[petsc-users] Question about using MatSNESMFWPSetComputeNormU

[최경준]

Is there a part that you considered this as finite-difference approximation?
I thought I used matrix-free method with MatCreateSNESMF() function

Also I used
- call PCSetType(pc, PCNONE, ier)  --> so the pc type shows 'none' at the
log


I didn't use any of command line options.


Kyungjun

2016-08-19 4:27 GMT+09:00 Barry Smith <bsmith at mcs.anl.gov>:

>
>    You can't use that Jacobian function SNESComputeJacobianDefault  with
> matrix free, it tries to compute the matrix entries and stick them into the
> matrix. You can use MatMFFDComputeJacobian
>
> > On Aug 18, 2016, at 2:03 PM, 최경준 <kyungjun.choi92 at gmail.com> wrote:
> >
> > I got stuck at FormJacobian stage.
> >
> > - call SNESComputeJacobianDefault(snes, v, J, pJ, FormResidual, ier)
> --> J & pJ are same with A matrix-free matrix (input argument)
> >
> >
> >
> > with these kind of messages..
> >
> > [0]PETSC ERROR: No support for this operation for this object type
> > [0]PETSC ERROR: Mat type mffd
> >
> >
> >
> > Guess it's because I used A matrix-free matrix (which is mffd type) into
> pJ position.
> >
> > Is there any solution for this kind of situation?
> >
> >
> > 2016-08-19 2:05 GMT+09:00 Matthew Knepley <knepley at gmail.com>:
> > On Thu, Aug 18, 2016 at 12:04 PM, 최경준 <kyungjun.choi92 at gmail.com> wrote:
> > Then in order not to use preconditioner,
> >
> > is it ok if I just put A matrix-free matrix (made from
> MatCreateSNESMF()) into the place where preA should be?
> >
> > Yes, but again the solve will likely perform very poorly.
> >
> >   Thanks,
> >
> >      Matt
> >
> > The flow goes like this
> > - call SNESCreate
> > - call SNESSetFunction(snes, r, FormResidual, userctx, ier)
> > - call MatCreateSNESMF(snes, A, ier)
> > - call SNESSetJacobian(snes, A, A, FormJacobian, userctx, ier)
> > - call SNESSetFromOptions()
> >
> > - call SNESGetKSP(snes, ksp, ier)
> > - call KSPSetType(ksp, KSPGMRES, ier)
> > - call KSPGetPC(ksp, pc, ier)
> > - call PCSetType(pc, PCNONE, ier)
> > - call KSPGMRESSetRestart(ksp, 30, ier)
> >
> > - call SNESSolve()
> > .
> > .
> >
> >
> > and inside the FormJacobian routine
> > - call SNESComputeJacobian(snes, v, J, pJ, userctx, ier)  --> J and pJ
> must be pointed with A and A.
> >
> >
> >
> > Thank you again,
> >
> > Kyungjun.
> >
> > 2016-08-19 1:44 GMT+09:00 Matthew Knepley <knepley at gmail.com>:
> > On Thu, Aug 18, 2016 at 11:42 AM, 최경준 <kyungjun.choi92 at gmail.com> wrote:
> > Thanks for your helpful answers.
> >
> > Here's another question...
> >
> > As I read some example PETSc codes, I noticed that there should be a
> preconditioning matrix (e.g. approx. jacobian matrix) when using
> MatCreateSNESMF().
> >
> > I mean,
> > after calling MatCreateSNESMF(snes, A, ier),
> > there should be another matrix preA(preconditioning matrix) to use
> SNESSetJacobian(snes, A, preA, FormJacobian, ctx, ier).
> >
> >
> > 1) Is there any way that I can use matrix-free method without making
> preconditioning matrix?
> >
> > Don't use a preconditioner. As you might expect, this does not often
> work out well.
> >
> > 2) I have a reference code, and the code adopts
> >
> > MatFDColoringCreate()
> > and finally uses
> > SNESComputeJacobianDefaultColor() at FormJacobian stage.
> >
> > But I can't see the inside of the fdcolor and I'm curious of this
> mechanism. Can you explain this very briefly or tell me an example code
> that I can refer to. ( I think none of PETSc example code is using
> fdcolor..)
> >
> > This is the default, so there is no need for all that code. We use naive
> graph 2-coloring. I think there might be a review article by Alex Pothen
> about that.
> >
> >   Thanks,
> >
> >     Matt
> >
> >
> > Best,
> >
> > Kyungjun.
> >
> > 2016-08-19 0:54 GMT+09:00 Matthew Knepley <knepley at gmail.com>:
> > On Thu, Aug 18, 2016 at 10:39 AM, 최경준 <kyungjun.choi92 at gmail.com> wrote:
> > 1) I wanna know the difference between applying option with command line
> and within source code.
> > From my experience, command line option helps set other default settings
> that I didn't applied, I guess.
> >
> > The command line arguments are applied to an object when
> *SetFromOptions() is called, so in this case
> > you want SNESSetFromOptions() on the solver. There should be no
> difference from using the API.
> >
> > 2) I made a matrix-free matrix with MatCreateSNESMF function, and every
> time I check my snes context with SNESView,
> >
> >     Mat Object:     1 MPI processes
> >       type: mffd
> >       rows=11616, cols=11616
> >         Matrix-free approximation:
> >           err=1.49012e-08 (relative error in function evaluation)
> >           The compute h routine has not yet been set
> >
> > at the end of line shows there's no routine for computing h value.
> > I used MatMFFDWPSetComputeNormU function, but it didn't work I think.
> > Is it ok if I leave the h value that way? Or should I have to set h
> computing routine?
> >
> > I am guessing you are calling the function on a different object from
> the one that is viewed here.
> > However, there will always be a default function for computing h.
> >
> >   Thanks,
> >
> >     Matt
> >
> > Kyungjun.
> >
> > 2016-08-18 23:18 GMT+09:00 Matthew Knepley <knepley at gmail.com>:
> > On Thu, Aug 18, 2016 at 8:35 AM, 최경준 <kyungjun.choi92 at gmail.com> wrote:
> > Hi, I'm trying to set my SNES matrix-free with Walker & Pernice way of
> computing h value.
> >
> > I found above command (MatSNESMFWPSetComputeNormU) but my fortran
> compiler couldn't fine any reference of that command.
> >
> > I checked Petsc changes log, but there weren't any mentions about that
> command.
> >
> > Should I have to include another specific header file?
> >
> > We have this function
> >
> >   http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/
> MatMFFDWPSetComputeNormU.html
> >
> > but I would recommend using the command line option
> >
> >   -mat_mffd_compute_normu
> >
> >   Thanks,
> >
> >      Matt
> >
> > Thank you always.
> >
> >
> >
> > --
> > 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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