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Recent Changes
To resolve address a problem with PATH ordering when using anaconda3 modules, a warning in the module was put in place to avoid caution loading an anaconda3 module while in a virtual environment, or if conda init has been used to modify one's environment.
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Non-python/conda HPC users would see per-job stderr from the conda deactivate above:
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[arnoldg@dt-login03 ~]$ conda deactivate
bash: conda: command not found
[arnoldg@dt-login03 ~]$
# or
[arnoldg@dt-login03 ~]$ conda deactivate
CommandNotFoundError: Your shell has not been properly configured to use 'conda deactivate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
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Jupyter and jupyter-lab will find the environments in your $HOME/.conda/envs -- your login shell should reflect what you want to see from Jupyter.
We think the The list of avail. kernels for Jupyter should be the same as what you see from a login shell and python3 ( https://github.com/Anaconda-Platform/nb_conda_kernels ).
Jupyter needs to be installed in every virtual environment where you want to use with Jupyter-lab or Jupyter-notebook.
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[arnoldg@dt-login03 jupyter_notebook_config.d]$ python3 -m nb_conda_kernels list [ListKernelSpecs] WARNING | Config option `kernel_spec_manager_class` not recognized by `ListKernelSpecs`. [ListKernelSpecs] [nb_conda_kernels] enabled, 8 kernels found Available kernels: conda-env-westpa20-py /projects/bbka/arnoldg/westpa20/share/jupyter/kernels/python3 conda-root-py /sw/external/python/anaconda3/share/jupyter/kernels/python3 conda-env-anaconda3_Rcpu-r /sw/external/python/anaconda3_rcpu/share/jupyter/kernels/ir conda-env-anaconda3_Rcpu-py /sw/external/python/anaconda3_rcpu/share/jupyter/kernels/python3 conda-env-westpa-2022.03-py /sw/external/python/westpa-2022.03/share/jupyter/kernels/python3 conda-env-.conda-myclone-py /u/arnoldg/.conda/envs/myclone/share/jupyter/kernels/python3 conda-env-.conda-mynewenv-r /u/arnoldg/.conda/envs/mynewenv/share/jupyter/kernels/ir conda-env-.conda-mynewenv-py /u/arnoldg/.conda/envs/mynewenv/share/jupyter/kernels/python3 python3 /sw/external/python/anaconda3_gpu/share/jupyter/kernels/python3 |
Debugging:
For debugging purposes, try jupyter-lab from a terminal:
Of interest are the Searching path at the beginning, and the nb_conda_kernels outputs.
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[arnoldg@dt-login03 jupyter_notebook_config.d]$ jupyter-lab --log-level=0
[D 2023-02-20 12:48:50.533 ServerApp] Searching ['/u/arnoldg/.jupyter', '/u/arnoldg/.local/etc/jupyter', '/sw/external/python/anaconda3/etc/jupyter', '/usr/local/etc/jupyter', '/etc/jupyter'] for config files
[D 2023-02-20 12:48:50.533 ServerApp] Looking for jupyter_config in /etc/jupyter
[D 2023-02-20 12:48:50.533 ServerApp] Looking for jupyter_config in /usr/local/etc/jupyter
[D 2023-02-20 12:48:50.533 ServerApp] Looking for jupyter_config in /sw/external/python/anaconda3/etc/jupyter
[D 2023-02-20 12:48:50.534 ServerApp] Loaded config file: /sw/external/python/anaconda3/etc/jupyter/jupyter_config.json
[D 2023-02-20 12:48:50.534 ServerApp] Looking for jupyter_config in /u/arnoldg/.local/etc/jupyter
[D 2023-02-20 12:48:50.534 ServerApp] Looking for jupyter_config in /u/arnoldg/.jupyter
[D 2023-02-20 12:48:50.537 ServerApp] Looking for jupyter_server_config in /etc/jupyter
[D 2023-02-20 12:48:50.537 ServerApp] Looking for jupyter_server_config in /usr/local/etc/jupyter
[D 2023-02-20 12:48:50.537 ServerApp] Looking for jupyter_server_config in /sw/external/python/anaconda3/etc/jupyter
