Commit 5a263e90 authored by Christian Tischer's avatar Christian Tischer

Update README.md

parent 76618489
......@@ -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
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