This article will guide you to run Jupyter Notebook via Miniconda on a LANTA HPC system, which requires ssh tunneling to the LANTA HPC.
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Creating an environment to run the Jupyter Notebook
Load Miniconda module
Use the
ml av Miniconda
command to see which version of Miniconda is available on the LANTA HPC system.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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(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 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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http://127.0.0.1:8714/?token=2923d6fab4ef109f30e63a77014e632eed3fd2a5fa561929 |
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