Linking problems with Anaconda when using LD_LIBRARY_PATH

Question

I just tried installing Anaconda on Linux 64 bit. Everything seems to have worked well, but when I tried to start IPython from a terminal, I get the following error:

$ ipython
Traceback (most recent call last):
  File "/home/josh/installs/conda/1.7.0/bin/ipython", line 4, in <module>
    from IPython import start_ipython
  File "/home/josh/installs/conda/1.7.0/lib/python2.7/site-packages/IPython/__init__.py", line 43, in <module>
    from .config.loader import Config
  File "/home/josh/installs/conda/1.7.0/lib/python2.7/site-packages/IPython/config/__init__.py", line 16, in <module>
    from .application import *
  File "/home/josh/installs/conda/1.7.0/lib/python2.7/site-packages/IPython/config/application.py", line 27, in <module>
    from collections import defaultdict
  File "/home/josh/installs/conda/1.7.0/lib/python2.7/collections.py", line 9, in <module>
    from operator import itemgetter as _itemgetter, eq as _eq
ImportError: /home/josh/installs/conda/1.7.0/lib/python2.7/lib-dynload/operator.so: undefined symbol: _PyUnicodeUCS4_AsDefaultEncodedString

I get the same error if I try to update conda:

$ conda update conda                                                                                                      
Traceback (most recent call last):
  File "/home/josh/installs/conda/1.7.0/bin/conda", line 3, in <module>
    from conda.cli import main
  File "/home/josh/installs/conda/1.7.0/lib/python2.7/site-packages/conda/cli/__init__.py", line 8, in <module>
    from conda.cli.main import main
  File "/home/josh/installs/conda/1.7.0/lib/python2.7/site-packages/conda/cli/main.py", line 43, in <module>
    import argparse
  File "/home/josh/installs/conda/1.7.0/lib/python2.7/argparse.py", line 85, in <module>
    import collections as _collections
  File "/home/josh/installs/conda/1.7.0/lib/python2.7/collections.py", line 9, in <module>
    from operator import itemgetter as _itemgetter, eq as _eq
ImportError: /home/josh/installs/conda/1.7.0/lib/python2.7/lib-dynload/operator.so: undefined symbol: _PyUnicodeUCS4_AsDefaultEncodedString

It is also strange because it looks like it installed Python 2.7.4 and not Python 2.7.5. I literally downloaded it just now (October 1st).

$ python
Python 2.7.4 (default, Apr 21 2013, 18:37:10)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-50)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

and I have the following on my .bashrc: PATH=/home/josh/installs/conda/1.7.0/bin:$PATH which seems to be doing its job: $ which python /home/josh/installs/conda/1.7.0/bin/python I installed the version available here. Below is the full installation log:

