Update README.md

README.md

@@ -57,3 +57,25 @@ conda activate <ENV_NAME>
 ### Advanced: setting up a conda environment for multiple maintainers and users
 
 TODO
+
+
+### Launching an interactive jupyter notebook on a GPU cluster node
+
+1. Make sure you are in the EMBL intranet
+2. Login to the cluster with `ssh` from your terminal. 
+    - Mac and Linux: a terminal and ssh is included. 
+    - Windows: please install [git for windows](https://git-scm.com/download/win) which includes a ssh command client (choose *Run Git and included Unix tools form Windows Command Prompt* on installation).
+3. Open a terminal
+4. Log into the EMBL cluster: 
+    - `ssh EMBLUSERNAME@login.cluster.embl.de`
+    - when asked enter you EMBLK password.
+4. Ask for an interactive job on a GPU node: 
+    - `srun -t 60:00 -N1 -n4 --mem 32G -p gpu -C "gpu=2080Ti|gpu=1080Ti" --gres=gpu:1 -W 0 --pty -E $SHELL
+IP=$(ip a s $(ip r l | grep default | awk '{ print $5 }') | grep -Po 'inet \K[\d.]+')
+source /g/almf/software/miniconda3/run_conda.sh
+conda activate stardist-gpu
+cd /g/cba/exchange/stardist/examples/2D
+jupyter notebook --ip $IP 2_training.ipynb
+
+
+