UNIX

Most of our systems (and general HPC resources) run some UNIX derivative. Much of the software is command line based, so it's worthwhile to learn the basics.

There are tons of free resources on the web for getting started (Basic UNIX Commands). There should also be a "for dummies" book in the lab.

As you find resources that are helpful, please update this page.

Connecting (SSH)

Windows 8 and older: PuTTY SSH Client WinSCP file transfer tool

MacOS and Linux users can use OpennSSH on the command line (it generally comes with the OS). Windows 10 versions and newer will also have built in ssh capabilities.

Resources for setting up ssh keys

Visual guide to how ssh-keys and ssh-agent work: An Illustrated Guide to SSH Agent Forwarding

For setting up ssh-agent (so you don't have to type your password over and over): Understanding ssh-agent and ssh-add

Script for automatically starting ssh-agent on login of a machine (place in your .profile/.bash_profile): StackOverflow: Start ssh-agent on login

Visual guide to ssh tunnels (ie. port forwarding)

A good resource to understand port-forwarding, and more advanced uses of port-forwarding: A visual guide to SSH tunnels

Command Line Basics

Explain Shell: Copy/paste a CLI command, and it will tell you what all the flags mean

How to think when using grep, awk, and sed: Article going over the basic uses of grep, awk, and sed and how to think through their use cases.

Learning Awk by Example: Tutorials going over how to use awk, while actually using examples.

Advanced Bash-Scripting Guide

Graphical Sessions (VNC)

See VNC

File Permissions and ACL

See File Permissions Basics and ACL