[petsc-users] GAMG and zero pivots follow up

[David Knezevic]

On Tue, Nov 10, 2015 at 10:28 PM, David Knezevic <david.knezevic at akselos.com
> wrote:

> On Tue, Nov 10, 2015 at 10:24 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> On Tue, Nov 10, 2015 at 9:21 PM, David Knezevic <
>> david.knezevic at akselos.com> wrote:
>>
>>> On Tue, Nov 10, 2015 at 10:00 PM, Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> On Tue, Nov 10, 2015 at 8:39 PM, David Knezevic <
>>>> david.knezevic at akselos.com> wrote:
>>>>
>>>>> I'm looking into using GAMG, so I wanted to start with a simple 3D
>>>>> elasticity problem. When I first tried this, I got the following "zero
>>>>> pivot" error:
>>>>>
>>>>> -----------------------------------------------------------------------
>>>>>
>>>>> [0]PETSC ERROR: Zero pivot in LU factorization:
>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html#zeropivot
>>>>> [0]PETSC ERROR: Zero pivot, row 3
>>>>> [0]PETSC ERROR: See
>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>>>> shooting.
>>>>> [0]PETSC ERROR: Petsc Release Version 3.6.1, Jul, 22, 2015
>>>>> [0]PETSC ERROR:
>>>>> /home/dknez/akselos-dev/scrbe/build/bin/fe_solver-opt_real on a
>>>>> arch-linux2-c-opt named david-Lenovo by dknez Tue Nov 10 21:26:39 2015
>>>>> [0]PETSC ERROR: Configure options --with-shared-libraries=1
>>>>> --with-debugging=0 --download-suitesparse --download-parmetis
>>>>> --download-blacs
>>>>> --with-blas-lapack-dir=/opt/intel/system_studio_2015.2.050/mkl
>>>>> --CXXFLAGS=-Wl,--no-as-needed --download-scalapack --download-mumps
>>>>> --download-metis --download-superlu_dist
>>>>> --prefix=/home/dknez/software/libmesh_install/opt_real/petsc
>>>>> --download-hypre --download-ml
>>>>> [0]PETSC ERROR: #1 PetscKernel_A_gets_inverse_A_5() line 48 in
>>>>> /home/dknez/software/petsc-3.6.1/src/mat/impls/baij/seq/dgefa5.c
>>>>> [0]PETSC ERROR: #2 MatSOR_SeqAIJ_Inode() line 2808 in
>>>>> /home/dknez/software/petsc-3.6.1/src/mat/impls/aij/seq/inode.c
>>>>> [0]PETSC ERROR: #3 MatSOR() line 3697 in
>>>>> /home/dknez/software/petsc-3.6.1/src/mat/interface/matrix.c
>>>>> [0]PETSC ERROR: #4 PCApply_SOR() line 37 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/impls/sor/sor.c
>>>>> [0]PETSC ERROR: #5 PCApply() line 482 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/interface/precon.c
>>>>> [0]PETSC ERROR: #6 KSP_PCApply() line 242 in
>>>>> /home/dknez/software/petsc-3.6.1/include/petsc/private/kspimpl.h
>>>>> [0]PETSC ERROR: #7 KSPInitialResidual() line 63 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/interface/itres.c
>>>>> [0]PETSC ERROR: #8 KSPSolve_GMRES() line 235 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/impls/gmres/gmres.c
>>>>> [0]PETSC ERROR: #9 KSPSolve() line 604 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/interface/itfunc.c
>>>>> [0]PETSC ERROR: #10 KSPSolve_Chebyshev() line 381 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/impls/cheby/cheby.c
>>>>> [0]PETSC ERROR: #11 KSPSolve() line 604 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/interface/itfunc.c
>>>>> [0]PETSC ERROR: #12 PCMGMCycle_Private() line 19 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/impls/mg/mg.c
>>>>> [0]PETSC ERROR: #13 PCMGMCycle_Private() line 48 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/impls/mg/mg.c
>>>>> [0]PETSC ERROR: #14 PCApply_MG() line 338 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/impls/mg/mg.c
>>>>> [0]PETSC ERROR: #15 PCApply() line 482 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/interface/precon.c
>>>>> [0]PETSC ERROR: #16 KSP_PCApply() line 242 in
>>>>> /home/dknez/software/petsc-3.6.1/include/petsc/private/kspimpl.h
>>>>> [0]PETSC ERROR: #17 KSPSolve_CG() line 139 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/impls/cg/cg.c
>>>>> [0]PETSC ERROR: #18 KSPSolve() line 604 in
>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/interface/itfunc.c
>>>>>
>>>>> -----------------------------------------------------------------------
>>>>>
>>>>> I saw that there was a thread about this in September (subject: "gamg
>>>>> and zero pivots"), and that the fix is to use "-mg_levels_pc_type
>>>>> jacobi." When I do that, the solve succeeds (I pasted the -ksp_view at the
>>>>> end of this email).
>>>>>
>>>>> So I have two questions about this:
>>>>>
>>>>> 1. Is it surprising that I hit this issue for a 3D elasticity problem?
>>>>> Note that matrix assembly was done in libMesh, I can look into the
>>>>> structure of the assembled matrix more carefully, if needed. Also, note
>>>>> that I can solve this problem with direct solvers just fine.
>>>>>
>>>>
>>>> Yes, this seems like a bug, but it could be some strange BC thing I do
>>>> not understand.
>>>>
>>>
>>>
>>> OK, I can look into the matrix in more detail. I agree that it should
>>> have a non-zero diagonal, so I'll have a look at what's happening with that.
>>>
>>>
>>>
>>>
>>>> Naively, the elastic element matrix has a nonzero diagonal. I see that
>>>> you are doing LU
>>>> of size 5. That seems strange for 3D elasticity. Am I missing
>>>> something? I would expect
>>>> block size 3.
>>>>
>>>
>>>
>>> I'm not sure what is causing the LU of size 5. Is there a setting to
>>> control that?
>>>
>>> Regarding the block size: I set the vector and matrix block size to 3
>>> via VecSetBlockSize and MatSetBlockSize. I also
>>> used MatNullSpaceCreateRigidBody on a vector with block size of 3, and set
>>> the matrix's near nullspace using that.
>>>
>>
>> Can you run this same example with -mat_no_inode? I think it may be a
>> strange blocking that is causing this.
>>
>
>
> That works. The -ksp_view output is below.
>


I just wanted to follow up on this. I had a more careful look at the
matrix, and confirmed that there are no zero entries on the diagonal (as
expected for elasticity). The matrix is from one of libMesh's example
problems: a simple cantilever model using HEX8 elements.

Do you have any further thoughts about what might cause the "strange
blocking" that you referred to? If there's something non-standard that
libMesh is doing with the blocks, I'd be interested to look into that. I
can send over the matrix if that would be helpful.

Thanks,
David
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20151111/2e3cda75/attachment.html>