[petsc-dev] Add natural-to-global and global-to-natural operations for DM?

[Matthew Knepley]

On Wed, Mar 20, 2013 at 9:49 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>    Richard,
>
>       Once you have the vector in the "natural order" what do you do with
> it?
>

Also, I am not sure that making an ordering is the best way to do this. I
just do it on
the fly for Plex when outputting to VTK.

   Matt


> 1) visualize it?
> 2) store to disk?
> 3) send to one process so you can do something on it?
> 3) ???
>
>      Note that VecView() on DMDA vectors automatically manage the mapping
> to natural ordering when saving to disk so the user does not ever need to
> apply globaltonatural themselves.
>
>      I would argue that the only "legitimate" use of
> DMDAGlobalToNatural/NaturalToGlobal() is for IO (or similarly transferring
> a DMDA vector between two MPI communicators of different sizes) so my
> inclination is to make DMDAGlobalToNatural() less public, not bring it down
> to the DM level.
>
>     If you are using GlobalToNatural in your IO I would argue that better
> approach is to imbed the mapping inside the VecLoad and VecView for your DM
> unstructured then you do not need need a universal DMGlobalToNatural();
>
>     I do not object to a DMLocalToLocalBegin/End(), though local is not
> universal we do have the local concept at the DM level already and it will
> remain there.
>
>    Barry
>
>
>
> On Mar 19, 2013, at 9:54 PM, Richard Tran Mills <rtm at eecs.utk.edu> wrote:
>
> > Hi Barry,
> >
> > What we call the "natural" ordering in PFLOTRAN is what is referred to
> as the "application" ordering in PETSc parlance.  In the structured grid
> case this "application" ordering is the natural ordering used by the DMDA
> routines like DMDANaturalToGlobalBegin()/End(), and in the unstructured
> case it is whatever ordering was used to assign cell IDs when the
> unstructured grid was created.  Rather than having code for two cases, I
> would prefer to be able to just call DMNaturalToGlobalBegin()/End() for
> either case.  I do realize, of course, that for the DMDA case there is
> always a default meaning for the "natural" ordering, whereas for the case
> of a general DM the notion of "natural" will be application dependent and
> will have to be specified by user code (which I'd like to do in this case
> by having a DMShellSetNaturalToGlobalVecScatter()).
> >
> > Obviously, there may be subtypes of DM for which no "natural to global"
> operation makes sense.  What I'm saying is that I nonetheless would like to
> have a general DMNaturalToGlobalBegin()/End() that will do the appropriate
> thing if it makes sense for that DM and complain otherwise.  I guess this
> is a question of what the PETSc philosophy is regarding such things.  I
> note that there is at least one example of a current DMDA method that ought
> to just be a DM one: I don't see why we should have
> DMDALocalToLocalBegin()/End() and not just DMLocalToLocalBegin()/End(), and
> I'd like to go ahead and change this.  But LocalToLocal makes sense for
> lots of DMs, and NaturalToGlobal may not.
> >
> > --Richard
> >
> > On 3/7/13 10:51 PM, Barry Smith wrote:
> >> On Mar 7, 2013, at 9:46 PM, Richard Tran Mills <rtm at eecs.utk.edu>
> wrote:
> >>
> >>> Continuing on my quest to be able to wrap all of the unstructured grid
> operations in PFLOTRAN inside a DM: Would it be OK to add
> DMGlobalToNaturalBegin()/End() and DMNatualToGlobalBegin()/End()? These are
> currently DMDA routines, not DM ones.  We do something that we call
> natural-to-global and global-to-natural operations with our unstructured
> grid cases in PFLOTRAN (though I'm not sure if "natural" is quite the thing
> to call it... I always think of that in terms of a structured grid layout).
>  I would like to just call DMGlobalToNaturalBegin()/End(), etc., on our DM,
> whether it is a DMDA or a DMShell.
> >>>
> >>> I had already mentioned that I plan to add DM interface routines for
> local-to-local operations.  I am thinking that global-to-natural, etc.,
> also ought to be added, though I'm not sure if the concept of "natural"
> ordering necessarily makes sense in some cases.
> >>    What does natural mean for you on anything but a DA in what you do
> with pflotran? Once we all understand than we can come up with ideas on how
> that fits with DM.
> >>
> >>    Barry
> >>
> >>> --Richard
> >>>
> >>> --
> >>> Richard Tran Mills, Ph.D.
> >>> Computational Earth Scientist      | Joint Assistant Professor
> >>> Hydrogeochemical Dynamics Team     | EECS and Earth & Planetary
> Sciences
> >>> Oak Ridge National Laboratory      | University of Tennessee, Knoxville
> >>> E-mail: rmills at ornl.gov  V: 865-241-3198
> http://climate.ornl.gov/~rmills
> >>>
> >
> >
> > --
> > Richard Tran Mills, Ph.D.
> > Computational Earth Scientist      | Joint Assistant Professor
> > Hydrogeochemical Dynamics Team     | EECS and Earth & Planetary Sciences
> > Oak Ridge National Laboratory      | University of Tennessee, Knoxville
> > E-mail: rmills at ornl.gov  V: 865-241-3198 http://climate.ornl.gov/~rmills
> >
>
>


-- 
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
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