[petsc-dev] DMplex: Natural Ordering and subDM

[Matthew Knepley]

On Mon, Nov 27, 2017 at 9:24 PM, Jed Brown <jed at jedbrown.org> wrote:

> Matthew Knepley <knepley at gmail.com> writes:
>
> > On Mon, Nov 27, 2017 at 8:08 PM, Jed Brown <jed at jedbrown.org> wrote:
> >
> >> I don't know the answer to your question (Matt?), but do you really need
> >> to reorder the entire mesh or would it be sufficient to label your
> >> points with their original numbering?
> >
> >
> > Maybe I am wrong, but I think it amounts to the same thing. If we are
> going
> > to output things in parallel,
> > we would need to communicate to he writing process, which this
> essentially
> > does.
>
> Writing a label doesn't require redistribution of the mesh.  It's possible
> to do parallel IO.
>

My understanding is that 3rd party programs want the mesh in the original
order, so we
want it ordered in the HDF5 file in the original order. You could I guess
write it in the order,
but it seems messy to write stuff all over the place in the file. Is that
what you mean?

  Matt


> > I thought I responded, but what has to happen is that the SF for this
> > reordering must be decimated to
> > produce a subSF for the subDM. Its just not simple, so I have not had the
> > free time to work it out.
> >
> >    Matt
> >
> >
> >> Blaise A Bourdin <bourdin at lsu.edu> writes:
> >>
> >> > Hi,
> >> > I am fighting with natural ordering in DMplex with multi-fields /
> multi
> >> components DM.
> >> > I need to read / write files in a distribution-independent ordering.
> The
> >> natural way to do so is to define the natural ordering as that of the
> file,
> >> then call DMPlexGlobalToNaturalBegin/End before VecView:
> >> > The pseudo code would be
> >> >
> >> >   DMPlexCreateFromFile(PETSC_COMM_WORLD,ifilename,
> interpolate,&dmUAS);
> >> >   // create default section associated with a complicated layout of
> >> multiple fields
> >> >   // (U,\alpha,\sigma)
> >> >   DMSetUseNatural(dmUAS,PETSC_TRUE);
> >> >   DMPlexDistribute(dmUAS,0,&migrationSF,&dmDist);
> >> >
> >> >   DMGetGlobalVector(dmDist,&UAS);
> >> >   DMGetGlobalVector(dmDist,&UASNatural);
> >> >   DMPlexGlobalToNaturalBegin(dmDist,UAS,UASNatural);
> >> >   DMPlexGlobalToNaturalEnd(dmDist,UAS,UASNatural);
> >> >   // Do my I/O stuff using UASNatural
> >> >
> >> > If I try to do the same thing one field at a time, things break:
> >> > Say that I get the subDM for the first field (U):
> >> >
> >> >   DMCreateSubDM(dmDist,1,&fieldU,&ISU,&dmU);
> >> >
> >> > Then dmU->useNatural is PETSC_FALSE and  I cannot compute
> dmU->sfnatural
> >> using DMPlexCreateGlobalToNaturalSF since I do not have the “sequential”
> >> version of dmU.
> >> >
> >> > What is the proper way to handle this situation? Creating sequential
> >> subDMs and calling DMDistribute on each of them is ugly and possibly
> costly.
> >> >
> >> > Regards,
> >> >
> >> > Blaise
> >> >
> >> > --
> >> > Department of Mathematics and Center for Computation & Technology
> >> > Louisiana State University, Baton Rouge, LA 70803, USA
> >> > Tel. +1 (225) 578 1612, Fax  +1 (225) 578 4276
> http://www.math.lsu.edu/~
> >> bourdin
> >>
> >
> >
> >
> > --
> > 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.caam.rice.edu/~mk51/>
>



-- 
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.caam.rice.edu/~mk51/>
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