Clean conda Windows install, followed by 'conda update --all' results in wrong mkl dlls being used for Spyder

Problem Description

A clean conda install from https://www.anaconda.com/download/#windows (version 5.2.0) works for Spyder, but if I then do a ‘conda update --all’, the resulting configuration is broken. When you run Spyder, launching from Anaconda navigator, you get a message about a missing ordinal 242 in Anaconda3\Library\bin\mkl_intel_thread.dll

This turns out to be because the dlls from mkl-2018.0.3-1 are installed in Anaconda3\Library\bin, but something in Spyder needs the dlls from mkl-2018.0.2-1 instead. If you copy the dlls from Anaconda3\pkgs\mkl-2018.0.2-1\Library\bin into Anaconda3\Library\bin, Spyder then launches normally. (This probably breaks something else, but if so, it’s something I haven’t yet tried to use 😉

What steps reproduce the problem?

1. Install Anaconda for Windows
2. run conda update --all
3. Launch Spyder

What is the expected output? What do you see instead?

Paste Traceback/Error Below (if applicable)

PASTE TRACEBACK HERE

Versions

• Spyder version: 3.2.8
• Python version: 3.6.5
• Qt version: 5.9.4
• PyQt5 version: 5.9.2
• Operating system: Windows 10

Dependencies

pyflakes >=0.6.0 :  2.0.0 (OK)
pycodestyle >=2.3:  2.4.0 (OK)
pygments >=2.0   :  2.2.0 (OK)
pandas >=0.13.1  :  0.23.1 (OK)
numpy >=1.7      :  1.14.5 (OK)
sphinx >=0.6.6   :  1.7.5 (OK)
rope >=0.9.4     :  0.10.7 (OK)
jedi >=0.9.0     :  0.12.0 (OK)
nbconvert >=4.0  :  5.3.1 (OK)
sympy >=0.7.3    :  1.1.1 (OK)
cython >=0.21    :  0.28.3 (OK)
qtconsole >=4.2.0:  4.3.1 (OK)
IPython >=4.0    :  6.4.0 (OK)
pylint >=0.25    :  1.9.2 (OK)

[msarahan]

We have spoken with Intel about this issue. They said that there are some backwards incompatible changes in mkl 2019. We had been operating under the assumption that software built against 2018 would work with 2019, but that is not necessarily true. We will be rebuilding packages so that constraints are more accurate, and so thata complete set of software built with mkl 2019 is available.

[CAM-Gerlach]

@ccordoba12 @mingwandroid @msarahan This appears to be potentially more serious than previously stated, to the point of essentially making a Anaconda environment with mkl 2018.0.3 completely unusable. I installed Spyder 3.3.0 (conda-forge) and its optional dependencies (numpy, pandas, matplotlib, scipy, sympy and cython) into a fresh conda environment on my on my Win 8.1 x64 system, and while import pandas doesn’t trigger the error message in that environment, anything with matplotlib will, among other things, e.g.

import matplotlib.pyplot as plt
ax = plt.subplot(111, projection='polar')

This not only happens in Spyder, but also QtConsole, ipython, and even a bare python interpreter; each crashes with the above two lines. I also tested in another new, clean environment with just Python 3.6.6 and matplotlib installed, and got the bug immediately on import matplotlib.pyplot as plt in the basic Python interpreter, crashing it. I then installed pandas, and got the same bug immediately upon importing it, again crashing the interpreter. I then downgraded to mkl 2018.0.2-1 from 2018.0.3-1 with conda, and everything worked fine.

So, users can fix it relatively painlessly (for now) by just running conda install mkl=2018.0.2 under Anaconda Prompt in any affected environment. However, this would appear to be very serious for those creating a new environment that uses numpy or other packages that depend on it, anyone running conda update --all, or anyone installing or updating a package that triggers an install of that new version, since it will cause their environment to be essentially broken and unusable unless and until they are aware of and implement the above fix.