SSH keys

Generate your SSH key pair

The SSH key pair contains two files:

Private key: id_rsa

Public key: id_rsa.pub

To generate the key pair, follow the steps:

1. Open Terminal on your PC and locate at your home folder by using cd ~

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    ssh-keygen -t rsa
   

2. Set the configurations

   Press key Enter or return (on Mac) to confirm generating the key pair in your current location.

   The ssh-keygen requires a password. You may use an empty password by directly entering key Enter or return but this is not recommended for security issues.

   Enter your password again to confirm your setting.

   Then, the configurations has been saved in ~/.ssh/id_rsa and the public key has been saved in ~/.ssh/id_rsa.pub.

3. Upload the public key

   Copy the content in ~/.ssh/id_rsa.pub on your PC, and paste it into ~/.ssh/authorized_keys on your HPC user homefolder.

   This process can be done by using two terminal windows. One is locating on your PC homefolder and you can copy the contents of your public key by using

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    pbcopy < ~/.ssh/id_rsa.pub
   

   Open another window to log in the HPC server and create the authorized_keys file by

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    touch ~/.ssh/authorized_keys
   

   Then edit it by vim

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    vim ~/.ssh/authorized_keys
   

   and paste the public key content into this file.

Additional Resources

1. For windows users, Bitvise SSH Client

2. Cheatsheet for vim

SSH Host Setting

SSH Config File

The SSH config file config is located in the .ssh configuration folder under your home directory: ~/.ssh/config.

Usually you need to created it by yourself as this is not coming as default.

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touch ~/.ssh/config

You can edit the SSH config file in your terminal by vim

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vim ~/.ssh/config

or you may use sublime, atom or any editor to change the configurations.

Configuration File Structure

Here is the general format:

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Host host_name_1
    HostName host.server.com
    User username
    Port 1234
    IdentityFile ~/.ssh/id_rsa


Host *
    # change the default_value

Transfering Files

In Terminal

Use scp to transfer your file.

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scp path/on/your/pc/file username@host.server.com:path/on/your/HPC/

Example on Habanero:

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scp MyDataFile <UNI>@habaxfer.rcs.columbia.edu:<DESTINATION_PATH>

Globus.org

Get unified access to your research data, across all systems, using any existing identity.

• It charges, but entering Globus through Xsede is free for use.

Globus is strongly recommended especially for the HPCs which need Token to verify your login.

Softwares

The recommended softwares are:

• FileZilla

• Cyberduck

• CloudMounter

• Mountain Duck

How to make terminal beautiful

Switch shell to zsh

Installation

1. Install zsh

   • Via source code

   • Recommended

     MacOS: use homebrew

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       brew install zsh
     

     Ubuntu / Debian Linux: use apt-get

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       sudo apt-get install zsh
     

2. Verify installation by running zsh --version.

3. Make ZSH your default shell chsh -s $(which zsh)

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    chsh -s /bin/zsh
   

4. The configuration file is: ~/.zshrc. After editing it, close the current terminal window and reopen it to activate the new configuration. Or run source ~/.zshrc to activate it immediately.

   For example, you can copy your alias setting at ~/.bashrc into ~/.zshrc.

   Some recommended alias that improves typing efficiency:

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    alias ll='ls -l'
    alias la='ls -a'
    alias haba='ssh <uni>@haba***.columbia.edu'
    alias sz='source ~/.zshrc'
   

   Some useful ones that work well on Habanero HPC:

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    alias mysq='squeue -u <uni>' # View your job lists
    alias work='cd path/to/my/project' # Quick jump to your folder
   

Documents

• User Guide

• Installling ZSH

Oh My ZSH!

Oh My ZSH is a delightful, open source, community-driven framework for managing your Zsh configuration. It comes bundled with thousands of helpful functions, helpers, plugins, themes.

Installation

Install Oh My ZSH through curl:

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sh -c "$(curl -fsSL https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh)"

or via wget

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sh -c "$(wget https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh -O -)"

Customization

The configurations are in the ~/.zshrc file. You can use vim to edit it inside your terminal.

Supported materials:

1. Theme

2. Plugins

   Highly recommended:

   • autojump: view its github repo

   • git

Zprezto

Prezto is the configuration framework for Zsh; it enriches the command line interface environment with sane defaults, aliases, functions, auto completion, and prompt themes.

Installation

1. In Zsh, clone the Zprezto repository:

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    git clone --recursive https://github.com/sorin-ionescu/prezto.git "${ZDOTDIR:-$HOME}/.zprezto"
   

2. Create a new Zsh configuration .zshrc by copying the following:

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    setopt EXTENDED_GLOB
    for rcfile in "${ZDOTDIR:-$HOME}"/.zprezto/runcoms/^README.md(.N); do
    ln -s "$rcfile" "${ZDOTDIR:-$HOME}/.${rcfile:t}"
    done
   

   If there already exists a Zsh configuration, backup it and replace it with a new one.

Customization

The configuration for Zprezto is in ~/.zpreztorc file.

• Themes

Why not use Tmux?

Installation

MacOS: use homebrew

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brew install tmux

Ubuntu / Debian Linux: use apt-get

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sudo apt-get install tmux

Start & Exit

To start, you can use the simple instruction tmux new in your terminal. There will be an information bar occuring in the bottom of the terminal window to confirm the using of tmux.

To get out, you can use exit to close the current pane.

Operate a Session

1. Create a named session

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    tmux new -s [session name]
   

2. List all the sessions in the current host

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    tmux ls
   

3. Retrieve the last session

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    tmux a
   

4. Retrieve a named session

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    tmux a -t foo [session name]
   

5. Delete a named session

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    tmux kill-session -t [session name]
   

6. Delete all the sessions

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    tmux kill-server
   

Detach

Shortcuts

All the command shortcuts in tmux require the prefix shortcut ctrl+b, which is ^b on Mac.

Commands for Panes

• % Horizontally split the pane into two

• " Vertically split the pane into two

• x Close current pane

• { Move forward current pane

• } Move backward current pane

• ; Select the last pane

• o Select next pane

• ↑, ↓, ←, → Jump to the pane in that direction

• space Change the layout of panes

• z Maximize current pane, use it again to recover

• q Show the index of all the panes, type the corresponding index to jump to the pane

Commands for Window

• c Create new window

• p Switch to the previous window

• n Switch to the next window

• w Select in the window list

• & Close current window

• , Rename the window

• 0 Switch to window No. 0. You may switch to any window using the number id.

• f Search for the window name

Commands for Session

• $ Rename current session

• s Select in session list

• d Detach the current session, exit the tmux and return to shell

Custom Themes

You can customize tmux through .tmux.conf file.

A recommended theme collecion: Jim Myhrberg’s tmux-themepack

Additional Resource

• CheatSheet by MohamedAlaa

• The Tao of tmux by Tony Narlock

• Oh My Tmux! by Gregory Pakosz

• 
  Notes: Density Functional Theory
• 
  Cancel your HPC Job Efficiently