Re: [cctbxbb] Boost Import Error

Ok, now I'm getting a little further at least. But is encounter a new error message, which I don’t understand: 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 129, in <module> floating_point_exceptions = floating_point_exceptions() File "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py", line 122, in floating_point_exceptions import libtbx.load_env File "/Users/magnus/Downloads/cctbx_sources/libtbx/load_env.py", line 5, in <module> libtbx.env = libtbx.env_config.unpickle() File "/Users/magnus/Downloads/cctbx_sources/libtbx/env_config.py", line 2194, in unpickle set_preferred_sys_prefix_and_sys_executable(build_path=build_path) File "/Users/magnus/Downloads/cctbx_sources/libtbx/env_config.py", line 2110, in set_preferred_sys_prefix_and_sys_executable if (op.samefile(build_path, dirname)): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/posixpath.py", line 162, in samefile s1 = os.stat(f1) OSError: [Errno 2] No such file or directory: '' Somewhere it was suggested to launch by: python ./script.py instead of python script.py but in my case, that didn't help Suggestions how to proceed from here? Thanks, Magnus On 04 Jun 2014, at 15:01, Gabor Bunkoczi wrote:

Hi Magnus,

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but what is $DYLIB_LIBRARY_PATH?

Sorry, this should be DYLD_LIBRARY_PATH, as suggested by Luc's original answer below.

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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.

Yeah, but this may not work if there is some binary incompatibility. So far it looks you are lucky, and it may. If not, you have to rebuild. This will not change "your" python in any way, i.e. other extensions remain functional.

Gabor

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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"):

Thanks for you help in this matter - I appreciate it, Magnus dlopen(/Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so,

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2): Symbol not found: boost::python::objects::function_object(boost::python::objects::py_function const&, std::__1::pair 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 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 _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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Dr Gabor Bunkoczi

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