HPC Linux Tutorial
Emergency Linux Procedures
HELP! I'm stuck and can't get out!
How do I logout?
You can logout of Linux using one, or a combination, of these methods.
exitat the terminal prompt.
logoutat the terminal prompt. This sometimes doesn't work, and you must use
exitinstead because of ... reasons.
- Hold down the
CTRLkey and press
d. CTRL-d in the universal Unix/Linux end-of-input key sequence.
Oh no, VI
Somehow you managed to stumble into the vi text editor. VI comes with with every Linux distribution and is a good editor learn, but right now you just want to get out of it. Follow these steps.
- Press the
ESCkey. It doesn't hurt to press it 2 or 3 times.
- Press the
ENTERkey (depending on what it is called on your keyboard)
You should now be back at a terminal prompt. You're welcome.
But the Internet told me to do it
So you've been using the Internet to figure out how to get some piece of software working that you need for your research. It probably told you to run
sudo apt-get blahblahblah so you did that. Now the system is telling you that "This incident will be reported." Don't panic. Everything is okay.
Sudo stands for "super user do" and is a command to elevate your privileges to the mighty root user who has full access to the entire system. The root user is needed to install software and make system-wide changes. Unfortunately (or fortunately for the HPC administrator) you don't have access to do this, hence the incident message.
On a side note, even without using sudo, you won't be able to use the command apt-get since it is a tool for installing packages on Debian Linux variants like Ubuntu. The ELSA cluster uses CentOS Linux which does not use apt-get but instead uses yum which is another package manager. But don't worry, you don't have permissions to run either of these with or without sudo. If you need software installed system-wide, contact the HPC administrator for some helpful, friendly assistance.
Software Carpentry's Unix Shell Lesson
Software Carpentry focuses on teaching researchers the computing skills they need to get more done in less time and with less pain. Their lesson on the Unix Shell is listed below. Note that while they refer to it as Unix, the lesson also applies to its younger cousin Linux.
Ryan's Tutorials are also excellent. Two relevant tutorials are linked below.
On-line Manual Pages
Linux consists of thousands of commands. While the
command options arguments syntax is common among most of them, it can be daunting to remember the various options for each command. Options don't necessary have the same meaning between different commands. For example, the
-i option has a different meaning when used with
ls than with
grep. To eliminate the need to keep a thick Linux command "bible" next to you at all times (or more likely a browser window open to your favorite search engine), the system provides "manual pages" built into Linux that can be called up as needed. These are called man pages in Linux lingo. You use the
man command to display the manual pages for a command, e.g.
man cat will display the manual page for the cat command.
Let's review an example man page. The command
man followed by most Linux commands will display a helpful screen with its syntax, description of what the it does, all of the available options, and a few examples. For more help using man try running
$ man cat
CAT(1) User Commands CAT(1) NAME cat - concatenate files and print on the standard output SYNOPSIS cat [OPTION]... [FILE]... DESCRIPTION Concatenate FILE(s), or standard input, to standard output. -A, --show-all equivalent to -vET -b, --number-nonblank number nonempty output lines, overrides -n -e equivalent to -vE -E, --show-ends display $ at end of each line -n, --number number all output lines -s, --squeeze-blank suppress repeated empty output lines -t equivalent to -vT -T, --show-tabs display TAB characters as ^I -u (ignored) -v, --show-nonprinting use ^ and M- notation, except for LFD and TAB --help display this help and exit --version output version information and exit With no FILE, or when FILE is -, read standard input. EXAMPLES cat f - g Output f's contents, then standard input, then g's contents. cat Copy standard input to standard output. GNU coreutils online help: <http://www.gnu.org/software/coreutils/> Report cat translation bugs to <http://translationproject.org/team/> AUTHOR Written by Torbjorn Granlund and Richard M. Stallman. COPYRIGHT Copyright © 2013 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. SEE ALSO tac(1) The full documentation for cat is maintained as a Texinfo manual. If the info and cat programs are properly installed at your site, the command info coreutils 'cat invocation' should give you access to the complete manual. GNU coreutils 8.22 November 2015 CAT(1)
To search all man pages for a certain keyword, try using the -k option like the example below.
$ man -k concatenate
g3cat (1) - concatenate multiple g3 documents strcat (3) - concatenate two strings strncat (3) - concatenate two strings wcscat (3) - concatenate two wide-character strings wcsncat (3) - concatenate two wide-character strings cat (1) - concatenate files and print on the standard output cat (1p) - concatenate and print files nc (1) - Concatenate and redirect sockets ncat (1) - Concatenate and redirect sockets pmlogextract (1) - reduce, extract, concatenate and merge Performance Co-Pilot archives strcat (3p) - concatenate two strings strncat (3p) - concatenate a string with part of another tac (1) - concatenate and print files in reverse Tcl_Concat (3) - concatenate a collection of strings wcscat (3p) - concatenate two wide-character strings wcsncat (3p) - concatenate a wide-character string with part of another zcat (1p) - expand and concatenate data