[petsc-dev] Seeking Advice on Petsc Preconditioners to Try
Mark F. Adams
mark.adams at columbia.edu
Thu Dec 29 13:11:05 CST 2011
First you need to set the block size for the matrix as I said before.
Then if this is a vector Laplacian like operator then the code can construct the null space with the node/cell coordinates, which is required for the method to be complete for a vector Lapalcian. Here is a 3D example:
ierr = PetscMalloc( (m+1)*sizeof(PetscReal), &coords ); CHKERRQ(ierr);
/* forms the element stiffness for the Laplacian and coordinates */
for(i=Ni0,ic=0,ii=0;i<Ni1;i++,ii++){
for(j=Nj0,jj=0;j<Nj1;j++,jj++){
for(k=Nk0,kk=0;k<Nk1;k++,kk++,ic++){
/* coords */
x = coords[3*ic] = h*(PetscReal)i;
y = coords[3*ic+1] = h*(PetscReal)j;
z = coords[3*ic+2] = h*(PetscReal)k;
}
}
}
ierr = KSPSetOperators( ksp, Amat, Amat, SAME_NONZERO_PATTERN ); CHKERRQ(ierr);
ierr = PCSetCoordinates( pc, 3, coords ); CHKERRQ(ierr);
On Dec 29, 2011, at 12:15 PM, Dave Nystrom wrote:
> 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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