> On Jul 15, 2022, at 11:20 AM, Matthew Knepley <knep...@gmail.com> wrote:
>
> On Fri, Jul 15, 2022 at 11:01 AM Randall Mackie <rlmackie...@gmail.com
> <mailto:rlmackie...@gmail.com>> wrote:
> I am also interested in converting my DMDA code to DMPlex so that I can use
> OcTree grids.
>
> Is there a simple example that would show how to do a box grid in DMPlex, or
> more information about how to convert a DMDA grid to DMPlex?
>
> Hi Randy,
>
> Creating a box mesh is easy and can be done from the command line.
>
> The hard part is usually converting the loop structure. Plex is setup to
> support FEM and FVM, which are both
> cell-oriented. DMDA, on the other hand, tends to support a stencil of
> cells/vertices. Is this how your code looks?
Hi Matt,
I figured the hard part was the loop structure.
Yes, my DMDA code is pretty standard and I have fields defined on block edges
(it’s a staggered grid implementation, but written long before petsc had
staggered grid capability) and I just loop over the DMDA grid points like:
do k=zs,ze
do j=ys,ye
do i=xs,xe
I’d be very interested to see what you can show us.
Thanks, Randy
>
> I have a student working on a PetscFD which I could show you, but it is far
> from production.
>
> Thanks,
>
> Matt
>
> Thanks, Randy
>
>> On Jun 21, 2022, at 10:57 AM, Mark Adams <mfad...@lbl.gov
>> <mailto:mfad...@lbl.gov>> wrote:
>>
>> (keep on the list, you will need Matt and Toby soon anyway).
>>
>> So you want to add AMRex to your code.
>>
>> I think the first thing that you want to do is move your DMDA code into a
>> DMPLex code. You can create a "box" mesh and it is not hard.
>> Others like Matt can give advice on how to get started on that translation.
>> There is a simple step to create a DMForest (p4/8est) that Matt mentioned
>> from the DMPlex .
>>
>> Now at this point you can run your current SNES tests and get back to where
>> you started, but AMR is easy now.
>> Or as easy as it gets.
>>
>> As far as AMRex, well, it's not clear what AMRex does for you at this point.
>> You don't seem to have AMRex code that you want to reuse.
>> If there is some functionality that you need then we can talk about it or if
>> you have some programmatic reason to use it (eg, they are paying you) then,
>> again, we can talk about it.
>>
>> PETSc/p4est and AMRex are similar with different strengths and design, and
>> you could use both but that would complicate things.
>>
>> Hope that helps,
>> Mark
>>
>>
>> On Tue, Jun 21, 2022 at 1:18 PM Bernigaud Pierre <pierre.bernig...@onera.fr
>> <mailto:pierre.bernig...@onera.fr>> wrote:
>> Hello Mark,
>>
>> We have a working solver employing SNES, to which is attached a DMDA to
>> handle ghost cells / data sharing between processors for flux evaluation
>> (using DMGlobalToLocalBegin / DMGlobalToLocalEnd) . We are considering to
>> add an AMReX layer to the solver, but no work has been done yet, as we are
>> currently evaluating if it would be feasible without too much trouble.
>>
>> Our main subject of concern would be to understand how to interface
>> correctly PETSc (SNES+DMDA) and AMRex, as AMRex also appears to have his own
>> methods for parallel data management. Hence our inquiry for examples, just
>> to get a feel for how it would work out.
>>
>> Best,
>>
>> Pierre
>>
>> Le 21/06/2022 à 18:00, Mark Adams a écrit :
>>> Hi Bernigaud,
>>>
>>> To be clear, you have SNES working with DMDA in AMRex, but without adapting
>>> dynamically and you want to know what to do next.
>>>
>>> Is that right?
>>>
>>> Mark
>>>
>>>
>>>
>>>
>>> On Tue, Jun 21, 2022 at 11:46 AM Bernigaud Pierre
>>> <pierre.bernig...@onera.fr <mailto:pierre.bernig...@onera.fr>> wrote:
>>> Greetings,
>>>
>>> I hope you are doing great.
>>>
>>> We are currently working on parallel solver employing PETSc for the main
>>> numerical methods (GMRES, Newton-Krylov method). We would be interested
>>> in combining the PETSc solvers with the AMR framework provided by the
>>> library AMReX (https://amrex-codes.github.io/amrex/
>>> <https://amrex-codes.github.io/amrex/>). I know that within
>>> the AMReX framework the KSP solvers provided by PETSc can be used, but
>>> what about the SNES solvers? More specifically, we are using a DMDA to
>>> manage parallel communications during the SNES calculations, and I am
>>> wondering how it would behave in a context where the data layout between
>>> processors is modified by the AMR code when refining the grid.
>>>
>>> Would you have any experience on this matter ? Is there any
>>> collaboration going on between PETsc and AMReX, or would you know of a
>>> code using both of them?
>>>
>>> Respectfully,
>>>
>>> Pierre Bernigaud
>>>
>> --
>> <jlgjjjnkhffoclfc.gif>Pierre Bernigaud
>> Doctorant
>> Département multi-physique pour l’énergétique
>> Modélisation Propulsion Fusée
>> Tél: +33 1 80 38 62 33
>>
>> ONERA - The French Aerospace Lab - Centre de Palaiseau
>> 6, Chemin de la Vauve aux Granges - 91123 PALAISEAU
>> Coordonnées GPS : 48.715169, 2.232833
>>
>> Nous suivre sur : www.onera.fr <https://www.onera.fr/> | Twitter
>> <http://www.twitter.com/@onera_fr> | LinkedIn
>> <http://www.linkedin.com/company/onera> | Facebook
>> <http://www.facebook.fr/thefrenchaerospacelab> | Instagram
>> <https://www.instagram.com/onera_the_french_aerospace_lab>
>>
>> Avertissement/disclaimer https://www.onera.fr/en/emails-terms
>> <https://www.onera.fr/en/emails-terms><dldmcfkmcojhebgb.png>
>>
>>
>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
