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

[Utkarsh Ayachit]

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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>