[petsc-users] PETSc / AMRex

Fri Jul 15 13:58:43 CDT 2022

On Fri, Jul 15, 2022 at 1:46 PM Randall Mackie <rlmackie862 at gmail.com>
wrote:

> On Jul 15, 2022, at 11:20 AM, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Fri, Jul 15, 2022 at 11:01 AM Randall Mackie <rlmackie862 at 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.
>

What information do you need when computing an entry, for the cell and then
for the face?

  Thanks,

     Matt

> 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 <mfadams at 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.bernigaud at 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.bernigaud at 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/). 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*
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>>
>
> --
> 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/>
>
>
>

-- 
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/>
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