[petsc-dev] DMplex reader / viewers

[Blaise A Bourdin]

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