On Fri, Jul 15, 2022 at 1:46 PM Randall Mackie <rlmackie...@gmail.com> wrote:
> 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> > 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 <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> 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> 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* >>> 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 | 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 >>> <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/> > > > -- 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/>