[vtkusers] [vtk-developers] problems with VTK python module installation on OSX (after a custom build)

David Cole david.cole at kitware.com
Fri Sep 5 18:00:14 EDT 2008 

VTK_USE_RPATH should be sufficient...


On Fri, Sep 5, 2008 at 5:51 PM, Darren Weber
<darren.weber.lists at gmail.com>wrote:

> On Wed, Sep 3, 2008 at 3:28 PM, Mike Jackson
> <mike.jackson at bluequartz.net> wrote:
> > Cross posting to vtkusers list as that may be more appropriate:
> >
> >
> > Can you rebuild VTK with these two settings:
> >
> > CMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=ON \
>
> Where is this?  I don't see it in ccmake.  How do you set it?
>
> > VTK_USE_RPATH=ON
>
> This I can see in ccmake
>
> >
> > Run ccmake on your vtk build directory and set those two cmake variables.
> > Configure and build. After the build completes, then run "make install".
> >
> > The default installation location is in /usr/local. I would change it to
> > /usr/local/vtk-5.2.
> >
> > Next, Get rid of extra Python builds on your system. The only python
> build
> > should be in /System/Library/Frameworks.
> >
> > Now try to build your project. If everything goes correctly you should
> NOT
> > need to mess with DYLD_LIBRARY_PATH. The reason why you are having to set
> > that variable is because, as you found out, the vtk libraries do NOT have
> an
> > "install_path" (same as rpath on linux) set in them. Without that set to
> > anything besides the library name the linker will not be able to encode
> the
> > correct path in anything else that depends on the vtk libraries. Which is
> > some of your problems.
> >
> > Let us know if you can get this far.
> >
> > Mike
> > On Sep 3, 2008, at 2:19 PM, Darren Weber wrote:
> >
> >> I think we may be on the "right" track with addition(s) to the DYLD
> path,
> >> ie:
> >>
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$ echo $DYLD_LIBRARY_PATH
> >>
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$ export
> >> DYLD_LIBRARY_PATH=/usr/local/lib/vtk-5.2
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$ echo $DYLD_LIBRARY_PATH
> >> /usr/local/lib/vtk-5.2
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$ python
> >> Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53)
> >> [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
> >> Type "help", "copyright", "credits" or "license" for more information.
> >>>>>
> >>>>> import vtk
> >>
> >> Traceback (most recent call last):
> >>  File "<stdin>", line 1, in <module>
> >>  File "/usr/local/lib/python2.5/site-packages/vtk/__init__.py", line
> >> 43, in <module>
> >>   from io import *
> >>  File "/usr/local/lib/python2.5/site-packages/vtk/io.py", line 7, in
> >> <module>
> >>   from libvtkIOPython import *
> >> ImportError:
> >> dlopen(/usr/local/lib/python2.5/site-packages/vtk/libvtkIOPython.so,
> >> 10): Library not loaded: libpq.5.dylib
> >>  Referenced from:
> >> /usr/local/lib/python2.5/site-packages/vtk/libvtkIOPython.so
> >>  Reason: image not found
> >>>>>
> >>
> >> This is another failure, but this time it is related to the PostgreSQL
> >> library that resides in another location (under /Library path).  So, I
> >> conclude from this test that dlopen is now finding the vtk dylib
> >> files.
> >>
> >> Now, we can get the following "diagnostics" on the .so from the prior
> >> import problem:
> >>
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$ otool -L
> >> /usr/local/lib/python2.5/site-packages/vtk/libvtkCommonPython.so
> >> /usr/local/lib/python2.5/site-packages/vtk/libvtkCommonPython.so:
> >>        libvtkCommonPythonD.5.2.dylib (compatibility version 0.0.0,
> current
> >> version 0.0.0)
> >>        /Library/Frameworks/Python.framework/Versions/2.5/Python
> >> (compatibility version 2.5.0, current version 2.5.0)
> >>        libvtkCommon.5.2.dylib (compatibility version 0.0.0, current
> >> version 0.0.0)
> >>        libvtksys.5.2.dylib (compatibility version 0.0.0, current version
> >> 0.0.0)
> >>        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> >> version 111.1.1)
> >>        /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> >> version 7.4.0)
> >>        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> >> version 1.0.0)
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$
> >>
> >>
> >> Notice how some of the system libaries have full paths (ie,
> >> /usr/lib/....), but the vtk dylib files have no paths.  Hence, when we
> >> specify the DYLD_LIBRARY_PATH, the python import process is now
> >> finding these extra libraries because dlopen is now searching at least
> >> the /usr/local/lib/vtk... path (recursively? maybe not, because it
> >> doesn't work if we use /usr/local/lib without the specific vtk path).
