Ubuntu SSH Machine Learning Server Setup

OS Installation

1. Download Ubuntu Server
2. Create a bootable USB using balenaEtcher
3. Go to your PC's BIOS and enable Booting from Storage Device (UEFI)
4. Insert USB, reboot and select USB as boot medium (or drag to top and reboot)
5. Follow the on-screen instructions to install Ubuntu Server, below are my preferences
   • Use whole SSD disk, no logical volumes (it is just a mess to manage, so painful when upgrading SSDs)
   • No pre-installed packages
   • Ethernet connection only
   • Install OpenSSH without importing identity

Note: it takes quite some time to reach the installation screen, be patient and don't panic if you see stuff like stdin: invalid argument

Admin User Setup

Install Essentials

sudo apt-get -y update && sudo apt-get -y upgrade
sudo apt-get install -y build-essential

Install NVIDIA Driver

sudo apt-get install -y nvidia-driver-495
sudo reboot

Install Docker

Add Docker repo:

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
echo \ "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu \ $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

Install Docker:

sudo apt-get update
sudo apt-get install -y docker-ce docker-ce-cli containerd.i

Install NVIDIA Container Toolkit

Setup stable repository and GPG key:

distribution=$(. /etc/os-release;echo $ID$VERSION_ID) \
   && curl -s -L https://nvidia.github.io/nvidia-docker/gpgkey | sudo apt-key add - \
   && curl -s -L https://nvidia.github.io/nvidia-docker/$distribution/nvidia-docker.list | sudo tee /etc/apt/sources.list.d/nvidia-docker.list

Install nvidia-docker2:

sudo apt-get update
sudo apt-get install -y nvidia-docker2

Restart Docker and test:

sudo systemctl restart docker
sudo docker run --rm --gpus all nvidia/cuda:11.0-base nvidia-smi

Formatting Data Drive(s)

For example, if your SSD is /dev/nvme0n1. ref

Start interation:

sudo fdisk /dev/nvme0n1

Dialogue:

Command (m for help): n
Select (default p): p
Partition number (1-4, default 1): 1
Command (m for help): w

Make filesystem:

sudo mkfs -t ext4 /dev/nvme0n1p1

Automount Data Drive(s)

Find data partition:

sudo fdisk -l

Find UUID of data partition:

sudo blkid

Create mount point:

sudo mkdir /data

Add fstab entry:

sudo nano /etc/fstab

Add the entry:

UUID=14D82C19D82BF81E /data    auto defaults 0 0

• UUID: safer to use UUID than e.g. /dev/sdb because UUID never changes
• /data: mount point
• auto: automatically determine filesystem
• defaults: default options
• 0: determines which filesystems need to be dumped (default is 0)
• 0: determine the order in which filesystem checks are done at boot time (default is 0)

Change permissions and mount all:

sudo chmod -R 777 /data
sudo mount -a

Prevent sleep

sudo systemctl mask sleep.target suspend.target hibernate.target hybrid-sleep.target
sudo reboot

Install ZSH and Starship

sudo apt-get install -y zsh
sh -c "$(curl -fsSL https://starship.rs/install.sh)"

New User Setup (by admin)

These steps assume that you have created a new user with a home directory. These steps should also be run for the admin user.

• Add SSH public key: <home_dir>/.ssh/authorized_keys
• Add user to docker group: sudo usermod -aG docker <user> (use newgrp docker to activate new group without logging out)
• Add user to data directory: sudo usermod -aG data <user>

New User Setup (by user)

These steps should also be run for the admin user.

Oh-my-zsh

Install Oh-my-zsh and plugins:

wget https://github.com/robbyrussell/oh-my-zsh/raw/master/tools/install.sh -O - | sh
git clone https://github.com/zsh-users/zsh-syntax-highlighting.git ${ZSH_CUSTOM:-~/.oh-my-zsh/custom}/plugins/zsh-syntax-highlighting
git clone https://github.com/zsh-users/zsh-autosuggestions ${ZSH_CUSTOM:-~/.oh-my-zsh/custom}/plugins/zsh-autosuggestions

Change default shell:

chsh -s $(which zsh)

Sample ~/.zshrc:

export ZSH="$HOME/.oh-my-zsh"
ZSH_THEME="robbyrussell"

export HISTSIZE=1000000
export SAVEHIST=1000000
setopt INC_APPEND_HISTORY
setopt HIST_IGNORE_DUPS
setopt EXTENDED_HISTORY

plugins=(
 zsh-syntax-highlighting
 zsh-autosuggestions
)  

source $ZSH/oh-my-zsh.sh

Starship

Add this to ~/.zshrc:

eval "$(starship init zsh)"

Sample ~/.config/starship.toml:

[username]
disabled = true

[hostname]
disabled = true

[conda]
format = "\\([[$style|$environment]]\\) "
ignore_base = false

[git_status]
conflicted = "⚔️ "
ahead = "🔺×$count "
behind = "🔻×$count "
diverged = "🔀 🔺×${ahead_count} 🔻×${behind_count} "
untracked = "🔓×$count "
stashed = "📥 "
modified = "📝×$count "
staged = "🔒×$count "
renamed = ""
deleted = "🔥×$count "
style = "bright-white"
format = "$all_status$ahead_behind"

Install Mambaforge

Installation:

wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh
bash Mambaforge-$(uname)-$(uname -m).sh

Setup (please re-open your shell):

mamba init --all
rm Mambaforge-$(uname)-$(uname -m).sh
conda config --set changeps1 False

Shell Alias

Add this to ~/.zshrc:

source $HOME/.local/.shellrc

Sample $HOME/.local/.shellrc:

extract() {
        for archive in $*; do
                if [ -f $archive ]; then
                        case $archive in
                        *.tar.bz2) tar xvjf $archive ;;
                        *.tar.gz) tar xvzf $archive ;;
                        *.tar.xz) tar xvf $archive ;;
                        *.bz2) bunzip2 $archive ;;
                        *.rar) rar x $archive ;;
                        *.gz) gunzip $archive ;;
                        *.tar) tar xvf $archive ;;
                        *.tbz2) tar xvjf $archive ;;
                        *.tgz) tar xvzf $archive ;;
                        *.zip) unzip $archive ;;
                        *.Z) uncompress $archive ;;
                        *.7z) 7z x $archive ;;
                        *) echo "don't know how to extract '$archive'..." ;;
                        esac
                else
                        echo "'$archive' is not a valid file!"
                fi
        done
}

# Git
alias ga="git add -A"
alias gc="git commit -m"
alias gac="git add -A && git commit -m"
alias grm="git rm -r --cached ."
alias gp="git push --tags"
alias gir="git rebase -i HEAD~15"

# List
alias l="ls -lAh"
alias cp="cp -r"
alias mk="mkdir -p"
alias rm="rm -rf --preserve-root"

# Apt-get
alias i="sudo apt-get install -y"
alias update="sudo apt-get update -y && sudo apt-get upgrade -y"

# Mamba
alias mi="mamba install -y -c conda-forge"
alias ma="mamba activate"
alias mc="mamba create python=3.9 jupyter notebook flake8 autopep8 pandas numpy scipy matplotlib seaborn -y -n"
alias mcf="mamba env create -f env.yaml"
alias mu="mamba env update -f env.yaml --prune"

# History
alias hg="history | rg"

# RC
alias zrc="code ~/.zshrc"
alias brc="code ~/.bashrc"
alias src="source ~/.zshrc"

# Utils
alias tv="tidy-viewer"
alias machine="macchina"
alias bw="bandwhich"