This article will guide you to run the Jupyter Notebook via Miniconda on the LANTA HPC system, which requires ssh tunneling to the LANTA HPC. An overview of the content can be found in the table of contents below for immediate visualization of the interesting parts.
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Creating an environment to run the Jupyter Notebook
Load Miniconda module
Use the
ml av Minicondacommand to see which version of Miniconda is available on the LANTA HPC system.Use the
ml Miniconda3/xx.xx.xcommand to load the Miniconda version that you want to use. If you don't specify a version, the default version (D) is loaded, which is Miniconda3/23.3.1-0.
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(myenv) username@lanta:~> conda install jupyter ... (myenv) username@lanta:~> conda install -c anaconda tensorflow-gpu ... |
Running Jupyter Notebook via ssh tunneling
Example of Slurm script for running Jupyter Notebook
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#!/bin/bash #SBATCH -p gpu # Specify partition [Compute/Memory/GPU] #SBATCH -N 1 -c 16 # Specify number of nodes and processors per task #SBATCH --gpus-per-task=1 # Specify the number of GPUs #SBATCH --ntasks-per-node=4 # Specify tasks per node #SBATCH -t 2:00:00 # Specify maximum time limit (hour: minute: second) #SBATCH -A ltxxxxxx # Specify project name #SBATCH -J JOBNAME # Specify job name module purge # Unload all modules module load Miniconda3/22.11.1-1 # Load the module that you want to use conda activate myenv # Activate your environment port=$(shuf -i 6000-9999 -n 1) USER=$(whoami) node=$(hostname -s) # jupyter notebookng instructions to the output file echo -e " Jupyter server is running on: $(hostname) Job starts at: $(date) Copy/Paste the following command into your local terminal -------------------------------------------------------------------- ssh -L $port:$node:$port $USER@lanta.nstda.or.th -i id_rsa -------------------------------------------------------------------- Open a browser on your local machine with the following address -------------------------------------------------------------------- http://localhost:${port}/?token=XXXXXXXX (see your token below) -------------------------------------------------------------------- " # start a cluster instance and launch jupyter server unset XDG_RUNTIME_DIR if [ "$SLURM_JOBTMP" != "" ]; then export XDG_RUNTIME_DIR=$SLURM_JOBTMP fi jupyter notebook --no-browser --port $port --notebook-dir=$(pwd) --ip=$node |
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http://127.0.0.1:8714/?token=2923d6fab4ef109f30e63a77014e632eed3fd2a5fa561929 |
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Shutting down the Jupyter Notebook
When you’re done with the Jupyter Notebook session, you can start the shutdown process by closing the browser and terminal on your local machine. Then, you must cancel your job in the Slurm system of the LANTA HPC with the scancel JOBID command.
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username@lanta:~> scancel xxxxx |
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