[petsc-users] PETSc with mesh refinement

[Zou, Ling]

Thanks both of you.
Great suggestions.

Ling

On Sun, Sep 3, 2017 at 12:55 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>   The TS/SNES/KSP/PC allocate various work vectors and matrices which they
> keep around for additional solvers. Thus if you want to change the size of
> your problem and/or number of degrees of freedom per process you need to do
> one of 2 things
>
>    1) destroy the old TS/SNES/ or KSP and create a new one each time you
> change your vectors to a different size or
>
>    2) call TSReset/SNESReset/or KSPReset each time you change your
> vectors, this causes all the internal work vectors and matrices to be freed
> so they can get replaced but keeps all the solver options etc.
>
>    2) is preferred to 1.
>
>    Barry
>
> > On Sep 3, 2017, at 1:44 PM, Matthew Knepley <knepley at gmail.com> wrote:
> >
> > On Sun, Sep 3, 2017 at 1:02 PM, Zou, Ling <ling.zou at inl.gov> wrote:
> > Hi All,
> >
> > I wonder if there is a good example on how PETSc should work with mesh
> refinement. I have done some online search/PETSc-user email search, but did
> not find a good one.
> >
> > Here is my case. Currently, assuming NO mesh refinement (so I know
> exactly the problem size, mesh connectivity, non-zero pattern of matrices,
> etc.)
> > In a transient simulation, my PETSc code looks like:
> >
> > ========================================================================
> > SetupVectors(); // unknown vec, old unknown, etc.
> > SetupResFunc(); // residual function, basically pointing to the
> discretized PDE
> > SetupMatrices(); // allocate memory for preconditioning matrix based on
> non-zero pattern (so it is mesh dependent)
> >                            // I also use finite differencing to get
> preconditioning matrix, so there is another MatFDColoring object associated
> with the matrix
> > for (int step = 0; step < max_step; step++)
> > {
> >   SNESSolve();
> > }
> > ========================================================================
> >
> > This setup works perfectly for my problems.
> > (I understand it is low efficient to use FD to get the preconditioning
> matrix, but it is not a priority to me at this moment).
> >
> > However, now I would like to do some mesh refinement, so the previous
> setup would not work, because the problem size, non-zero pattern of the
> matrix and MatFDColoring change with mesh size (and connectivity).
> > I suppose my code should be changed like this:
> >
> > ========================================================================
> > SetupVectors();
> > SetupResFunc();
> > SetupMatrices();
> >
> > for (int step = 0; step < max_step; step++)
> > {
> >   MeshRefinement(); // I will manage my mesh
> >
> >   AdjustVectors();   // resize vector
> >   AdjustMatrices(); // resize matrix, re-allocate memory, adjust
> non-zero pattern, etc.
> >
> >   SNESSolve();
> > }
> > ========================================================================
> >
> > The issue is that I understand one should not re-allocate memory to both
> PETSc vector and matrix dynamically during simulation, which has been
> discussed here:
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__
> scicomp.stackexchange.com_questions_373_is-2Dit-
> 2Dpossible-2Dto-2Ddynamically-2Dresize-2Da-2Dsparse-
> 2Dmatrix-2Din-2Dthe-2Dpetsc-2Dlibrary&d=DwIFAg&c=
> 54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=
> kuHHom1yjd94zUrBWecnYg&m=lEB-2RrZ7_xUBhwaeQnezW0fuTVkBbMZVcRtx8Fn
> tz0&s=6JH1-QnmGFstCWaXbdRsDRn-lSHYB-gqGOlsCFyhDVQ&e=
> >
> > So, the final questions are:
> > 1) Any good example on PETSc working with mesh refinement?
> > 2) Any suggestion on my proposed code structure?
> >
> > 1) No
> >
> > 2) Yes. We advocate using the DM to describe your data layout. This
> allows all Vec and Mats to be created automatically, and
> > also tells the solver (SNESSetDM, etc.) the sizes and potential
> decomposition.
> >
> > We are working on a mesh adaptivity interface which will allow
> adaptivity to be used with all DM problems without any extra
> > code. We should have some examples with this soon.
> >
> >   Thanks,
> >
> >      Matt
> >
> > Best,
> >
> > Ling
> >
> >
> >
> >
> >
> > --
> > 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
> >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
> caam.rice.edu_-7Emk51_&d=DwIFAg&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB_
> _aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=lEB-2RrZ7_
> xUBhwaeQnezW0fuTVkBbMZVcRtx8Fntz0&s=URW-NglPj9JSNGOxqvL8qv9WilvxNzmYIw
> 8A6IEn5tg&e=
>
>
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