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

[Chaffra Affouda]

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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