[petsc-users] Error when use DMPlexGetVertexNumbering

[Danyang Su]

On 18-02-16 10:50 AM, Matthew Knepley wrote:
> On Fri, Feb 16, 2018 at 1:45 PM, Danyang Su <danyang.su at gmail.com 
> <mailto: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 will try this. Thanks.
>
>     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.
Sorry for confusion. There are linux-gnu-dbg (debug version) and 
linux-gnu-opt (optimized version) configuration, the one I used to 
compile is debug version and the attached one is optimized version. I 
will try you recommendation first.

Thanks,

Danyang
>
>    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/%7Emk51/>

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