gpu_server_setup/setup_apps_miniforge.sh

#!/bin/bash

#variant to use conda insted of pip, tested

#Src: https://medium.com/swlh/how-to-install-jupyterhub-using-conda-without-runing-as-root-and-make-it-a-service-59b843fead12
#     https://jupyterhub.readthedocs.io/en/1.2.1/installation-guide-hard.html

set -e

if [ "$EUID" -ne 0 ]
  then echo "Please run as root"
  exit
fi

CERTIFICATE_HOSTNAME=$1

if [ -z "$CERTIFICATE_HOSTNAME" ] 
then
	echo "Please specify hostname for the certificate generation"
  exit
fi


#apt-get install -y --no-install-recommends libnvinfer7=7.1.3-1+cuda11.0 \
#    libnvinfer-dev=7.1.3-1+cuda11.0 \
#    libnvinfer-plugin7=7.1.3-1+cuda11.0

#add public ssh keys
#if [ ! -s "~/.ssh/authorized_keys" ]; then
#  cat id_*.pub >> ~/.ssh/authorized_keys
#fi

#echo ""
#echo "Install supermicro system tools..."
#apt-get update
#apt-get install -y ipmitool && modprobe ipmi_devintf

apt-get update
apt-get install -y language-pack-de python3.10-venv

echo "Install a recent notejs for jupyterhub from nodesource..."
#src: https://github.com/nodesource/distributions/blob/master/README.md
curl -fsSL https://deb.nodesource.com/setup_current.x | bash -
apt-get install -y nodejs

echo "create virtualenv and install JupyterHub..."
python3 -m venv /opt/jupyterhub/
/opt/jupyterhub/bin/python3 -m pip install wheel
/opt/jupyterhub/bin/python3 -m pip install jupyterhub jupyterlab
/opt/jupyterhub/bin/python3 -m pip install ipywidgets jupyterlab-git jupyter-server-proxy
npm install -g configurable-http-proxy

echo "setup jupyterhub config..."
mkdir -p /opt/jupyterhub/etc/jupyterhub/
cp jupyterhub_config_https.py /opt/jupyterhub/etc/jupyterhub/jupyterhub_config.py

echo "setup systemd service..."
mkdir -p /opt/jupyterhub/etc/systemd
cp jupyterhub_conda.service /opt/jupyterhub/etc/systemd/jupyterhub.service
ln -s /opt/jupyterhub/etc/systemd/jupyterhub.service /etc/systemd/system/jupyterhub.service
systemctl daemon-reload
systemctl enable jupyterhub.service

echo "Generate self signed certificate..."
mkdir -p /opt/jupyterhub/etc/jupyterhub/ssl-certs
openssl req -x509 -newkey rsa:4096 -sha256 -days 3650 -nodes \
  -keyout /opt/jupyterhub/etc/jupyterhub/ssl-certs/jhubssl.key \
  -out /opt/jupyterhub/etc/jupyterhub/ssl-certs/jhubssl.crt \
  -subj "/C=DE/ST=NRW/L=na/O=na Systems/OU=Self_Signed/CN=$CERTIFICATE_HOSTNAME" \
  -addext "subjectAltName=DNS:$CERTIFICATE_HOSTNAME"

#echo "jupyterhub.service status: (opens vim)"
#systemctl status jupyterhub.service

echo "Install conda..."
CONDA_DIR=/opt/conda
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh -b -p $CONDA_DIR

#symlinking the conda shell setup script to the profile ‘drop in’ folder so that it gets run on login:
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh

mkdir -p /opt/conda/envs/

#remove existing environment and ipykernel:
#/opt/conda/envs/default_python/jupyter kernelspec remove python3
#/opt/conda/bin/conda env remove -p /opt/conda/envs/default_python

#setup default conda environment
/opt/conda/bin/conda env create --prefix /opt/conda/envs/default_python -f work-environment.yml

#setup kernel for using the enviroment in jupyter lab
/opt/conda/envs/default_python/bin/python -m ipykernel install --name 'python3' --display-name "Python (default)"


#users have to setup their kernel like this:
#create conder enviroment:
#conda create ipykernel --name mypersonal_enviroment
#python -m ipykernel install --user --name mypersonal_enviroment --display-name "Python My Env"

#echo "Install Tensorflow..."
#conda install --yes tensorflow-gpu -c conda-forge


#Other tools:

#System monitoring
#echo "Install netdata..."
#wget -O /tmp/netdata-kickstart.sh https://my-netdata.io/kickstart.sh && sh /tmp/netdata-kickstart.sh
#echo "nvidia_smi: yes" >> /usr/lib/netdata/conf.d/python.d.conf
#service netdata restart
#on http://0.0.0.0:19999

#echo "Install gpuview..."
#/opt/jupyterhub/bin/python3 -m pip install gpuview
#/opt/jupyterhub/bin/python3 -m gpuview service --host 127.0.0.1 --port 9988 <-- fails

#echo "Disable services that delays startup by wating for network connectivity..."
#systemctl disable cloud-config
#systemctl disable cloud-final.service
#systemctl disable iscsid.service
#systemctl disable open-iscsi.service

echo "Start JupyterHub..."
systemctl start jupyterhub.service

echo ""
echo "Setup successfully finished"