[petsc-users] how to control snes_mf_operator

[Matthew Knepley]

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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