Key Features

Unix Architecture page on Wikipedia

Files are stored on disk in a hierarchical file system, with a single top location throughout the system (root, or “/”), with both files and directories, subdirectories, sub-subdirectories, and so on below it.

With few exceptions, devices and some types of communications between processes are managed and visible as files or pseudo-files within the file system hierarchy. This is known as everything’s a file.

Doug McIlroy (inventor of Unix pipes)

This is the Unix philosophy: Write programs that do one thing and do it well. Write programs to work together. Write programs to handle text streams, because that is a universal interface

File system

Key differences from Windows

there are mount points instead of A:, C:, etc.,
directories and files are case sensitive, and
the separation character is / instead of \

What would appear as a separate media hierarchy in Windows (e.g., A:\MyDir\MyCode.c) simply appears under a separate directory (known as a mount point) in Unix (e.g., /media/disk/MyDir/MyCode.c).

Root (`/`)

/boot - boot loader files
/etc- configuration files
/dev - device files
/bin - user programs required for booting
/sbin - system programs required for booting
/lib{,32,64} - libraries required for booting
/usr - programs, libraries, and such not required for booting
/root - superuser directory
/home - users directories (shared by all nodes)
/tmp - temporary files
/var - variable data (spool files, log files, etc.)
/opt - add on package directory
/media - mount point for removable media
/proc - process information pseudo-file system
/sys - system information pseudo-file system

User (`/usr`)

The /usr directory is split off from the / directory mostly because disk space used to be precious.

/usr/bin - user programs not required for booting
/usr/sbin - system programs not required for booting
/usr/lib{,32,64} - libraries not required for booting
/usr/games - game programs
/usr/share - architecture independent data
/usr/man - on-line manuals
/usr/src - source code
/usr/include - header files

User Local (`/usr/local`)

The /usr/local directory is a place to locally install programs without messing up /usr.

/usr/bin - user programs not required for booting
/usr/sbin - system programs not required for booting
/usr/lib{,32,64} - libraries not required for booting
/usr/games - game programs
/usr/share - architecture independent data
/usr/man - on-line manuals
/usr/src - source code
/usr/include - header files

Alliance supercomputers

/project - group data files (shared by all nodes and all group members)
/scratch - user temporary data files (local to each cluster)

Devices

Some of the special /dev files are

/dev/null - discards all data written and provides no data
/dev/zero - provides a constant stream of NULL characters
/dev/random - provides a stream of random characters
/dev/urandom - provides a constant stream of pseudo-random characters

Commands

Programs are run by specifying the command followed by the arguments separated by spaces.

program [argument…]

By convention, arguments are switches followed by strings (e.g., regexps, paths, file names, etc.). Switches are usually single dashes followed by letter for each switch or a double dash followed by a descriptive string (e.g., rm -fr mydir or rm --force --recurse mydir). Most commands also understand

- - as a file name means read or write to the terminal
-- - the end of switches and the start of the strings (in case the string needs to start with - or --).

Help

Traditionally man pages (a single help page) have been the de facto documentation source, however, some software suites have been switching to info pages (a collection of hyperlinked pages). Help for the shell built in commands is available by the built in help.

man command - on-line reference manuals
apropos [-a] keyword … - search on-line reference manuals (same as man -k)
info item - info documents

Directories

The current directory is . and the parent directory is ...

pwd - current directory
cd directory - change directory
mkdir directory - make directory
rmdir directory - remove directory

Files

Files beginning with . are considered hidden and not normally shown.

ls [-a] [-l] destination - list files
cp [-a|-p] [-r] [-s] source … destination - copy files
ln [-s] target name - link to file
mv source … destination - move files
rm [-r] [-f] destination … - remove files

Permissions

Standard permissions are read, write, and execute for user, group, and other. They are frequently abbreviated as three octal numbers (0=000, 1=001, 2=010, 3=011, 4=100, 5=101, 6=110, 7=111) corresponding to user read, write, and execute; group read, write, and execute; other read, write, and execute.

For directories, read allows the contents to be listed, write allows files to be added or removed, and execute allows the directory to be traversed.

chmod [u|g|o|a]…[+|-|=][r|w|x|X]… [-R] destination … - change mode (user/group/other permissions)
chown [-R] user destination … - change owner
chgrp [-R] group destination … - change group
setfacl [-m|-x] [-R] [[u|g|o|m]...:user:[r|w|x|X]...] destination* … - set file access control list *(individual users)
getfacl destination … - get file access control list (individual users)

View Files

The space key will advance a page and the q key will quit in more and less. In addition, the arrow keys will move in the appropriate direction in less.

more file - view one page at a time
less file - view forward and backwards
cat [file …] - concatenate files in sequence
head [-n lines] [file …] - first part of files
tail [-n lines] [-f] [file …] - last part of files
paste [-d deliminator] [file …] - concatenate files in parallel
cut [-d deliminator] [-f range] [file …] - extract columns
sort [-g] [-f] [-u] [file …] - sort lines

Comparison

Digests are numbers computed from the content of files such that it is extremely difficult to come up with two different files with the same number.

diff [-w] [-i] [-u number|-y] file1 file2 - compare files line by line
sdiff [-W] file1 file2 - compare files side by side (similar to diff -y)
md5sum [file …] - compute MD5 digest
sha256sum [file …] - compute SHA256 digest

Searching

egrep [-i] [-v] regexp [file …] - find lines matching regexp in files (same as grep -E)
fgrep [-i] [-v] strings [file …] - find lines matching strings in files (same as grep -F)
find directory … predicates - find files satisfying predicates in directories

Process

Each process (a running programs) is identified by a unique number.

