[petsc-users] how to control snes_mf_operator

[Zou (Non-US), Ling]

Thank you Matt.

Ling

On Tue, Dec 11, 2012 at 4:02 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Dec 11, 2012 at 2:59 PM, Zou (Non-US), Ling <ling.zou at inl.gov>wrote:
>
>> ok. I tried. Seems there is no effect.
>>
>> ./my-moose-project -i input.i -snes_type test -mat_mffd_umin
>> 1.e-10 -snes_test_display > out
>>
>> Also, the webpage says:
>> *-mat_mffd_unim <umin>
>>
>> *I am not quite sure if 'unim' is a typo. I tried both 'umin' and 'unim'
>> anyway.
>>
>
> You can check what is coming in, right? But this is all academic, with
> that scaling, you will get almost
> no significant figures in the Jacobian for those unknowns, so why worry
> about it. Nondimensionalize.
>
>     Matt
>
>
>> Ling
>>
>>
>>
>> On Tue, Dec 11, 2012 at 3:50 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>
>>> On Tue, Dec 11, 2012 at 2:40 PM, Zou (Non-US), Ling <ling.zou at inl.gov>
>>> wrote:
>>> > Hmm... I have an 'approximated' analytical Jacobian to compare. And I
>>> did
>>> > this:
>>> >
>>> > ./my-moose-project -i input.i -snes_type test -snes_test_display > out
>>> >
>>> > I actually found out that the PETSc provided FD Jacobian gives 'nan'
>>> > numbers, while my approximated Jacobian does not give 'nan' at the same
>>> > positions.
>>> >
>>> > As we discussed in the previous emails, the perturbation on U0 is too
>>> large,
>>> > which makes 'nan' appear in the FD Jacobians. So....I am trying to use
>>> a
>>> > smaller '-mat_mffd_err <number here>', to see if I could get an easy
>>> fix by
>>> > now, like this,
>>>
>>> I don't think 'err' has anything to do with it. If you read the page I
>>> mailed you, I
>>> believe umin can be made very small.
>>>
>>>    Matt
>>>
>>> > ./my-moose-project -i input.i -snes_type test -md_mffd_err 1.e-10
>>> > -snes_test_display > out
>>> >
>>> > seems not working :-(
>>> > no matter what number I give to -md_mffd_err, the print out results
>>> seem not
>>> > changed.
>>> >
>>> > But of course, non-dimensionalization might be the ultimate solution.
>>> >
>>> > Ling
>>> >
>>> > On Tue, Dec 11, 2012 at 3:29 PM, Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>> >>
>>> >> On Tue, Dec 11, 2012 at 2:19 PM, Zou (Non-US), Ling <ling.zou at inl.gov
>>> >
>>> >> wrote:
>>> >> > Matt, one more question.
>>> >> >
>>> >> > Can I combine the options
>>> >> > -snes_type test
>>> >> > and
>>> >> > -mat_mffd_err 1.e-10
>>> >> > to see the effect?
>>> >>
>>> >> I do not understand your question. test does compare the analytic and
>>> >> FD Jacobian
>>> >> actions, but I thought you did not have an analytic action.
>>> >>
>>> >>    Matt
>>> >>
>>> >> > Best,
>>> >> >
>>> >> > Ling
>>> >> >
>>> >> >
>>> >> >
>>> >> > On Tue, Dec 11, 2012 at 2:47 PM, Zou (Non-US), Ling <
>>> ling.zou at inl.gov>
>>> >> > wrote:
>>> >> >>
>>> >> >> thank you Matt. I will try to figure it out.
>>> Non-dimensionalization is
>>> >> >> certainly something worth to try.
>>> >> >>
>>> >> >> Best,
>>> >> >>
>>> >> >> Ling
>>> >> >>
>>> >> >>
>>> >> >> On Tue, Dec 11, 2012 at 2:41 PM, Matthew Knepley <
>>> knepley at gmail.com>
>>> >> >> wrote:
>>> >> >>>
>>> >> >>> On Tue, Dec 11, 2012 at 1:40 PM, Matthew Knepley <
>>> knepley at gmail.com>
>>> >> >>> wrote:
>>> >> >>> > On Tue, Dec 11, 2012 at 1:34 PM, Zou (Non-US), Ling
