Pyinstaller numpy "Intel MKL FATAL ERROR: Cannot load mkl_intel_thread.dll"

Question

I'm new with python apps. I'm trying to build my python GUI app with pyinstaller. My app depends on the following packages: PyQt4, numpy, pyqtgraph, h5py. I'm working with WinPython-32bit-3.4.4.1.

I build the app with this command:

pyinstaller --hidden-import=h5py.defs --hidden-import=h5py.utils --hidden-import=h5py.h5ac --hidden-import=h5py._proxy VOGE.py

I launch my app with the exe file in the dist directory created by pyinstaller and it seems work fine until the program call numpy and crash with this error:

Intel MKL FATAL ERROR: Cannot load mkl_intel_thread.dll

The mkl_intel_thread.dll is not present in the software directory; but with the file copied in the root dir of the program I got the same error

Thanks for your help

Answer 1

I had the same issue using Pyinstaller and Numpy. By default pyinstaller seems to not take into account numpy binaries so you have to specify it manually. You can add the files editing the ".spec" file "binaries" variable, but that will only work for your current program. If you want it working for all the programs your freeze you should make a "hook" and save it in C:\Python3*\Lib\site-packages\PyInstaller\hooks.

I had to adapt LeonidR's code to make the numpy-hook working. I rewrited it using a more modern, pythonic approach using list comprehensions:

from PyInstaller import log as logging 
from PyInstaller import compat
from os import listdir

mkldir = compat.base_prefix + "/Lib/site-packages/numpy/core" 
logger = logging.getLogger(__name__)
logger.info("MKL installed as part of numpy, importing that!")
binaries = [(mkldir + "/" + mkl, '') for mkl in listdir(mkldir) if mkl.startswith('mkl_')] 

"Binaries" is a list of tuples. The second item of the tuple corresponds to the folder where you want to place the 'dlls'. In this case is empty so it copies them directly in the main folder where your '.exe' is.