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This article will guide you to run Jupyter Notebook via Miniconda on a LANTA HPC system, which requires ssh tunneling to the LANTA HPC.

Table of Contents

Creating an environment to run the Jupyter Notebook

Load Miniconda module

  1. Use the ml av Miniconda command to see which version of Miniconda is available on the LANTA HPC system.

  2. Use the ml Miniconda3/xx.xx.x command 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 Miniconda3/22.11.1-1.

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Code Block
(myenv) username@lanta:~> conda install jupyter
...
(myenv) username@lanta:~> conda install -c anaconda tensorflow-gpu
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Running Jupyter Notebook via ssh tunneling

Example of Slurm script for running Jupyter Notebook

Code Block
#!/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 xxxxxx  projxxxx                     # 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 this in your local terminal to ssh tunnel with remote
    -----------------------------------------------------------------
    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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Code Block
http://127.0.0.1:8714/?token=2923d6fab4ef109f30e63a77014e632eed3fd2a5fa561929

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