[Paraview-developers] paraview superbuild

Mon Jul 1 13:06:05 EDT 2013

No, Python isn't requiring HDF5. But somehow enabling Python is
interacting with the hdf5 build (either internal to ParaView/VTK or
the one in ParaViewSuperbuild) that I am not exactly understanding.

Utkarsh

On Mon, Jul 1, 2013 at 12:52 PM, Paul Edwards <paul.m.edwards at gmail.com> wrote:
> Ok thanks.  Why is it that python requires HDF5?  I was actually
> hoping to use my own version - is this possible? (but not the system
> one....)
>
> On 1 July 2013 17:48, Utkarsh Ayachit <utkarsh.ayachit at kitware.com> wrote:
>> Hmm, looks like hdf5 is having trouble building on your setup. You can
>> try to figure out what configuration parameters would work for hdf5
>> and then update hdf5.cmake in the ParaView superbuild to make it work.
>> The hdf5 source and build tree under the superbuild are
>> ParaViewSuperbuild_build/hdf/src/hdf5 and
>> ParaViewSuperbuild_build/hdf/src/hdf5-build.
>>
>> Utkarsh
>>
>> On Mon, Jul 1, 2013 at 12:23 PM, Paul Edwards <paul.m.edwards at gmail.com> wrote:
>>> That fails here now:
>>>
>>> ....
>>> /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/hdf5/src/hdf5/hl/src/H5LT.c:873:44:
>>> warning: (near initialization for ‘callbacks’) [enabled by default]
>>> /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/hdf5/src/hdf5/hl/src/H5LT.c:920:18:
>>> error: request for member ‘udata’ in something not a structure or
>>> union
>>> /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/hdf5/src/hdf5/hl/src/H5LT.c:923:9:
>>> warning: implicit declaration of function
>>> ‘H5Pset_file_image_callbacks’ [-Wimplicit-function-declaration]
>>> /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/hdf5/src/hdf5/hl/src/H5LT.c:930:5:
>>> warning: implicit declaration of function ‘H5Pset_file_image’
>>> [-Wimplicit-function-declaration]
>>> gmake[5]: *** [hl/src/CMakeFiles/hdf5_hl.dir/H5LT.c.o] Error 1
>>> gmake[5]: *** Waiting for unfinished jobs....
>>> gmake[4]: *** [hl/src/CMakeFiles/hdf5_hl.dir/all] Error 2
>>> gmake[3]: *** [all] Error 2
>>> CMake Error at /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/pv-hdf5-build.cmake:26
>>> (message):
>>>   Failed!!!
>>>
>>> Regards,
>>> Paul
>>>
>>> On 1 July 2013 16:14, Utkarsh Ayachit <utkarsh.ayachit at kitware.com> wrote:
>>>> Can you try turning on HDF5 from the Superbuild as well?
>>>>
>>>> On Mon, Jul 1, 2013 at 11:05 AM, Paul Edwards <paul.m.edwards at gmail.com> wrote:
>>>>> Hi Utkarsh,
>>>>>
>>>>> Rerunning the build in serial gives this:
>>>>>
>>>>> 8<-------------------------------------------------------------------------
>>>>> ...
>>>>> ...
>>>>> Scanning dependencies of target vtkWrappingPythonCore
>>>>> [  6%] Building CXX object
>>>>> VTK/Utilities/PythonInterpreter/CMakeFiles/vtkPythonInterpreter.dir/vtkPythonInterpreter.cxx.o
>>>>> [  6%] Scanning dependencies of target vtkCommonSystem
>>>>> Building CXX object
>>>>> VTK/Wrapping/PythonCore/CMakeFiles/vtkWrappingPythonCore.dir/vtkPythonArgs.cxx.o
>>>>> [  6%] Scanning dependencies of target vtkCommonMath
>>>>> Building CXX object
>>>>> VTK/Common/System/CMakeFiles/vtkCommonSystem.dir/vtkClientSocket.cxx.o
>>>>> [  6%] Building CXX object
>>>>> VTK/Common/Math/CMakeFiles/vtkCommonMath.dir/vtkAmoebaMinimizer.cxx.o
>>>>> [  6%] Building C object
>>>>> VTK/ThirdParty/hdf5/vtkhdf5/src/CMakeFiles/vtkhdf5.dir/H5FDlog.c.o
