I think you are fine with DMForest. I just mentioned ForestClaw for background. It has a bunch of hyperbolic stuff in there that is specialized.
On Thu, Sep 19, 2019 at 8:16 AM Mohammad Hassan <mhbagh...@mail.sjtu.edu.cn> wrote: > In fact, I would create my base mesh in DMPlex and use DMForest to > construct the non-conformal meshing obtained by my own block-based AMR > functions. ForestClaw is based on p4est. However, I may need to implement > the AMR algorithm on DM in p4est library and then convert it to DMPlex. Do > you think DMForest alone will not allow me to create the AMR for DMPlex? > > > > Thanks > > Amir > > > > *From:* Mark Adams [mailto:mfad...@lbl.gov] > *Sent:* Thursday, September 19, 2019 7:23 PM > *To:* Mohammad Hassan <mhbagh...@mail.sjtu.edu.cn> > *Cc:* Matthew Knepley <knep...@gmail.com>; PETSc users list < > petsc-users@mcs.anl.gov> > *Subject:* Re: [petsc-users] DMPlex Distribution > > > > Note, Forest gives you individual elements at the leaves. Donna Calhoun, a > former Chombo user, has developed a block structured solver on p4est ( > https://math.boisestate.edu/~calhoun/ForestClaw/index.html), but I would > imagine that you could just take the Plex that DMForest creates and just > call DMRefine(...) on it to get a block structured AMR mesh. > > > > On Wed, Sep 18, 2019 at 11:02 AM Mohammad Hassan via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > Thanks for your suggestion, Matthew. I will certainly look into DMForest > for refining of my base DMPlex dm. > > > > *From:* Matthew Knepley [mailto:knep...@gmail.com] > *Sent:* Wednesday, September 18, 2019 10:35 PM > *To:* Mohammad Hassan <mhbagh...@mail.sjtu.edu.cn> > *Cc:* PETSc <petsc-users@mcs.anl.gov> > *Subject:* Re: [petsc-users] DMPlex Distribution > > > > On Wed, Sep 18, 2019 at 10:27 AM Mohammad Hassan < > mhbagh...@mail.sjtu.edu.cn> wrote: > > I want to implement block-based AMR, which turns my base conformal mesh to > non-conformal. My question is how DMPlex renders a mesh that it cannot > support non-conformal meshes. > > > > Mark misspoke. Plex _does_ support geometrically non-conforming meshing, > e.g. "hanging nodes". The easiest way to > > use Plex this way is to use DMForest, which uses Plex underneath. > > > > There are excellent p4est tutorials. What you would do is create your > conformal mesh, using Plex if you want, and > > use that for the p4est base mesh (you would have the base mesh be the > forest roots). > > > > Thanks, > > > > Matt > > > > If DMPlex does not work, I will try to use DMForest. > > > > *From:* Matthew Knepley [mailto:knep...@gmail.com] > *Sent:* Wednesday, September 18, 2019 9:50 PM > *To:* Mohammad Hassan <mhbagh...@mail.sjtu.edu.cn> > *Cc:* Mark Adams <mfad...@lbl.gov>; PETSc <petsc-users@mcs.anl.gov> > *Subject:* Re: [petsc-users] DMPlex Distribution > > > > On Wed, Sep 18, 2019 at 9:35 AM Mohammad Hassan via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > If DMPlex does not support, I may need to use PARAMESH or CHOMBO. Is there > any way that we can construct non-conformal layout for DM in petsc? > > > > Lets see. Plex does support geometrically non-conforming meshes. This is > how we support p4est. However, if > > you want that, you can just use DMForest I think. So you jsut want > structured AMR? > > > > Thanks, > > > > Matt > > > > > > *From:* Mark Adams [mailto:mfad...@lbl.gov] > *Sent:* Wednesday, September 18, 2019 9:23 PM > *To:* Mohammad Hassan <mhbagh...@mail.sjtu.edu.cn> > *Cc:* Matthew Knepley <knep...@gmail.com>; PETSc users list < > petsc-users@mcs.anl.gov> > *Subject:* Re: [petsc-users] DMPlex Distribution > > > > I'm puzzled. It sounds like you are doing non-conforming AMR (structured > block AMR), but Plex does not support that. > > > > On Tue, Sep 17, 2019 at 11:41 PM Mohammad Hassan via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > Mark is right. The functionality of AMR does not relate to > parallelization of that. The vector size (global or local) does not > conflict with AMR functions. > > Thanks > > > > Amir > > > > *From:* Matthew Knepley [mailto:knep...@gmail.com] > *Sent:* Wednesday, September 18, 2019 12:59 AM > *To:* Mohammad Hassan <mhbagh...@mail.sjtu.edu.cn> > *Cc:* PETSc <petsc-ma...@mcs.anl.gov> > *Subject:* Re: [petsc-users] DMPlex Distribution > > > > On Tue, Sep 17, 2019 at 12:03 PM Mohammad Hassan < > mhbagh...@mail.sjtu.edu.cn> wrote: > > Thanks for suggestion. I am going to use a block-based amr. I think I need > to know exactly the mesh distribution of blocks across different processors > for implementation of amr. > > > > Hi Amir, > > > > How are you using Plex if the block-AMR is coming from somewhere else? > This will help > > me tell you what would be best. > > > > And as a general question, can we set block size of vector on each rank? > > > > I think as Mark says that you are using "blocksize" is a different way > than PETSc. > > > > Thanks, > > > > Matt > > > > Thanks > > Amir > > > > *From:* Matthew Knepley [mailto:knep...@gmail.com] > *Sent:* Tuesday, September 17, 2019 11:04 PM > *To:* Mohammad Hassan <mhbagh...@mail.sjtu.edu.cn> > *Cc:* PETSc <petsc-users@mcs.anl.gov> > *Subject:* Re: [petsc-users] DMPlex Distribution > > > > On Tue, Sep 17, 2019 at 9:27 AM Mohammad Hassan via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > Hi > > I am using DMPlexCreateFromDAG() to construct my DM. Is it possible to set > the distribution across processors manually. I mean, how can I set the > share of dm on each rank (local)? > > > > You could make a Shell partitioner and tell it the entire partition: > > > > > https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/DMPLEX/PetscPartitionerShellSetPartition.html > > > > However, I would be surprised if you could do this. It is likely that you > just want to mess with the weights in ParMetis. > > > > Thanks, > > > > Matt > > > > Thanks > > Amir > > > > > -- > > 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/> > > > > > -- > > 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/> > >