Additionally, a principal goal of the course is to
develop/enhance your programming prowess and, at an operational
level, developing command-line proficiency requires the
acquisition of, and appreciation for, basic skills that
are essential for successful programming in virtually any
computer language. In this regard it is crucial to emphasize
the following, which is obvious to those of us who have lived
through the computer revolution, but may not be so to you:
Given this, two of the key issues that neophyte programmers must
grapple with are
I think it fair to say that many of the students who have
previously taken this course have not fully appreciated
the above points, at least in the early phases of the
course. Understandably, they have often been mystified
and/or confused and/or irritated by the command-line approach, not
only due its arcane nature, but because using the GUI is
more intuitive and is more natural. Understandably,
they thus tend to avoid the command-line so that at course-end,
for example, if I ask one of them to move a file from one place to
another from the command line they struggle, whereas it is
absolutely obvious to them how to do the job from the GUI.
So, in ending this preamble, I ask you to trust me that
learning to use the command-line is well worth your time.
When you type commands in Unix, you are actually interacting with
the OS through a special program called a shell, which
provides a more user-friendly command-line interface than that
defined by the basic Unix commands themselves. In this course, we
will focus on the use of bash
("bourne again shell") which over the years has become the most
commonly used shell in the Linux community. However, you should be
aware that there are other shells available for your use (in fact,
on many systems you can change your default shell using the chsh command. In particular, tcsh
is still in widespread use and if you are interested in learning a
bit about its features, you can start with a version
of
these notes that discusses it in some detail. However,
particularly if you are new to Linux I recommend that you stick
with bash for the duration of the course.
In the notes that follow, commands that you type to the shell, as well as the output from the commands and the shell prompt (usually denoted "% ") will appear in typewriter font and in a colored box. Here's an example
% pwdNote that the appearance of the prompt is the shell's way of telling you that is waiting for you to enter a command.
/home/choptuik
% date
Mon Sep 1 10:14:57 PDT 2014
%
One very useful feature of bash
is the ability to recall previously executed commands, and
to edit them via the "arrow" keys (as well as "Delete" and
"Backspace"). After you have typed a few commands, hit the "up
arrow" key a few times and note how you scroll back through the
commands you have previously issued. Use the "down arrow" the same
number of times to return to the basic prompt.
There is another handy feature of bash and other shells (which should be enabled by
default on your lab accounts),
which is generically known as completion.
The basic idea is that you can type the first few characters of a
command name (i.e. the first word typed after the prompt), or a
filename (i.e. essentially any word that follows a command name),
and then depress the TAB key. If there is a unique command
name (filename) that begins with the characters that you have
typed, the shell will automatically complete the command name
(filename). Especially for long command names this can save a
considerable amount of typing. If the initial few characters
that you have typed do not
uniquely identify a command or filename, then the shell will
either display all of the commands (filenames) that start with the
string of characters that you have typed, or, if there are a lot
of such commands (filenames), will prompt you to enter y
should you wish to see them all. In the former case (i.e.
when there aren't many matches) you can type additional characters
and use TAB at any point to attempt a completion.
You should also become familiar with
the use of the mouse (or equivalent mouse device) to select, cut
and paste text within a shell, as well as within many other Unix
applications. Historically, Unix systems have tended to use a three button mouse, and the
following instructions assume that you are using one: in the
current era, mice usually have only two buttons. In this case,
third-button-actions can often be emulated by depressing the two
buttons simultaneously. Additionally, for those mice that
have a roller, depressing the roller will act as a third-button
click. Here, then, are the basic text manipulation actions that
can be achieved using the mouse:
The Mageia
distribution that we are using allows you to select at login time
which desktop you wish to use, but the configuration of the lab
machines and the course note assume that you are using
KDE/Plasma. User
documentation for KDE is available HERE,
as well as via the desktop itself, once you login to one of
the lab machines. Unfortunately, the KDE documentation often
leaves something to be desired. However, in our
early lab sessions you will become familiar with key features of
KDE that will be needed for course work, and I am confident that
it will be a straightforward matter for you to become expert in
its use as the course progresses.
/home/choptuik/junkrefers to a file named junk that resides in a directory with absolute pathname
/home/choptuikthat itself lives in directory
/homethat is contained in the root directory
/In addition to specifying the absolute pathname, files may be uniquely specified using relative pathnames. The shell maintains a notion of your current location in the directory hierarchy, known, appropriately enough, as the working directory (hereafter abbreviated WD). The name of the working directory may be printed using the pwd command:
% pwdIf you refer to a filename such as
/home/choptuik
fooor a pathname such as
dir1/dir2/fooso that the reference does not begin with a /, the reference is identical to an absolute pathname constructed by prepending the WD, followed by a /, to the relative reference. Thus, assuming that my working directory is
/home/choptuikthe two previous relative pathnames are identical to the absolute pathnames
/home/choptuik/fooNote that although these files have the same filename foo, they have different absolute pathnames, and hence are distinct files.
/home/choptuik/dir1/dir2/foo
Home directories: Each user of a Unix system typically has a single directory called his/her home directory that serves as the base of his/her personal files. The command cd (change [working] directory) with no arguments will always take you to your home directory. On the lab machines you should see something like this
% cdWhen using bash, you may refer to your home directory using a tilde (~). Thus, assuming my home directory is
% pwd
/home/phys210t
/home/choptuikthen
% cd ~and
% cd ~/dir1/dir2are identical to
% cd /home/choptuikand
% cd /home/choptuik/dir1/dir2respectively. (Note that cd dirname causes the shell to change the working directory to dirname, assuming that dirname is a directory.) bash will also let you abbreviate other users' home directories by prepending a tilde to the user name. Thus, provided I have permission to change to phys210t's home directory,
% cd ~phys210twill take me there.
"Dot" and "Dot-Dot": Unix uses a single period (.) and two periods (..) to refer to the working directory and the parent of the working directory, respectively:
% cd ~phys210t/dir1Note that
% pwd
/home/phys210t/dir1
% cd ..
% pwd
/home/phys210t
% cd .
% pwd
/home/phys210t
% cd .does nothing---the working directory remains the same. However, the . notation is often used when copying or moving files into the working directory.
