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pythonmacospymctheanopsycopg

psycopg2, pymc, theano and DYLD_FALLBACK_LIBRARY_PATH

I am unable to use pymc along with psycopg2. The following simple snippet from the tutorial:

import pymc as pm
with pm.Model() as model:
    x = pm.Normal('x', mu=0., sd=1)

results in the following error:

Exception: The environment variable 'DYLD_FALLBACK_LIBRARY_PATH' does not contain the '/Users/josh/anaconda/envs/py27/lib' path in its value. This will make Theano unable to compile c code. Update 'DYLD_FALLBACK_LIBRARY_PATH' to contain the said value, this will fix this error.

I was able to fix this problem by adding:

export DYLD_FALLBACK_LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH:/Users/josh/anaconda/envs/py27/lib

to my shell init file .bashrc. However, and this is the part I don't understand, that line breaks psycopg2:

---> 50 from psycopg2._psycopg import BINARY, NUMBER, STRING, DATETIME, ROWID
     51 
     52 from psycopg2._psycopg import Binary, Date, Time, Timestamp

ImportError: dlopen(/Users/josh/anaconda/envs/py27/lib/python2.7/site-packages/psycopg2/_psycopg.so, 2): Library not loaded: @loader_path/../../../libpq.5.dylib                                                                                                 
  Referenced from: /Users/josh/anaconda/envs/py27/lib/python2.7/site-packages/psycopg2/_psycopg.so
  Reason: image not found

How can I have psycopg2 and pymc (here theano) live happily together?

This is on OS X with a Python 2.7.6 installation with an Python environment created with conda.

Solution

  • The development version of Theano don't need changes to DYLD_FALLBACK_LIBRARY_PATH. So undo the change to it and update your Theano version. From:

    http://www.deeplearning.net/software/theano/install.html#bleeding-edge-install-instructions

    Run one of those 2 command depending of your need:

    pip install --upgrade --no-deps git+git://github.com/Theano/Theano.git --install-option='--prefix=~/.local'
pip install --upgrade --no-deps git+git://github.com/Theano/Theano.git

    EDIT: I removed the link to an answer elsewhere and copied the answer here. Thanks