Cannot import PyOpenCL in Juypter Notebook

Question

I'm running inside an anacoda environment with pyopencl installed:

$> conda list | grep pyopencl
pyopencl                  2018.2.5         py37h9888f84_0    conda-forge

And from that same window I launch:

$> anaconda3/bin/jupyter_mac.command

Which is:

cat /Anaconda3/bin/jupyter_mac.command

DIR=$(dirname $0)

$DIR/jupyter-notebook

So, now we're running a notebook. When I attempt to import pyopencl:

import pyopencl as cl

I get the following error:

ModuleNotFoundError: No module named 'pyopencl'

I am able to run the examples locally in the same shell w/out any errors via:

$> python test6.py
Choose platform:
[0] <pyopencl.Platform 'Portable Computing Language' at 0x11512cf00>
[1] <pyopencl.Platform 'Apple' at 0x7f984cd1e010>
Choice [0]:1
Choose device(s):
[0] <pyopencl.Device 'Intel(R) Core(TM) i7-8850H CPU @ 2.60GHz' on 'Apple' at 0x7f984cc1f090>
[1] <pyopencl.Device 'Intel(R) UHD Graphics 630' on 'Apple' at 0x7f984cc19370>
[2] <pyopencl.Device 'AMD Radeon Pro 560X Compute Engine' on 'Apple' at 0x7f984cc19390>
Choice, comma-separated [0]:2
Set the environment variable PYOPENCL_CTX='1:2' to avoid being asked again.
PASSED
[-0.13433748]
[-0.13433748]

Any help is appreciated! Thanks.

Answer 1

Background

I managed to reproduce the behavior:

• On Win - but this shouldn't be a problem since (I assume that) things are the same on OSX
• The Python from the (current) Anaconda environment and Anaconda's default one (which corresponds to base environment) are distinct. If this is not the case, the answer (or parts of it) might be incorrect. Note that there are the only 2 Pythons that I'm going to reference, they are both internal to Anaconda (even if the Anaconda "keyword" will not be present)
• I used PyGraphviz in my test scenarios (instead of PyOpenCL)

code0.py:

#!/usr/bin/env python3

import sys
import os
import pprint


print(f"Python Executable: {sys.executable}")
print(f"Version {sys.version} on {sys.platform}\n")

conda_env_var = "CONDA_DEFAULT_ENV"
conda_env = os.environ[conda_env_var]
print(f"{conda_env_var}: {conda_env}\n")

sys_path = pprint.pformat(sys.path)
print(f"sys.path: {sys_path}\n")

path_var = "PATH"
env_path = pprint.pformat([item for item in os.environ[path_var].split(os.pathsep) if item.find(conda_env) > -1])
print(f"os.environ[\"{path_var}\"] (relevant): {env_path}\n")

import pygraphviz
print(pygraphviz)

Output:

(py_064_030701_test0) [cfati@CFATI-5510-0:e:\Work\Dev\StackOverflow\q055251357]> python code0.py
Python Executable: E:\Install\x64\Anaconda\Anaconda\2018.12\envs\py_064_030701_test0\python.exe
Version 3.7.1 (default, Dec 10 2018, 22:54:23) [MSC v.1915 64 bit (AMD64)] on win32

CONDA_DEFAULT_ENV: py_064_030701_test0

sys.path: ['e:\\Work\\Dev\\StackOverflow\\q055251357',
 'E:\\Work\\Dev\\Utils',
 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0\\python37.zip',
 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0\\DLLs',
 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0\\lib',
 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0',
 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0\\lib\\site-packages']

os.environ["PATH"] (relevant): ['E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0',
 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0\\Library\\mingw-w64\\bin',
 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0\\Library\\usr\\bin',
 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0\\Library\\bin',
 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0\\Scripts',
 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0\\bin']

<module 'pygraphviz' from 'E:\\Install\\x64\\Anaconda\\Anaconda\\2018.12\\envs\\py_064_030701_test0\\lib\\site-packages\\pygraphviz\\__init__.py'>


(py_064_030701_test0) [cfati@CFATI-5510-0:e:\Work\Dev\StackOverflow\q055251357]> where jupyter-notebook
E:\Install\x64\Anaconda\Anaconda\2018.12\Scripts\jupyter-notebook.exe