Filenames: There are relatively few restrictions on filenames in Unix. On most systems (including Linux systems), the length of a filename cannot exceed 255 characters. Any character except slash (/) (for obvious reasons) and "null" may be used. However, you should avoid using characters that are special to the shell (such as ( ) * ? $ !) as well as blanks (spaces). In fact, it is probably a good idea to stick to the set:
a-z A-Z 0-9 _ . -As with other operating systems, the period is often used to separate the "body" of a filename from an "extension" as in:
program.c (extension .c)Note that in contrast to some other operating systems, extensions are not required, and are not restricted to some fixed length (often 3 on other systems). In general, extensions are meaningful only to specific applications, or classes of applications, not to all applications. The underscore and minus sign are often used to create more "human readable" filenames such as:
paper.tex (extension .tex)
the.longextension (extension .longextension)
noextension (no extension)
this_is_a_long_file_nameYou can embed blanks in Unix filenames, but it is not recommended.
this-is-another-long-file-name
Unix generally makes it difficult for you to create a filename that starts with a minus. It is also non-trivial to get rid of such a file, so be careful. If you accidentally create a file with a name containing characters special to the shell (such as * or ?), the best thing to do is remove or rename (move) the file immediately by enclosing its name in single quotes to prevent shell evaluation:
% rm -i 'file_name_with_an_embedded_*_asterisk'Note that the single quotes in this example are forward-quotes (' '). Backward quotes (` `) have a completely different meaning to the shell.
% mv 'file_name_with_an_embedded_*_asterisk' sane_name
command_name [options] [arguments]where square brackets ('[...]') denote optional quantities. Options to Unix commands are frequently single alphanumeric characters preceded by a minus sign as in:
% ls -lOn Linux systems, many commands also accept options that are longer than a single character; by convention, these options are preceded by two minus signs as in:
% cp -R ...
% man -k ...
% ls --color=auto -CFArguments are typically names of files or directories or other text strings that do not start with - (or --). Individual arguments are separated by whitespace (one or more spaces or tabs):
% cp file1 file2There are two arguments in both of the above examples; note the use of single quotes to supply the grep command with an argument that contains a space. The command
% grep 'a string' file1
% grep a string file1which has three arguments has a completely different meaning.
Executables and Paths: In Unix, a command such as ls or cp is usually the name of a file that is known to the system to be executable (see the discussion of chmod below). To invoke the command, you must either type the absolute pathname of the executable file or ensure that the file can be found in one of the directories specified by your path. In bash, the current list of directories that constitute your path is maintained in the environment variable, PATH (note that case is significant for bash variables). To display the contents of this variable, type:
% echo $PATH(Observe that the $ mechanism is the standard way of evaluating local variables and environment (global) variables alike, and that the echo command simply "echoes" its arguments). On the lab machines the resulting output should look something like
.:/home/phys210t/bin:/home/phys210/bin:/usr/local/bin:/usr/bin:/usr/games: ...Note that the directories in the path are separated by a colon (:) and no whitespace and that the . in the output indicates that the working directory is in your path. The order in which path-components appear in the path (first . (dot), then /home/phys210t/bin, then /home/phys210/bin, etc.) is important. When you invoke a command without using an absolute pathname as in
% lsthe system looks in each directory in your path---and in the specified order---until it finds a file with the appropriate name. If no such file is found, an error message is printed:
% helpmeThe path variable is often set for you in a special system file each time a shell starts up, and it is conventional to modify the default setting by setting the PATH environment variable in your ~/.bashrc file. For an example, view the contents of the course default ~/.bashrc below.
-bash: helpme: command not found
Control Characters: The following control characters typically have the following special meanings or uses within bash. (If they don't, then your keyboard bindings are "non-standard" and you may wish to contact the system administrator about it.) You should familiarize yourself with the action and typical usage of each. I will use a caret (^) to denote the Control (Ctrl) key. Then
% ^Zfor example, means depress the z-key (upper or lower case) while simultaneously holding down the Control key.
% Mail -s "test message" choptuik@physics.ubc.caIf you try the above exercise, you will notice that the shell does not "echo" the ^D. This is typical of control characters---you must know when and where to type them and what sort of behaviour to expect. In this case, Mail prompts for an optional list of addresses to which the message is to be carbon-copied, but other commands, such as cat, will not echo anything. In almost all cases, however, you should be presented with a command prompt once you have typed ^D. Also, by default, bash exits when it encounters EOF, so if you type ^D at a shell prompt, you may find that you are logged out from the terminal session. If you don't like this behaviour (I don't), include the following line in your ~/.bashrc (it is included in the course default ~/.bashrc):
This is a one line message.
^D
Cc:
%
set -o ignoreeofNote that set is a bash builtin command (i.e. a sub-command of the bash interpreter) that controls many features of the operation of bash, and is discussed in slightly more detail in the shell options section below.
Example 1: Search for [TAB] characters in file foo using grep:
% grep '^V[TAB]' foo
Example 2: Removing "Carriage returns" (^M) using vi
:%s/^V^M//g
bash Startup Files: You can customize the
environment that results whenever a new bash starts by creating and/or modifying certain startup files that reside in
your home directory. Before proceeding, however, we
must note that bash makes
a distinction between login
shells and purely
interactive shells, and executes a different startup file
(assuming that it exists) in each case. You will start a bash login shell if, for
example, you connect to the main physics server, hyper, from a remote machine such as
your home computer. In this case you will have to go through
the login procedure of typing your user (account) name and your
password. On the other hand, shells that you start from the
Linux GUI on one of the workstations in the computer lab, for
example, will be purely interactive. In this instance the computer
already "knows" who you are and that you are logged in, and does
not ask you for your login name or password. Given this, the
two most important startup files (there are more, but we don't
have to discuss them here, and you can get the full details from
the bash man page) are as
follows:
if [ -f ~/.bashrc ]; thenNote that the first line of the above constitutes a test for the existence of the ~/.bashrc file, while the source ~/.bashrc command then executes the contents of the ~/.bashrc file, provided that it exists (i.e. the source command tells the shell to execute the commands in the file that is supplied as an argument to it). When sourcing or otherwise manipulating files in startup files, you should always perform this type of existence check. Otherwise an error message is apt to be generated, and this can sometimes cause problems with the overall startup process.
source ~/.bashrc
fi
% cp ~/.bashrc ~/.bashrc.O
% cp ~/.bashrc.O ~/.bashrc
% cd; ls -afor example, to print the names of all files in your home directory. Note that I have introduced another piece of shell syntax in the above example; the ability to type multiple commands separated by semicolons (;) on a single line. There is no guaranteed way to list only the hidden files in a directory, however
% ls -d .??*will usually come close. At this point it may not be clear to you why this works; if it isn't, you may want try to figure it out after you have gone through these notes and possibly looked at the man page for ls.
