[petsc-dev] DMplex reader / viewers

[Matthew Knepley]

On Tue, Jan 21, 2014 at 9:30 AM, Blaise A Bourdin <bourdin at lsu.edu> wrote:

> Hi,
>
> It looks like DMplex is steadily gaining maturity but I/O is lagging
> behind. As far as I understand, right now, PETSc can _read_ a mesh in
> exodus format, and  write binary VTS format, but many issues remain, IMHO:
>    - The exodus reader relies on a hard-coded nodeset named “marker”.
> Generating such a nodeset is not trivial
>      (at least not for complex meshes generated with Cubit / Trelis).
>

I will fix this right away. I will put in some registration mechanism for
labels, and we can iterate.

   - Reading from or writing to exodus files is not supported.
>

Yes, I think this is the best target. It should be similar to writing HDF5
that we do for PyLith.

   Matt


>    - The VTS viewer only allows to read and write _all_ fields in a DM.
> This may be overkill if one only
>      wants to read boundary values, for instance.
>    - The VTS viewer loses all informations on exodus nodesets and cell
> sets. These may have some significance
>      and may be required to exploit the output of a computations.
>    - VTS seems to have a concept of “blocks”. My understanding is that the
> parallel VTS viewer uses blocks to
>      save subdomains, and that continuity of piecewise linear fields
> across subdomain boundaries is lost.
>      It is not entirely clear to me if with this layout, it would be
> possible to reopen a file with a
>      different processor count.
>
> I can dedicate some resources to improving DMplex I/O. Perhaps we can
> start a discussion by listing the desired features such readers / writers
> should have. I will pitch in by listing what matters to me:
>    - A well documented and adopted file format that most post-processors /
> visualization tools can use
>    - Ability to read / write individual fields
>    - Preserve _all_ information from the exodus file (node / side / cell
> sets), do not lose continuity of fields
>      across subdomain boundaries.
>    - Ability to reopen file on a different cpu count
>    - Support for higher order elements
>
> Am I missing something? If not, we can follow up with discussion on
> formats and implementation.
>
> 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
>
>
>
>
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>


-- 
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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