[vtk-developers] can't link to MPI libraries when building on Ubuntu 15.04, VTK6.3

[Chaffra J. Affouda]

Ok I did and it built. What hdf5/mpi variables do I need to update?

Thanks,
Chaffra

On Mon, Sep 14, 2015, 14:19 Utkarsh Ayachit <utkarsh.ayachit at kitware.com>
wrote:

> For starters, turn off USE_SYSTEM_HDF5 and then confirm it builds.
> Once that's confirmed, you can turn the flag back on and then update
> the HDF5 library variables to include the MPI variables as well.
>
> On Mon, Sep 14, 2015 at 11:49 AM, Chaffra Affouda <chaffra at gmail.com>
> wrote:
> > Utkarsh,
> >
> > Yes I am:
> > I built with -DUSE_SYSTEM_HDF5=ON. Should I be doing something else?
> >
> > Chaffra
> >
> >
> > On 09/14/2015 10:56 AM, Utkarsh Ayachit wrote:
> >>
> >> Chaffra,
> >>
> >> Are you by any change using system HDF5?
> >>
> >> Utkarsh
> >>
> >> On Mon, Sep 14, 2015 at 8:46 AM, Chaffra Affouda <chaffra at gmail.com>
> >> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I am getting a lot of undefined references when linking. I know it is
> not
> >>> linking to MPI or the right MPI but I cannot see how.
> >>> I have openmpi installed and mpicc is pointing to the openmpi version.
> >>> Can
> >>> any reproduce or help? Error is below
> >>>
> >>> Thanks,
> >>> Chaffra
> >>>
> >>>     Linking CXX shared library ../../lib/libvtkIOAMR-6.3.so
> >>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In
> function
> >>> `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&),
> >>> bool)':
> >>>
> >>>
> vtkAMREnzoParticlesReader.cxx:(.text._ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[_ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb]+0x15):
> >>> undefined reference to `ompi_mpi_cxx_op_intercept'
> >>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In
> function
> >>> `MPI::Intracomm::Create_graph(int, int const*, int const*, bool)
> const':
> >>>
> >>>
> vtkAMREnzoParticlesReader.cxx:(.text._ZNK3MPI9Intracomm12Create_graphEiPKiS2_b[_ZNK3MPI9Intracomm12Create_graphEiPKiS2_b]+0x39):
> >>> undefined reference to `MPI::Comm::Comm()'
> >>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In
> function
> >>> `MPI::Graphcomm::Clone() const':
> >>>
> >>>
> vtkAMREnzoParticlesReader.cxx:(.text._ZNK3MPI9Graphcomm5CloneEv[_ZNK3MPI9Graphcomm5CloneEv]+0x35):
> >>> undefined reference to  `MPI::Comm::Comm()'
> >>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In
> function
> >>> `MPI::Cartcomm::Clone() const':
> >>>
> >>>
> vtkAMREnzoParticlesReader.cxx:(.text._ZNK3MPI8Cartcomm5CloneEv[_ZNK3MPI8Cartcomm5CloneEv]+0x35):
> >>> undefined reference to   `MPI::Comm::Comm()'
> >>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In
> function
> >>> `MPI::Intercomm::Merge(bool) const':
> >>>
> >>>
> vtkAMREnzoParticlesReader.cxx:(.text._ZNK3MPI9Intercomm5MergeEb[_ZNK3MPI9Intercomm5MergeEb]+0x37):
> >>> undefined reference to  `MPI::Comm::Comm()'
> >>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In
> function
> >>> `MPI::Intracomm::Create(MPI::Group const&) const':
> >>>
> >>>
> vtkAMREnzoParticlesReader.cxx:(.text._ZNK3MPI9Intracomm6CreateERKNS_5GroupE[_ZNK3MPI9Intracomm6CreateERKNS_5GroupE]+0x3a):
> >>> undefined    reference to `MPI::Comm::Comm()'
> >>>
> >>>
> CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o:vtkAMREnzoParticlesReader.cxx:
> >>> (.text._ZNK3MPI9Intracomm5SplitEii[_ZNK3MPI9Intracomm5SplitEii]+0x36):
> >>> more
> >>> undefined references to `MPI::Comm::Comm()' follow
> >>>
> >>>
> CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[_ZTVN3MPI8DatatypeE]+0x78):
> >>> undefined reference to `    MPI::Datatype::Free()'
> >>>
> >>>
> CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o:(.data.rel.ro._ZTVN3MPI3WinE[_ZTVN3MPI3WinE]+0x48):
> >>> undefined reference to  `MPI::Win::Free()'
> >>>     collect2: error: ld returned 1 exit status
> >>>     IO/AMR/CMakeFiles/vtkIOAMR.dir/build.make:363: recipe for target
> >>> 'lib/libvtkIOAMR-6.3.so.1' failed
> >>> make[2]: *** [lib/libvtkIOAMR-6.3.so.1] Error 1
> >>>     CMakeFiles/Makefile2:6388: recipe for target
> >>> 'IO/AMR/CMakeFiles/vtkIOAMR.dir/all' failed
> >>> make[1]: *** [IO/AMR/CMakeFiles/vtkIOAMR.dir/all] Error 2
> >>> Makefile:107: recipe for target 'all' failed
> >>> make: *** [all] Error 2
> >>>
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