[petsc-users] Setting up a PETSc section for field-split
Matthew Knepley
knepley at gmail.com
Tue Jan 28 10:20:43 CST 2014
On Tue, Jan 28, 2014 at 10:11 AM, Luc Berger-Vergiat <lb2653 at columbia.edu>wrote:
> What I don't really understand is why the size of all the sub fields is
> zero?
> As you can see all the matrix object in my fieldsplit preconditioner have
> total:nonzeros=0, allocated nonzeros=0.
>
> This seems strange since I issued the following command:
> call DMSetDefaultSection(FSDM, FSSection, ierr)
>
That section looks like you never called PetscSectionSetUp().
Matt
> with a the following FSSection:
> PetscSection with 4 fields
> field 0 with 1 components
> Process 0:
> ( 0) dim 0 offset 0
> ( 1) dim 1 offset 0
> ( 2) dim 0 offset 0
> ( 3) dim 0 offset 0
> ( 4) dim 1 offset 0
> ( 5) dim 0 offset 0
> ( 6) dim 0 offset 0
> ( 7) dim 0 offset 0
> ( 8) dim 0 offset 0
> ( 9) dim 0 offset 0
> ( 10) dim 0 offset 0
> ( 11) dim 0 offset 0
> ( 12) dim 0 offset 0
> ( 13) dim 0 offset 0
> ( 14) dim 0 offset 0
> ( 15) dim 0 offset 0
> field 1 with 1 components
> Process 0:
> ( 0) dim 1 offset 0
> ( 1) dim 0 offset 1
> ( 2) dim 1 offset 0
> ( 3) dim 1 offset 0
> ( 4) dim 0 offset 1
> ( 5) dim 1 offset 0
> ( 6) dim 0 offset 0
> ( 7) dim 0 offset 0
> ( 8) dim 0 offset 0
> ( 9) dim 0 offset 0
> ( 10) dim 0 offset 0
> ( 11) dim 0 offset 0
> ( 12) dim 0 offset 0
> ( 13) dim 0 offset 0
> ( 14) dim 0 offset 0
> ( 15) dim 0 offset 0
> field 2 with 1 components
> Process 0:
> ( 0) dim 0 offset 1
> ( 1) dim 0 offset 1
> ( 2) dim 0 offset 1
> ( 3) dim 0 offset 1
> ( 4) dim 0 offset 1
> ( 5) dim 0 offset 1
> ( 6) dim 1 offset 0
> ( 7) dim 1 offset 0
> ( 8) dim 1 offset 0
> ( 9) dim 1 offset 0
> ( 10) dim 1 offset 0
> ( 11) dim 1 offset 0
> ( 12) dim 0 offset 0
> ( 13) dim 0 offset 0
> ( 14) dim 0 offset 0
> ( 15) dim 0 offset 0
> field 3 with 1 components
> Process 0:
> ( 0) dim 0 offset 1
> ( 1) dim 0 offset 1
> ( 2) dim 0 offset 1
> ( 3) dim 0 offset 1
> ( 4) dim 0 offset 1
> ( 5) dim 0 offset 1
> ( 6) dim 0 offset 1
> ( 7) dim 0 offset 1
> ( 8) dim 0 offset 1
> ( 9) dim 0 offset 1
> ( 10) dim 0 offset 1
> ( 11) dim 0 offset 1
> ( 12) dim 1 offset 0
> ( 13) dim 1 offset 0
> ( 14) dim 1 offset 0
> ( 15) dim 1 offset 0
>
> I thought that by using DMSetDefaultSection() I would be done setting the
> fields and that the fieldsplit would detect that section and use it to
> construct the splits.
>
> Should I use another command to tell the PC to use the DM section?
>
> Best,
> Luc
>
> On 01/28/2014 10:25 AM, Matthew Knepley wrote:
>
> On Mon, Jan 27, 2014 at 1:35 PM, Luc Berger-Vergiat <lb2653 at columbia.edu>wrote:
>
>> Thanks Matt,
>> this indeed setting the number of fields earlier solve my issue!
>>
>> I have now made some progress getting my DM setup but I am having
>> troubles setting my splitfield options.
>> I ran my problem with the -ksp_view option to see what is going on and I
>> guess that somehow the section that I define in my DM is not used by the
>> preconditioner to split the fields.
>> Here is the output of PETSc
>>
>> KSP Object: 1 MPI processes
>> type: gmres
>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>> Orthogonalization with no iterative refinement
>> GMRES: happy breakdown tolerance 1e-30
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-08, absolute=1e-16, divergence=1e+16
>> left preconditioning
>> using PRECONDITIONED norm type for convergence test
>> PC Object: 1 MPI processes
>> type: fieldsplit
>> FieldSplit with MULTIPLICATIVE composition: total splits = 4
>> Solver info for each split is in the following KSP objects:
>> Split number 0 Defined by IS
>>
>
> There are 4 splits here and they are defined by an IS. Why do you think
> that is not what you asked for?