> >>
> >> Similarly, now we can see the full library dependency for the
> >> IOPython.so file using:
> >>
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$ otool -L
> >> /usr/local/lib/python2.5/site-packages/vtk/libvtkIOPython.so
> >> /usr/local/lib/python2.5/site-packages/vtk/libvtkIOPython.so:
> >>        libvtkIOPythonD.5.2.dylib (compatibility version 0.0.0, current
> >> version 0.0.0)
> >>        libvtkIO.5.2.dylib (compatibility version 0.0.0, current version
> >> 0.0.0)
> >>        /usr/local/lib/libpqxx-2.6.9.dylib (compatibility version 0.0.0,
> >> current version 0.0.0)
> >>        libpq.5.dylib (compatibility version 5.0.0, current version
> 5.1.0)
> >>        /usr/local/mysql/lib/libmysqlclient.15.dylib (compatibility
> version
> >> 16.0.0, current version 16.0.0)
> >>        /usr/lib/libz.1.dylib (compatibility version 1.0.0, current
> version
> >> 1.2.3)
> >>        libvtkFilteringPythonD.5.2.dylib (compatibility version 0.0.0,
> >> current version 0.0.0)
> >>        libvtkCommonPythonD.5.2.dylib (compatibility version 0.0.0,
> current
> >> version 0.0.0)
> >>        /Library/Frameworks/Python.framework/Versions/2.5/Python
> >> (compatibility version 2.5.0, current version 2.5.0)
> >>        libvtkFiltering.5.2.dylib (compatibility version 0.0.0, current
> >> version 0.0.0)
> >>        libvtkDICOMParser.5.2.dylib (compatibility version 0.0.0, current
> >> version 0.0.0)
> >>        libvtkNetCDF.5.2.dylib (compatibility version 0.0.0, current
> >> version 0.0.0)
> >>        libvtkmetaio.5.2.dylib (compatibility version 0.0.0, current
> >> version 0.0.0)
> >>        libvtksqlite.5.2.dylib (compatibility version 0.0.0, current
> >> version 0.0.0)
> >>        libvtkpng.5.2.dylib (compatibility version 0.0.0, current version
> >> 0.0.0)
> >>        libvtktiff.5.2.dylib (compatibility version 0.0.0, current
> version
> >> 0.0.0)
> >>        libvtkzlib.5.2.dylib (compatibility version 0.0.0, current
> version
> >> 0.0.0)
> >>        libvtkjpeg.5.2.dylib (compatibility version 0.0.0, current
> version
> >> 0.0.0)
> >>        libvtkexpat.5.2.dylib (compatibility version 0.0.0, current
> version
> >> 0.0.0)
> >>        libvtkCommon.5.2.dylib (compatibility version 0.0.0, current
> >> version 0.0.0)
> >>        libvtksys.5.2.dylib (compatibility version 0.0.0, current version
> >> 0.0.0)
> >>        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> >> version 111.1.1)
> >>        /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> >> version 7.4.0)
> >>        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> >> version 1.0.0)
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$
> >>
> >>
> >> It's curious that it has a full path to /usr/local/lib/libpqxx (which
> >> I had to build and install on this system), but it has no full path to
> >> the associated libpq.  I don't fully understand this link dependency,
> >> as I thought libpqxx would be the primary link target and, in turn, it
> >> would link to libpq. (This postgreSQL stuff is another topic on the
> >> list somewhere.)
> >>
> >> It's also curious that 'locate' can find the libpq, but dlopen does
> >> not.  So, something about the locate environment of default settings
> >> is different from the dlopen environment, eg:
> >>
> >> {{{
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$ locate libpq.5.dylib
> >> /Library/PostgreSQL/8.3/lib/libpq.5.dylib
> >> /Library/PostgreSQL/8.3/pgAdmin3.app/Contents/Frameworks/libpq.5.dylib
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$
> >> }}}
> >>
> >> So, now we modify the DYLD path to find libpq and WHA-LA, the import is
> >> working!
