Cannot load libmkl_intel_thread.dylib

[crondonm]

Hi, I'm new to Julia and I am still learning. I am on MacOS 10.13 (High Sierra) and using Julia 0.6, and installed anaconda3 with python 3.6.2. Every time I run PyPlot like this:
using PyPlot
plot(rand(10))

I got the following error:

Intel MKL FATAL ERROR: Cannot load libmkl_intel_thread.dylib
Julia has stopped: 2

I have tried everything. I uninstalled Julia and Python, I switched back and forth between the private Conda version from PyCall and Python 3.6. Moreover, I plot directly from Python using matlibplot it works fine. The problem seems to be Julia. I ran out of ideas.

Any help is appreciated.

Carlos

[iamed2]

@willtebbutt is also experiencing this, with Python 2.7 installed with Conda.jl, and El Capitan.

[stevengj]

Possibly a conflict between the BLAS libraries linked to Julia and those linked to NumPy (which is used by Matplotlib). Are you using the standard Julia binary, built with OpenBLAS, or a Julia binary linked with MKL?

[iamed2]

Will was using the binaries (OpenBLAS). We're currently building Julia from source on his machine to see if we get the same problem.

[jonalm]

I'm having the same issue on OSX Sierra.

julia> using PyPlot
julia> plot(rand(10))
Intel MKL FATAL ERROR: Cannot load libmkl_intel_thread.dylib.

For what its worth:

My julia version is Version 0.6.0 (2017-06-19 13:05 UTC), installed from the v0.6.0 branch, using make -j 4, and I believe the python version PyPlot tries to use, is whatever PyCall installs by default.

julia> Pkg.build("PyPlot")
INFO: Building Conda
INFO: Building PyCall
INFO: PyCall is using /Users/jon.alm.eriksen/.julia/v0.6/Conda/deps/usr/bin/python (Python 2.7.13) at /Users/jon.alm.eriksen/.julia/v0.6/Conda/deps/usr/bin/python, libpython = /Users/jon.alm.eriksen/.julia/v0.6/Conda/deps/usr/lib/libpython2.7
INFO: /Users/jon.alm.eriksen/.julia/v0.6/PyCall/deps/deps.jl has not changed
INFO: /Users/jon.alm.eriksen/.julia/v0.6/PyCall/deps/PYTHON has not changed

[stevengj]

Is there a libmkl_intel_thread.dylib anywhere in ~/.julia/v0.6/Conda/deps/usr? Maybe the anaconda packagers didn't link things correctly so that it is just not finding the path?

[jonalm]

@stevengj I don't know if this is expected? It looks like there are three of them.

~/opt/julia > find ~/.julia/v0.6/Conda/deps/usr -name "libmkl_intel_thread.dylib"
/Users/jon.alm.eriksen/.julia/v0.6/Conda/deps/usr/lib/libmkl_intel_thread.dylib
/Users/jon.alm.eriksen/.julia/v0.6/Conda/deps/usr/pkgs/mkl-2017.0.1-0/lib/libmkl_intel_thread.dylib
/Users/jon.alm.eriksen/.julia/v0.6/Conda/deps/usr/pkgs/mkl-2018.0.0-hc285769_4/lib/libmkl_intel_thread.dylib

I don't know how this linking work, but is there someway to manually point to the dylib file?

Curiously, this seems to work:

~/opt/julia > /Users/jon.alm.eriksen/.julia/v0.6/Conda/deps/usr/bin/python
Python 2.7.13 |Continuum Analytics, Inc.| (default, Dec 20 2016, 23:05:08)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import matplotlib
>>> import matplotlib.pyplot as plt
>>> plt.plot([1,2,3])
[<matplotlib.lines.Line2D object at 0x112375ad0>]

[stevengj]

Setting LD_LIBRARY_PATH explicitly works around the problem, i.e.export LD_LIBRARY_PATH=$HOME/.julia/v0.6/Conda/deps/usr/lib before launching Julia, and then it works for me.

This seems like a problem with Anaconda. The library paths are set up correctly if you launch the python executable, apparently, but not if you load libpython from another program (as we do in Julia).

[willtebbutt]

This solution also works for me. Thanks!

[jonalm]

Works for me too. Greatly appreciated suggestion @stevengj Thanks.

[crondonm]

It also works for me. Thank you very much!

[flamesofmoon]

Thank you very much @stevengj Works for me as well. I have struggled for two days!

[flamesofmoon]

@stevengj do you know how to set that forever? Cause every time I run Julia I have to type that command which is troublesome. Thanks a lot!

[stevengj]

@flamesofmoon , you can put it in your ~/.profile file.

Hopefully, we'll soon have better fix. If nothing else, as I mentioned in ContinuumIO/anaconda-issues#6423, I can add manual dlopen calls in PyPlot and PyCall. But hopefully we can get this fixed in Anaconda.