Hi,
I’ve installed Anaconda3-2020.02-MacOSX-x86_64 on OSX 10.13.6, launched Jupyter 6.0.3 from the Anaconda navigator interface, accessed to the web page.
When I type import pandas as pd, the kernel fails, here is the log in the jupyter_mac command
Last login: Sun Apr 12 18:17:37 on ttys000
(base) iMac:~ laurent$ /Users/laurent/opt/anaconda3/bin/jupyter_mac.command ; exit;
[I 18:40:26.241 NotebookApp] JupyterLab extension loaded from /Users/laurent/opt/anaconda3/lib/python3.7/site-packages/jupyterlab
[I 18:40:26.242 NotebookApp] JupyterLab application directory is /Users/laurent/opt/anaconda3/share/jupyter/lab
[I 18:40:26.797 NotebookApp] Serving notebooks from local directory: /Users/laurent
[I 18:40:26.797 NotebookApp] The Jupyter Notebook is running at:
[I 18:40:26.797 NotebookApp] http://localhost:8888/?token=0d0e5fb4379863a9309b95e8f76551438482efe985584d1d
[I 18:40:26.797 NotebookApp] or http://127.0.0.1:8888/?token=0d0e5fb4379863a9309b95e8f76551438482efe985584d1d
[I 18:40:26.797 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 18:40:26.833 NotebookApp]
To access the notebook, open this file in a browser:
file:///Users/laurent/Library/Jupyter/runtime/nbserver-19479-open.html
Or copy and paste one of these URLs:
http://localhost:8888/?token=0d0e5fb4379863a9309b95e8f76551438482efe985584d1d
or http://127.0.0.1:8888/?token=0d0e5fb4379863a9309b95e8f76551438482efe985584d1d
[I 18:41:35.208 NotebookApp] Kernel started: e727a8dc-4fba-4dc5-b922-a27399dcb8e6
[I 18:41:44.206 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
kernel e727a8dc-4fba-4dc5-b922-a27399dcb8e6 restarted
[I 18:42:06.415 NotebookApp] Saving file at /dev/python/MLPython/First step.ipynb
[I 18:42:11.228 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
kernel e727a8dc-4fba-4dc5-b922-a27399dcb8e6 restarted
[I 18:43:34.848 NotebookApp] Saving file at /dev/python/MLPython/First step.ipynb
I’ve checked in ~/opt/anaconda3/bin
./jupyter kernelspec list
Available kernels:
python3 /Users/laurent/opt/anaconda3/share/jupyter/kernels/python3
It sounds similar to https://github.com/xianyi/OpenBLAS/issues/2306 and related issues - a problem that your CPU is mis-detected by some libraries used by pandas. Maybe you can ask them on github/their preferred channel of communication how to continue? Possibly somebody needs to guide you through several steps until the real issue is found.
You could open the terminal in the Jupyter UI and and type “python”. Then you should see the error message like in the issue I commented. I suggest you ask people of the pandas community. I can’t guide you through this.
The information I gave, comes from the console that opened when I launched jupyter from anaconda’UI.
As you can see kernel started and after I typed and executed import pandas as pd in the jupyter UI, there is a kernel restart without any explanation or relevant message. I just discover these tools, but I can investigate if you tell me where is the log file (if any) ?
Is there a way to launch manually the jupyter python environnement : is there a virtual env configuration stored in ~/opt/anaconda3 ?
python
Python 3.7.7 (default, Mar 26 2020, 10:32:53)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pandas as pd
Illegal instruction: 4
(Pandas) iMac:~ laurent$ sysctl -a | grep machdep.cpu.features
machdep.cpu.features: FPU VME DE PSE TSC MSR PAE MCE CX8 APIC SEP MTRR PGE MCA CMOV PAT PSE36 CLFSH DS ACPI MMX FXSR SSE SSE2 SS HTT TM PBE SSE3 DTES64 MON DSCPL VMX SMX EST TM2 SSSE3 CX16 TPR PDCM SSE4.1 SSE4.2 POPCNT
This seems to be related to numpy version built in
conda list numpy
# packages in environment at /Users/laurent/opt/anaconda3/envs/Pandas:
#
# Name Version Build Channel
numpy 1.18.1 py37h7241aed_0
numpy-base 1.18.1 py37h6575580_1
Searching now the best way to downgrade numpy to 1.17.4 …
I would not be so sure whether it is directly numpy or maybe some third-party library they use. AVX sounds more like openBLAS (but maybe because that was the source for me). Have you tried playing around with the environment variables like in the first link (my first answer)? I only received that hint and I used it. If you are interested where exactly the AVX message is sent off, you can try Python debugger and find out which statement of the pandas import makes it break. It could be great if you share your experience with the community at https://github.com/pandas-dev/pandas so that they know that there is some need to improve.
Then it is great that we have figured that one out. Too bad that they dropped the support for old Macs but for the meantime at least some kind of solution (downgrading) seems to exist. Those silent failures are even worse and can take ages if nobody else has already reported a similar thing.
Last login: Mon Apr 13 12:30:53 on tty??
(base) iMac:~ laurent$ . /Users/laurent/opt/anaconda3/bin/activate && conda activate /Users/laurent/opt/anaconda3/envs/Pandas;
(Pandas) iMac:~ laurent$ python
Python 3.7.7 (default, Mar 26 2020, 10:32:53)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pandas as pd
>>>
No more crash … let’s see if it’s working on jupyter now …
Maybe you can ask a new question instead of posting your personal question below the answer to another topic? How are the two even related? It is better style to link to other topics in your own question if that seems helpful. And for me your question is by far too short to really understand what you are troubled by.
@Christopher_C are you sure that you exported that environment variable in a way that numpy had a chance to see it? I currently see two options of what have gone wrong:
Please be aware that any code cell starting with an exclamation mark are executed in a subshell. Please check the value of the environment variable at a later stage.
Is the environment variable already set at the time numpy is imported?
