Closed
Description
Actual Behavior
Python crashes when I try to import any library (numpy, matplotlib, etc..) and also whe i open spyder with the following error:
Intel MKL FATAL ERROR: Cannot load mkl_intel_thread.dll.
Expected Behavior
No crashy
Steps to Reproduce
When I open the cmd I put:
python
import numpy
and i have the following message from windows
and in the cmd
Intel MKL FATAL ERROR: Cannot load mkl_intel_thread.dll.
I have the following on system PATH
and i don't have the file " mkl_intel_thread.dll" on my system32 directory
Thanks for the support!
Anaconda or Miniconda version: Anaconda 5.3
Operating System: Windows 10 1809
conda info
active environment : base
active env location : C:\Users\augus\Anaconda3
shell level : 1
user config file : C:\Users\augus\.condarc
populated config files : C:\Users\augus\.condarc
conda version : 4.5.11
conda-build version : 3.16.1
python version : 3.7.0.final.0
base environment : C:\Users\augus\Anaconda3 (writable)
channel URLs : https://conda.anaconda.org/intel/win-64
https://conda.anaconda.org/intel/noarch
https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/win-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/win-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/pro/win-64
https://repo.anaconda.com/pkgs/pro/noarch
https://repo.anaconda.com/pkgs/msys2/win-64
https://repo.anaconda.com/pkgs/msys2/noarch
package cache : C:\Users\augus\Anaconda3\pkgs
C:\Users\augus\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\augus\Anaconda3\envs
C:\Users\augus\AppData\Local\conda\conda\envs
C:\Users\augus\.conda\envs
platform : win-64
user-agent : conda/4.5.11 requests/2.19.1 CPython/3.7.0 Windows/10 Windows/10.0.17763
administrator : False
netrc file : None
offline mode : False
conda list --show-channel-urls
# packages in environment at C:\Users\augus\Anaconda3:
#
# Name Version Build Channel
_ipyw_jlab_nb_ext_conf 0.1.0 py37_0 defaults
alabaster 0.7.12 py37_0 defaults
anaconda custom py37_0 defaults
anaconda-client 1.7.2 py37_0 defaults
anaconda-navigator 1.9.2 py37_0 defaults
anaconda-project 0.8.2 py37_0 defaults
appdirs 1.4.3 py37h28b3542_0 defaults
asn1crypto 0.24.0 py37_0 defaults
astroid 2.0.4 py37_0 defaults
astropy 3.0.4 py37hfa6e2cd_0 defaults
atomicwrites 1.2.1 py37_0 defaults
attrs 18.2.0 py37h28b3542_0 defaults
automat 0.7.0 py37_0 defaults
babel 2.6.0 py37_0 defaults
backcall 0.1.0 py37_0 defaults
backports 1.0 py37_1 defaults
backports.os 0.1.1 py37_0 defaults
backports.shutil_get_terminal_size 1.0.0 py37_2 defaults
beautifulsoup4 4.6.3 py37_0 defaults
bitarray 0.8.3 py37hfa6e2cd_0 defaults
bkcharts 0.2 py37_0 defaults
blas 1.0 mkl defaults
blaze 0.11.3 py37_0 defaults
bleach 3.0.2 py37_0 defaults
blosc 1.14.4 he51fdeb_0 defaults
bokeh 0.13.0 py37_0 defaults
boto 2.49.0 py37_0 defaults
bottleneck 1.2.1 py37h452e1ab_1 defaults