[D 2023-02-20 12:48:50.537 ServerApp] Looking for jupyter_server_config in /u/arnoldg/.local/etc/jupyter
[D 2023-02-20 12:48:50.537 ServerApp] Looking for jupyter_server_config in /u/arnoldg/.jupyter
[D 2023-02-20 12:48:50.538 ServerApp] Paths used for configuration of jupyter_server_config:
/etc/jupyter/jupyter_server_config.json
[D 2023-02-20 12:48:50.538 ServerApp] Paths used for configuration of jupyter_server_config:
/usr/local/etc/jupyter/jupyter_server_config.json
[D 2023-02-20 12:48:50.539 ServerApp] Paths used for configuration of jupyter_server_config:
/sw/external/python/anaconda3/etc/jupyter/jupyter_server_config.d/jupyterlab.json
/sw/external/python/anaconda3/etc/jupyter/jupyter_server_config.d/nbclassic.json
/sw/external/python/anaconda3/etc/jupyter/jupyter_server_config.d/notebook_shim.json
/sw/external/python/anaconda3/etc/jupyter/jupyter_server_config.d/panel-client-jupyter.json
/sw/external/python/anaconda3/etc/jupyter/jupyter_server_config.json
[D 2023-02-20 12:48:50.541 ServerApp] Paths used for configuration of jupyter_server_config:
/u/arnoldg/.local/etc/jupyter/jupyter_server_config.d/ipyparallel.json
/u/arnoldg/.local/etc/jupyter/jupyter_server_config.json
[D 2023-02-20 12:48:50.541 ServerApp] Paths used for configuration of jupyter_server_config:
/u/arnoldg/.jupyter/jupyter_server_config.json
Note: detected 128 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable.
Note: NumExpr detected 128 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
NumExpr defaulting to 8 threads.
[I 2023-02-20 12:48:51.954 ServerApp] ipyparallel | extension was successfully linked.
[W 2023-02-20 12:48:51.957 LabApp] Config option `kernel_spec_manager_class` not recognized by `LabApp`.
[W 2023-02-20 12:48:51.958 LabApp] Config option `kernel_spec_manager_class` not recognized by `LabApp`.
[W 2023-02-20 12:48:51.960 LabApp] Config option `kernel_spec_manager_class` not recognized by `LabApp`.
[I 2023-02-20 12:48:51.961 ServerApp] jupyterlab | extension was successfully linked.
[W 2023-02-20 12:48:51.962 NotebookApp] Config option `kernel_spec_manager_class` not recognized by `NotebookApp`.
[W 2023-02-20 12:48:51.963 NotebookApp] Config option `kernel_spec_manager_class` not recognized by `NotebookApp`.
[W 2023-02-20 12:48:51.965 NotebookApp] Config option `kernel_spec_manager_class` not recognized by `NotebookApp`.
[I 2023-02-20 12:48:51.965 ServerApp] nbclassic | extension was successfully linked.
[D 2023-02-20 12:48:51.968 ServerApp] Paths used for configuration of jupyter_notebook_config:
/u/arnoldg/.jupyter/jupyter_notebook_config.json
[D 2023-02-20 12:48:51.968 ServerApp] Paths used for configuration of jupyter_notebook_config:
/etc/jupyter/jupyter_notebook_config.json
[D 2023-02-20 12:48:51.969 ServerApp] Paths used for configuration of jupyter_notebook_config:
/usr/local/etc/jupyter/jupyter_notebook_config.json
[D 2023-02-20 12:48:51.969 ServerApp] Paths used for configuration of jupyter_notebook_config:
/sw/external/python/anaconda3/etc/jupyter/jupyter_notebook_config.d/jupyterlab.json
/sw/external/python/anaconda3/etc/jupyter/jupyter_notebook_config.d/panel-client-jupyter.json
/sw/external/python/anaconda3/etc/jupyter/jupyter_notebook_config.json
[D 2023-02-20 12:48:51.971 ServerApp] Paths used for configuration of jupyter_notebook_config:
/u/arnoldg/.local/etc/jupyter/jupyter_notebook_config.d/ipyparallel.json
/u/arnoldg/.local/etc/jupyter/jupyter_notebook_config.json
[D 2023-02-20 12:48:51.971 ServerApp] Paths used for configuration of jupyter_notebook_config:
/u/arnoldg/.jupyter/jupyter_notebook_config.json
[I 2023-02-20 12:48:51.971 ServerApp] notebook_shim | extension was successfully linked.