(py_064_030701_test0) [cfati@CFATI-5510-0:e:\Work\Dev\StackOverflow\q055251357]> jupyter-notebook
[I 01:16:10.345 NotebookApp] JupyterLab extension loaded from E:\Install\x64\Anaconda\Anaconda\2018.12\lib\site-packages\jupyterlab
[I 01:16:10.346 NotebookApp] JupyterLab application directory is E:\Install\x64\Anaconda\Anaconda\2018.12\share\jupyter\lab
[I 01:16:10.349 NotebookApp] Serving notebooks from local directory: e:\Work\Dev\StackOverflow\q055251357
[I 01:16:10.350 NotebookApp] The Jupyter Notebook is running at:
[I 01:16:10.352 NotebookApp] http://localhost:8888/?token=14412a6d6d0c895d059a86bcd71e10cbface4a479c5843c2
[I 01:16:10.353 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 01:16:10.437 NotebookApp]

    To access the notebook, open this file in a browser:
        file:///C:/Users/cfati/AppData/Roaming/jupyter/runtime/nbserver-24700-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/?token=14412a6d6d0c895d059a86bcd71e10cbface4a479c5843c2
[I 01:17:18.569 NotebookApp] 302 GET /?token=14412a6d6d0c895d059a86bcd71e10cbface4a479c5843c2 (::1) 0.98ms
[I 01:17:25.161 NotebookApp] Creating new notebook in
[I 01:17:26.147 NotebookApp] Kernel started: 8b702b2d-97d0-40e3-bbca-42107efd1de5
[I 01:17:27.186 NotebookApp] Adapting to protocol v5.1 for kernel 8b702b2d-97d0-40e3-bbca-42107efd1de5

And the same script ran into the Jupyter Notebook:

As seen, it fails and that is because it's ran by Anaconda's default Python (which doesn't have the package installed). Took a look and noticed that the jupyter-notebook executable launches (Anaconda's default) Python on jupyter-notebook-script.py (from the same dir).

Possible solutions:

1. Install the missing package(s) in the main Python

This was the 1^st that came to my mind: installing PyGraphviz (and all the other required ones). Didn't try it, but it should work. The reason why I didn't try it, is because I am against polluting the main Python with packages. But, since it already contains an awful amount of site-packages, things are debatable.

2. Register the current environment Python as a kernel

I tried to make jupyter-notebook launching the current environment Python installation instead, using its configuration, or altering %CONDA_PYTHON_EXE%, but no success (note that it's my 1^st time working with Jupyter). Anyway after some investigations, I realized that jupyter-notebook executable launches the Python that Jupyter is installed in. This is a common technique, and it's done by hardcoding the Python path into the executables (although strangely, looking at it with a hex editor didn't find it).

While searching, I ran into [SO]: Changing Python Executable (@Matt's answer) and from there to [ReadTheDocs.IPython]: Installing the IPython kernel, and gave that a shot:

py_064_030701_test0) [cfati@CFATI-5510-0:e:\Work\Dev\StackOverflow\q055251357]> where pip
E:\Install\x64\Anaconda\Anaconda\2018.12\envs\py_064_030701_test0\Scripts\pip.exe
E:\Install\x64\Anaconda\Anaconda\2018.12\Scripts\pip.exe

(py_064_030701_test0) [cfati@CFATI-5510-0:e:\Work\Dev\StackOverflow\q055251357]> pip freeze
certifi==2019.3.9
pygraphviz==1.5
wincertstore==0.2

(py_064_030701_test0) [cfati@CFATI-5510-0:e:\Work\Dev\StackOverflow\q055251357]> pip install ipykernel
Collecting ipykernel

...
# Some pip useless output
...