Shell Aliases: As you will discover, the syntax of many Unix commands is quite complicated and furthermore, the "bare-bones" version of some commands is less than ideal for interactive use, particularly by novices. bash provides a simple mechanism called aliasing that allows you to easily remedy these deficiencies in many cases. The basic syntax for aliasing is
% alias name=stringwhere name is the name (use the same considerations for choosing an alias name as for filenames; i.e. avoid special characters) of the alias and string is a text string that is substituted for name when name is used as if it were a command. The following examples should illustrate the basic idea, (see the bash documentation (man bash) for a few more details, should you wish):
% alias ls='ls -FC'provides an alias for the ls command that uses the -F and -C options (these options are described in the discussion of the ls command below). Note that the single quotes in the alias definition are essential if the definition contains special characters, including whitespace (recall that whitespace = spaces/blanks and or TAB characters); it is good defensive programming to always include them.
The following lines define aliases for rm, cp and mv (see below) that will not clobber (destroy/overwrite) files without first asking you for explicit confirmation. They are highly recommended for novices and experts alike.
% alias rm='rm -i'The following lines define aliases RM, CP, and MV that act like the "bare" Unix commands rm, cp and mv (i.e. that are not cautious). Use them when you are sure you are about to do the correct thing: the presumption here is that you have to think a little more to type the upper-case command.
% alias cp='cp -i'
% alias mv='mv -i'
% alias RM='/bin/rm'To see a list of all your current aliases, simply type
% alias CP='/bin/cp'
% alias MV='/bin/mv'
% aliasNote that all of the preceding aliases (and a few more) are defined in the file ~phys210/.aliases on the lab machines. If you adopt your .bashrc and .profile from ~phys210/.bashrc and ~phys210/.profile, respectively, as we will ask you to do in an early lab session, and also copy ~phys210/.aliases to your home directory, then the aliases will automatically be available for your use when bash starts up, since the lines
if [ -f ~/.aliases ]; thenappear in the template .bashrc. (Recall that source file tells the shell to execute the commands in the file file). Although the use of a separate ~/.alias file is not a "standardized" approach, I commend it to you as a means of keeping your ~/.bashrc relatively uncluttered if you define a lot of aliases. However, if you wish, you can simply add alias definitions to your ~/.bashrc, or define them interactively at the command line at any time.
source ~/.aliases
fi
% echo $SHELLOPTSwhere the output from the echo command is typical of what you can expect to see on your lab account.
braceexpand:emacs:hashall:histexpand:history:ignoreeof:interactive-comments:...
man
Use man (short for manual) to print
information about a specific Unix command, or to print a list of
commands that have something to do with a specified topic (-k
option, for keyword). Although these days it is often easy to get
info about a command via an online search (Google e.g.) it is
still worth becoming familiar with man. Although the level
of intelligibility for commands (especially for novices) varies
widely, most basic commands are thoroughly described in their man
pages, with usage examples in many cases. It helps to develop an
ability to scan quickly through text looking for specific
information you feel will be of use. Examples of man
invocations include:
% man manto get detailed information on the man command itself,
% man cpfor information on cp and
% man -k compilerto get a list of commands having something to do with the topic 'compiler'. The command apropos, found on most Unix systems, is essentially an alias for man -k.
Output from man will typically look like
% man manfor a specific command and,
man(1) General Commands Manual man(1)
NAME
man - format and display the on-line manual pages
SYNOPSIS
man [-acdfFhkKtwW] [--path] [-m system] [-p string] [-C config_file]
[-M pathlist] [-P pager] [-B browser] [-H htmlpager] [-S section_list]
[section] name ...
DESCRIPTION
man formats and displays the on-line manual pages. If you specify sec-
tion, man only looks in that section of the manual. name is normally
the name of the manual page, which is typically the name of a command,
function, or file. However, if name contains a slash (/) then man
interprets it as a file specification, so that you can do man ./foo.5
or even man /cd/foo/bar.1.gz.
See below for a description of where man looks for the manual page
files.
MANUAL SECTIONS
The standard sections of the manual include:
1 User Commands
.
.
.
% man -k languagefor a keyword-based search. Note that the output from man -k ... is a list of commands and brief synopses. You can then get detailed information about any specific command (say python in the current example), with another man command:
ALTER_LANGUAGE (7) - change the definition of a procedural language
CREATE_LANGUAGE (7) - define a new procedural language
DROP_LANGUAGE (7) - remove a procedural language
.
.
.
.
octave (1) - A high-level interactive language for numerical computations
perl (1) - The Perl 5 language interpreter
perlfaq7 (1) - General Perl Language Issues
perlxs (1) - XS language reference manual
pt::json_language [pt_json_language] (n) - The JSON Grammar Exchange Format
pt::peg_language [pt_peg_language] (n) - PEG Language Tutorial
python [python2] (1) - an interpreted, interactive, object-oriented programming ...
python [python3] (1) - an interpreted, interactive, object-oriented programming ...
ruby (1) - Interpreted object-oriented scripting language
% man pythonAlso note that the output from man is fed (piped) into the more command, so refer to the description of more below (or the man page for more!) for some details that will allow you to page forward and backward, and search for text, in a particular man page.
ssh
Use ssh to establish a secure (i.e. encrypted)
connection from one Unix machine to another. This is the basic
mechanism that can be used to (1) start a Unix shell on a remote
host and (2) execute one or more Unix commands on such a machine.
During this course, you will probably find this command most
useful if you are using a ssh client such as putty
on one of your personal machines to login to the main physics
server, hyper.phas.ubc.ca. However, ssh is
extensively used in the "real world" for logging in from one
machine to another, where each machine is typically running some
flavour of Unix.
Typical usage of ssh is
bh0% ssh hyper.phas.ubc.ca -l choptuikwhich will initiate a remote-login for user choptuik on the machine hyper.phas.ubc.ca. When I enter this command, I will be prompted for my password (for the account choptuik) on hyper.
choptuik@hyper.phas.ubc.ca's password:The following commands are equivalent to the above invocation:
% ssh choptuik@hyper.phas.ubc.ca
% slogin hyper.phas.ubc.ca -l choptuik
% slogin choptuik@hyper.phas.ubc.ca
The first of the above alternate forms is generally the most
convenient to type, and is the one that I use.
