Hi Matt, Basically, I have a simple meshing script that generates a set of points for my FEM mesh and outputs a C file that compiles into my program. Along with those points is a static data field that I need to be associated with the correct data point. I don't have a function that evaluates at each point, it's just pre-generated data.
Since I called DMPlexDistribute() early on, I think my mesh points get re-ordered, right? So I need a way to re-order my data field to match that ordering. Is there a good way to do this? I tried using DMPlexDistributeField as a first attempt, but I get some kind of error no matter what I do (presumably I'm not giving the right input), and there aren't any examples in the docs. Ellen On 10/12/2018 11:31 AM, Matthew Knepley wrote: > On Fri, Oct 12, 2018 at 11:12 AM Ellen M. Price > <ellen.pr...@cfa.harvard.edu <mailto:ellen.pr...@cfa.harvard.edu>> wrote: > > So I found *that* problem -- turns out that using DMPlexCreateSection > was messing things up, and it seems PETSc is handling that part > internally? > > > DMPlexSection creates the Section based on the discretization > information in the DM (stored in a PetscDS). > If no discretization info is available, then it defaults to P0 I think, > which is what you got. > > After discretization info is put into the DM, if I ask for the Section, > the DM will create it automatically if it is missing. > > > However, I've run into a related problem now. I need to > project some field data onto the mesh; it's a static array of > integration weights, and each one corresponds to a single point in the > mesh. Based on this answer: > > https://lists.mcs.anl.gov/pipermail/petsc-users/2015-December/027964.html > > I think I need DMPlexDistributeField. > > > I don't think that is what you want. That is just sending data around. > > You want to define an FEM field. We use DMProject*() for this. These > take as input either > a function of the coordinates (regular function) or another FEM field. > > Can you tell me how your function is defined? I mean apart from the > particular data you > have at points. > > Thanks, > > Matt > > > However, *that* function takes a > section as an argument, and I had to take out the part where I create a > section to get things working! Calling DMGetDefaultSection or > DMGetDefaultGlobalSection doesn't seem to help matters, either, because > then I seem to get a null section? > > So I either need to figure out how to set the section properly or how to > get the section properly. As always, any help is appreciated. > > Ellen > > > On 10/11/2018 05:41 PM, Matthew Knepley wrote: > > On Thu, Oct 11, 2018 at 4:39 PM Ellen M. Price > > <ellen.pr...@cfa.harvard.edu <mailto:ellen.pr...@cfa.harvard.edu> > <mailto:ellen.pr...@cfa.harvard.edu > <mailto:ellen.pr...@cfa.harvard.edu>>> wrote: > > > > I was working with a DMPLEX and FEM, following SNES example > 12. I get > > the following error when I call DMProjectFunction, but I don't > know what > > it means. Can anyone explain where I might have gone wrong, or > at least > > what this error is telling me? I think the point closure size is > > correct, since my mesh is 3d simplex, > > > > > > Yes, if you have 3D SIMPLEX mesh and are using P1 elements, then you > > would have > > 4 dofs in the closure of a cell. The dual space dimension is the > number > > of dual space > > basis vectors assigned to points in the closure. Since it is 1, it > looks > > like you have a P0 > > dual space. I assume you changed something in ex12? > > > > Thanks, > > > > Matt > > > > > > but what is the dual space > > dimension, and where might I have set it incorrectly? > > > > [0]PETSC ERROR: Nonconforming object sizes > > [0]PETSC ERROR: The section point closure size 4 != dual space > > dimension 1 > > [0]PETSC ERROR: See > http://www.mcs.anl.gov/petsc/documentation/faq.html > > for trouble shooting. > > [0]PETSC ERROR: Petsc Release Version 3.9.2, May, 20, 2018 > > ... > > [0]PETSC ERROR: Configure options > > --prefix=/home/eprice/software/petsc-opt --with-hdf5=1 > > --with-hdf5-dir=/home/eprice/software/hdf5-parallel --with-mpe=1 > > --with-mpe-dir=/home/eprice/software/mpe --with-debugging=0 > > LDFLAGS="-pthread -lz" COPTFLAGS="-O3 -march=native -mtune=native" > > CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3 > > -march=native -mtune=native" --with-mpi=1 > > --with-mpi-dir=/home/eprice/software/mpich --with-mumps=1 > > --with-mumps-dir=/home/eprice/software/mumps --with-parmetis=1 > > --with-parmetis-dir=/home/eprice/software/parmetis --with-metis=1 > > --with-metis-dir=/home/eprice/software/parmetis --with-ptscotch=1 > > --with-ptscotch-dir=/home/eprice/software/scotch > --with-scalapack=1 > > --with-scalapack-dir=/home/eprice/software/scalapack > > [0]PETSC ERROR: #1 DMProjectLocal_Generic_Plex() line 347 in > > /h/sabriel0/src/petsc-3.9.2/src/dm/impls/plex/plexproject.c > > [0]PETSC ERROR: #2 DMProjectFunctionLocal_Plex() line 428 in > > /h/sabriel0/src/petsc-3.9.2/src/dm/impls/plex/plexproject.c > > [0]PETSC ERROR: #3 DMProjectFunctionLocal() line 6265 in > > /h/sabriel0/src/petsc-3.9.2/src/dm/interface/dm.c > > [0]PETSC ERROR: #4 DMProjectFunction() line 6250 in > > /h/sabriel0/src/petsc-3.9.2/src/dm/interface/dm.c > > ... > > > > (I know this is an optimized PETSc build, but I get the same > error from > > my debug build, it's just much slower.) > > > > Ellen > > > > > > > > -- > > 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/ > <https://www.cse.buffalo.edu/%7Eknepley/> > > <http://www.cse.buffalo.edu/%7Eknepley/> > > > > -- > 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.cse.buffalo.edu/%7Eknepley/>
