[petsc-users] PetscDSSetJacobianPreconditioner causing DIVERGED_LINE_SEARCH for multi-field problem
Matthew Knepley
knepley at gmail.com
Sun Apr 3 08:17:37 CDT 2016
On Sun, Apr 3, 2016 at 6:55 AM, Sander Arens <Sander.Arens at ugent.be> wrote:
> Any thoughts on this, Matt?
>
Shoot, this fell out of my working set, and I am behind on incorporating
your pull request. I will
look at both this week.
Thanks,
Matt
> Thanks,
> Sander
>
> On 21 March 2016 at 09:49, Sander Arens <Sander.Arens at ugent.be> wrote:
>
>> Matt,
>>
>> I think the problem is in DMCreateSubDM_Section_Private. The block size
>> can be counted there (very similar as in DMCreateMatrix_Plex) and then
>> passed down to the IS. I can create a pull request for this if you'd like
>> (or should I just add this to my other pull request for the Neumann bc's)?
>>
>> On 3 March 2016 at 18:02, Sander Arens <Sander.Arens at ugent.be> wrote:
>>
>>> Ok, thanks for clearing that up!
>>>
>>> On 3 March 2016 at 18:00, Matthew Knepley <knepley at gmail.com> wrote:
>>>
>>>> On Thu, Mar 3, 2016 at 10:48 AM, Sander Arens <Sander.Arens at ugent.be>
>>>> wrote:
>>>>
>>>>> So is the block size here refering to the dimension of the
>>>>> near-nullspace or has it something to do with the coarsening?
>>>>>
>>>>> I would have thought to also see the block size in this part:
>>>>>
>>>>
>>>> Dang, that is a problem. It should have the correct block size when FS
>>>> pulls it out of the overall matrix. This should be
>>>> passed down using the block size of the IS. Something has been broken
>>>> here. I will put it on my list of things to look at.
>>>>
>>>> Thanks,
>>>>
>>>> Matt
>>>>
>>>>
>>>>> Mat Object: 1 MPI processes
>>>>> type: seqaij
>>>>> rows=1701, cols=1701
>>>>> total: nonzeros=109359, allocated nonzeros=109359
>>>>> total number of mallocs used during MatSetValues
>>>>> calls =0
>>>>> has attached near null space
>>>>> using I-node routines: found 567 nodes, limit
>>>>> used is 5
>>>>>
>>>>> Thanks,
>>>>> Sander
>>>>>
>>>>>
>>>>> On 3 March 2016 at 17:29, Matthew Knepley <knepley at gmail.com> wrote:
>>>>>
>>>>>> You can see the block size in the output
>>>>>>
>>>>>> Mat Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=12, cols=12, bs=6
>>>>>> total: nonzeros=144, allocated nonzeros=144
>>>>>> total number of mallocs used during MatSetValues
>>>>>> calls =0
>>>>>> using I-node routines: found 3 nodes, limit
>>>>>> used is 5
>>>>>> linear system matrix = precond matrix:
>>>>>> Mat Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=12, cols=12, bs=6
>>>>>> total: nonzeros=144, allocated nonzeros=144
>>>>>> total number of mallocs used during MatSetValues
>>>>>> calls =0
>>>>>> using I-node routines: found 3 nodes, limit used is
>>>>>> 5
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Matt
>>>>>>
>>>>>> On Thu, Mar 3, 2016 at 10:28 AM, Sander Arens <Sander.Arens at ugent.be>
>>>>>> wrote:
>>>>>>
>>>>>>> Sure, here it is.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Sander
>>>>>>>
>>>>>>> On 3 March 2016 at 15:33, Matthew Knepley <knepley at gmail.com> wrote:
>>>>>>>
>>>>>>>> On Thu, Mar 3, 2016 at 8:05 AM, Sander Arens <Sander.Arens at ugent.be
>>>>>>>> > wrote:
>>>>>>>>
>>>>>>>>> Yes, the matrix is created by one of the assembly functions in
>>>>>>>>> Plex, so that answers my question. I was confused by this because I
>>>>>>>>> couldn't see this information when using -snes_view.
>>>>>>>>>
>>>>>>>>
>>>>>>>> Hmm, then something is wrong because the block size should be
>>>>>>>> printed for the matrix at the end of the solver in -snes_view, Can you
>>>>>>>> send that to me?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Matt
>>>>>>>>
>>>>>>>>
>>>>>>>>> Thanks for the helpful replies,
>>>>>>>>> Sander
>>>>>>>>>
>>>>>>>>> On 3 March 2016 at 14:52, Matthew Knepley <knepley at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> On Thu, Mar 3, 2016 at 7:49 AM, Sander Arens <
>>>>>>>>>> Sander.Arens at ugent.be> wrote:
>>>>>>>>>>
>>>>>>>>>>> And how can I do this? Because when I look at all the options
>>>>>>>>>>> with -help I can strangely enough only find
>>>>>>>>>>> -fieldsplit_pressure_mat_block_size and not
>>>>>>>>>>> -fieldsplit_displacement_mat_block_size.
