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Jupyter

The ABiMS Cluster integrates a JupyterHub service that let you spawn Jupyter servers over the cluster.

This service is accessible from a simple web browser by connecting with your ABiMS Cluster account to https://ondemand.sb-roscoff.fr

You need to have at least one active project on the cluster to be able to spawn Jupyter servers

Add custom environment to the JupyterLab#

To add custom environment for JupyterLab you need first to open a ssh session to the cluster (see Logging in).

Add a user-defined Python environment#

Create a conda environment:

module load conda
conda create -n <your-env-name> python=3.7 ipykernel

Install any specific Python librairies in this environment...

Register this new environment for Jupyter :

~/.conda/envs/<your-env-name>/bin/python -m ipykernel install --user --name '<your-env-name>' --display-name "My Python"

Add a user-defined R environment#

Create a conda environment with R:

module load conda
conda create -n <your-env-name> r-base=3.6.3 r-irkernel jupyter_client

Install any specific R librairies in this environment...

Start R:

conda activate <your-env-name>
R

Register the R environment for Jupyter

IRkernel::installspec(name = '<your-env-name>', displayname = 'My R', user = TRUE)

Add any existing conda R environment#

For example R 4.0.2 already installed on the cluster.

Start R:

module load r/4.0.2
R

Register the R environment for Jupyter:

IRkernel::installspec(name = 'r-4.0.2', displayname = 'Cluster R 4',  user = TRUE)