>
> Thanks,
>
> Matt
>
>
>> KSP Object: (fieldsplit_Field_0_) 1 MPI processes
>> type: preonly
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>> left preconditioning
>> using NONE norm type for convergence test
>> PC Object: (fieldsplit_Field_0_) 1 MPI processes
>> type: ilu
>> ILU: out-of-place factorization
>> 0 levels of fill
>> tolerance for zero pivot 2.22045e-14
>> using diagonal shift on blocks to prevent zero pivot
>> matrix ordering: natural
>> factor fill ratio given 1, needed 1
>> Factored matrix follows:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=0, cols=0
>> package used to perform factorization: petsc
>> total: nonzeros=0, allocated nonzeros=0
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> linear system matrix = precond matrix:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=0, cols=0
>> total: nonzeros=0, allocated nonzeros=0
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> Split number 1 Defined by IS
>> KSP Object: (fieldsplit_Field_1_) 1 MPI processes
>> type: preonly
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>> left preconditioning
>> using NONE norm type for convergence test
>> PC Object: (fieldsplit_Field_1_) 1 MPI processes
>> type: ilu
>> ILU: out-of-place factorization
>> 0 levels of fill
>> tolerance for zero pivot 2.22045e-14
>> using diagonal shift on blocks to prevent zero pivot
>> matrix ordering: natural
>> factor fill ratio given 1, needed 1
>> Factored matrix follows:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=0, cols=0
>> package used to perform factorization: petsc
>> total: nonzeros=0, allocated nonzeros=0
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> linear system matrix = precond matrix:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=0, cols=0
>> total: nonzeros=0, allocated nonzeros=0
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> Split number 2 Defined by IS
>> KSP Object: (fieldsplit_Field_2_) 1 MPI processes
>> type: preonly
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>> left preconditioning
>> using NONE norm type for convergence test
>> PC Object: (fieldsplit_Field_2_) 1 MPI processes
>> type: ilu
>> ILU: out-of-place factorization
>> 0 levels of fill
>> tolerance for zero pivot 2.22045e-14
>> using diagonal shift on blocks to prevent zero pivot
>> matrix ordering: natural
>> factor fill ratio given 1, needed 1
>> Factored matrix follows:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=0, cols=0
>> package used to perform factorization: petsc
>> total: nonzeros=0, allocated nonzeros=0
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> linear system matrix = precond matrix:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=0, cols=0
>> total: nonzeros=0, allocated nonzeros=0
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> Split number 3 Defined by IS
>> KSP Object: (fieldsplit_Field_3_) 1 MPI processes
>> type: preonly
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>> left preconditioning
>> using NONE norm type for convergence test
>> PC Object: (fieldsplit_Field_3_) 1 MPI processes
>> type: ilu
>> ILU: out-of-place factorization
>> 0 levels of fill
>> tolerance for zero pivot 2.22045e-14
>> using diagonal shift on blocks to prevent zero pivot
>> matrix ordering: natural
>> factor fill ratio given 1, needed 1
>> Factored matrix follows:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=0, cols=0
>> package used to perform factorization: petsc
>> total: nonzeros=0, allocated nonzeros=0
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> linear system matrix = precond matrix:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=0, cols=0
>> total: nonzeros=0, allocated nonzeros=0
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> linear system matrix = precond matrix:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=16, cols=16
>> total: nonzeros=256, allocated nonzeros=256
>> total number of mallocs used during MatSetValues calls =0
>> using I-node routines: found 4 nodes, limit used is 5
>>
>> I am also attaching part of my code which I use to generate the DM, the
>> KSP and the PC objects.
>>
>> Best,
>> Luc
>>
>> On 01/25/2014 10:31 AM, Matthew Knepley wrote:
>>
>> On Fri, Jan 24, 2014 at 5:10 PM, Luc Berger-Vergiat <lb2653 at columbia.edu
>> > wrote:
>>
>>> Hi all,
>>> I want to use PETSc as a solver for an FEM problem: modelization of
>>> shear bands using a 4 fields mixed formulation.
>>>
>>> So far I am just trying to set up a two fields in a Petsc section,
>>> assign dof too each field and then set up the section to pass it to a DM. I
>>> am taking this approach because in general I want for fieldsplit to work
>>> purely on the algebraic level without knowledge of boundary conditions or
>>> geometry.
>>>
>>> As of now I have issues when I try to assign a point and its associated
>>> degree of freedom to a field using: PetscSectionSetFieldDof.
>>> Is this the correct way to associate a dof/point to a field?
>>>
>>
>> You have to set the number of fields before the chart. I am updating
>> the docs.
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> I attached an example code and its makefile.
>>>
>>> --
>>> Best,
>>> Luc
>>>
>>>
>>
>>
>> --
>> 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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