If a final non-option argument is supplied to ssh, it is interpreted as a command to be executed remotely. In this case, control immediately returns to the invoking shell after completion (successful, or otherwise) of the command(s), as seen in the following examples, where the password prompts have been suppressed:
hyper% ssh matt@bh0.phas.ubc.ca dateIf you wish to execute more than one command on the remote host, separate them with
Mon Sep 1 10:39:21 PDT 2014
hyper% ssh matt@bh0.phas.ubc.ca 'pwd; date' /home/matt Mon Sep 1 10:40:03 PDT 2014 hyper%Important: Note that you cannot ssh into any of the lab machines per se, but this is irrelevant since your home directory on hyper is the same as it is on the lab machines (so that all of your directories/files are accessible on hyper), and all of the software used in the course (xmaple and matlab in particular) is available on hyper.
lab-machine% ssh -X matt@bh0.phas.ubc.caand, assuming that I was logged into one of the lab machines, the kate window running on bh0 would be displayed on my workstation desktop. If I had not enabled X11 forwarding in the ssh command, then when I tried starting kate, I would get an error message such as the following:
bh0% kate
bh0% kateNote that X is the venerable windowing software---developed at MIT---on which almost all Unix desktop environments are ultimately based. X11 is the current version of the software, and has actually been current since 1987! See the Wikipedia entry for X11 additional information should you be interested.
kate: cannot connect to X server
Gory Details of ssh: In contrast to many of the other commands described here, the behaviour of ssh depends crucially on the current context for the command, which, by convention, ssh stores as a number of files in the directory ~/.ssh (i.e. as a number of files in a directory named .ssh, located in your home directory). If ~/.ssh does not exist (which nominally means that you have yet to issue the ssh command from that specific account), it will automatically be created, and certain files within ~/.ssh will be created and/or modified.
For example, assume that as choptuik@hyper.phas.ubc.ca, I have never used the ssh command. However, I can and do login into hyper.phas.ubc.ca (as choptuik) using one of the workstations in the computer lab, and start up a command shell. I can now establish a secure connection to my account on bh0.phas.ubc.ca via ssh as follows:
hyper% ssh matt@bh0.phas.ubc.caThis message from ssh is a warning that essentially tells me that I have not connected before to the host bh0.phas.ubc.ca. It gives me a chance to check the ssh invocation to ensure that I've typed everything correctly, to safeguard against security issues that we won't delve into here. Because I'm sure that I want to connect, I enter yes. The output from the ssh command then continues:
The authenticity of host 'bh0.phas.ubc.ca (142.103.234.164)' can't be established.
RSA key fingerprint is ff:12:42:f2:37:2d:5c:d6:d2:be:59:f8:34:b3:1b:c8.
Are you sure you want to continue connecting (yes/no)?
Warning: Permanently added 'bh0.phas.ubc.ca,142.103.234.164' (RSA) to the list ...After correctly typing my password for matt@bh0, I am left in a shell running on bh0, and I can now "work" (i.e. issue Unix commands) within that shell.
matt@bh0.phas.ubc.ca's password:
When I'm done my work on bh0, I can use the logout (or exit) command
bh0% logoutto return to hyper.
Connection to bh0.phas.ubc.ca closed.
hyper%
Assuming I've done the above, I now see that the directory ~/.ssh has been created, and contains the file known_hosts:
hyper% cd ~/.sshThe purpose of the known_hosts file is to maintain identification information for hosts to which I've previously ssh'ed. In particular, the next time I ssh from hyper to bh0, the message 'The authenticity of host ...' will not appear, and ssh will "automatically" connect to bh0.
hyper% ls
known_hosts
hyper% ssh matt@bh0.phas.ubc.caRefer to the man page on ssh for full details on this command.
matt@bh0.phas.ubc.ca's password:
Mail
All of you are undoubtedly already
expert in the sending and receiving of e-mail, using one or more
of your favourite mail clients, and I will use the
"Connect/Blackboard" system to communicate electronically with
the class as a whole. Note that this mechanism does not allow me to directly
see your individual e-mail addresses, so if you want to get
personalized e-mail from myself or the TAs, you will need to
first send us a message to which we can reply.
In this course, you will
not be required to use a mail client on your physics account.
However, in the spirit of mastering command-line Unix, we
consider a brief illustration of the use of a very old, and,
especially for your generation, a very primitive mail client known
as Mail (we've already
encountered this program in our discussion of control characters):
Again, here's a basic example showing how to use Mail to send a message:
% Mail -s "this is the subject" choptuik@phas.ubc.caNote that multiple recipients can be specified on the command line. Another form involves redirection from a file.
This is a one line test message.
^D
Cc:
%
% Mail -s "sending a file as a message" matt@laplace.phas.ubc.ca < messagesends the contents of file message with the subject field of the e-mail set to 'sending a file as a message'.
If you are interested, you can consult the man page for Mail for additional information on its use. Most importantly, you should note that although it may seem like obsolete technology, the type of usage illustrated above can be quite useful. For example, you might write a script that takes a long time to accomplish some task. It can then be convenient to have the script send you a message when it has completed. This is cumbersome, if not impossible, to accomplish using GUI-based mail clients, but is essentially trivial with Mail.
exit
Type exit to leave both login and purely interactive
shells.
If there are suspended jobs (see job control below), you will get a warning message, and you will not be logged out.
% exitIf you then type exit a second time (with no intervening command), the system assumes you have decided you don't care about the suspended jobs, and will log you out. Alternatively, you can deal with the suspended jobs, and then exit.
There are stopped jobs
logout
logout has the same effect as exit, but can only be used in
login shells. If you enter logout
in a purely interactive shell, you will receive the message
% logoutChanging your passwd
bash: logout: not login shell: use `exit'
bh0% ssh phys210e@hyper.physics.ubc.caImportant note: Again, do not use passwd directly on the lab machines (i.e. without having ssh-ed into hyper). The passwd command will appear to work on those computers, but in fact it does not.
phys210e@hyper.physics.ubc.ca's password:
Last login: Mon Sep 1 10:24:02 2014 from bh0.phas.ubc.ca
I'm now logged into hyper
% passwd
Old password:
Password:
Checking, please wait ...
Reenter Password:
Password okay. Changing password ...
Please wait.....done.
%
Creating, Manipulating and Viewing Files
(including Directories):
Text editors: kate, gedit, vi (vim / gvim) or emacs (xemacs)
Although you may find it somewhat painful (especially if you've
developed a serious relationship with Microsoft Word), I consider
it an absolutely key goal for everyone in this course to become
reasonably proficient in at least one of the text editors: kate, gedit, vi, gvim or emacs (or some other text
editor installed on the lab machines that is instructor-approved).
Note that a text editor, although similar in spirit to a word
processor, really has a different fundamental purpose. As the name
suggests, this is to create and manipulate files that contain plain text (i.e. files for
which many of the features of modern word processors, such as the
ability to create documents that use different fonts, font-sizes,
styles, colours ... and/or that include tables, figures etc. etc.
are completely irrelevant). Plain text files are central to
the use of most programming languages and programming environments
in Unix, as well as to the configuration and customization of the
operating system itself. During the course, many of the homework
assignments, as well as your term projects, will require the
creation of this type of file.
