[petsc-users] Solving Poisson equation with multigrid
Michele Rosso
mrosso at uci.edu
Wed May 29 19:29:40 CDT 2013
1) How do I solve this?
2) So upgrading to version 3.4 would take care of the shift without the
need to specify any option?
Michele
On 05/29/2013 05:17 PM, Matthew Knepley wrote:
> On Wed, May 29, 2013 at 7:22 PM, Michele Rosso <mrosso at uci.edu
> <mailto:mrosso at uci.edu>> wrote:
>
> I attached the complete output.
> I used 2 processors for this run. I wanted to use only one to have
> a cleaner output but I could not because of this error:
>
>
> There are 2 problems here:
>
> 1) GAMG is not accepting options for the coarse grid solver
>
> 2) You do not appear to using PETSc 3.4, or the shift you are trying
> to set would be there by default
>
> Matt
>
> [0]PCSetData_AGG bs=1 MM=32768
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Arguments are incompatible!
> [0]PETSC ERROR: MatMatMult requires A, mpiaij, to be compatible
> with B, seqaij!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 3, Wed Aug 29
> 11:26:24 CDT 2012
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: ./hit on a named nid15343 by Unknown Wed May 29
> 18:15:24 2013
> [0]PETSC ERROR: Libraries linked from
> [0]PETSC ERROR: Configure run at
> [0]PETSC ERROR: Configure options
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: MatMatMult() line 8614 in src/mat/interface/matrix.c
> [0]PETSC ERROR: PCGAMGOptprol_AGG() line 1358 in
> src/ksp/pc/impls/gamg/agg.c
> [0]PETSC ERROR: PCSetUp_GAMG() line 673 in
> src/ksp/pc/impls/gamg/gamg.c
> [0]PETSC ERROR: PCSetUp() line 832 in src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: KSPSetUp() line 278 in src/ksp/ksp/interface/itfunc.c
> hit: gamg.c:568: PCSetUp_GAMG: Assertion `pc->setupcalled' failed.
>
> On 05/29/2013 02:29 PM, Matthew Knepley wrote:
>> On Wed, May 29, 2013 at 5:25 PM, Michele Rosso <mrosso at uci.edu
>> <mailto:mrosso at uci.edu>> wrote:
>>
>> Hi,
>>
>> I proceeded as Matt suggested. I am running without nullspace
>> (Dirichlet's BCs) with the following options:
>>
>> -pc_type gamg -pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1
>> -mg_coarse_sub_pc_factor_shift_type NONZERO -ksp_view
>> -options_left
>>
>> The results are fine and the run finishes. The output of
>> -ksp_view does not say anything about the coarse solver being
>> shifted.
>> In fact the option -mg_coarse_sub_pc_factor_shift_type
>> NONZERO is not used:
>>
>>
>> Please show us the COMPLETE output.
>>
>> Thanks,
>>
>> Matt
>>
>> #PETSc Option Table entries:
>> -ksp_view
>> -mg_coarse_sub_pc_factor_shift_type NONZERO
>> -options_left
>> -pc_gamg_agg_nsmooths 1
>> -pc_mg_cycle_type v
>> -pc_type gamg
>> #End of PETSc Option Table entries
>> There is one unused database option. It is:
>> Option left: name:-mg_coarse_sub_pc_factor_shift_type value:
>> NONZERO
>>
>> Michele
>>
>>
>> On 05/24/2013 03:20 PM, Matthew Knepley wrote:
>>> On Fri, May 24, 2013 at 5:18 PM, Michele Rosso
>>> <mrosso at uci.edu <mailto:mrosso at uci.edu>> wrote:
>>>
>>> Using
>>>
>>> -pc_type gamg -pc_mg_cycle_type v -pc_gamg_agg_nsmooths
>>> 1 -mg_coarse_sub_pc_factor_shift_type NONZERO
>>> -option_left -ksp_view
>>>
>>>
>>> This is what debugging is about. We are not running your
>>> problem. How could this be debugged?
>>>
>>> 1) Run the problem w/o a null space so that it finishes
>>>
>>> 2) Look at the output for -ksp_view
>>>
>>> 3) Does the coarse solver say that it is shifted?
>>>
>>> 4) Are there options which were unused?
>>>
>>> Matt
>>>
>>> still produces the same error:
>>>
>>> [0]PCSetData_AGG bs=1 MM=131072
>>> [0]PETSC ERROR: --------------------- Error Message
>>> ------------------------------------
>>> [0]PETSC ERROR: Detected zero pivot in LU factorization:
>>> see
>>> http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot!