bzip2 1.0.6 vc14_17 [vc14] intel
ca-certificates 2018.03.07 0 defaults
certifi 2018.10.15 py37_0 defaults
cffi 1.11.5 py37h74b6da3_1 defaults
chardet 3.0.4 py37_1 defaults
click 7.0 py37_0 defaults
cloudpickle 0.6.1 py37_0 defaults
clyent 1.2.2 py37_1 defaults
colorama 0.4.0 py37_0 defaults
comtypes 1.1.7 py37_0 defaults
conda 4.5.11 py37_0 defaults
conda-build 3.16.1 py37_0 defaults
conda-env 2.6.0 1 defaults
console_shortcut 0.1.1 3 defaults
constantly 15.1.0 py37h28b3542_0 defaults
contextlib2 0.5.5 py37_0 defaults
cryptography 2.3 py37h74b6da3_0 defaults
cryptography-vectors 2.3.1 py37_0 defaults
curl 7.61.1 h7602738_0 defaults
cycler 0.10.0 py37_0 defaults
cython 0.28.5 py37h6538335_0 defaults
cytoolz 0.9.0.1 py37hfa6e2cd_1 defaults
dask 0.19.4 py37_0 defaults
dask-core 0.19.4 py37_0 defaults
datashape 0.5.4 py37_1 defaults
decorator 4.3.0 py37_0 defaults
defusedxml 0.5.0 py37_1 defaults
distributed 1.23.3 py37_0 defaults
docutils 0.14 py37_0 defaults
entrypoints 0.2.3 py37_2 defaults
et_xmlfile 1.0.1 py37_0 defaults
fastcache 1.0.2 py37hfa6e2cd_2 defaults
filelock 3.0.9 py37_0 defaults
flask 1.0.2 py37_1 defaults
flask-cors 3.0.6 py37_0 defaults
freetype 2.9.1 ha9979f8_1 defaults
get_terminal_size 1.0.0 h38e98db_0 defaults
gevent 1.3.6 py37hfa6e2cd_0 defaults
glob2 0.6 py37_1 defaults
greenlet 0.4.15 py37hfa6e2cd_0 defaults
h5py 2.8.0 py37h3bdd7fb_2 defaults
hdf5 1.10.2 vc14_2 [vc14] intel
heapdict 1.0.0 py37_2 defaults
html5lib 1.0.1 py37_0 defaults
hyperlink 18.0.0 py37_0 defaults
icc_rt 2019.0 intel_117 intel
icu 58.2 ha66f8fd_1 defaults
idna 2.7 py37_0 defaults
imageio 2.4.1 py37_0 defaults
imagesize 1.1.0 py37_0 defaults
importlib_metadata 0.6 py37_0 defaults
incremental 17.5.0 py37_0 defaults
intel-openmp 2019.0 intel_117 intel
intelpython 2019.0 2 intel
ipykernel 5.0.0 py37h39e3cac_0 defaults
ipython 7.0.1 py37h39e3cac_0 defaults
ipython_genutils 0.2.0 py37_0 defaults
ipywidgets 7.4.2 py37_0 defaults
isort 4.3.4 py37_0 defaults
itsdangerous 0.24 py37_1 defaults
jdcal 1.4 py37_0 defaults
jedi 0.13.1 py37_0 defaults
jinja2 2.10 py37_0 defaults
jpeg 9b hb83a4c4_2 defaults
jsonschema 2.6.0 py37_0 defaults
jupyter 1.0.0 py37_7 defaults
jupyter_client 5.2.3 py37_0 defaults
jupyter_console 6.0.0 py37_0 defaults
jupyter_core 4.4.0 py37_0 defaults
jupyterlab 0.35.1 py37_0 defaults
jupyterlab_launcher 0.13.1 py37_0 defaults
jupyterlab_server 0.2.0 py37_0 defaults
keyring 15.1.0 py37_0 defaults
kiwisolver 1.0.1 py37h6538335_0 defaults
lazy-object-proxy 1.3.1 py37hfa6e2cd_2 defaults
libarchive 3.3.2 h843f8d1_5 defaults
libcurl 7.61.1 h7602738_0 defaults
libiconv 1.15 h1df5818_7 defaults
libpng 1.6.34 vc14_3 [vc14] intel
libsodium 1.0.16 h9d3ae62_0 defaults
libssh2 1.8.0 hd619d38_4 defaults
libtiff 4.0.9 h36446d0_2 defaults
libxml2 2.9.8 hadb2253_1 defaults
libxslt 1.1.32 hf6f1972_0 defaults
llvmlite 0.24.0 py37h6538335_0 defaults