[/home/josh/installs/conda] >>> /home/josh/installs/conda/1.7.0/
PREFIX=/home/josh/conda/1.7.0
installing: python-2.7.5-2 ...
installing: conda-1.9.1-py27_0 ...
installing: _license-1.1-py27_0 ...
installing: apptools-4.2.0-py27_0 ...
installing: astropy-0.2.4-np17py27_1 ...
installing: atom-0.3.2-py27_0 ...
installing: binstar-0.3.1-py27_0 ...
installing: biopython-1.61-np17py27_0 ...
installing: bitarray-0.8.1-py27_0 ...
installing: bokeh-0.1.1-np17py27_0 ...
installing: boto-2.12.0-py27_0 ...
installing: cairo-1.12.2-1 ...
installing: casuarius-1.1-py27_0 ...
installing: chaco-4.3.0-np17py27_1 ...
installing: configobj-4.7.2-py27_0 ...
installing: cubes-0.10.2-py27_3 ...
installing: curl-7.30.0-0 ...
installing: cython-0.19.1-py27_0 ...
installing: dateutil-2.1-py27_2 ...
installing: disco-0.4.4-py27_0 ...
installing: distribute-0.6.45-py27_0 ...
installing: docutils-0.11-py27_0 ...
installing: dynd-python-0.4.2-np17py27_0 ...
installing: enable-4.3.0-np17py27_0 ...
installing: enaml-0.7.19-py27_1 ...
installing: envisage-4.3.0-py27_0 ...
installing: erlang-R15B01-0 ...
installing: flask-0.10.1-py27_1 ...
installing: freetype-2.4.10-0 ...
installing: gevent-0.13.8-py27_0 ...
installing: gevent-websocket-0.3.6-py27_2 ...
installing: gevent_zeromq-0.2.5-py27_2 ...
installing: greenlet-0.4.1-py27_0 ...
installing: grin-1.2.1-py27_1 ...
installing: h5py-2.2.0-np17py27_0 ...
installing: hdf5-1.8.9-0 ...
installing: imaging-1.1.7-py27_3 ...
installing: ipython-1.0.0-py27_0 ...
installing: ipython-notebook-1.0.0-py27_0 ...
installing: ipython-qtconsole-1.0.0-py27_0 ...
installing: itsdangerous-0.23-py27_0 ...
installing: jinja2-2.7.1-py27_0 ...
installing: jpeg-8d-0 ...
installing: keyring-3.0.1-py27_0 ...
installing: launcher-0.1.2-py27_0 ...
installing: libdynd-0.4.2-0 ...
installing: libevent-2.0.20-0 ...
installing: libnetcdf-4.2.1.1-1 ...
installing: libpng-1.5.13-1 ...
installing: libtiff-4.0.2-0 ...
installing: libxml2-2.9.0-0 ...
installing: libxslt-1.1.28-0 ...
installing: llvm-3.3-0 ...
installing: llvmmath-0.1.1-np17py27_2 ...
installing: llvmpy-0.12.0-py27_0 ...
installing: lxml-3.2.3-py27_0 ...
installing: markupsafe-0.18-py27_0 ...
installing: matplotlib-1.3.0-np17py27_0 ...
installing: mayavi-4.3.0-np17py27_1 ...
installing: mdp-3.3-np17py27_0 ...
installing: meta-0.4.2.dev-py27_0 ...
installing: mpi4py-1.3-py27_0 ...
installing: mpich2-1.4.1p1-0 ...
installing: netcdf4-1.0.5-np17py27_0 ...
installing: networkx-1.8.1-py27_0 ...
installing: nltk-2.0.4-np17py27_0 ...
installing: nose-1.3.0-py27_0 ...
installing: numba-0.10.2-np17py27_0 ...
installing: numexpr-2.0.1-np17py27_3 ...
installing: numpy-1.7.1-py27_0 ...
installing: opencv-2.4.6-np17py27_0 ...
installing: openssl-1.0.1c-0 ...
installing: pandas-0.12.0-np17py27_0 ...
installing: patsy-0.2.1-np17py27_0 ...
installing: pep8-1.4.6-py27_0 ...
installing: pip-1.4.1-py27_0 ...
installing: pixman-0.26.2-0 ...
installing: ply-3.4-py27_0 ...
installing: psutil-1.0.1-py27_0 ...
installing: py-1.4.14-py27_0 ...
installing: py2cairo-1.10.0-py27_1 ...
installing: pycosat-0.6.0-py27_0 ...
installing: pycparser-2.9.1-py27_0 ...
installing: pycrypto-2.6-py27_0 ...
installing: pycurl-7.19.0-py27_2 ...
installing: pyface-4.3.0-py27_0 ...
installing: pyflakes-0.7.3-py27_0 ...
installing: pygments-1.6-py27_0 ...
installing: pyparsing-1.5.6-py27_0 ...
installing: pysal-1.6.0-np17py27_1 ...
installing: pysam-0.6-py27_0 ...
installing: pyside-1.2.1-py27_0 ...
installing: pytables-2.4.0-np17py27_0 ...
installing: pytest-2.3.5-py27_0 ...
installing: pytz-2013b-py27_0 ...
installing: pyyaml-3.10-py27_0 ...
installing: pyzmq-2.2.0.1-py27_1 ...
installing: qt-4.8.5-0 ...
installing: readline-6.2-0 ...
installing: redis-2.6.9-0 ...
installing: redis-py-2.7.2-py27_0 ...
installing: requests-1.2.3-py27_0 ...
installing: rope-0.9.4-py27_0 ...
installing: scikit-image-0.8.2-np17py27_2 ...
installing: scikit-learn-0.14.1-np17py27_0 ...
installing: scipy-0.12.0-np17py27_0 ...
installing: shiboken-1.2.1-py27_0 ...
installing: six-1.4.1-py27_0 ...
installing: sphinx-1.1.3-py27_4 ...
installing: spyder-2.2.4-py27_0 ...
installing: spyder-app-2.2.4-py27_0 ...
installing: sqlalchemy-0.8.2-py27_0 ...
installing: sqlite-3.7.13-0 ...
installing: statsmodels-0.5.0-np17py27_0 ...
installing: sympy-0.7.3-py27_0 ...
installing: system-5.8-1 ...
installing: theano-0.5.0-np17py27_1 ...
installing: tk-8.5.13-0 ...
installing: tornado-3.1.1-py27_0 ...
installing: traits-4.3.0-py27_0 ...
installing: traitsui-4.3.0-py27_0 ...
installing: util-linux-2.21-0 ...
installing: vtk-5.10.1-py27_0 ...
installing: werkzeug-0.9.4-py27_0 ...
installing: xlrd-0.9.2-py27_0 ...
installing: xlwt-0.7.5-py27_0 ...
installing: yaml-0.1.4-0 ...
installing: zeromq-2.2.0-1 ...
installing: zlib-1.2.7-0 ...
installing: anaconda-1.7.0-np17py27_0 ...
installing: _cache-0.0-x0 ...
Python 2.7.5 :: Continuum Analytics, Inc.
creating default environment...
installation finished.

Do you wish the installer to prepend the Anaconda install location
to PATH in your /home/josh/.bashrc ? [yes|no]
[no] >>> yes

Prepending PATH=/home/josh/installs/conda/1.7.0/bin to PATH in /home/josh/.bashrc
A backup will be made to: /home/josh/.bashrc-anaconda.bak


For this change to become active, you have to open a new terminal.

Thank you for installing Anaconda!

Answer 1

On your system Anaconda is picking up a "system version" of libpython which is compiled with 2-byte Unicode where-as Anaconda is built with 4-byte Unicode. This is an unusual situation for some reason the dynamic loader for operator.so file indicated is picking up your system libpython library.

Also, it looks like when you run python you are getting the standard "system" Python regardless of what your PATH is.

Have you started a new terminal, or run # source .bashrc ? Which Linux distribution are you using? Do you have LD_LIBRARY_PATH set in your environment?

Note that this question is also asked at https://github.com/ContinuumIO/conda/issues/296 so an answer may be there.