>>> [0]PETSC ERROR: Zero pivot row 280 value 6.56964e-17
>>> tolerance 2.22045e-14!
>>> [0]PETSC ERROR:
>>> ------------------------------------------------------------------------
>>> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 3,
>>> Wed Aug 29 11:26:24 CDT 2012
>>> [0]PETSC ERROR: See docs/changes/index.html for recent
>>> updates.
>>> [0]PETSC ERROR: See docs/faq.html for hints about
>>> trouble shooting.
>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>> [0]PETSC ERROR:
>>> ------------------------------------------------------------------------
>>> [0]PETSC ERROR: ./hit on a named nid15363 by Unknown Fri
>>> May 24 17:06:50 2013
>>> [0]PETSC ERROR: Libraries linked from
>>> [0]PETSC ERROR: Configure run at
>>> [0]PETSC ERROR: Configure options
>>> [0]PETSC ERROR:
>>> ------------------------------------------------------------------------
>>> [0]PETSC ERROR: MatPivotCheck_none() line 583 in
>>> src/mat/impls/aij/seq//ptmp/skelly/petsc/3.3.03/cray_interlagos_build/real/src/include/petsc-private/matimpl.h
>>> [0]PETSC ERROR: MatPivotCheck() line 602 in
>>> src/mat/impls/aij/seq//ptmp/skelly/petsc/3.3.03/cray_interlagos_build/real/src/include/petsc-private/matimpl.h
>>> [0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 585 in
>>> src/mat/impls/aij/seq/aijfact.c
>>> [0]PETSC ERROR: MatLUFactorNumeric() line 2803 in
>>> src/mat/interface/matrix.c
>>> [0]PETSC ERROR: PCSetUp_LU() line 160 in
>>> src/ksp/pc/impls/factor/lu/lu.c
>>> [0]PETSC ERROR: PCSetUp() line 832 in
>>> src/ksp/pc/interface/precon.c
>>> [0]PETSC ERROR: KSPSetUp() line 278 in
>>> src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock()
>>> line 715 in src/ksp/pc/impls/bjacobi/bjacobi.c
>>> [0]PETSC ERROR: PCSetUpOnBlocks() line 865 in
>>> src/ksp/pc/interface/precon.c
>>> [0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in
>>> src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: KSPSolve() line 403 in
>>> src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock()
>>> line 715 in src/ksp/pc/impls/bjacobi/bjacobi.c
>>> [0]PETSC ERROR: PCSetUpOnBlocks() line 865 in
>>> src/ksp/pc/interface/precon.c
>>> [0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in
>>> src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: KSPSolve() line 403 in
>>> src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: PCMGMCycle_Private() line 20 in
>>> src/ksp/pc/impls/mg/mg.c
>>> [0]PETSC ERROR: PCMGMCycle_Private() line 49 in
>>> src/ksp/pc/impls/mg/mg.c
>>> [0]PETSC ERROR: PCMGMCycle_Private() line 49 in
>>> src/ksp/pc/impls/mg/mg.c
>>> [0]PETSC ERROR: PCMGMCycle_Private() line 49 in
>>> src/ksp/pc/impls/mg/mg.c
>>> [0]PETSC ERROR: PCApply_MG() line 326 in
>>> src/ksp/pc/impls/mg/mg.c
>>> [0]PETSC ERROR: PCApply() line 384 in
>>> src/ksp/pc/interface/precon.c
>>> [0]PETSC ERROR: KSPSolve_CG() line 139 in
>>> src/ksp/ksp/impls/cg/cg.c
>>> [0]PETSC ERROR: KSPSolve() line 446 in
>>> src/ksp/ksp/interface/itfunc.c
>>>
>>> On 05/24/2013 02:51 PM, Jed Brown wrote:
>>>> Michele Rosso<mrosso at uci.edu> <mailto:mrosso at uci.edu> writes:
>>>>
>>>>>> With petsc-3.4 (which you should upgrade to), use
>>>>>> -mg_coarse_sub_pc_factor_shift_type NONZERO
>>>> Actually, use this with petsc-3.3 also (and please upgrade to
>>>> petsc-3.4).
>>>>
>>>> The option you were passing was not being used.
>>>>
>>>
>>>
>>>
>>>
>>> --
>>> 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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