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

[Utkarsh Ayachit]

This merge request should fix this issue:
https://gitlab.kitware.com/vtk/vtk/merge_requests/678

Utkarsh

On Tue, Sep 15, 2015 at 6:23 PM, Chaffra Affouda <chaffra at gmail.com> wrote:
> Thanks it does.
>
>
> On 09/14/2015 04:34 PM, Utkarsh Ayachit wrote:
>>
>> Can you try if the attached patch addresses the issue?
>>
>> Thanks
>> Utkarsh
>>
>> On Mon, Sep 14, 2015 at 3:21 PM, Chaffra J. Affouda <chaffra at gmail.com>
>> wrote:
>>>
>>> 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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>