Unless you are already familiar with another Linux text editor
which is installed on the lab machines, I recommend you use kate, which is the default
editor for the KDE desktop (gedit, which is the
default for GNOME, is very similar, and you are free to
use it should you wish).
kate provides an intuitive user interface (i.e. a GUI) which, although perhaps not as visually striking, or feature-rich, closely resembles that of word processors with which you will no doubt be familiar. I expect that most of you will be able to readily master kate, with little if any help, If you do need assistance, the application provides an extensive help facility that is available from the main menu bar. Note that kate implements the mouse-text-manipulation features discussed in the introductory section: various pieces of text can be selected using the sweeping, double and triple clicking actions described above, and then can be pasted by positioning the cursor and depressing the middle mouse button. Also observe that kate may not be available on some non-Linux Unix systems that you may need to work on, but given the introductory nature of this course, I don't consider that sufficient reason to dissuade you from its use.
For those interested in becoming Unix/Linux gurus
vi and emacs are the two major
"traditional" text-editors that are found on most Unix
implementations (certainly vi
should be!) Both are themselves text-based; that is, they do not
provide a GUI, and for the most part, do not allow for
manipulation of the text being edited with the mouse.
Moreover, vi developed a
reputation for being suitable mainly for "hardcore" users, who
didn't mind dealing with its rather unique, simplistic, and not
entirely intuitive (to put it mildly!) user interface. emacs, on the other hand, was
viewed as a much more elegant, powerful and full-featured editor,
to the point that with a suitable configuration, you could get emacs to do just about
everything but make coffee. Personally, I use vi, since that's the editor I
first encountered on Unix, and although it is a good idea for any Unix user to know a bit
about vi (if only
because some of its syntax appears in many other standard Unix
commands), I would strongly recommend that any of you who know
neither vi or emacs, and who wish to learn
one of them, seriously consider learning emacs, at least to
start. In addition, if you intend to become a serious Unix user, then you
really should learn how
to use one of these text-based editors, since you will almost
certainly encounter situations where you need to edit files using
a basic terminal session that will not support the use of a GUI.
Over the years, vi on
Linux systems has evolved to become vim (for Vi IMproved), so that, for example, if
you execute vi on the
lab machines, it is
actually vim that starts
up. This is a minor point, but something to keep in mind
should you be looking online for information concerning vi (i.e. you should probably
search for information on vim).
The good news is that there is now a GUI-based version of vi
/ vim called, gvim,
and the version of emacs
installed on the lab machines uses a GUI by default. You are more
than welcome to use these rather than their text-based antecedents
for course work. Again note, however, that these GUIs are not as
user friendly as the word processing software that you are
probably accustomed to (or kate
for that matter) but they will, for example, allow you to use the
mouse to position the cursor as well as to highlight text and cut. Again, it is up
to you which text editor you choose to use, but we really want you to learn to
use at least one that isn't a Microsoft or Mac/Apple product!
Use more to view the contents of one or more files,
one page at a time. For example:
% more /usr/share/dict/wordsIn this case I have executed the more command in a shell window containing only a few lines (i.e. my pages are short). The
1080
10-point
10th
11-point
12-point
16-point
18-point
1st
2
20-point
2,4,5-t
2,4-d
2D
2nd
30-30
3-D
3-d
3D
3M
3rd
--More--(0%)
--More--(0%)message is actually a prompt: hit the space bar to see the next page, type b to backup a page, and type q to quit viewing the file. You can also search for a string in the output by typing a '/' (forward slash) followed by the text to be located:
/misspellRefer to the man page for additional features of the command. We have already noted that output from man is typically piped through more.
...skipping
misspeed
mis-spell
misspell
misspelled
misspelling
misspellings
misspells
misspelt
mis-spend
misspend
misspender
misspending
misspends
misspent
misspoke
misspoken
mis-start
misstart
misstarted
--More--(49%)
lpr
Although many of the applications that
you will be using in the computer lab will have their own
printing facilities which will be of the type that is likely
familiar to you, is also possible to print files from the
command line with the lpr command. If no options are
passed to lpr, files are sent to the system-default
printer, or to the printer specified by your PRINTER environment variable, if it is set.
Typical usage is
% lpr file_to_be_printedThe default printer on the lab machines is the Xerox ColorQube 8870 in Hennings 203 and, by default, printing will be two-sided (duplex). Should you need to make one-sided hard copy, print the file using the -o sides=one-sided option:
% lpr -o sides=one-sided file_to_be_printed
cd and pwd
Use cd and pwd to change (set) and print,
respectively, your working directory. We have already seen
examples of these commands above. Here's a summary of typical
usages (again note the use of semi-colons to separate distinct
Unix commands issued on the same line):
% cdRecall that .. refers to the parent directory of the working directory so that
% pwd
/home/choptuik
% cd ~; pwd
/home/choptuik
% cd /tmp; pwd
/tmp
% cd ~phys210; pwd
/home/phys210
% cd ..; pwd
/home
% cd phys210; pwd
/home/phys210
% cd ..takes you up one level (closer to the root) in the file system hierarchy.
ls
Use ls to list the contents of one or more
directories. On Linux systems, I advocate the use of the alias
% alias ls='ls --color=auto -FC'which will cause ls to
% cd ~phys210tNote that the file cmd is marked executable while dir1 and dir2 are directories. To see hidden files and directories, use the -a option:
% ls
cmd* dir1/ dir2/
%
% cd ~phys210tand to view the files in "long" format, use -l:
% ls -a
./ .Xauthority .bash_history .gnupg/ cmd* dir2/
../ .aliases .bashrc .profile dir1/
% cd ~phys210tThe output in this case is worthy of a bit of explanation. First observe that ls produces one line of output per file/directory listed. The first field in each listing line consists of 10 characters that are further subdivided as follows:
% ls -l
-rwxr-xr-x 1 phys210t public 39 Aug 23 2012 cmd*
drwxr-xr-x 4 phys210t public 4096 Aug 23 2012 dir1/
drwxr-xr-x 2 phys210t public 4096 Aug 23 2012 dir2/
If any of the arguments to ls is a directory, then the contents of that directory are listed. Finally, note that the -R option will recursively list sub-directories:
% cd ~phys210t; pwdNote how each sub-listing begins with the relative pathname to the directory followed by a colon. For kicks, you might want to try
/home/phys210t
% ls -R
.:
cmd* dir1/ dir2/
./dir1:
file_1 subdir1/ subdir2/
./dir1/subdir1:
file_s
./dir1/subdir2:
file_3
./dir2:
file_4
% cd /which will list essentially all the files on the system which you can read (have read permission for). Type ^C when you get bored.
% ls -R
mkdir
Use mkdir to make (create) one or more directories.
