[Paraview] MacOSX Linking problems

Thu Oct 11 21:07:00 EDT 2012

That speaks to an issue with the environment being used to compile paraview. Uninstall HDF5 from MacPorts and use the one from VTK. This seems like the best course of action and is what I do here when I build my OS X versions of ParaView.
  I also build HDF5 for a few other projects so I got pretty good at building HDF5 myself with the CMake support that HDF5 has had for the last few years.
___________________________________________________________
Mike Jackson                    Principal Software Engineer
BlueQuartz Software                            Dayton, Ohio
mike.jackson at bluequartz.net              www.bluequartz.net

On Oct 11, 2012, at 9:02 PM, 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> 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              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> 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> 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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