[petsc-users] DMPLEX project function error

Ellen M. Price ellen.price at cfa.harvard.edu
Fri Oct 12 14:51:18 CDT 2018 

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.price at cfa.harvard.edu <mailto:ellen.price at 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.price at cfa.harvard.edu <mailto:ellen.price at cfa.harvard.edu>
>     <mailto:ellen.price at cfa.harvard.edu
>     <mailto:ellen.price at 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/>

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