Sample usage:
% cd ~If you need to make a 'deep' directory (i.e. a directory for which one or more parents do not exist) use the -p option to automatically create parents as needed:
% mkdir tempdir
% cd tempdir; pwd
/home/choptuik/tempdir
% cd ~In this case, the mkdir command made the directories
% mkdir -p a/long/way/down
% cd a/long/way/down; pwd
/home/choptuik/a/long/way/down
/home/choptuik/a /home/choptuik/a/long /home/choptuik/a/long/wayand, finally
/home/choptuik/a/long/way/down
cp
Use cp to (1) make a copy of a file, (2) copy one or
more files to a directory, or (3) duplicate an entire directory
structure. The simplest usage is the first, as in:
% cp foo barwhich copies the contents of file foo to file bar in the working directory. Assuming that cp is aliased to cp -i, as recommended, you will be prompted to confirm overwrite if bar already exists in the current directory; otherwise a new file named bar is created. Typical of the second usage is
% cp foo bar /tmpwhich will create (or overwrite) files
/tmp/foo /tmp/barwith contents identical to foo and bar respectively. Note that /tmp is a special directory on Unix system for which all users have write access, and can thus be used as a convenient "temporary" location to create/store files/directories, which will not clutter up your home directory.
% cd ~phys210t; ls -aStudy the above example carefully to make sure you understand what happened when the command
./ .aliases .bashrc dir1/ .profile .Xauthority
../ .bash_history cmd* dir2/ .viminfo
% mkdir -p /tmp/choptuik
% cp -r ~phys210t /tmp/choptuik
cp: cannot open '/home/phys210t/.bash_history' for reading: Permission denied
cp: cannot open '/home/phys210t/.Xauthority' for reading: Permission denied
cp: cannot access '/home/phys210t/.gnupg': Permission denied
% cd /tmp/choptuik/phys210t; ls -a
./ ../ .aliases .bashrc .gnupg/ .profile cmd* dir1/ dir2/
% cp -r ~phys210t /tmpwas issued. In brief, the directory /tmp/choptuik/phys210t was created and all contents of /home/phys210t (including hidden files) for which I had read permission were recursively copied into that new directory: sub-directories of /tmp/choptuik/phys210t were automatically created as required.
mv
Use mv to rename files, or to move files from one
directory to another. Again, I assume that mv is aliased
to mv -i so that you will be prompted if an existing file
will be clobbered by the command. Here's a "rename" example
% lswhile the following sequence illustrates how several files might be moved up one level in the directory hierarchy:
thisfile
% mv thisfile thatfile
% ls
thatfile
% pwd
/tmp/lev1
% ls
lev2/
% cd lev2
% ls
file1 file2 file3 file4
% mv file1 file2 file3 ..
% ls
file4
% cd ..
% ls
file1 file2 file3 lev2/
rm
Use rm to remove (delete) files or directory
hierarchies. The use of the alias rm -i for cautious
removal is highly recommended. Once you've removed a file
in Unix there is essentially nothing you can do to (easily)
recover it other than restoring a copy from backup media
(assuming the system is regularly backed up), and if the
file was created since the last backup, you're really out of luck!
Examples include:
% rm thisfileto remove a single file,
% rm file1 file2 file3to remove several files at once, and
% rm -r thisdirto remove all contents of directory thisdir, including the directory itself. Be particularly careful with this form of the command and note that
% rm thisdirwill not work. Unix will complain that thisdir is a directory.
chmod
Use chmod to change the permissions on a file. See
the discussion of ls above for a brief
introduction to file-permissions and check the man pages
for ls and chmod for additional information.
Basically, file permissions control who can do what with your
files. Who includes yourself (the user u), users
in your group (g) and the rest of the world (the others o).
What includes reading (r), writing (w, which
itself includes removing/renaming) and executing (x, and
recall that execution permission on a directory is required in
order to cd to
it). When you create a new file, the system sets the
permissions (or mode) of a file to default values that you can
modify using the umask command. (See the discussion of umask in the man page
for bash for more
information).
On the lab machines your defaults should be such that you can do anything you want to a file you've created, while the rest of the world (including fellow group members) normally has read and, where appropriate, execute permission. As the man page will tell you, you can either specify permissions in numeric (octal) form or symbolically. I prefer the latter. Some examples that should be useful to you include:
% chmod go-rwx file_or_directory_to_hidewhich removes all permissions from 'group' and 'others', effectively hiding the file/directory,
% chmod a+x executable_fileto make a file executable by everyone (a stands for all and is the union of user, group and other) and
% chmod a-w file_to_write_protectto remove everyone's write permission to a file, including yours (i.e. the user's), which prevents accidental modification of particularly valuable information. Note that permissions are added with a + and removed with a -. You can also set permissions absolutely using an =, for example
% chmod a=r file_for_all_to_read
scp
Use scp (whose syntax is an extension of cp)
to copy files or hierarchies from one Unix system to another. scp
is part of the ssh distribution, so will prompt you for a
password for access to the remote account.
For example, assume I am logged into hyper and that I want to copy my ~/.bashrc file to a file named ~/.bashrc-hyper in my home directory on matt@bh0.phas.ubc.ca. The following will do the trick
hyper% scp ~/.bashrc matt@bh0.phas.ubc.ca:~/.bashrc-hyperThe last line in the above output is a status report that lists, in order, the name of file that was transferred, the percentage of the file transmitted (for large files, or on slow connections, you will see this number being updated in "real time"), the number of bytes transferred, the approximate speed of the transfer, and the elapsed time for the copy. If you wish to suppress this output use the -q (for quiet) option to the command:
matt@bh0.phas.ubc.ca's password:
.bashrc 100% 1813 1.8KB/s 00:00
hyper% scp -q ~/.bashrc matt@bh0.phas.ubc.ca:~/.bashrc-hyperThe above example copies a file from the local host to a remote host. You can use scp to go the other way as well: i.e. the command can be used bi-directionally between hosts. Thus, for example, the following invocation will copy my ~/.aliases file on bh0 to the file ~/.aliases-bh0 on my account on hyper:
hyper% scp -q matt@bh0.phas.ubc.ca:~/.aliases ~/.aliases-bh0
WARNING!! Be very careful using scp, particularly since there is no -i (cautious) option to warn you if existing files will be overwritten (there actually is a -i option, but it serves a completely different purpose!). Also note that there is a -r option for remote-copying entire hierarchies.
Local Variables: bash allows for the
definition of variables,
which are used to store various pieces of information in the form
of text strings. Indeed this basic notion of "variable" should be
familiar to you if you have experience programming in a language
such as C, Maple, Mathematica, python, Matlab etc. Further, bash distinguishes between two
types of variables: local
variables, whose values are available only in the current
shell, and environment
or global variables, whose values are inherited (accessible) by
processes (including other shells) that are started within the
current shell.