ps [-A|-U user] [-H] [-f] - process list
kill [-s signal] process … - signal process
nohup command - disconnect command
nice command - low priority command

Remote

ssh [user@]host [command] - login to remote system
scp [[user@]host:] source … [[user@]host:]destination - copy remote files
unix2dos file … - convert to DOS line breaks
dos2unix file … - convert to Unix line breaks

Other

sleep seconds - waits given number of seconds
echo [-n] [-e] strings - prints strings
test tests - perform various string (e.g., equality) of file (e.g., existence) tests

Editors

The two most popular Unix editors are vi and emacs. Both are extremely powerful and very complex. A simpler editor is nano.

vi [file …] - common Unix editor
emacs [-nw] [file …] - common Unix editor
nano [file …] - simple Unix editor

Vi

Vi distinguishes between command and insert mode. Command mode allows you to move around and enter commands. Insert mode allows you to edit text.

:h - help
:w[!] [file] - write file (excalmation forces it)
:e file - edit file
:q[!] - quit Vi (exclamation forces it)
:n[!] - next file (excalmation forces it)
[a|A] - append after cursor or at end of line
[i|I] - insert (capital for beginning of line)
[v|V] - select to cursor or to end of line
[c[w|c]|C] - change selection/word/line or to end of line
[d[w|d]|D] - delete selection/word/line or to end of line
[y[w|y]|Y] - copy selection/word/line or to end of line
[p|P] - paste before or after cursor/line
J - join lines
[u|U] - undo (capital for current line)
ESC - revert to command mode

Emacs

Emacs is a more traditional single mode editor. Partially typed entries can be completed by pressing TAB (twice to list).

CTRL+h - help (b list keys and k describes keys)
CTRL+g - abort current operation
CTRL+[1|2|3] - single window or split vertical/horizontal window
CTRL+x CTRL+s - save current buffer
CTRL+x CTRL+b - switch current buffer
CTRL+x CTRL+k - quit current buffer
CTRL+x CTRL+c - quit Emacs
CTRL+SPACE - mark start of region
CTRL+w - copy from start of region to cursor
CTRL+y - past copied region
CTRL+k - delete to end of line or line if start of line
CTRL+s - search for text
CTRL+_ - undo
ALT+x - enter command (TAB twice to list)

Command Line

The shell is a command line interpreter that lets users run programs. It proves ways to start programs and to manipulate/setup the context in which they run. The main parts of this are

arguments,
environment,
standard input (stdin),
standard output (stdout),
standard error (stderr), and
return value

A standard command looks like so

command [<stdinfile] [>[>]stdoutfile] [2>[>]stderrfile] [&]

Arguments

Options passed to the program to tweak it’s behaviour. Traditionally switches (e.g., -xzf or --extract --gzip --file) followed by strings (e.g., regexp, paths, file names, etc.). Partially typed file names and directories can be completed by pressing TAB (twice to list).

…{…}… (brace expansion) - if not quoted, expands once for each comma separated list or once for each number in .. separated range
~… (tilde expansion) - if not quoted, expands to home directory of user following the tilde or the current user if no user specified
${...} (parameter and variable expansion) - if not single quoted, expands to environment variable specified or the corresponding parameter if number specified ({ and } are not always required)
$(...) (command substitution) - if not single quoted, expands to output for command (`…` is an alternative syntax)
$((...)) (arithmetic substitution) - if not single quoted, expands to evaluated result of the expression
… (word splitting) - if not quoted, splits into separate arguments anywhere an IFS character (by default space, tab, and newline) occurs
…[*|?|[…]]… (path name expansion) - if not quoted, is considered a pattern and replaced with matching file names (* matches any string, ? matches any character, and […] matches all the enclosed characters)

Quoting

Special characters can be escaped with \ to remove their special meaning. Single and double quoting strings affect escaping as well as which expansions and substitutions are preformed.

'…' - no expansion or substitutions is preformed
"…" - only escaping, parameter and variable expansion, command substitutions, and arithmetic substitutions occur

Environment

A set of key value pairs (e.g., USER=root) that programs can look up and use. Each program gets a fresh copy (i.e., changing it will not change the original) of all environment variables marked for export.

key=value - make a local environment variable
export key[=value] - mark an environment variable for export
unset key - delete an environment variable

Two important environment variables are

PATH - list of : separated directories to look for programs in
LD_LIBRARY_PATH - list of : separated directories to look for libraries in (ahead of the system defaults specified in /etc/ld.so.conf)

Input and Output

Programs are run with a standard place to read input from, a standard place to write output to, and a standard place to write error messages to. By default these are all the terminal window in which the program is run. This can be changed via

< file - read standard input from file
[>|>>] file - write standard output to file (overwriting or appending)
[2>|2>>] file - write standard error to file (overwriting or appending)
[&>|&>>] file - write standard output and error to file (overwriting or appending)

Status

Programs return an integer exit status. The stats of the most recent executed foreground command is available as $?.

0 - program completed successfully
1…127 - program specific error code
128…255 - program terminated by signal 127+signal

Job Control

Programs run in the foreground by default. Background jobs will suspended if they require input. Existing jobs will be sent SIGHUP when the shell exits.

jobs - list jobs
fg id - switch job to foreground
bg id … - switch jobs to background
disown id … - release jobs from job control

Foreground jobs usually respond to the following key combinations

CTRL+Z - suspend program
CTRL+C - abort program
CTRL+D - end of input

Multiple Commands

Commands can be combined in several ways.

… ; … - run first command and then second (same as pressing ENTER)
… & … - run first command in background at the same time as second
… | … - run first command in background with its output going to the second as input
… && … - run first command and then second only if first returns success
… || … - run first command and then second only if first returns failure