[petsc-users] Error when use DMPlexGetVertexNumbering

[Matthew Knepley]

On Fri, Feb 16, 2018 at 1:45 PM, Danyang Su <danyang.su at gmail.com> wrote:

> Hi Matt,
>
> I try to get the global vertex index and cell index from local mesh and
> run into problem. What I need is local to global index (the original index
> used in DMPlexCreateFromCellList is best, as user know exactly where the
> node/cell is) for vertices and cells, which will be used to assign material
> properties and some parameters to the specified cell/vertex.


I would recommend doing this before you distribute the mesh. Just set these
properties using a DMLabel and it will be automatically distributed.


> I can use coordinates to select vertex/cell which has already included,
> but still want to keep this feature. This is pretty straightforward when
> using structured grid. For the unstructured grid, I just got compiling
> error saying "You need a ISO C conforming compiler to use the glibc headers"
>

For any compilation problem, you have to send the configure.log and
make.log. However, it appears that you are not using the same compiler that
you configured with.

   Matt


> Would you please let me know if I need to change the configuration of
> PETSc or is there any alternative ways to avoid using
> DMPlexGetVertexNumbering and DMPlexGetCellNumbering but get local to global
> index?
>
> The error information during compilation is shown below, followed by PETSc
> configuration.
>
>  -o ../../solver/solver_ddmethod.o ../../solver/solver_ddmethod.F90
>
> In file included from /usr/include/features.h:375:0,
>                  from /usr/include/stdio.h:28,
>                  from /home/dsu/Soft/PETSc/petsc-3.7
> .5/include/petscsys.h:161,
>                  from /home/dsu/Soft/PETSc/petsc-3.7
> .5/include/petscis.h:8,
>                  from /home/dsu/Soft/PETSc/petsc-3.7
> .5/include/petscvec.h:10,
>                  from /home/dsu/Soft/PETSc/petsc-3.7
> .5/include/petscmat.h:7,
>                  from /home/dsu/Soft/PETSc/petsc-3.7
> .5/include/petsc/private/dmpleximpl.h:5,
>                  from ../../solver/solver_ddmethod.F90:4122:
> /usr/include/x86_64-linux-gnu/sys/cdefs.h:30:3: error: #error "You need a
> ISO C conforming compiler to us\
> e the glibc headers"
>  # error "You need a ISO C conforming compiler to use the glibc headers"
>    ^
> In file included from /usr/include/features.h:399:0,
>                  from /usr/include/stdio.h:28,
>                  from /home/dsu/Soft/PETSc/petsc-3.7
> .5/include/petscsys.h:161,
>                  from /home/dsu/Soft/PETSc/petsc-3.7
> .5/include/petscis.h:8,
>                  from /home/dsu/Soft/PETSc/petsc-3.7
> .5/include/petscvec.h:10,
>                  from /home/dsu/Soft/PETSc/petsc-3.7
> .5/include/petscmat.h:7,
>                  from /home/dsu/Soft/PETSc/petsc-3.7
> .5/include/petsc/private/dmpleximpl.h:5,
>                  from ../../solver/solver_ddmethod.F90:4122:
> /usr/include/x86_64-linux-gnu/gnu/stubs.h:7:0: fatal error:
> gnu/stubs-32.h: No such file or directory
>  # include <gnu/stubs-32.h>
>  ^
> compilation terminated.
> make: [../../solver/solver_ddmethod.o] Error 1 (ignored)
>
>
> PETSc configuration
> --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mumps
> --download-scalapack --download-parmetis --download-metis
> --download-ptscotch --download-fblaslapack --download-mpich
> --download-hypre --download-superlu_dist --download-hdf5=yes
> --with-debugging=0 COPTFLAGS="-O3 -march=native -mtune=native"
> CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3 -march=native
> -mtune=native"
>
> Thanks and regards,
>
> Danyang
>
>


-- 
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.caam.rice.edu/~mk51/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20180216/84ba1108/attachment.html>