The syntax for defining a new local variable (or for changing its
value) is simple:
% varname=valueAs with file names and aliases, you should avoid names for shell variables (of either type) that contain special characters. Also, a variable name cannot begin with a number. To access the value of a variable (or, synonymously, to evaluate the variable) we simply prefix the variable name with a $ (dollar sign). We can then use the echo command, which, as already mentioned in the section on executables and paths, simply "echoes" its arguments (see man echo for full details), to display the value. Here are some examples:
% var1=val1You should observe that the use of the prefix $ to evaluate a shell variable is quite different from the evaluation mechanism found in many other programming languages (e.g. Maple, C, Matlab), where use of the variable name itself generally results in evaluation (except when the name appears on the left hand side of an assignment). When writing scripts that use variables it is a common mistake to forget to use the $ when needed, so be extra vigilant about this point if and when you do write scripts.
% echo $var1
val1
% var1='val1'
% echo $var1
val1
% var2='val1 val2 val3'
% echo $var2
val1 val2 val3
Environment Variables: As mentioned
above, bash uses
another type of variable---called an environment variable---which
is often used for communication between the shell and
other processes (possibly another shell, which does not
necessarily have to be bash).
To see a list of all currently defined environment variables, use
the env command:
% envor the printenv command:
LC_PAPER=en_CA.UTF-8
LC_ADDRESS=en_CA.UTF-8
XDG_SESSION_ID=c216
LC_MONETARY=en_CA.UTF-8
HOSTNAME=cord
GPG_AGENT_INFO=/tmp/gpg-fspov7/S.gpg-agent:27903:1
TERM=xterm
SHELL=/bin/bash
CANBERRA_DRIVER=pulse
LC_SOURCED=1
HISTSIZE=1000
TMPDIR=/tmp
SSH_CLIENT=142.103.234.164 58952 22
MGA_MENU_STYLE=mageia
LC_NUMERIC=en_CA.UTF-8
QTDIR=/usr/lib64/qt4
SSH_TTY=/dev/pts/3
.
.
.
% printenvand to display the values of one or more specific environment variables, supply the variable name(s) to printenv, or use the echo command in conjunction with the $ evaluation mechanism:
LC_PAPER=en_CA.UTF-8
LC_ADDRESS=en_CA.UTF-8
XDG_SESSION_ID=c216
LC_MONETARY=en_CA.UTF-8
HOSTNAME=cord
GPG_AGENT_INFO=/tmp/gpg-fspov7/S.gpg-agent:27903:1
TERM=xterm
SHELL=/bin/bash
CANBERRA_DRIVER=pulse
LC_SOURCED=1
HISTSIZE=1000
TMPDIR=/tmp
SSH_CLIENT=142.103.234.164 58952 22
MGA_MENU_STYLE=mageia
LC_NUMERIC=en_CA.UTF-8
QTDIR=/usr/lib64/qt4
SSH_TTY=/dev/pts/3
.
.
.
% printenv PWDMany environment variables are automatically defined whenever bash starts; a list of a few of these is given below. If you want to define your own environment variable, MYENV, say, and set its (initial) value, use the syntax
/home/phys210t
% printenv HOME PATH
/home/phys210t
.:/home/phys210t/bin:/home/phys210/bin:/usr/local/bin:/usr/bin:/usr/games: ...
% echo $LOGNAME
phys210t
% echo $SHELL $USER
/bin/bash phys210t
% export MYENV='value'The export keyword tells the shell that you are defining an environment variable, and not a local variable, but otherwise the assignment syntax is identical to that of local variables. It is conventional, but not mandatory, to use all-uppercase names for environment variables. Also, once an environment variable is defined, and you wish to change its value, it is not necessary to use the export keyword again:
% printenv MYENV
value
% MYENV='newvalue'; printenv MYENV
newvalue
Note that a key aspect of the global nature of environment
variables is that they (and their values) are "inherited" by any
shell that is executed within a running bash (which includes the shells that are always
started whenever a bash
script is executed). Thus, if after having executed the
assignments above, I now start a new shell, the environment
variable MYENV will be defined with its expected value:
% bash
A new shell starts ...
% printenv MYENV
newvalue
Following is a list of a few of the environment variables that are generally predefined and/or redefined as necessary by bash:
% cd $HOME/dir1is equivalent to
% cd ~/dir1
Using bash Pattern Matching: bash provides facilities that allow you to concisely refer to one or more files whose names match a given pattern. The process of translating patterns to actual filenames is known as filename expansion or globbing. Patterns are constructed using plain text strings and the following constructs, known as wildcards
Continuing, match sets may also be specified explicitly, as in
? Matches any single character
* Matches any string of characters (including no
characters)
[a-z] (Example) Matches any single character contained
in the specified range (the match set)---unfortunately
(from the viewpoint of a Unix neophyte), the precise characters
that comprise the match set can vary from system to system,
due to the inherent ambiguity in how to order upper
and lower case letters (see note below).
[^a-z] (Example) Matches any single character
not contained in the specified range
[02468]Examples:
% ls ??lists all regular (not hidden) files and directories whose names contain precisely two characters.
% cp a* /tmpcopies all files whose name begins with 'a' to the temporary directory /tmp.
% mv *.f ../newdirmoves all files whose names end with '.f' to directory ../newdir. Note that the command
% mv *.f *.forwill not rename all files ending with '.f' to files with the same prefixes, but ending in '.for'. (This was the case on some other operating systems, many of which are now defunct). This is easily understood by noting that expansion occurs before the final argument list is passed along to the mv command. If there aren't any '.for' files in the working directory, *.for will expand to nothing and the last command will be identical to
% mv *.fwhich is not at all what was intended.
[a-c]is equivalent to
[aBbCc]
bash maintains a numbered
history of previously entered command lines. Type
% history(which I personally alias as hi) to view your command-line history.
Examples:
% !20
reexecutes the 20th command in the history.
% !c
reexecutes the most recently issued command that starts with a
'c'.
Standard Input, Standard Output and Standard Error: A typical Unix command (process, program, job, task, application) reads some input, performs some operations on, or depending on, the input, then produces some output. It proves to be extremely powerful to be able to write programs (including bash scripts) that read and write their input and output from "standard" locations. Thus, Unix defines the notions of
% catHere, cat reads lines from stdin (the terminal) and writes those lines to stdout (also the terminal) so that every line you type is "echoed" by the command. A command that reads from stdin and writes to stdout is known as a filter.
foo
foo
bar
bar
^D
Input and Output Redirection: The power and flexibility of the stdin/stdout mechanism becomes apparent when we consider the operations of input and output redirection that are implemented in bash (and many other shells). As the name suggests, redirection means that stdin and/or stdout are associated with some source/sink other than the terminal.
Input Redirection is accomplished using the < (less-than) character, followed by the name of a file from which the input is to be extracted. Thus the command-line
% cat < input_to_catcauses the contents of the file input_to_cat to be used as input to the cat command. In this case, the effect is exactly the same as if
% cat input_to_cathad been entered. Note that the whitespace before and after the '<' is not necessary, but is used here for clarity (the same comment applies to the other redirection operators discussed below).