locket 0.2.0 py37_1 defaults
lxml 4.2.5 py37hef2cd61_0 defaults
lz4-c 1.8.1.2 h2fa13f4_0 defaults
lzo 2.10 h6df0209_2 defaults
m2w64-gcc-libgfortran 5.3.0 6 defaults
m2w64-gcc-libs 5.3.0 7 defaults
m2w64-gcc-libs-core 5.3.0 7 defaults
m2w64-gmp 6.1.0 2 defaults
m2w64-libwinpthread-git 5.0.0.4634.697f757 2 defaults
markupsafe 1.0 py37hfa6e2cd_1 defaults
matplotlib 3.0.0 py37hd159220_0 defaults
mccabe 0.6.1 py37_1 defaults
menuinst 1.4.14 py37hfa6e2cd_0 defaults
mistune 0.8.3 py37hfa6e2cd_1 defaults
mkl 2019.0 intel_117 intel
mkl-service 1.1.2 py37hb217b18_5 defaults
mkl_fft 1.0.6 py37hdbbee80_0 defaults
mkl_random 1.0.1 py37h77b88f5_1 defaults
more-itertools 4.3.0 py37_0 defaults
mpmath 1.0.0 py37_2 defaults
msgpack-python 0.5.6 py37he980bc4_1 defaults
msys2-conda-epoch 20160418 1 defaults
multipledispatch 0.6.0 py37_0 defaults
navigator-updater 0.2.1 py37_0 defaults
nbconvert 5.3.1 py37_0 defaults
nbformat 4.4.0 py37_0 defaults
networkx 2.2 py37_1 defaults
nltk 3.3.0 py37_0 defaults
nose 1.3.7 py37_2 defaults
notebook 5.7.0 py37_0 defaults
numba 0.39.0 py37h830ac7b_0 defaults
numexpr 2.6.8 py37h9ef55f4_0 defaults
numpy 1.15.2 py37ha559c80_0 defaults
numpy-base 1.15.2 py37h8128ebf_0 defaults
numpydoc 0.8.0 py37_0 defaults
odo 0.5.1 py37_0 defaults
olefile 0.46 py37_0 defaults
openpyxl 2.5.8 py37_0 defaults
openssl 1.0.2o vc14_3 [vc14] intel
packaging 18.0 py37_0 defaults
pandas 0.23.4 py37h830ac7b_0 defaults
pandoc 2.2.3.2 0 defaults
pandocfilters 1.4.2 py37_1 defaults
parso 0.3.1 py37_0 defaults
partd 0.3.9 py37_0 defaults
path.py 11.5.0 py37_0 defaults
pathlib2 2.3.2 py37_0 defaults
patsy 0.5.0 py37_0 defaults
pep8 1.7.1 py37_0 defaults
pickleshare 0.7.5 py37_0 defaults
pillow 5.2.0 py37h08bbbbd_0 defaults
pip 10.0.1 py37_0 defaults
pkginfo 1.4.2 py37_1 defaults
pluggy 0.7.1 py37h28b3542_0 defaults
ply 3.11 py37_0 defaults
prometheus_client 0.4.2 py37_0 defaults
prompt_toolkit 2.0.6 py37_0 defaults
psutil 5.4.7 py37hfa6e2cd_0 defaults
py 1.7.0 py37_0 defaults
pyasn1 0.4.4 py37h28b3542_0 defaults
pyasn1-modules 0.2.2 py37_0 defaults
pycodestyle 2.4.0 py37_0 defaults
pycosat 0.6.3 py37hfa6e2cd_0 defaults
pycparser 2.19 py37_0 defaults
pycrypto 2.6.1 py37hfa6e2cd_9 defaults
pycurl 7.43.0.2 py37h74b6da3_0 defaults
pyflakes 2.0.0 py37_0 defaults
pygments 2.2.0 py37_0 defaults
pylint 2.1.1 py37_0 defaults
pyodbc 4.0.24 py37h6538335_0 defaults
pyopenssl 18.0.0 py37_0 defaults
pyparsing 2.2.2 py37_0 defaults
pyqt 5.9.2 py37h6538335_2 defaults
pysocks 1.6.8 py37_0 defaults
pytables 3.4.4 py37he6f6034_0 defaults
pytest 3.8.2 py37_0 defaults
pytest-arraydiff 0.2 py37h39e3cac_0 defaults
pytest-astropy 0.4.0 py37_0 defaults
pytest-doctestplus 0.1.3 py37_0 defaults
pytest-openfiles 0.3.0 py37_0 defaults
pytest-remotedata 0.3.0 py37_0 defaults
python 3.7.0 hea74fb7_0 defaults
python-dateutil 2.7.3 py37_0 defaults
