Unable to import numpy: Error: /usr/lib/liblapack.so.3: undefined symbol: gotoblas

Question

When I try to import numpy, I get the following error:

/usr/local/lib/python2.7/dist-packages/numpy/linalg/__init__.py in <module>()
     49 from .info import __doc__
     50 
---> 51 from .linalg import *
     52 
     53 from numpy.testing import Tester

/usr/local/lib/python2.7/dist-packages/numpy/linalg/linalg.py in <module>()
     27     )
     28 from numpy.lib import triu, asfarray
---> 29 from numpy.linalg import lapack_lite, _umath_linalg
     30 from numpy.matrixlib.defmatrix import matrix_power
     31 from numpy.compat import asbytes

ImportError: /usr/lib/liblapack.so.3: undefined symbol: gotoblas

I have already tried solutions posted Error by import numpy: lapack_lite.so: undefined symbol and GotoBLAS error when installing matplotlib with pip in a virtualenv on debian wheezy

I already tried all the options in:

vvkulkarni@galileo:~$ sudo update-alternatives --config liblapack.so.3
There are 3 choices for the alternative liblapack.so.3 (providing /usr/lib/liblapack.so.3).

  Selection    Path                                      Priority   Status
------------------------------------------------------------
* 0            /usr/lib/openblas-base/liblapack.so.3      40        auto mode
  1            /usr/lib/atlas-base/atlas/liblapack.so.3   35        manual mode
  2            /usr/lib/lapack/liblapack.so.3             10        manual mode
  3            /usr/lib/openblas-base/liblapack.so.3      40        manual mode

I am using Ubuntu 14.1 and python 2.7

how did you install numpy? Your problem is more than likely having conflicting `liblapack.so.3` I only have `/usr/lib/lapack/liblapack.so.3` running ubuntu 14.04. Can you remove `libopenblas-base`? — Padraic Cunningham, Sep 28 '14 at 18:55
I installed it using apt-get install:sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose — vkmv, Sep 28 '14 at 18:57
You could also try using pip but may well get the same issue, I had no issue installing the `scipy-stack` originally — Padraic Cunningham, Sep 28 '14 at 19:00
I tried that too but hit this and the workaround provided does not work for me:http://stackoverflow.com/questions/22388519/problems-with-pip-install-numpy-runtimeerror-broken-toolchain-cannot-link-a — vkmv, Sep 28 '14 at 19:08
I am on ubuntu for sure... to be clear things were working fine until a system apt-upgrade was done to patch for shellshock after which I am hitting these issues. — vkmv, Sep 28 '14 at 19:12
This is surprising. I removed libopenblas-base, reinstalled libatlas3-dev and now the error goes away. But now I have a slower numpy :(. I believe OpenBLAS is much faster — vkmv, Sep 28 '14 at 19:21
Yes, I did mention that in my first comment ;) Well the numpy you have now is definitely faster than the one you had a few minutes ago! — Padraic Cunningham, Sep 28 '14 at 19:24
Indeed ! A working numpy is better than no numpy at all :). Thanks ! — vkmv, Sep 28 '14 at 19:30

score 5 · Answer 1 · answered Sep 01 '17 at 18:39

To solve these issues, I followed the install bash script here: https://gist.github.com/amirsani/d2aa0763cc138902bf73

I still had the same error occur during testing at the ending of all the installation so I did this

sudo apt-get remove libopenblas-base

Which I got from here: Installing lapack for numpy

This appears to have solved my original problem (similar to yours but not identical) where I was attempting to run the following from ipython

from ortools.linear_solver import pywraplp

which produced an identical error to the one you had.

score 1 · Answer 2 · answered Apr 21 '17 at 07:46

The error message shows that your numpy installation is in '/usr/local/lib', but apt-get will put numpy in '/usr/lib'. This suggests to me that you have another copy of numpy which was installed by another method (e.g. pip install). Check if you have a directory called /usr/lib/python2.7/dist-packages/numpy/. If so, you just need to make sure that Python imports numpy from here and not from '/usr/local/lib'.

Try deleting, renaming or moving the directory /usr/local/lib/python2.7/dist-packages/numpy/, alternatively you can change sys.path from within Python.

Unable to import numpy: Error: /usr/lib/liblapack.so.3: undefined symbol: gotoblas

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