I think the problem is that it is picking up libboost_python.dylib that was supplied with the system (in /usr/local/lib), and not the one that was used in compilation (in $LIBTBX_BUILD/lib). Could you check that there is a libboost_python.dylib in this directory?
Yes, it's there.
What happens if you change the search order for the linker (if this was Linux, export DYLIB_LIBRARY_PATH=$LIBTBX_BUILD/lib:$DYLIB_LIBRARY_PATH would work, but on the Mac I do not know).
I assume $LIBTBX_BUILD is /Users/magnus/Downloads/cctbx_build/
in my case,
but what is $DYLIB_LIBRARY_PATH?
It would probably be easier for you to rebuild the cctbx Python bindings with the Python you want to use, and then all things would work.
I think that's what I'm trying to do. I want to avoid the cctbx wrapper and therefore are launching python from my /opt/local/bin install where I keep all the rest of the modules I need. It is only cctbx that causes trouble. So I try to get "my" python to accept it.
Thanks for you help in this matter - I appreciate it,
Magnus
It only takes 10-20 minutes to compile even on a vintage computer.
BW, Gabor
On 2014-06-04 13:15, Magnus Andersson wrote:
Thanks Luc,
I have now updated by PYTHONPATH as you suggested:
export
PYTHONPATH=/Users/magnus/Downloads/cctbx_sources:/opt/local/bin:/Users/magnus/Downloads/cctbx_build/lib:/Users/magnus/Downloads/cctbx_sources:/Users/magnus/Downloads/cctbx_sources/boost_adaptbx:/Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath:/usr/local/lib
, which indeed makes my /opt/local/bin/python2.7 find boost. However,
now I get a new error message, which is a little harder to interpret:
import iotbx.pdb
File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py",
line 2, in <module>
from cctbx.array_family import flex
File
"/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py",
line 2, in <module>
import scitbx.array_family.flex
File
"/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py",
line 2, in <module>
import boost.optional # import dependency
File
"/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/optional.py",
line 2, in <module>
import boost.python
File
"/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py",
line 57, in <module>
ext = import_ext("boost_python_meta_ext")
File
"/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py",
line 36, in import_ext
+ [" "+p for p in sys.path]))
ImportError: __import__("boost_python_meta_ext"):
dlopen(/Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so,
2): Symbol not found:
boost::python::objects::function_object(boost::python::objects::py_function
const&, std::__1::pair<boost::python::detail::keyword const*,
boost::python::detail::keyword const*> const&)
Referenced from:
/Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so
Expected in: /usr/local/lib/libboost_python.dylib
in /Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so
sys.path:
/Users/magnus/Documents/TR-WAXS/magnus_testing/PyWAXS
/Users/magnus/.venvburrito/lib/python/distribute-0.6.32-py2.7.egg
/Users/magnus/.venvburrito/lib/python/virtualenv-1.8.4-py2.7.egg
/Users/magnus/.venvburrito/lib/python/virtualenvwrapper-3.6-py2.7.egg
/Users/magnus/.venvburrito/lib/python/stevedore-0.8-py2.7.egg
/Users/magnus/.venvburrito/lib/python/virtualenv_clone-0.2.4-py2.7.egg
/Users/magnus/.venvburrito/lib/python
/Users/magnus/Downloads/cctbx_sources
/opt/local/bin
/Users/magnus/Downloads/cctbx_build/lib
/Users/magnus/Downloads/cctbx_sources/boost_adaptbx
/Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath
/usr/local/lib
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/readline
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyObjC
/Library/Python/2.7/site-packages
I don't know how to deal with this - any suggestions?
Thanks,
Magnus
On 03 Jun 2014, at 23:44, Luc Bourhis <[email protected]> wrote:
Suggestions?
If you want to do it by hand, you need to parrot what cctbx.python
does. You need to set the following environment variables:
1. LIBTBX_BUILD
that must be the path of cctbx_build next to cctbx_sources or
cctbx_project
2. PYTHONPATH
at the very least it shall contain
$LIBTBX_BUILD/lib:$CCTBXSRC:$CCTBXSRC/boost_adaptbx:$CCTBXSRC/libtbx/pythonpath
where $CCTBXSRC is the full path of cctbx_sources or cctbx_project
3. DYLD_LIBRARY_PATH
It shall contain $LIBTBX_BUILD/lib
Best wishes,
Luc
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