python-libarchive-c 2.8 py37_6 defaults
pytz 2018.5 py37_0 defaults
pywavelets 1.0.0 py37h452e1ab_0 defaults
pywin32 223 py37hfa6e2cd_1 defaults
pywinpty 0.5.4 py37_0 defaults
pyyaml 3.13 py37hfa6e2cd_0 defaults
pyzmq 17.1.2 py37hfa6e2cd_0 defaults
qt 5.9.6 vc14h62aca36_0 defaults
qtawesome 0.5.1 py37_1 defaults
qtconsole 4.4.1 py37_0 defaults
qtpy 1.5.1 py37_0 defaults
requests 2.19.1 py37_0 defaults
rope 0.11.0 py37_0 defaults
ruamel_yaml 0.15.46 py37hfa6e2cd_0 defaults
scikit-image 0.14.0 py37h6538335_1 defaults
scikit-learn 0.20.0 py37heebcf9a_1 defaults
scipy 1.1.0 py37h4f6bf74_1 defaults
seaborn 0.9.0 py37_0 defaults
send2trash 1.5.0 py37_0 defaults
service_identity 17.0.0 py37h28b3542_0 defaults
setuptools 40.4.3 py37_0 defaults
simplegeneric 0.8.1 py37_2 defaults
singledispatch 3.4.0.3 py37_0 defaults
sip 4.19.8 py37h6538335_0 defaults
six 1.11.0 py37_1 defaults
snappy 1.1.7 h777316e_3 defaults
snowballstemmer 1.2.1 py37_0 defaults
sortedcollections 1.0.1 py37_0 defaults
sortedcontainers 2.0.5 py37_0 defaults
sphinx 1.8.1 py37_0 defaults
sphinxcontrib 1.0 py37_1 defaults
sphinxcontrib-websupport 1.1.0 py37_1 defaults
spyder 3.3.1 py37_1 defaults
spyder-kernels 0.2.6 py37_0 defaults
sqlalchemy 1.2.11 py37hfa6e2cd_0 defaults
sqlite 3.23.1 vc14_1 [vc14] intel
statsmodels 0.9.0 py37h452e1ab_0 defaults
sympy 1.3 py37_0 defaults
tbb 2019.1 vc14_intel_0 [vc14] intel
tblib 1.3.2 py37_0 defaults
terminado 0.8.1 py37_1 defaults
testpath 0.4.2 py37_0 defaults
tk 8.6.8 hfa6e2cd_0 defaults
toolz 0.9.0 py37_0 defaults
tornado 5.1.1 py37hfa6e2cd_0 defaults
tqdm 4.26.0 py37h28b3542_0 defaults
traitlets 4.3.2 py37_0 defaults
twisted 18.7.0 py37hfa6e2cd_1 defaults
unicodecsv 0.14.1 py37_0 defaults
urllib3 1.23 py37_0 defaults
vc 14.0 2 intel
vs2015_runtime 14.0.25420 intel_2 intel
wcwidth 0.1.7 py37_0 defaults
webencodings 0.5.1 py37_1 defaults
werkzeug 0.14.1 py37_0 defaults
wheel 0.32.1 py37_0 defaults
widgetsnbextension 3.4.2 py37_0 defaults
win_inet_pton 1.0.1 py37_1 defaults
win_unicode_console 0.5 py37_0 defaults
wincertstore 0.2 py37_0 defaults
winpty 0.4.3 4 defaults
wrapt 1.10.11 py37hfa6e2cd_2 defaults
xlrd 1.1.0 py37_1 defaults
xlsxwriter 1.1.1 py37_0 defaults
xlwings 0.12.1 py37_0 defaults
xlwt 1.3.0 py37_0 defaults
xz 5.2.3 vc14_2 [vc14] intel
yaml 0.1.7 hc54c509_2 defaults
zeromq 4.2.5 he025d50_1 defaults
zict 0.1.3 py37_0 defaults
zlib 1.2.11 vc14h21ff451_5 [vc14] intel
zope 1.0 py37_1 defaults
zope.interface 4.5.0 py37hfa6e2cd_0 defaults
Metadata
Metadata
Assignees
Labels
No labels
Type
Projects
Milestone
Relationships
Development
No branches or pull requests
Participants
Activity
mingwandroid commentedon Oct 18, 2018
Either let the installer add to your PATH - it adds multiple entries (worst option) or use Anaconda Prompt or Anaconda Navigator to launch the software or else use conda's activate script.