>>> >> >>> > <ling.zou at inl.gov>
>>> >> >>> > wrote:
>>> >> >>> >> Dear All,
>>> >> >>> >>
>>> >> >>> >> I have recently had an issue using snes_mf_operator. I've
>>> tried to
>>> >> >>> >> figure it
>>> >> >>> >> out from PETSc manual and PETSc website but didn't get any
>>> luck, so
>>> >> >>> >> I
>>> >> >>> >> submit
>>> >> >>> >> my question here and hope some one could help me out.
>>> >> >>> >>
>>> >> >>> >> (1)
>>> >> >>> >>
>>> =================================================================
>>> >> >>> >> A little bit background here: my problem has 7 variables, i.e.,
>>> >> >>> >>
>>> >> >>> >> U = [U0, U1, U2, U3, U4, U5, U6]
>>> >> >>> >>
>>> >> >>> >> U0 is in the order of 1.
>>> >> >>> >> U1, U2, U4 and U5 in the oder of 100.
>>> >> >>> >> U3 and U6 are in the order of 1.e8.
>>> >> >>> >>
>>> >> >>> >> I believe this should be quite common for most PETSc users.
>>> >> >>> >>
>>> >> >>> >> (2)
>>> >> >>> >>
>>> =================================================================
>>> >> >>> >> My problem here is, U0, by its physical meaning, has to be
>>> limited
>>> >> >>> >> between 0
>>> >> >>> >> and 1. When PETSc starts to perturb the initial solution of U
>>> >> >>> >> (which I
>>> >> >>> >> believe properly set) to approximate the operation of J (dU),
>>> the
>>> >> >>> >> U0
>>> >> >>> >> get a
>>> >> >>> >> perturbation size in the order of 100, which causes problem as
>>> U0
>>> >> >>> >> has
>>> >> >>> >> to be
>>> >> >>> >> smaller than 1.
>>> >> >>> >>
>>> >> >>> >> From my observation, this same perturbation size, say eps, is
>>> >> >>> >> applied
>>> >> >>> >> on all
>>> >> >>> >> U0, U1, U2, etc. <=== Is this the default setting?
>>> >> >>> >> I also guess that this eps, in the order of 100, is determined
>>> from
>>> >> >>> >> my
>>> >> >>> >> initial solution vector and other related PETSc parameters.
>>>  <===
>>> >> >>> >> Is
>>> >> >>> >> my
>>> >> >>> >> guessing right?
>>> >> >>> >>
>>> >> >>> >> (3)
>>> >> >>> >>
>>> =================================================================
>>> >> >>> >> My question: I'd like to avoid a perturbation size ~100 on U0,
>>> >> >>> >> i.e., I
>>> >> >>> >> have
>>> >> >>> >> to limit it to be ~0.01 (or some small number) to avoid the U0
>>> > 1
>>> >> >>> >> situation. Is there any way to control that?
>>> >> >>> >> Or, is there any advanced option to control the perturbation
>>> size
>>> >> >>> >> on
>>> >> >>> >> different variables when using snes_mf_operator?
>>> >> >>> >
>>> >> >>> > Here is a description of the algorithm for calculating h. It
>>> seems
>>> >> >>> > to
>>> >> >>> > me a better way to do this
>>> >> >>> > is to non-dimensionalize first.
>>> >> >>>
>>> >> >>> I forgot the URL:
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/Mat/MatCreateMFFD.html#MatCreateMFFD
>>> >> >>>
>>> >> >>>    Matt
>>> >> >>>
>>> >> >>> >    Matt
>>> >> >>> >
>>> >> >>> >>
>>> >> >>> >> Hope my explanation is clear. Please let me know if it is not.
>>> >> >>> >>
>>> >> >>> >>
>>> >> >>> >> Best Regards,
>>> >> >>> >>
>>> >> >>> >> 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
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> >> >>> --
>>> >> >>> 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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