On Thu, Nov 5, 2015 at 12:11 PM, tschroeder <tschroe...@daad-alumni.de> wrote:
> I decided to start fresh. Here is a little bit more detail: > There's an issue here: the optional INCLUDES should show your installed PETSc directory, but it doesn't. > libmesh_optional_INCLUDES........ : -I/usr/include/eigen3 -I/usr/include > > libmesh_optional_LIBS............ : -L/lib -lhdf5 -Wl,-rpath,/lib -lz > -L/usr/lib -ltbb -ltbbmalloc > LibMesh also thinks your PETSc installation has no MPI: configure:29534: result: <<< Warning: configuring in serial - no MPI in PETSC config >>> but I can see from the attached files that you did --download-mpich. In short, something still isn't quite right about your PETSc installation. > Then, I executed make. > > That failed, seemingly because it could not find the PETSc include file > directory: > > In file included from src/base/libmesh.C:62:0: > ./include/libmesh/petsc_macro.h:93:19: fatal error: petsc.h: No such file > or directory > This makes sense, as the path to the PETSc headers does not appear in your list of libmesh_optional_INCLUDES. I'm not really sure why configure seems to find PETSc but then doesn't add the path to the list of includes... there may have been some bug in libmesh 0.9.4 that is causing this, but I don't recall there being one... Starting over, I called make as follows: > > C_INCLUDE_PATH=/home/tobias/PETSc/petsc-install/include > export C_INCLUDE_PATH > CPLUS_INCLUDE_PATH=/home/tobias/PETSc/petsc-install/include > export CPLUS_INCLUDE_PATH > make > > > Not, I get this error: > > > CXX src/partitioning/libmesh_dbg_la-parmetis_partitioner.lo > In file included from > /home/tobias/PETSc/petsc-install/include/mpi.h:2216:0, > from ./contrib/parmetis/include/parmetis.h:17, > from src/partitioning/parmetis_partitioner.C:40: > /home/tobias/PETSc/petsc-install/include/mpicxx.h:2737:34: error: > declaration of C function 'void Parmetis::MPI::Init(int&, char**&)' > conflicts with > extern void Init(int &, char **& ); > ^ > /home/tobias/PETSc/petsc-install/include/mpicxx.h:2736:13: error: previous > declaration 'void Parmetis::MPI::Init()' here > extern void Init(void); > This issue is caused because libmesh's parmetis installation is conflicting with PETSc's. We fixed this back in March [0], but 0.9.4 was released in February. Grabbing a zip file of current libmesh master [1] would fix this issue, and probably shed more light on why the PETSc installation's include path is not being set. [0]: https://github.com/libMesh/libmesh/commit/51f52627cfb10462166f8661aabcde936404cecc [1]: https://github.com/libMesh/libmesh/archive/master.zip -- John ------------------------------------------------------------------------------ _______________________________________________ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
