[petsc-users] Error when use DMPlexGetVertexNumbering

[Danyang Su]

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 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"

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