On Tue, Jan 21, 2014 at 9:30 AM, Blaise A Bourdin <bour...@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 > > > > > > > > -- 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
