[Paraview] MacOSX Linking problems
Brickle Macho
bricklemacho at gmail.com
Fri Oct 12 02:07:21 EDT 2012
I uninstalled HDF5 and it builds.
Thanks for the help.
Michael.
--
On 12/10/12 9:02 AM, Pat Marion wrote:
> I think this is exactly the same problem that I've seen on all mac
> platforms where HDF5 is installed from macports. You can either
> uninstall hdf5 from macports, or you need to feed even more detailed
> information to paraview. You can edit the CMakeCache.txt file in the
> paraview build directory and put this:
>
> VTK_USE_SYSTEM_HDF5:BOOL=ON
> HDF5_INCLUDE_DIR=/opt/local/include
> HDF5_INCLUDE_DIRS=/opt/local/include
> HDF5_LIBRARIES=/opt/local/lib/libhdf5.dylib;/opt/local/lib/libhdf5_cpp.dylib
>
>
> Mike, I think that the problem is that with VTK_USE_SYSTEM_HDF5=OFF,
> vtk will build its own hdf5, but some conflicting hdf5 headers from
> the system install under /opt/local/include sneak in, and cause link
> errors.
>
> Pat
>
> On Thu, Oct 11, 2012 at 9:00 PM, Michael Jackson
> <mike.jackson at bluequartz.net <mailto:mike.jackson at bluequartz.net>> wrote:
>
> do a "make VERBOSE=1" and you can see exactly what the compiler is
> being sent as far as -I include directories. I would say that
> something is missing either in your HDF5 installation, or an HDF5
> include path is not being found.
>
> Doesn't VTK come with HDF5 at this point? Why not just let VTK
> build its own.
> ___________________________________________________________
> Mike Jackson Principal Software Engineer
> BlueQuartz Software Dayton, Ohio
> mike.jackson at bluequartz.net <mailto:mike.jackson at bluequartz.net>
> www.bluequartz.net <http://www.bluequartz.net>
>
> On Oct 11, 2012, at 7:50 PM, Brickle Macho wrote:
>
> > Thanks to both for your quick response.
> >
> > From a clean/new build directory I tried your suggestion of
> -DVTK_USE_SYSTEM_HDF5=ON I received a different error (fragment
> below), which looks like it not finding some HDF5 headers.
> >
> > I will keep investigating. Obviously something strange about my
> setup or use of Macports.
> >
> > Thanks again.
> >
> > Michael.
> >
> >
> > ------------ new error
> > Linking CXX executable ../../../../bin/ChartsCxxTests
> > [ 34%] Built target ChartsCxxTests
> > Scanning dependencies of target Xdmf
> > [ 34%] Building CXX object
> Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/XdmfArray.cxx.o
> > In file included from
> /Users/michael/PhD/ExistingSoftware/ParaView-3.14.1-Source/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:29,
> > from
> /Users/michael/PhD/ExistingSoftware/ParaView-3.14.1-Source/Utilities/Xdmf2/libsrc/XdmfArray.h:28,
> > from
> /Users/michael/PhD/ExistingSoftware/ParaView-3.14.1-Source/Utilities/Xdmf2/libsrc/XdmfArray.cxx:25:
> >
> /Users/michael/PhD/ExistingSoftware/ParaView-3.14.1-Source/Utilities/Xdmf2/libsrc/XdmfHDFSupport.h:30:22:
> error: H5public.h: No such file or directory
> >
> /Users/michael/PhD/ExistingSoftware/ParaView-3.14.1-Source/Utilities/Xdmf2/libsrc/XdmfHDFSupport.h:36:18:
> error: hdf5.h: No such file or directory
> >
> >
> > On 12/10/12 4:03 AM, Pat Marion wrote:
> >> Oops, I meant to say you should set VTK_USE_SYSTEM_HDF5 to ON.
> >>
> >> Pat
> >>
> >> On Thu, Oct 11, 2012 at 4:02 PM, Pat Marion
> <pat.marion at kitware.com <mailto:pat.marion at kitware.com>> wrote:
> >> It looks the compiler included system HDF5 headers even though
> VTK_USE_SYSTEM_HDF5 is disabled. Then, at link time it doesn't
> link the system HDF5 libraries because VTK_USE_SYSTEM_HDF5 if off.
> You could try running cmake in the build dir and setting
> VTK_USE_SYSTEM_HDF5 to OFF.
> >>
> >> I think this might be caused by a tricky a bug in VTK's cmake
> scripts. I guess CMake would need to add -IVTK/Utilities/vtkhdf5
> before -I/opt/local/include when system hdf5 is off.
> >>
> >> Pat
> >>
> >>
> >> On Thu, Oct 11, 2012 at 3:46 PM, Brickle Macho
> <bricklemacho at gmail.com <mailto:bricklemacho at gmail.com>> wrote:
> >> Hi,
> >>
> >> I am trying to build ParaView on my MacBook and I am getting a
> list of undefined symbols. Below is the first of about 35+
> similar errors. For info all of the required supporting packages
> were installed by Macports. I downloaded ParaView-3.14.1-Source
> from the website and created a separate build directory. I
> received a that I was running Qt 4.8.3 whereas the officially
> supported version is Qt 4.6.
> >>
> >> In case it is related, I had an earlier problem where during
> compiling the generated makefile was expecting some Qt file under
> files in /opt/local/lib/Resources/... whereas they were in
> /opt/local/Library/Frameworks/QtGui.framework/Versions/4/Resources/...
> I resolved this by creating a symbolic link in /opt/local/lib
> >>
> >> Not sure where to start to solve the problem. Any help appreciated.
> >>
> >> Regards,
> >>
> >> Michael.
> >> --
> >>
> >> ------- Linking problem below ---------------
> >>
> >> [ 75%] Built target vtkPVVTKExtensionsCS
> >> Linking CXX executable
> ../../../bin/ParaViewCoreVTKExtensionsPrintSelf
> >> Undefined symbols for architecture x86_64:
> >> "_H5check_version", referenced from:
> >> vtkEnzoReaderInternal::GetAttributeNames() in
> libvtkPVVTKExtensions.a(vtkEnzoReader.cxx.o)
> >> vtkEnzoReader::LoadAttribute(char const*, int)in
> libvtkPVVTKExtensions.a(vtkEnzoReader.cxx.o)
> >> vtkEnzoReader::GetParticles(int, vtkPolyData*, int,
> int)in libvtkPVVTKExtensions.a(vtkEnzoReader.cxx.o)
> >> vtkFlashReaderInternal::ReadMetaData() in
> libvtkPVVTKExtensions.a(vtkFlashReader.cxx.o)
> >> vtkFlashReaderInternal::GetTime() in
> libvtkPVVTKExtensions.a(vtkFlashReader.cxx.o)
> >> vtkFlashReaderInternal::GetCycle() in
> libvtkPVVTKExtensions.a(vtkFlashReader.cxx.o)
> >> (maybe you meant: _vtk__H5check_version)
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> >
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