JupyterLab

To install and run JupyterLab Server, proceed as follows

log on to the eagle/altari cluster heandode

generate yourself an interactive session on nodes, with the necessary resources. e.g. like this :

trojan@eagle:~$ srun -N1 --ntasks-per-node=24 --mem=70gb --time=48:00:00                                                                                                              --pty /bin/bash
srun: job 25964247 queued and waiting for resources
srun: job 25964247 has been allocated resources
trojan@e1280:~$

in the directory grant_XXX/project_data/$USER download and install anaconda software

trojan@e1280:~$ wget wget https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh
--2022-12-22 14:32:17--  http://wget/
Resolving wget (wget)... failed: Name or service not known.
wget: unable to resolve host address ‘wget’
--2022-12-22 14:32:17--  https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh
Resolving repo.anaconda.com (repo.anaconda.com)... 104.16.130.3, 104.16.131.3, 2606:4700::6810:8303, ...
Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.130.3|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 773428196 (738M) [application/x-sh]
Saving to: ‘Anaconda3-2022.10-Linux-x86_64.sh’

Anaconda3-2022.10-Linux-x86_64.sh               100%[================================
====================================================================>] 737.60M   197MB/s    in 4.1s

2022-12-22 14:32:22 (181 MB/s) - ‘Anaconda3-2022.10-Linux-x86_64.sh’ saved [773428196/773428196]

FINISHED --2022-12-22 14:32:22--
Total wall clock time: 5.1s
Downloaded: 1 files, 738M in 4.1s (181 MB/s)
(base) trojan@e1280:~$./Anaconda3-2022.10-Linux-x86_64.sh 

declare the variable NUMEXPR_MAX_THREADS to be 24

(base) trojan@e1280:~$ export NUMEXPR_MAX_THREADS=24

after initialisation, start jupyter-lab (select port from the range 9000 - 50000 ):

(base) trojan@e1280:~$ jupyter-lab --no-browser --port=9999 --ip=0.0.0.0
[I 2022-12-22 13:21:11.929 ServerApp] jupyterlab | extension was successfully linked.
[I 2022-12-22 13:21:15.518 ServerApp] nbclassic | extension was successfully linked.
[I 2022-12-22 13:21:15.518 ServerApp] panel.io.jupyter_server_extension | extension was successfully linked.
[I 2022-12-22 13:21:15.710 ServerApp] nbclassic | extension was successfully loaded.
[I 2022-12-22 13:21:15.711 LabApp] JupyterLab extension loaded from /home/users/trojan/anaconda3/lib/python3.9/site-packages/jupyterlab
[I 2022-12-22 13:21:15.711 LabApp] JupyterLab application directory is /home/users/trojan/anaconda3/share/jupyter/lab
[I 2022-12-22 13:21:15.716 ServerApp] jupyterlab | extension was successfully loaded.
[I 2022-12-22 13:21:15.717 ServerApp] panel.io.jupyter_server_extension | extension was successfully loaded.
[I 2022-12-22 13:21:15.718 ServerApp] Serving notebooks from local directory: /home/users/trojan
[I 2022-12-22 13:21:15.718 ServerApp] Jupyter Server 1.18.1 is running at:
[I 2022-12-22 13:21:15.718 ServerApp] http://e1280:9999/lab?token=f3e54adf1c4880885b501a59f5cc374c42e429f70be77aa1
[I 2022-12-22 13:21:15.718 ServerApp]  or http://127.0.0.1:9999/lab?token=f3e54adf1c4880885b501a59f5cc374c42e429f70be77aa1
[I 2022-12-22 13:21:15.718 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2022-12-22 13:21:15.726 ServerApp]

    To access the server, open this file in a browser:
        file:///home/users/trojan/.local/share/jupyter/runtime/jpserver-6499-open.html
    Or copy and paste one of these URLs:
        http://e1280:9999/lab?token=f3e54adf1c4880885b501a59f5cc374c42e429f70be77aa1
     or http://127.0.0.1:9999/lab?token=f3e54adf1c4880885b501a59f5cc374c42e429f70be77aa1

then set up ssh tunneling using the command ( the node number in the command should match the one assigned earlier in the interactive session , in this case e1280). On Linux, start a new terminal and type the following command. On Windows, on the other hand, use a text-based SSH client such as PowerShell and execute the command:

ssh -L 9999:e1280:9999 trojan@eagle.man.poznan.pl

after the tunneling has been set up, we launch the browser and type in the address:

http://127.0.0.1:9999/

we will be asked to provide a key (token), then you should provide the key value that was automatically generated by the JupyterLab server in our case f3e54adf1c4880885b501a59f5cc374c42e429f70be77aa1

JupyterLab will then be launched