> >>
> >> {{{
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$ export
> >> DYLD_LIBRARY_PATH=/usr/local/lib/vtk-5.2:/Library/PostgreSQL/8.3/lib
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$ echo $DYLD_LIBRARY_PATH
> >> /usr/local/lib/vtk-5.2:/Library/PostgreSQL/8.3/lib
> >> [ dweber at elegans ~/src/kitware/VTK_build ]$ python
> >> Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53)
> >> [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
> >> Type "help", "copyright", "credits" or "license" for more information.
> >>>>>
> >>>>> import vtk
> >>>>>
> >> }}}
> >>
> >>
> >> I'll have to double check the default settings on DYLD path for the
> >> system.  This is A fix on this particular system, so the problem
> >> remains for any general OSX distribution to fix this in an elegant
> >> manner.  What would you recommend for a system-wide fix to these path
> >> settings and how would you implement this within cmake?  (Again, I
> >> need to RTFM, it's overdue.  I will persist with OSX.)
> >>
> >> Thanks heaps for getting me back on track with OSX!  Power to the people
> >> ;-)
> >>
> >> Darren
> >>
> >>
> >> [PS, I suppose I could remove the /Library/Frameworks/Python.framework
> >> installs to fall back on the /System/.... python installation, but it
> >> probably makes little difference apart from disk space.  I know it's
> >> not wise to touch the /System area, so that's off limits.  I guess the
> >> only advantage to the /Library installs from python.org is to keep up
> >> with patches and new releases.  Actually I can't decide on whether to
> >> use the binary packages direct from python.org or the macports /opt
> >> installation, the latter seems to provide an option for ipython and
> >> that would be a real bonus.  The macports install may be as close as I
> >> need to get to a source build for python.  I've opted to use macports
> >> rather than fink, but that may be a mistake too ;-)  I do like the
> >> Debian package system, which is the basis for fink.  I just don't know
> >> whether fink is keeping up with things the way that Ubuntu does; it
> >> takes the best of Debian on popular platforms.  I've opted for
> >> macports only because I know they will be specific to the OSX way of
> >> doing things - but why did they choose /opt/ instead of the default
> >> /usr or /usr/local path?  Gheez.]
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Wed, Sep 3, 2008 at 10:16 AM, Prabhu Ramachandran
> >> <prabhu at aero.iitb.ac.in> wrote:
> >>>
> >>> Darren Weber wrote:
> >>>>
> >>>> I've discovered a minor problem with the VTK python installation (from
> >>>> build) on OSX.  I'm basically having library path issues and I don't
> >>>> know
> >>>> how to bend VTK build-install to fit OSX python or how to bend OSX
> >>>> python to
> >>>> use the default VTK install paths.
> >>>
> >>> [...]
> >>>>
> >>>> However, despite my attempt to get the module installed in the "right"
> >>>> place, I get this traceback during the import:
> >>>>
> >>>> dweber at weber-mbp ~/src/kitware/VTK_build ]$ which python
> >>>
> >>> [...]
> >>>>
> >>>> ImportError:
> >>>>
> >>>>
> dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/vtk/libvtkCommonPython.so,
> >>>> 10): Library not loaded: libvtkCommonPythonD.5.2.dylib
> >>>> Referenced from:
> >>>>
> >>>>
> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/vtk/libvtkCommonPython.so
> >>>> Reason: image not found
> >>>>>>>
> >>>>
> >>>>
> >>>> This is where the libvtkCommon* libs are at:
> >>>>
> >>>> /usr/local/lib/python2.5/site-packages/vtk/libvtkCommonPython.so
> >>>> /usr/local/lib/vtk-5.2/libvtkCommonPythonD.5.2.0.dylib
> >>>> /usr/local/lib/vtk-5.2/libvtkCommonPythonD.5.2.dylib
> >>>> /usr/local/lib/vtk-5.2/libvtkCommonPythonD.dylib
> >>>
> >>> Try this:
> >>>
> >>> export DYLD_LIBRARY_PATH=/usr/local/lib/vtk-5.2
> >>>
> >>> Then rerun Python and see if import vtk works at all.
> >>>
> >>> cheers,
> >>> prabhu
> >>>
> >>
> >
> >  _________________________________________________
> > | Mike Jackson - Principal Software Engineer      |
> > | BlueQuartz Software                             |
> > | mike.jackson at bluequartz.net                     |
> > | www.bluequartz.net                              |
> > ---------------------------------------------------
> >
> >
> >
> >
> >
> >
> >
> >
> _______________________________________________
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> vtk-developers at vtk.org
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>
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