[petsc-users] DMPlex Distribution

Thu Sep 19 06:23:28 CDT 2019

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 at 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:knepley at gmail.com]
> *Sent:* Wednesday, September 18, 2019 10:35 PM
> *To:* Mohammad Hassan <mhbaghaei at mail.sjtu.edu.cn>
> *Cc:* PETSc <petsc-users at mcs.anl.gov>
> *Subject:* Re: [petsc-users] DMPlex Distribution
>
>
>
> On Wed, Sep 18, 2019 at 10:27 AM Mohammad Hassan <
> mhbaghaei at 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:knepley at gmail.com]
> *Sent:* Wednesday, September 18, 2019 9:50 PM
> *To:* Mohammad Hassan <mhbaghaei at mail.sjtu.edu.cn>
> *Cc:* Mark Adams <mfadams at lbl.gov>; PETSc <petsc-users at 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 at 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:mfadams at lbl.gov]
> *Sent:* Wednesday, September 18, 2019 9:23 PM
> *To:* Mohammad Hassan <mhbaghaei at mail.sjtu.edu.cn>
> *Cc:* Matthew Knepley <knepley at gmail.com>; PETSc users list <
> petsc-users at 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 at 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:knepley at gmail.com]
> *Sent:* Wednesday, September 18, 2019 12:59 AM
> *To:* Mohammad Hassan <mhbaghaei at mail.sjtu.edu.cn>
> *Cc:* PETSc <petsc-maint at mcs.anl.gov>
> *Subject:* Re: [petsc-users] DMPlex Distribution
>
>
>
> On Tue, Sep 17, 2019 at 12:03 PM Mohammad Hassan <
> mhbaghaei at 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:knepley at gmail.com]
> *Sent:* Tuesday, September 17, 2019 11:04 PM
> *To:* Mohammad Hassan <mhbaghaei at mail.sjtu.edu.cn>
> *Cc:* PETSc <petsc-users at 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 at 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/>
>
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