Add instruction in README

README.md

@@ -1,5 +1,64 @@
+# Example notebook
+
+- Using small file: [visualize_demo_output.ipynb](./visualize_demo_output.ipynb)
+- Using big file on Odyssey: [visualize_large_output.ipynb](./visualize_large_output.ipynb)
+
+# Environment
 
 Install Miniconda, and then:
 
  conda env create -n ac290 -f ./environment.yaml
  conda activate ac290
+ which ipython jupyter
+
+# Note on using Jupyter on Odyssey
+
+## Jupyter on login node
+
+ ssh [email protected] -L 8889:localhost:8889
+ conda activate ac290
+ jupyter notebook --NotebookApp.token='' --no-browser --port=8889
+
+Visit `localhost:8889` in browser.
+
+## Jupyter on compute node (with sbatch)
+
+Make a script like:
+
+ #!/bin/bash
+ #SBATCH -p test
+ #SBATCH -N 1
+ #SBATCH -n 6
+ #SBATCH -t 1:00:00
+ #SBATCH --mem-per-cpu 3000
+ #SBATCH --job-name notebook
+ #SBATCH --output jupyter-address-%J.log
+
+ ## get tunneling info
+ jupyter_port=8889 # other number also works
+ jupyter_ip=$(hostname -i)
+
+ ## print tunneling instructions to jupyter-log-{jobid}.txt
+ echo -e "
+  Copy/Paste this in your local terminal to ssh tunnel with remote
+  -----------------------------------------------------------------
+  ssh [email protected] -N -L ${jupyter_port}:${jupyter_ip}:${jupyter_port}
+  -----------------------------------------------------------------
+
+  Then open a browser on your local machine to the following address
+  ------------------------------------------------------------------
+  localhost:${jupyter_port} (prefix w/ https:// if using password)
+  ------------------------------------------------------------------
+  "
+
+ ## launch jupyter
+ conda activate ac290
+ jupyter-notebook --NotebookApp.token='' --no-browser --port=${jupyter_port} --ip=$(jupyter_ip}
+
+Follow instruction in the generated log file.
+
+## Jupyter on compute node (with srun; doesn't work)
+
+Ref: https://informatics.fas.harvard.edu/port-forwarding-on-odyssey-nodes.html
+
+In principle it should work, but I keep getting `srun: Force Terminated job` after launching notebook.