>>> Los Alamos, NM 87544
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> 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
> >>>>
> >>>
> >>
> >
>
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