Issue as in title.
I am trying to get Jupyter notebooks running python remotely on my work computer (far better resources than my personal machine).
I think the issue may be originating from how something in the environment is set up (Linux), but I have been troubleshooting for over a day now and could really do with some help.
I am using a virtual environment, and had some issues with getting it to use the jupyter executable in my virtual environment. I have now resolved this. I have installed the venv as a kernel and can run on this in the notebook (A) or I can launch the notebook explicitly using the venv executable (B). However there is still an inconsistency between python paths of which and sys.executable:
In terminal (venv active):
(venv) npc8.pauln> which python
/home/pauln/wtf/venv/bin/python
(venv) npc8.pauln> python
Python 3.6.8 (default, Apr 2 2020, 13:34:55)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-39)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.executable
'/home/pauln/wtf/venv/bin/python'
Jupyter (identical in the cases of A and B described above):
! which python
/bin/python
import sys
sys.executable
'/home/pauln/wtf/venv/bin/python3'
As a sanity check, I replicated the above on my home machine - both return the same value, as I think would be expected. I also noted that if I start a terminal from within the notebook, it does not enter the venv by default on my work machine, but it does on my home machine.
I also checked jupyter-troubleshoot, and include it incase it is useful:
Terminal (venv active):
(venv) npc8.pauln> jupyter-troubleshoot
WARNING: You are using pip version 20.2.2; however, version 20.2.4 is available.
You should consider upgrading via the '/home/pauln/wtf/venv/bin/python -m pip install --upgrade pip' command.
$PATH:
/home/pauln/wtf/venv/bin
/w/work3/home/pauln/TeXLive/2020/bin/x86_64-linux
/mnt/share/cern_CentOS7/root/v6.20.04/bin
./
/bin
/usr/bin
/usr/local/bin
/home/pauln/apps/clas12root/bin
/home/pauln/apps/chanser/bin
sys.path:
/home/pauln/wtf/venv/bin
/mnt/share/cern_CentOS7/root/v6.20.04/lib
/home/pauln/wtf
/usr/lib64/python36.zip
/usr/lib64/python3.6
/usr/lib64/python3.6/lib-dynload
/home/pauln/wtf/venv/lib64/python3.6/site-packages
/home/pauln/wtf/venv/lib/python3.6/site-packages
sys.executable:
/home/pauln/wtf/venv/bin/python
sys.version:
3.6.8 (default, Apr 2 2020, 13:34:55)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-39)]
platform.platform():
Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
which -a jupyter:
/home/pauln/wtf/venv/bin/jupyter
/usr/local/bin/jupyter
pip list:
Package Version
------------------- ---------
argon2-cffi 20.1.0
async-generator 1.10
attrs 20.3.0
awkward 0.14.0
backcall 0.2.0
bleach 3.2.1
cachetools 4.1.1
certifi 2020.11.8
cffi 1.14.3
cycler 0.10.0
decorator 4.4.2
defusedxml 0.6.0
entrypoints 0.3
importlib-metadata 2.0.0
ipykernel 5.3.4
ipython 7.16.1
ipython-genutils 0.2.0
ipywidgets 7.5.1
jedi 0.17.2
Jinja2 2.11.2
jsonschema 3.2.0
jupyter 1.0.0
jupyter-client 6.1.7
jupyter-console 6.2.0
jupyter-core 4.6.3
jupyterlab-pygments 0.1.2
kiwisolver 1.3.1
MarkupSafe 1.1.1
matplotlib 3.3.2
mistune 0.8.4
nbclient 0.5.1
nbconvert 6.0.7
nbformat 5.0.8
nest-asyncio 1.4.2
notebook 6.1.5
numpy 1.19.4
packaging 20.4
pandas 1.1.4
pandocfilters 1.4.3
parso 0.7.1
pexpect 4.8.0
pickleshare 0.7.5
Pillow 8.0.1
pip 20.2.2
prometheus-client 0.8.0
prompt-toolkit 3.0.8
ptyprocess 0.6.0
pycparser 2.20
Pygments 2.7.2
pyparsing 2.4.7
pyrsistent 0.17.3
python-dateutil 2.8.1
pytz 2020.4
pyzmq 19.0.2
qtconsole 4.7.7
QtPy 1.9.0
Send2Trash 1.5.0
setuptools 49.6.0
six 1.15.0
terminado 0.9.1
testpath 0.4.4
tornado 6.1
traitlets 4.3.3
uproot 3.13.0
uproot-methods 0.8.0
wcwidth 0.2.5
webencodings 0.5.1
wheel 0.35.1
widgetsnbextension 3.5.1
zipp 3.4.0
From notebook (again A and B):
WARNING: You are using pip version 19.3.1; however, version 20.2.4 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
$PATH:
/mnt/share/cern_CentOS7/root/v6.20.04/bin
./
/bin
/usr/bin
/usr/local/bin
/home/pauln/apps/clas12root/bin
/home/pauln/apps/chanser/bin
/w/work3/home/pauln/TeXLive/2020/bin/x86_64-linux
sys.path:
/mnt/share/local_CentOS7/bin
/mnt/share/cern_CentOS7/root/v6.20.04/lib
/home/pauln/wtf
/usr/local/lib/python37.zip
/usr/local/lib/python3.7
/usr/local/lib/python3.7/lib-dynload
/usr/local/lib/python3.7/site-packages
sys.executable:
/usr/local/bin/python3.7
sys.version:
3.7.0 (default, Sep 17 2018, 10:25:45)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)]
platform.platform():
Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
which -a jupyter:
/usr/local/bin/jupyter
pip list:
Package Version
------------------ --------
attrs 19.3.0
backcall 0.1.0
bleach 3.1.0
corner 2.0.1
cycler 0.10.0
Cython 0.29.6
decorator 4.4.1
defusedxml 0.6.0
emcee 2.2.1
entrypoints 0.3
importlib-metadata 0.23
ipykernel 5.1.3
ipython 7.9.0
ipython-genutils 0.2.0
ipywidgets 7.5.1
jedi 0.15.1
Jinja2 2.10.3
jsonschema 3.1.1
jupyter 1.0.0
jupyter-client 5.3.4
jupyter-console 6.0.0
jupyter-core 4.6.1
kiwisolver 1.0.1
MarkupSafe 1.1.1
matplotlib 3.0.3
mistune 0.8.4
more-itertools 7.2.0
nbconvert 5.6.1
nbformat 4.4.0
notebook 6.0.2
numpy 1.17.4
pandas 0.25.3
pandocfilters 1.4.2
parso 0.5.1
pexpect 4.7.0
pickleshare 0.7.5
pip 19.3.1
prometheus-client 0.7.1
prompt-toolkit 2.0.10
ptyprocess 0.6.0
Pygments 2.4.2
pymc 2.3.6
pyparsing 2.3.1
pyrsistent 0.15.5
pystan 2.18.1.0
python-dateutil 2.8.1
pytz 2019.3
pyzmq 18.1.0
qtconsole 4.4.3
root-numpy 4.8.0
root-pandas 0.7.0
Send2Trash 1.5.0
setuptools 41.6.0
six 1.13.0
terminado 0.8.2
testpath 0.4.4
tornado 6.0.3
traitlets 4.3.3
wcwidth 0.1.7
webencodings 0.5.1
widgetsnbextension 3.5.1
zipp 0.6.0
Any help would be greatly appreciated!
Cheers, Paul
