diff --git a/pages/merlin6/04-Jupyterhub/jupyterhub.md b/pages/merlin6/04-Jupyterhub/jupyterhub.md index 7109938..7f878df 100644 --- a/pages/merlin6/04-Jupyterhub/jupyterhub.md +++ b/pages/merlin6/04-Jupyterhub/jupyterhub.md @@ -28,7 +28,7 @@ The service is available inside of PSI (or through a VPN connection) at Slurm batch system. If the cluster is not currently overloaded and the resources you requested are available, your job will usually start within 30 seconds. - + @@ -63,21 +63,50 @@ conda info -e You can get more info on the use of the `conda` package management tool at its official [https://conda.io/projects/conda/en/latest/commands.html](documentation site). ## Using your own custom made environments with jupyterhub -Python environments can take up a lot of space due to the many dependencies that will be installed. You should always install your extra environments to the data area belonging to your account, e.g. `/data/user/${YOUR-USERNAME}/conda-envs` +Python environments can take up a lot of space due to the many dependencies that will be installed. You should always install your extra environments to the data area belonging to your account, e.g. `/data/user/${YOUR-USERNAME}/conda-envs` In order for jupyterhub (and jupyter in general) to recognize the provided environment as a valid kernel, make sure that you include the `nb_conda_kernels` package in your environment. This package provides the necessary activation and the dependencies. Example: ``` conda create -c conda-forge -p /data/user/${USER}/conda-envs/my-test-env python=3.7 nb_conda_kernels - ``` After this, your new kernel will be visible as `my-test-env` inside of your jupyterhub session. +## Requesting additional resources + +The **Spawner Options** page covers the most common options. These are used to +create a submission script for the jupyterhub job and submit it to the slurm +queue. Additional customization can be implemented using the *'Optional user +defined line to be added to the batch launcher script'* option. This line is +added to the submission script at the end of other `#SBATCH` lines. Parameters can +be passed to SLURM by starting the line with `#SBATCH`, like in [Running Slurm +Scripts](/merlin6/running-jobs.html). Some ideas: + +**Request additional memory** + +``` +#SBATCH --mem=100G +``` + +**Request multiple GPUs** (gpu partition only) + +``` +#SBATCH --gpus=2 +``` + +**Log additional information** + +``` +hostname; date; echo $USER +``` + +Output is found in `~/jupyterhub_batchspawner_.log`. ## Contact -In case of problems or requests, please either submit a **[PSI Service Now](https://psi.service-now.com/psisp)** incident containing *"Merlin Jupyterhub"* as part of the subject, or contact us by mail through . - - +In case of problems or requests, please either submit a **[PSI Service +Now](https://psi.service-now.com/psisp)** incident containing *"Merlin +Jupyterhub"* as part of the subject, or contact us by mail through +.