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Maybe I am missing something here. The matrix from which you
>>>>>>>>>> calculate the preconditioner using GAMG must be created somewhere. Why
>>>>>>>>>> is the block size not specified at creation time? If the matrix
>>>>>>>>>> is created by one of the assembly functions in Plex, and the PetscSection
>>>>>>>>>> has
>>>>>>>>>> a number of field components, then the block size will already be
>>>>>>>>>> set.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Matt
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Sander
>>>>>>>>>>>
>>>>>>>>>>> On 3 March 2016 at 14:21, Matthew Knepley <knepley at gmail.com>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> On Thu, Mar 3, 2016 at 6:20 AM, Sander Arens <
>>>>>>>>>>>> Sander.Arens at ugent.be> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Ok, I forgot to call SNESSetJacobian(snes, J, P, NULL, NULL)
>>>>>>>>>>>>> with J != P, which caused to write the mass matrix into the (otherwise
>>>>>>>>>>>>> zero) (1,1) block of the Jacobian and which was the reason for the
>>>>>>>>>>>>> linesearch to fail.
>>>>>>>>>>>>> However, after fixing that and trying to solve it with
>>>>>>>>>>>>> FieldSplit with LU factorization for the (0,0) block it failed because
>>>>>>>>>>>>> there were zero pivots for all rows.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Anyway, I found out that attaching the mass matrix to the
>>>>>>>>>>>>> Lagrange multiplier field also worked.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Another related question for my elasticity problem: after
>>>>>>>>>>>>> creating the rigid body modes with DMPlexCreateRigidBody and attaching it
>>>>>>>>>>>>> to the displacement field, does the matrix block size of the (0,0) block
>>>>>>>>>>>>> still have to be set for good performance with gamg? If so, how can I do
>>>>>>>>>>>>> this?
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Yes, it should be enough to set the block size of the
>>>>>>>>>>>> preconditioner matrix.
>>>>>>>>>>>>
>>>>>>>>>>>> Matt
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>> Sander
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 2 March 2016 at 12:25, Matthew Knepley <knepley at gmail.com>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Wed, Mar 2, 2016 at 5:13 AM, Sander Arens <
>>>>>>>>>>>>>> Sander.Arens at ugent.be> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I'm trying to set a mass matrix preconditioner for the Schur
>>>>>>>>>>>>>>> complement of an incompressible finite elasticity problem. I tried using
>>>>>>>>>>>>>>> the command PetscDSSetJacobianPreconditioner(prob, 1, 1, g0_pre_mass_pp,
>>>>>>>>>>>>>>> NULL, NULL, NULL) (field 1 is the Lagrange multiplier field).
>>>>>>>>>>>>>>> However, this causes a DIVERGED_LINE_SEARCH due to to Nan or
>>>>>>>>>>>>>>> Inf in the function evaluation after Newton iteration 1. (Btw, I'm using
>>>>>>>>>>>>>>> the next branch).
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Is this because I didn't use
>>>>>>>>>>>>>>> PetscDSSetJacobianPreconditioner for the other blocks (which uses the
>>>>>>>>>>>>>>> Jacobian itself for preconditioning)? If so, how can I tell Petsc to use
>>>>>>>>>>>>>>> the Jacobian for those blocks?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 1) I put that code in very recently, and do not even have
>>>>>>>>>>>>>> sufficient test, so it may be buggy
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 2) If you are using FieldSplit, you can control which blocks
>>>>>>>>>>>>>> come from A and which come from the preconditioner P
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCFieldSplitSetDiagUseAmat.html#PCFieldSplitSetDiagUseAmat
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCFieldSplitSetOffDiagUseAmat.html#PCFieldSplitSetOffDiagUseAmat
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I guess when using PetscDSSetJacobianPreconditioner the
>>>>>>>>>>>>>>> preconditioner is recomputed at every Newton step, so for a constant mass
>>>>>>>>>>>>>>> matrix this might not be ideal. How can I avoid recomputing this at every
>>>>>>>>>>>>>>> Newton iteration?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Maybe we need another flag like
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/SNES/SNESSetLagPreconditioner.html
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> or we need to expand
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/SNES/SNESSetLagJacobian.html
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> to separately cover the preconditioner matrix. However, both
>>>>>>>>>>>>>> matrices are computed by one call so this would
>>>>>>>>>>>>>> involve interface changes to user code, which we do not like
>>>>>>>>>>>>>> to do. Right now it seems like a small optimization.
>>>>>>>>>>>>>> I would want to wait and see whether it would really be
>>>>>>>>>>>>>> maningful.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>> Sander
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> 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
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>
>>>
>>
>
--
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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