Installing collected packages: tornado, colorama, six, ipython-genutils, decorator, traitlets, backcall, pygments, pickleshare, wcwidth, prompt-toolkit, parso, jedi, ipython, jupyter-core, python-dateutil, pyzmq, jupyter-client, ipykernel
Successfully installed backcall-0.1.0 colorama-0.4.1 decorator-4.4.0 ipykernel-5.1.0 ipython-7.4.0 ipython-genutils-0.2.0 jedi-0.13.3 jupyter-client-5.2.4 jupyter-core-4.4.0 parso-0.3.4 pickleshare-0.7.5 prompt-toolkit-2.0.9 pygments-2.3.1 python-dateutil-2.8.0 pyzmq-18.0.1 six-1.12.0 tornado-6.0.2 traitlets-4.3.2 wcwidth-0.1.7

(py_064_030701_test0) [cfati@CFATI-5510-0:e:\Work\Dev\StackOverflow\q055251357]> where python
E:\Install\x64\Anaconda\Anaconda\2018.12\envs\py_064_030701_test0\python.exe
E:\Install\x64\Anaconda\Anaconda\2018.12\python.exe

(py_064_030701_test0) [cfati@CFATI-5510-0:e:\Work\Dev\StackOverflow\q055251357]> python -m ipykernel install --name %CONDA_DEFAULT_ENV%
Installed kernelspec py_064_030701_test0 in C:\ProgramData\jupyter\kernels\py_064_030701_test0

After launching it, and selecting the newly created kernel (like in the image below) things went fine.

This is basically what @AndrásNagy also explained in his answer.

Although this was my 1^st choice at the beginning, using current environment Python to write its metadata in a location where main Python (and other Pythons not necessarily inside Anaconda) could read it from, doesn't seem so straightforward to me (although it might be the recommended approach).

3. Install Jupyter in the current environment Python

I also thought of this from the beginning, but I didn't get to it right away because of the previous approach. I thought that Jupyter has a lot of dependencies (which it's true), but so does IPyKernel. However, now I think it's the the simplest way.

(py_064_030701_test0) [cfati@CFATI-5510-0:e:\Work\Dev\StackOverflow\q055251357]> pip install jupyter
Collecting jupyter

...
# Some pip useless output
...

Installing collected packages: qtconsole, testpath, defusedxml, entrypoints, webencodings, bleach, mistune, MarkupSafe, jinja2, pandocfilters, attrs, pyrsistent, jsonschema, nbformat, nbconvert, Send2Trash, prometheus-client, pywinpty, terminado, notebook, widgetsnbextension, ipywidgets, jupyter-console, jupyter
Successfully installed MarkupSafe-1.1.1 Send2Trash-1.5.0 attrs-19.1.0 bleach-3.1.0 defusedxml-0.5.0 entrypoints-0.3 ipywidgets-7.4.2 jinja2-2.10 jsonschema-3.0.1 jupyter-1.0.0 jupyter-console-6.0.0 mistune-0.8.4 nbconvert-5.4.1 nbformat-4.4.0 notebook-5.7.8 pandocfilters-1.4.2 prometheus-client-0.6.0 pyrsistent-0.14.11 pywinpty-0.5.5 qtconsole-4.4.3 terminado-0.8.2 testpath-0.4.2 webencodings-0.5.1 widgetsnbextension-3.4.2


(py_064_030701_test0) [cfati@CFATI-5510-0:e:\Work\Dev\StackOverflow\q055251357]> where jupyter-notebook
E:\Install\x64\Anaconda\Anaconda\2018.12\envs\py_064_030701_test0\Scripts\jupyter-notebook.exe
E:\Install\x64\Anaconda\Anaconda\2018.12\Scripts\jupyter-notebook.exe

Needless to say that launching jupyter-notebook (notice that it's a different executable) did the trick (as installing Jupyter also registers the Python installation as a kernel).

Answer 2

I think I had the same problem as you! I had a problem that the anaconda environment kernel did not show up in my jupyter notebook when I started that jupyter notebook from my conda environment!

Please consider the following:

conda activate YourEnvironmentName
pip install ipykernel 
python -m ipykernel install --user --name=YourEnvironmentName

Hopefully after this you will be able to start your Jupyter notebook with

jupyter notebook --ip=0.0.0.0 --port=8080

And select the conda environment from the list of kernels where you have installed pyopencl

Answer 3

I had a similar issue, where I created a conda environment, activated the environment, installed a bunch of packages, then added the kernel to ipython, but the installed packages wouldn't load and I was getting import errors.

Solution: The new kernel was pointing to the wrong python executable (for the base environment). I had to edit the kernel.json file to point to the python executable in the appropriate environment. This was the first string in the "argv" array.