[cctbxbb] Boost Import Error

Magnus Andersson magnus.andersson at scilifelab.se
Wed Jun 4 06:18:28 PDT 2014 

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 <gb360 at cam.ac.uk> wrote:

> Hi Magnus,
> 
>> but what is $DYLIB_LIBRARY_PATH?
> 
> Sorry, this should be DYLD_LIBRARY_PATH, as suggested by Luc's original answer below.
> 
>>> 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
> 
>> 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 <luc_j_bourhis at mac.com> 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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>>> http://phenix-online.org/mailman/listinfo/cctbxbb
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> 
> -- 
> ##################################################
> 
>     Dr Gabor Bunkoczi
> 
>     Cambridge Institute for Medical Research
>     Wellcome Trust/MRC Building
>     Addenbrooke's Hospital
>     Hills Road
>     Cambridge CB2 0XY
> ##################################################
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> cctbxbb mailing list
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