Gentle Introduction to Linux

Reading:

• SWC: Novice Shell Workshop
• SWC: Bash Reference
• Bash Cheat Sheet
• The slides I presented with

Operating Systems

An operating system (OS) is one of the most basic bits of software that sits between you and the computer hardware. It "operates" the "system". Windows, or Mac OS X are both familiar examples of operating systems. An operating system allows you to do very fundamental things like:

• display things on your monitor
• react to typing and mouse movements
• read/write files from your harddrive
• connect to the internet

The Unix/Linux Operating Systems

Unix is an operating system developed in the 1970s. Linux is an open source clone of Unix. Linux is widely used in scientific computing because it is freely available, has a large community of users and developers, and many scientific computing tools are available for it.

Mac OS X is also started as a clone of Unix, and so shares many of the same features.

What is the SCC?

The Specialised Computing Cluster (SCC) is a research computer located at CAMH. Actually, it is several computers "clustered" together to make it easy to divide up computing work among them. This becomes important when you have lots of data, or many different tasks to perform, or both and a single computer does not have the power to do your work in a reasonable amount of time.

Linux (specifically a flavour of linux called CentOS) is the operating system for the SCC.

Every CAMH researcher can apply for access to the SCC. If you are interested, send an email to david.rotenberg@camh.ca.

The terminal / the shell / the command line

aka the scary black window.

In Windows and Mac OS X, you pretty much only use the operating system through the desktop, by pointing and clicking with your mouse, etc. For scientific computing, you will often want to also use a command-line interface -- that is, you will want a way of typing out the commands you want the computer to do, rather than gesturing with your mouse.

Why? Because:

• Many tools are only available as command line tools
• It is faster when you get used to it.
• It is more precise.
• You can automate what you you want to do. That is, you can record every step you take, and "play it back" on new datasets.
• The SCC and other compute clusters often only allow you command-line access (ie. no desktop).

The shell is just a program. It is an interactive command-line interface we will use to do work and run other programs, and it is what the next two workshops focus on. It is called the 'shell' because on the surface you use it by typing, but inside it speaks directly to the operating system. Not a very good name, I know. There are different kinds of shells; we will use bash.

The terminal is the program used to display the shell and allow you to interact with it. In Windows, you will need to install cygwin to get a terminal window for a bash shell, and in Mac OS, you can use the Terminal program.

SSH: the secure shell for remote access

SSH is a program that allows you to remotely connect to another computer and start a shell on it in order to do work. It is what you will have to use in order to access the SCC.

• On Windows, use mobaxterm for SSH
• On Mac, use Terminal

To connect to the SCC (if you are on the CAMH network):

ssh test_user@scc.pipitone.ca

Use the password: scc_user

The filesystem: how files and folders are organized on linux

• folders are organized in a heirarchy, a tree structure, with folders and files inside of folders.
• / is the top most folder. It is called the "root" folder.
• Each file and folder can be exactly named using its path, e.g.
  • /home, /home/jp, /home/jp/Documents/paper.doc

A brief tour of the shell

Basic commands:

• who, whoami
• pwd: print working directory
• ls: list files in a folder
• cd: change directory, e.g. cd /home
• mkdir: make a directory, e.g. mkdir newdir
• touch: make an empty file, e.g. touch file.txt
• cp: make a copy of a file, e.g. cp file.txt copy.txt
• mv: move a file to a new location, e.g. mv file.txt renamed.txt
• rm: remove a file, or folder, e.g. rm file.txt, rm -i file.txt, rm -rf newdir
• edit a file using: nano file.txt
• Command history - up key, history command
• getting help: man, help

Relative paths:

• ls ., ls .., ls /, ls ./
• ls /home/jp/../, ls /home/jp/../..
• mkdir ./newdir