[petsc-users] Question about using MatSNESMFWPSetComputeNormU

Matthew Knepley knepley at gmail.com
Thu Aug 18 14:05:19 CDT 2016 

On Thu, 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
>

1) Always give the ENTIRE error message

2) As I said in the last two messages, you can only use this without a
preconditioner, so you need

  -pc_type none

    Matt


>
> 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/manualpage
>>>>>>>> s/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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