Zeekk9 commentedon Oct 18, 2018
Thanks. But that is what the anaconda installer has added to the PATH. I tried with Anaconda Prompt and Navigator but the still have the problem.
mingwandroid commentedon Oct 18, 2018
Ah ok. Your problem is likely then non system DLLs in the system32 folder.
Some audio application installs them there, possibly some other software does too. I asked the audio people to stop, they didn't reply. They probably only care that their stuff runs correctly and have no concern about breaking people's systems.
Look for mkl DLLs in C:\Windows\System32.
Also please look at old bug reports before posting duplicates. In particular make sure to check closed issues.
Zeekk9 commentedon Oct 19, 2018
Thanks again. In fact there are several files with the same name "mkl_intel_thread.dll" in other folders not in system32. I have renamed them to .bak but I still have the same problem.
mingwandroid commentedon Oct 19, 2018
from a normal cmd.exe prompt, and also from the Anaconda Prompt please type
where mkl_intel_thread.dlland show the results of each.Zeekk9 commentedon Oct 19, 2018
On normal cmd.exe say
C:\Windows\System32\where.exeC:\Windows\System32\mkl_intel_thread.dllC:\Users\augus\Anaconda3\Library\bin\mkl_intel_thread.dlland on Anaconda prompt
C:\Users\augus\Anaconda3\Library\bin\mkl_intel_thread.dllC:\Windows\System32\mkl_intel_thread.dllmingwandroid commentedon Oct 19, 2018
Oh, you are mixing defaults with intel? Don't do that.
msarahan commentedon Oct 19, 2018
That really shouldn't be a problem. Especially on Windows, I believe Intel uses essentially identical build processes as us. Our MKL packages are just straight repacks of the intel packages.
mingwandroid commentedon Oct 19, 2018
The error message suggests an incompatibility, likely to do with version constraints across channels?
mingwandroid commentedon Oct 19, 2018
Once my Windows VM finishes downloading I'll take a look. Has taken about 4 hours so far!
msarahan commentedon Oct 19, 2018
I agree completely, I'm just confounded on what the conflict is. A conflict between defaults and intel is not impossible, but I don't think it's likely, either.
mingwandroid commentedon Oct 20, 2018
But looking again we see in your very first comment.
But you then posted the result of
where mkl_intel_thread.dllC:\Windows\System32\mkl_intel_thread.dllThis is you problem, only MS should put DLLs in C:\Windows\System32, no one else should as it risks breaking your other software.
Sorry it took so long to track down!
Zeekk9 commentedon Oct 27, 2018
I downgrade to anaconda 5.2 with python 3.6 and all works fine, the problem is with python 3.7 or mkl conda files.
msarahan commentedon Oct 27, 2018
Though it may seem that newer anaconda is the root cause, we are certain from our testing that our files are self consistent and working. You definitely have a conflict with something else on your system. Apparently that something else was compatible with the 5.2.0 release. What happens if you start with your 5.2.0 installation and then update numpy to version 1.15.3? I expect it will break in the same way that you see problems with anaconda 5.3.0 , but if you could help me test that theory, it would be helpful.
18 remaining items