[petsc-users] Solving Poisson equation with multigrid

Matthew Knepley knepley at gmail.com
Fri May 24 17:17:20 CDT 2013 

On Fri, May 24, 2013 at 4:46 PM, Michele Rosso <mrosso at uci.edu> wrote:

>  In both cases I used -ksp_view and -option_left.
>
> For case 1 ( -pc_type gamg -pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1  -mg_coarse_sub_pc_factor_shift_nonzero
> ) I posted the only output I had.
>
> For case 2 ( -pc_type gamg -pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1
> -mg_coarse_pc_type svd) the output was too long to fit into an e-mail.
> Please find it attached.
>

It looks like you are running in parallel (never do this until everything
works in serial), which probably means you are using
PCREDUNDANT for the coarse PC, so you need what Jed suggested:

  -mg_coarse_sub_pc_type svd

    Matt


> Michele
>
>  On 05/24/2013 02:37 PM, Matthew Knepley wrote:
>
> On Fri, May 24, 2013 at 4:35 PM, Michele Rosso <mrosso at uci.edu> wrote:
>
>>  I tried
>>
>> -pc_type gamg -pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1
>> -mg_coarse_sub_pc_factor_shift_nonzero
>>
>> but I still get
>>
>> [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 6.58999e-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 nid21818 by Unknown Fri May 24 16:08:33
>> 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: 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
>>
>>
>> If instead I use
>>
>> -pc_type gamg -pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1
>> -mg_coarse_pc_type svd
>>
>> as Matthew suggested, I am told that there is an invalid argument.
>>
>
>  1) When you send these in, we need to see -ksp_view, so we know what is
> begin used
>
>  2) This is not enough information above. I use this all the time, or I
> would not have suggested it
>
>     Matt
>
>
>>  Michele
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>  On 05/24/2013 01:04 PM, Matthew Knepley wrote:
>>
>> On Fri, May 24, 2013 at 2:55 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
>>
>>> Michele Rosso <mrosso at uci.edu> writes:
>>>
>>> > Hi Jed,
>>> >
>>> > I followed your suggestion by using:
>>> >
>>> > -pc_type gamg  -pc_mg_cycle_type v  -pc_gamg_agg_nsmooths 1
>>> >
>>> > This works perfectly if I have a non-singular matrix. When instead I
>>> use
>>> > periodic conditions for my system ( I set  the nullspace removal
>>> > correctly ),
>>> > I receive an error saying a zero pivot is detected in the LU
>>> > factorization. So, after some research, I found in the mailinglist a
>>> fix :
>>> >
>>> > -pc_type gamg -pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1
>>> > -mg_coarse_pc_factor_shift_nonzero
>>>
>>>  It'll need to be -mg_coarse_sub_pc_factor_shift_nonzero
>>>
>>> With petsc-3.4 (which you should upgrade to), use
>>> -mg_coarse_sub_pc_factor_shift_type NONZERO
>>>
>>> The reason you need this "sub" prefix is that the code always restricts
>>> using block Jacobi (usually localized so that all the entries are in one
>>> block), before applying the direct coarse solver.
>>
>>
>>  I think this is less elegant than
>>
>>    -mg_coarse_pc_type svd
>>
>>      Matt
>>
>>
>>>  > Still I am receiving the following error
>>> >
>>> >
>>> > [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 6.5908e-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 nid09458 by Unknown Fri May 24
>>> > 14:40:48 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: 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
>>> >
>>> > What could the reason be?
>>> > Thank you,
>>> >
>>> > Michele
>>> >
>>> >
>>> >
>>> > On 05/17/2013 07:35 PM, Michele Rosso wrote:
>>> >> Thank you very much. I will try and let you know.
>>> >>
>>> >> Michele
>>> >>
>>> >> On 05/17/2013 07:01 PM, Jed Brown wrote:
>>> >>> Michele Rosso<mrosso at uci.edu>  writes:
>>> >>>
>>> >>>> I noticed that the problem appears even if I use CG with the default
>>> >>>> preconditioner: commenting KSPSetDM() solves the problem.
>>> >>> Okay, this issue can't show up if you use SNES, but it's a
>>> consequence
>>> >>> of making geometric multigrid work with a pure KSP interface.  You
>>> can
>>> >>> either use KSPSetComputeOperators() to put your assembly in a
>>> function
>>> >>> (which will also be called on coarse levels if you use -pc_type mg
>>> >>> without Galerkin coarse operators) or you can can provide the
>>> Jacobian
>>> >>> using KSPSetOperators() as usual, but also call KSPSetDMActive() so
>>> that
>>> >>> the DM is not used for computing/updating the Jacobian.
>>> >>>
>>> >>> The logic is cleaner in petsc-3.4 and I think it just does the right
>>> >>> thing in your case.
>>> >>>
>>> >>>> So basically without a proper grid (it seems no grid with an even
>>> >>>> numbers of nodes qualifies) and with my own system matrix, I cannot
>>> use
>>> >>>> any type of multigrid
>>> >>>> pre-conditioner?
>>> >>> You can use all the AMG methods without setting a DM.
>>> >>>
>>> >>
>>>
>>
>>
>>
>>  --
>> 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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