[petsc-users] Question about using MatSNESMFWPSetComputeNormU
최경준
kyungjun.choi92 at gmail.com
Thu Aug 18 22:28:44 CDT 2016
Dear Matt.
I didn't use the command line options because it looked not working.
I called SNESSetFromOptions(snes, ier) in my source code,
but options like -snes_mf or -snes_monitor doesn't look working.
Is there anything that I should consider more?
2016-08-19 4:47 GMT+09:00 Matthew Knepley <knepley at gmail.com>:
> On Thu, Aug 18, 2016 at 2:44 PM, 최경준 <kyungjun.choi92 at gmail.com> wrote:
>
>> Is there a part that you considered this as finite-difference
>> approximation?
>> I thought I used matrix-free method with MatCreateSNESMF() function
>>
>
> You did not tell the SNES to use a MF Jacobian, you just made a Mat
> object. This is why
> we encourage people to use the command line. Everything is setup
> correctly and in order.
> Why would you choose not to. This creates long rounds of email.
>
> Matt
>
>
>> 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
>>> >
>>>
>>>
>>
>
>
> --
> 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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