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Running Jupyter Notebook (compute node)

Running Jupyter Notebook on the compute node using Slurm

The step to run Jupyter Notebook on the compute node of the Cluster using Slurm:

step1: SSH to cluster
ssh <<usrname>>@<hostname>>

step2: Create a Slurm sbatch file
vi jupyter_cn_run.sub
(ref. sample slurm batch file)

step3: Submit this sbatch to Slurm
sbatch jupyter_cn_run.sub

step4: Check that your job is running
squeue -u $USER

step5: Once it is running you can continue. Wait for a few minutes for Jupyter to start. Check the log output file to find out the IP we need to use to create an SSH tunnel
cat ~/jupyter.log

step6: Then on your laptop, open a new Terminal and create an SSH tunnel
ssh -L8888:<<IP>>:8888 <<username>>@<<hostname>>
Important: You must replace the IP address in the command below with your IP address from step5

step7: On your laptop open a browser window and you can then browse to the link from the log file of step5 to open the Jupyter Notebook
http://127.0.0.1:8888/<<token>>

Sample Slurm batch file (jupyter_cn_run.sub)

#!/bin/bash
#
#SBATCH --job-name=jupyter_run
#SBATCH --partition=short
#SBATCH --ntasks=1
#SBATCH --time=00:05:00
#SBATCH --mem=10GB
#SBATCH --output=jupyter.log
##SBATCH --error=jupyter.err
#
source /share/anaconda3/bin/activate
export XDG_RUNTIME_DIR=""
#
echo "node ip: " `hostname -i`
#
date
jupyter lab --no-browser --ip=0.0.0.0 --port=8888
date
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