>>>>> /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/paraview/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5FDlog.c:212:5:
>>>>> error: ‘off64_t’ undeclared here (not in a function)
>>>>> /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/paraview/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5FDlog.c:
>>>>> In function ‘H5FD_log_read’:
>>>>> /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/paraview/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5FDlog.c:1089:48:
>>>>> error: expected ‘)’ before ‘addr’
>>>>> /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/paraview/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5FDlog.c:
>>>>> In function ‘H5FD_log_write’:
>>>>> /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/paraview/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5FDlog.c:1201:47:
>>>>> error: expected ‘)’ before ‘addr’
>>>>> gmake[5]: *** [VTK/ThirdParty/hdf5/vtkhdf5/src/CMakeFiles/vtkhdf5.dir/H5FDlog.c.o]
>>>>> Error 1
>>>>> gmake[4]: *** [VTK/ThirdParty/hdf5/vtkhdf5/src/CMakeFiles/vtkhdf5.dir/all]
>>>>> Error 2
>>>>> gmake[4]: *** Waiting for unfinished jobs....
>>>>> ------------------------------------------------------------------------->8
>>>>>
>>>>> I think this must be a problem configuring something as this compiles
>>>>> here when using the superbuild without Python...
>>>>>
>>>>> ...and, I can make it work with python when building the dependencies
>>>>> myself (same versions) and then ParaView from source.
>>>>>
>>>>> I was hoping to make my life easier using the superbuild ;)
>>>>>
>>>>> Please let me know if you know what is going wrong.
>>>>>
>>>>> Thanks,
>>>>> Paul
>>>>>
>>>>>
>>>>>
>>>>> On 1 July 2013 15:30, Utkarsh Ayachit <utkarsh.ayachit at kitware.com> wrote:
>>>>>> Paul, are you doing a parallel build? Can you try without the "-j". It
>>>>>> should atleast make the error message a bit easier to read.
>>>>>>
>>>>>> Utkarsh
>>>>>>
>>>>>> On Mon, Jul 1, 2013 at 10:18 AM, Paul Edwards <paul.m.edwards at gmail.com> wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> I'm trying to use the ParaViewSuperbuild (for v4.0.1) on suse 12.1 but
>>>>>>> it is failing as soon as I try to include python.
>>>>>>>
>>>>>>> 8<---------------------------------------------------------------------
>>>>>>> ...
>>>>>>> [  5%] Generating ../H5lib_settings.c
>>>>>>> libhdf5.settings: No such file or directory
>>>>>>> gmake[5]: *** [VTK/ThirdParty/hdf5/vtkhdf5/H5lib_settings.c] Error 1
>>>>>>> gmake[4]: *** [VTK/ThirdParty/hdf5/vtkhdf5/src/CMakeFiles/vtkhdf5.dir/all]
>>>>>>> Error 2
>>>>>>> gmake[4]: *** Waiting for unfinished jobs....
>>>>>>> ...
>>>>>>> ...
>>>>>>> Linking C shared module ../../../lib/site-packages/mpi4py/MPI.so
>>>>>>> [  5%] Built target mpi4py.MPI
>>>>>>> gmake[3]: *** [all] Error 2
>>>>>>> CMake Error at /users/zephyr01/paul/dev/src/iconCFD-dev/ThirdParty/build/openmpi-1.6.4/ParaViewSuperbuild_build/pv-paraview-build.cmake:26
>>>>>>> (message):
>>>>>>>   Failed!!!
>>>>>>> --------------------------------------------------------------------->8
>>>>>>>
>>>>>>> I'm struggling to find out where the actual problem is here.  Any ideas?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Paul
>>>>>>> _______________________________________________
>>>>>>> Paraview-developers mailing list
>>>>>>> Paraview-developers at paraview.org
>>>>>>> http://public.kitware.com/mailman/listinfo/paraview-developers