[petsc-users] Solving Poisson equation with multigrid

Wed May 29 20:08:05 CDT 2013

On Wed, May 29, 2013 at 8:29 PM, Michele Rosso <mrosso at uci.edu> wrote:

>  1) How do I solve this?
>

We will fix this, but any fix will necessitate upgrading.

2) So upgrading to version 3.4 would take care of the shift without the
> need to specify any option?
>

Yes

    Matt

> 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> 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> 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> 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> <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
>
>
>

-- 
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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