====== Linux Tutorial ======

This tutorial is intended to be a practical and brisk tutorial of many of the basics of using Linux for people who have never used it before. Setting up a website, compiling LaTeX, firing up MatLAB, and other typical tasks math grads would want from the department computers are covered quickly.

By using the related tools mentioned here, you can do things such as modify your webpage, retrieve/send files, turn LaTeX files into PDFs, and all other tasks you can do on the department computers from where ever you have internet access!

===== Connecting to a Linux computer =====

If you are using one of the Ubuntu computers in the computer lab or in your office, there is nothing special you have to do. Just open the "terminal" application and you are ready to start typing unix commands.

If you are on your own computer, you first need to connect to the math's computers.  Just as you need a web browser (like Firefox) to connect to a web server (like www.gmail.com), you need an SSH client to connect to an SSH server. To connect, you need your username, password, and a SSH client. 

Some good SSH clients include 

  * Windows: [[http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html|PuTTY]]
  * Mac: See the Mac program "Terminal". Then type "ssh username@math-server" and hit enter. 

For details on how to connect to a math server, see the computer FAQ [[https://www.math.ucdavis.edu/resources/comp/comp-faq/#use_osx_ssh|here]] and [[https://www.math.ucdavis.edu/resources/comp/comp-faq/#use_putty_ssh|here]] and [[https://www.math.ucdavis.edu/resources/comp/comp-faq/#dept_login_servers|here]].


===== The Basics =====

The first thing you should do is watch this [[https://youtu.be/Ms5sNYyejEw|youtube video]] that covers the core set of unix commands that a Linux user would use almost every day. Then search online/youtube for "basic unix commands" and work through the examples. An important set of basic unix commands you should look up include

  * ls (for listing a directory)
  * pwd (printing current path)
  * cd (for moving around in folders)
  * mkdir (making folders)
  * mv (moving things)
  * rm (removing things)
  * cp (copy things)
  * man (help)
  * chmod (file permissions)
  * tab completion


Once you successfully connect to a terminal, you are given a prompt where you can type commands. This section is devoted to introducing some everyday commands. In what follows, when in doubt, Linux is typically case-sensitive!


==== The folder system and your home directory ====
Like on your own computer, Linux has a folder (sometimes called a directory) structure.  Any folder can contain any number of files. A folder can also have any number of folders called subfolders (and these folders can in turn have the same kind of content). When you log in, you are brought to your what is called your "home directory".  Your home directory is a subfolder of some other folder (called its parent directory).

Some special directories have special symbols.  The current directory is given the symbol <code>.</code> the parent directory of the current directory is given the symbol <code>..</code> and your home directory is given the tilde symbol <code>~</code>


==== Navigating directories ====


To see what directory you're in at a given moment, you can type <code>pwd</code> and press Enter.  This tells you your "present working directory". You can see a listing of the contents in the present directory by typing the command <code>ls</code> and pressing Enter. 

To move to a different directory, use the command "cd" with an additional parameter. For example, to go to the parent directory of the current directory, type <code>cd ..</code> and press Enter. You can try this again and again to get all the way to the top-level directory, the unique directory with no parent.  All along the way, you can check where you are with the command pwd

To get back to your home directory, use <code>cd ~</code> or the shortcut <code>cd</code>

==== Creating, deleting, moving, and renaming directories ====

In your home directory, suppose you want to create a subdirectory (to store, for example, the scratch work of the rest of this tutorial).  If you wish to make a directory called learnlinux in the current directory, type <code>mkdir learnlinux</code>. Now you can use <code>cd learnlinux</code> to get into it and <code>cd ..</code> to get back.

To delete the directory learnlinux type <code>rmdir learnlinux</code> As a safety feature "rmdir learnlinux" only works if the folder you wish to delete has nothing in it. Now try creating two folders, one called test1 and one called test2. You can move test1 into test2 by typing <code>mv test1 test2</code>

 Now, test1 is a subfolder of test2. You can rename test2 to test3 by typing <code>mv test2 test3</code>

==== Creating, deleting, and renaming files ====


To create a blank file called myfile.txt in the current directory, type <code>touch myfile.txt</code>

To rename the text file, type <code>mv myfile.txt renamed-file.txt</code>  

To delete the file, type <code>rm renamed-file.txt</code>

==== File permissions ====

This is very important. You do not want other people to read, edit or delete your important files. You can recursively set permissions with chmod.


==== Editing text files directly ====

You have two basic ways of modify files. One option is to download them to your computer, edit them like normal, and then save them back to the math servers. Your other basic way to modify files is directly in the terminal using a text-based text editor.  This makes sense for quick and minor edits.  It also may help you keep your files in order, because you only have one version of a file floating around.

The three most-popular text editors on Linux are called "pico", "vi", and "emacs".  You just have to pick one and stick with it.  pico is by far the easiest of the three.  Later, you may want to try vi and/or emacs because they are much more powerful (though much more difficult to use). You may find that you like "gedit", the graphical text-editor. This is nice to use in the department, and there is a way to use it via SSH (see the section on X Windows), but it may run slowly over a slow Internet connection, and for this reason alone, it may be useful to learn how to open, edit, and save a file in pico.


Search online for great tutorials on pico, vi, emacs.

==== Using LaTeX ====

See the [[:latex|LaTeX Tutorial]]. 

Suppose you have a valid LaTeX file called mytheorem.tex in the present working directory.  To make a PDF, you can run <code>pdflatex mytheorem.tex</code>

If your LaTeX file is invalid, you will not reach the normal prompt and instead be given a question mark.  You can type a capital X or "ctrl+c" to quit. 

===== Advanced Commands =====

These commands are also useful

  * grep (search in files)
  * find (search for files)
  * unix pipe operator (you can do magic with this)
  * sed
  * awk (good for super crazy things)
  * screen or tmux (good for running long compute jobs
  * top or htop 
  * input and output redirection

Basically, there is a command for everything. If you want to do something, just search the internet for "how to X unix command".


===== Transferring files =====

It is so easy to just use a (S)FTP program like WinSCP or FileZilla. 

You could also use unix commands to transfer files...see sftp, put and get.