<p dir="ltr">Ok I did and it built. What hdf5/mpi variables do I need to update?</p>
<p dir="ltr">Thanks,<br>
Chaffra<br>
</p>
<br><div class="gmail_quote"><div dir="ltr">On Mon, Sep 14, 2015, 14:19 Utkarsh Ayachit <<a href="mailto:utkarsh.ayachit@kitware.com">utkarsh.ayachit@kitware.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">For starters, turn off USE_SYSTEM_HDF5 and then confirm it builds.<br>
Once that's confirmed, you can turn the flag back on and then update<br>
the HDF5 library variables to include the MPI variables as well.<br>
<br>
On Mon, Sep 14, 2015 at 11:49 AM, Chaffra Affouda <<a href="mailto:chaffra@gmail.com" target="_blank">chaffra@gmail.com</a>> wrote:<br>
> Utkarsh,<br>
><br>
> Yes I am:<br>
> I built with -DUSE_SYSTEM_HDF5=ON. Should I be doing something else?<br>
><br>
> Chaffra<br>
><br>
><br>
> On 09/14/2015 10:56 AM, Utkarsh Ayachit wrote:<br>
>><br>
>> Chaffra,<br>
>><br>
>> Are you by any change using system HDF5?<br>
>><br>
>> Utkarsh<br>
>><br>
>> On Mon, Sep 14, 2015 at 8:46 AM, Chaffra Affouda <<a href="mailto:chaffra@gmail.com" target="_blank">chaffra@gmail.com</a>><br>
>> wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> I am getting a lot of undefined references when linking. I know it is not<br>
>>> linking to MPI or the right MPI but I cannot see how.<br>
>>> I have openmpi installed and mpicc is pointing to the openmpi version.<br>
>>> Can<br>
>>> any reproduce or help? Error is below<br>
>>><br>
>>> Thanks,<br>
>>> Chaffra<br>
>>><br>
>>>     Linking CXX shared library ../../lib/<a href="http://libvtkIOAMR-6.3.so" rel="noreferrer" target="_blank">libvtkIOAMR-6.3.so</a><br>
>>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In function<br>
>>> `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&),<br>
>>> bool)':<br>
>>><br>
>>> vtkAMREnzoParticlesReader.cxx:(.text._ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[_ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb]+0x15):<br>
>>> undefined reference to `ompi_mpi_cxx_op_intercept'<br>
>>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In function<br>
>>> `MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const':<br>
>>><br>
>>> vtkAMREnzoParticlesReader.cxx:(.text._ZNK3MPI9Intracomm12Create_graphEiPKiS2_b[_ZNK3MPI9Intracomm12Create_graphEiPKiS2_b]+0x39):<br>
>>> undefined reference to `MPI::Comm::Comm()'<br>
>>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In function<br>
>>> `MPI::Graphcomm::Clone() const':<br>
>>><br>
>>> vtkAMREnzoParticlesReader.cxx:(.text._ZNK3MPI9Graphcomm5CloneEv[_ZNK3MPI9Graphcomm5CloneEv]+0x35):<br>
>>> undefined reference to  `MPI::Comm::Comm()'<br>
>>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In function<br>
>>> `MPI::Cartcomm::Clone() const':<br>
>>><br>
>>> vtkAMREnzoParticlesReader.cxx:(.text._ZNK3MPI8Cartcomm5CloneEv[_ZNK3MPI8Cartcomm5CloneEv]+0x35):<br>
>>> undefined reference to   `MPI::Comm::Comm()'<br>
>>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In function<br>
>>> `MPI::Intercomm::Merge(bool) const':<br>
>>><br>
>>> vtkAMREnzoParticlesReader.cxx:(.text._ZNK3MPI9Intercomm5MergeEb[_ZNK3MPI9Intercomm5MergeEb]+0x37):<br>
>>> undefined reference to  `MPI::Comm::Comm()'<br>
>>>     CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o: In function<br>
>>> `MPI::Intracomm::Create(MPI::Group const&) const':<br>
>>><br>
>>> vtkAMREnzoParticlesReader.cxx:(.text._ZNK3MPI9Intracomm6CreateERKNS_5GroupE[_ZNK3MPI9Intracomm6CreateERKNS_5GroupE]+0x3a):<br>
>>> undefined    reference to `MPI::Comm::Comm()'<br>
>>><br>
>>> CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o:vtkAMREnzoParticlesReader.cxx:<br>
>>> (.text._ZNK3MPI9Intracomm5SplitEii[_ZNK3MPI9Intracomm5SplitEii]+0x36):<br>
>>> more<br>
>>> undefined references to `MPI::Comm::Comm()' follow<br>
>>><br>
>>> CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[_ZTVN3MPI8DatatypeE]+0x78):<br>
>>> undefined reference to `    MPI::Datatype::Free()'<br>
>>><br>
>>> CMakeFiles/vtkIOAMR.dir/vtkAMREnzoParticlesReader.cxx.o:(.data.rel.ro._ZTVN3MPI3WinE[_ZTVN3MPI3WinE]+0x48):<br>
>>> undefined reference to  `MPI::Win::Free()'<br>
>>>     collect2: error: ld returned 1 exit status<br>
>>>     IO/AMR/CMakeFiles/vtkIOAMR.dir/build.make:363: recipe for target<br>
>>> 'lib/libvtkIOAMR-6.3.so.1' failed<br>
>>> make[2]: *** [lib/libvtkIOAMR-6.3.so.1] Error 1<br>
>>>     CMakeFiles/Makefile2:6388: recipe for target<br>
>>> 'IO/AMR/CMakeFiles/vtkIOAMR.dir/all' failed<br>
>>> make[1]: *** [IO/AMR/CMakeFiles/vtkIOAMR.dir/all] Error 2<br>
>>> Makefile:107: recipe for target 'all' failed<br>
>>> make: *** [all] Error 2<br>
>>><br>
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><br>
</blockquote></div>