This website provides guidelines to use the cluster of the Centre de Recherche en Neurosciences de Lyon (CRNL).
It is managed and it has been configured by Thibaut Woog (thibaut.woog@inserm.fr).
If you encounter problems with the tutorials or methods described on this website or if you have solutions/tips/tricks to share, please tell us using the Giscus comment section below each page, or write to romain.ligneul@inserm.fr
Using Jupyter lab
Our new cluster has a built-in Jupyterhub system that will greatly facilitate the life of most users (and ITs!), as it helps managing the load on the “entry point” server (i.e. 10.69.168.93). Jupyterhub offers to everyone a very complete IDE for Python and Matlab programming, as well as a Desktop application (similar to former VNC connections).
The Jupyterhub environment is available at the following address (accessible within CRNL premises or with VPN): http://10.69.168.24:8000/
Yet, you will still need to learn how to create virtual environments (especially Python users) and how to submit jobs efficiently and ethically.
Obtain VPN access (optional)
If you want to access the cluster remotely, check this page.
Configure your Github (optional but recommended)
Learn how to connect your Github account to your terminal on the cluster here.
Learn to submit jobs (recommended)
The cluster uses SLURM to manage “jobs” (i.e. functions/scripts running in parallel). Check the two part tutorial for efficient and responsible job submission on the cluster using Slurm and Python (including interactive Notebooks).
Using VS code
Check the dedicated tutorial to use VS code within contained SLURM jobs, to avoid cluttering/saturating our login node (a common cause of institute-wise service disruption).
Note that the job submission tutorial is still applicable when using VS code.
Other resources
If you can access wiki.crnl.fr, then you may also check the following:
- https://wiki.crnl.fr/doku.php?id=en:wiki:informatique:services:computing_cluster_crnl
- https://wiki.crnl.fr/lib/exe/fetch.php?media=wiki:services_et_groupes:club_neuro_imageurs:commonusecrnl.pdf
How to contribute
To contribute to the development and conception of these guidelines, request access to the CRNL Github organization to Samuel Garcia.
Leave a message
Feel free to comment, make a question, report a bug, etc. If you want to notify a specific user (e.g. to get a faster response), you may include their Github handle in your message (e.g. @romainligneul or @samuelgarcia).