HPC Linux Tutorial

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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.

  • Type exit at the terminal prompt.
  • Type logout at the terminal prompt. This sometimes doesn't work, and you must use exit instead because of ... reasons.
  • Hold down the CTRL key 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 ESC key. It doesn't hurt to press it 2 or 3 times.
  • Type :q!
  • Press the RETURN or ENTER key (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

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 man.

$ man cat

CAT(1)                                                            User Commands                                                           CAT(1)

       cat - concatenate files and print on the standard output

       cat [OPTION]... [FILE]...

       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

              output version information and exit

       With no FILE, or when FILE is -, read standard input.

       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/>

       Written by Torbjorn Granlund and Richard M. Stallman.

       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.


       The  full documentation for cat is maintained as a Texinfo manual.  If the info and cat programs are properly installed at your site, the

              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