python matplotlib MKL fatal error on ubuntu 12.04

Question

Here's my python code

1 import matplotlib.pyplot as plt                                                 
2 plt.plot([1, 2, 3, 4])                                                          
3 plt.ylabel('some numbers')                                                      
4 plt.show()

When I run it, I got the following error message

$ python test.py 

*** libmkl_avx.so *** failed with error : /usr/local/enthought/lib/libmkl_avx.so: undefined symbol: i_free
*** libmkl_def.so *** failed with error : /usr/local/enthought/lib/libmkl_def.so: undefined symbol: i_free
MKL FATAL ERROR: Cannot load neither libmkl_avx.so nor libmkl_def.so

Here's my python version.

$ python --version
Python 2.7.2 -- EPD 7.2-2 (64-bit)

Looks like there is something wrong with my enthought python installation. When I use standard python2.7, everything is fine. — user1591487, Jan 25 '13 at 00:09
The `EPD` in your version indicates this is the Enthought Python Distributation. That should come with matplotlib already. It's *possible* that running `sudo apt-get install matplotlib` on top of that created some problems. — SethMMorton, May 21 '13 at 16:48

score 1 · Answer 1 · answered Mar 30 '16 at 14:17

I realize this is a pretty old question, but I was having the same issue and found a solution without needing to reinstall, so for any future readers here is what I did:

@root commented above with a link to the intel forum. One of the answers there suggested preloading some of the MKL libraries. (dated Tue, 10/20/2009 - 10:32, I can't figure out how to link to specific comment on there).

This solved the issue for me. Though, you'll need to find where tthe libmkl_core.so and libmkl_sequential.so libraries are stored for you. For me, it was:

export LD_PRELOAD=/usr/local/Canopy/v152/CanopyCore/appdata/canopy-1.5.2.2785.rh5-x86_64/lib/libmkl_sequential.so:/usr/local/Canopy/v152/CanopyCore/appdata/canopy-1.5.2.2785.rh5-x86_64/lib/libmkl_core.so

There were also copies in /usr/local/Canopy/v152/Canopy_64bit/User/lib/, but these versions did NOT work. Only the one above.

Hope this helps someone out in the future!

for anaconda the libraries are found in anaconda2/lib/ – Diego Apr 13 '16 at 21:36 — Diego, Apr 13 '16 at 21:36

score 0 · Answer 2 · edited May 23 '17 at 10:34

0

Update python packages. I had this problem twice on two different machines. Updating solves the problem. Upgrading all packages with pip

edited May 23 '17 at 10:34

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answered Jan 14 '15 at 16:30

Tomasz Turowski

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python matplotlib MKL fatal error on ubuntu 12.04

2 Answers2