CODEWITHSUNDEEP
pythonmacosgccscikit-learn
aquagremlin
aquagremlin

Reputation: 3549

import sklearn error with anaconda python 3.52

Fresh install of anaconda python3 onto secondary hard drive of mac running mavericks.

import sklearn

gives

Library not loaded: /usr/local/lib/libgcc_s.1.dylib
  Referenced from: /Volumes/SecondHD/anaconda/lib/python3.5/site-packages/scipy/sparse/linalg/isolve/_iterative.so
  Reason: image not found

gcc was installed with home-brew and exists.

which gcc

gives

/usr/bin/gcc

In /usr/local/Cellar/gcc/6.1.0/lib/gcc/6 I can find libgcc_s.1.dylib so I know it's there even tho it was not symlinked in /usr/local/lib.

Rather than adding more symlinks to /usr/local/lib from all the libraries in Cellar, I instead added the location of the libraries to the search path.

In my ~.profile I have

export LIBRARY_PATH="$LIBRARY_PATH:/usr/local/lib"
export LIBRARY_PATH="$LIBRARY_PATH:/usr/local/Cellar/gcc/6.1.0/lib/gcc/6"

But that does not work. However, the error goes away if I add this line to my .profile

export DYLD_FALLBACK_LIBRARY_PATH=/usr/local/Cellar/gcc/6.1.0/lib/gcc/6

My understanding from this post is that LIBRARY_PATH is a list of places a compiler (like gcc) will look for libraries when it is linking code. But in Mac OSX, DYLD_LIBRARY_PATH and DYLD_FALLBACK_LIBRARY_PATH contain a list of places any program will search for a shared library when it runs.

So if sklearn wants a gcc library, that would mean some compilation (and linking) will happen. Why is this line not sufficient

export LIBRARY_PATH="$LIBRARY_PATH:/usr/local/Cellar/gcc/6.1.0/lib/gcc/6"

and why is DYLD_FALLBACK_LIBRARY_PATH or DYLD_LIBRARY_PATH needed?

Upvotes: 2

Views: 742

Answers (1)

Fabio Fumarola
Fabio Fumarola

Reputation: 498

I had the same problem. What I did was creating symbolic links from my cellar folder of gcc to /usr/local/lib.

  1. look for the right path of you gcc

  2. ln -s /usr/local/Cellar/gcc/X.X.X/lib/gcc/6/* /usr/local/lib

Upvotes: 2

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