[I 2023-02-20 12:48:51.972 ServerApp] panel.io.jupyter_server_extension | extension was successfully linked.
[D 2023-02-20 12:48:51.972 ServerApp] Config changed: {'JupyterApp': {'kernel_spec_manager_class': 'nb_conda_kernels.CondaKernelSpecManager'}, 'NotebookApp': {}, 'ServerApp': {'log_level': 0, 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'ipyparallel': True, 'nbclassic': True, 'notebook_shim': True, 'panel.io.jupyter_server_extension': True}>}}
[D 2023-02-20 12:48:51.972 ServerApp] Raising open file limit: soft 1024->4096; hard 262144->262144
[D 2023-02-20 12:48:51.972 ServerApp] [nb_conda_kernels] refreshing conda info
[I 2023-02-20 12:48:54.607 ServerApp] [nb_conda_kernels] enabled, 8 kernels found
[I 2023-02-20 12:48:54.645 ServerApp] notebook_shim | extension was successfully loaded.
[I 2023-02-20 12:48:54.648 ServerApp] Loading IPython parallel extension
[I 2023-02-20 12:48:54.648 ServerApp] ipyparallel | extension was successfully loaded.
[I 2023-02-20 12:48:54.649 LabApp] JupyterLab extension loaded from /sw/external/python/anaconda3/lib/python3.9/site-packages/jupyterlab
[I 2023-02-20 12:48:54.649 LabApp] JupyterLab application directory is /sw/external/python/anaconda3/share/jupyter/lab
[I 2023-02-20 12:48:54.652 ServerApp] jupyterlab | extension was successfully loaded.
[I 2023-02-20 12:48:54.660 ServerApp] nbclassic | extension was successfully loaded.
[I 2023-02-20 12:48:54.660 ServerApp] panel.io.jupyter_server_extension | extension was successfully loaded.
[I 2023-02-20 12:48:54.661 ServerApp] The port 8888 is already in use, trying another port.
[I 2023-02-20 12:48:54.661 ServerApp] Serving notebooks from local directory: /u/arnoldg/.local/etc/jupyter/jupyter_notebook_config.d
[I 2023-02-20 12:48:54.661 ServerApp] Jupyter Server 1.23.4 is running at:
[I 2023-02-20 12:48:54.661 ServerApp] http://localhost:8889/lab?token=a728f76b935d157d2eecc6a32810cf4e88ae1bc53701f4f6
[I 2023-02-20 12:48:54.661 ServerApp] or http://127.0.0.1:8889/lab?token=a728f76b935d157d2eecc6a32810cf4e88ae1bc53701f4f6
[I 2023-02-20 12:48:54.661 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2023-02-20 12:48:54.880 ServerApp]
To access the server, open this file in a browser:
file:///u/arnoldg/.local/share/jupyter/runtime/jpserver-1287615-open.html
Or copy and paste one of these URLs:
http://localhost:8889/lab?token=a728f76b935d157d2eecc6a32810cf4e88ae1bc53701f4f6
or http://127.0.0.1:8889/lab?token=a728f76b935d157d2eecc6a32810cf4e88ae1bc53701f4f6
/usr/bin/xdg-open: line 862: x-www-browser: command not found
/usr/bin/xdg-open: line 862: firefox: command not found
/usr/bin/xdg-open: line 862: iceweasel: command not found
/usr/bin/xdg-open: line 862: seamonkey: command not found
/usr/bin/xdg-open: line 862: mozilla: command not found
/usr/bin/xdg-open: line 862: epiphany: command not found
/usr/bin/xdg-open: line 862: konqueror: command not found
/usr/bin/xdg-open: line 862: chromium: command not found
/usr/bin/xdg-open: line 862: chromium-browser: command not found
/usr/bin/xdg-open: line 862: google-chrome: command not found
/usr/bin/xdg-open: line 862: www-browser: command not found
/usr/bin/xdg-open: line 862: links2: command not found
/usr/bin/xdg-open: line 862: elinks: command not found
/usr/bin/xdg-open: line 862: links: command not found
/usr/bin/xdg-open: line 862: lynx: command not found
/usr/bin/xdg-open: line 862: w3m: command not found
xdg-open: no method available for opening 'file:///u/arnoldg/.local/share/jupyter/runtime/jpserver-1287615-open.html'
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