Output Redirection is accomplished using the > (greater than) character, again followed by the name of a file into which the (standard) output of the command is to be directed. Thus
% cat > output_from_catwill cause cat to read lines from the terminal (stdin is not redirected in this case) and copy them into the file output_from_cat. Care must be exercised in using output redirection since one of the first things that will happen in the above example is that the file output_from_cat will be clobbered. If the shell option noclobber has been set using
set -o noclobberwhich is highly recommended for novices (and included in the course default .bashrc), then output will not be allowed to be redirected to an existing file. Thus, in the above example, and assuming that noclobber is set, if output_from_cat already existed, the shell would respond as follows:
% cat > output_from_catand the command would be aborted.
output_from_cat: File exists
The standard output from a command can also be appended to a file using the two-character sequence >> (no intervening spaces). Thus
% cat >> existing_filewill append lines typed at the terminal to the end of existing_file.
From time to time it is convenient to be able to "throw away" the standard output of a command. Unix systems have a special file called /dev/null that is ideally suited for this purpose. Output redirection to this file, as in:
verbose_command > /dev/nullwill result in the stdout from the command disappearing without a trace.
Pipes: Part of the "Unix programming philosophy" is to keep input and output to and from commands in "machine-readable" form: this usually means keeping the input and output simple, structured and devoid of extraneous information which, while informative to humans, is likely to be a nuisance for other programs. Thus, rather than writing a command that produces output such as:
% pgm_wrongwe write one that produces
Time = 0.0 seconds Force = 6.0 Newtons
Time = 1.0 seconds Force = 6.1 Newtons
Time = 2.0 seconds Force = 6.2 Newtons
% pgm_rightThe advantage of this approach is that it is then often possible to combine commands (programs) on the command-line so that the standard output from one command is fed directly into the standard input of another. In this case we say that the output of the first command is piped into the input of the second. Here's an example:
0.0 6.0
1.0 6.1
2.0 6.2
% ls -1 | wcThe -1 ("one", not "ell") option to ls tells ls to list regular files and directories one per line. The command wc (for word count) when invoked with no arguments, reads stdin until EOF is encountered and then prints three numbers: (1) the total number of lines in the input (2) the total number of words in the input and (3) the total number of characters in the input (in this case, 82). The pipe symbol "|" tells the shell to connect the standard output of ls to the standard input of wc. The entire ls -1 | wc construct is known as a pipeline, and in this case, the first number (10) that appears on the standard output is simply the number of regular files and directories in the current directory.
10 10 82
Pipelines can be made as long as desired, and once you know a few
Unix commands, you can easily accomplish some fairly sophisticated
tasks by interactively building up multi-stage pipelines. Note
that it is often useful to build up a pipeline stage by stage, and
to do this the command recall mechanism provided via the up-arrow
key is helpful, as are the history commands discussed
above.
Regular Expressions and grep: Regular expressions may be formally defined as those character strings that are recognized (accepted) by finite state automata. If you haven't studied automata theory, this definition won't be of much use, so for our purposes we will define regular expressions as specifications for rather general patterns that we will wish to detect, usually in the contents of files. Although there are similarities in the Unix specification of regular expressions to bash wildcards (see above), there are important differences as well, so be careful. We begin with regular expressions that match a single character:
a (Example) Matches 'a', any character other thanMultiple-character regular expressions may then be built up as follows:
the special characters: . * [ ] \ ^ or $ may be
used as is
\* (Example) Matches the single character '*'.
Note that `\' is the "backslash" character. A
backslash may be used to "escape" any of the
special characters listed above
(including backslash itself)
. (Period/dot) Matches ANY single character.
[abc] (Example) Matches any one of 'a', 'b' or 'c'.
[^abc] (Example) Matches any character that ISN'T an
'a', 'b' or 'c'.
[a-z] (Example) Matches any character in the inclusive
range 'a' through 'z'.
[^a-z] (Example) Matches any character NOT in the
inclusive range 'a' through 'z'.
^ Matches the beginning of a line.
$ Matches the end of a line.
ahgfh (Example) Matches the string 'ahgfh'. Any string
of specific characters (including escaped special
characters) may be specified in this fashion.
a* (Example) Matches zero or more occurrences of the
character 'a'. Any single character expression
(except start and end of line) followed by a '*' will
match zero or more occurrences of that particular
sequence.
.* Matches an arbitrary string of characters.
Note that, in contrast to the bash globbing mechanism described
above, ranges involving lower case and upper case characters,
respectively, are always distinct. Thus
[a-z]
matches a single lower case letter only, while
[A-Z]
similarly matches a single upper case letter only (in particular,
then, the meaning of a character range in the context of regular
expressions does not
depend on the collating sequence defined by the locale).
All of this is may be a bit confusing, so it is best to consider the use of regular expressions in the context of the Unix grep command.
grep
grep (which loosely stands for (g)lobal search for
(r)egular (e)xpression with (p)rint) has the following general
syntax:
grep [options] regular_expression [file1 file2 ...]Note that only the regular_expression argument is required. Thus
% grep thewill read lines from stdin (normally the terminal) and echo only those lines that contain the string 'the'. If one or more file arguments are supplied along with the regular expression, then grep will search those files for lines matching the regular expression, and print the matching lines to standard output (again, normally the terminal). Thus
% grep the *will print all the lines of all the regular files in the working directory that contain the string 'the'.
Some of the options to grep are worth mentioning here. The first is -i which tells grep to ignore case when pattern-matching. Thus
% grep -i the textwill print all lines of the file text that contain 'the' or 'The' or 'tHe' etc. Second, the -v option instructs grep to print all lines that do not match the pattern; thus
% grep -v the textwill print all lines of text that do not contain the string 'the'. Finally, the -n option tells grep to include a line number at the beginning of each line printed. Thus
% grep -in the textwill print, with line numbers, all lines of the file text that contain the string 'the', 'The', 'tHe' etc. Note that multiple options can be specified with a single - followed by a string of option letters with no intervening blanks. Most Unix commands allow this syntax for providing several options.
Here are a few slightly more complicated examples. Note that when supplying a regular expression that contains characters such as '*', '?', '[', '!' ..., that are special to the shell, the regular expression should be surrounded by single quotes to prevent shell interpretation of the shell characters. In fact, you won't go wrong by always enclosing the regular expression in single quotes.
% grep '^.....$' file1prints all lines of file1 that contain exactly 5 characters (not counting the "newline" at the end of each line):
% grep 'a' file1 | grep 'b'prints all lines of file1 that contain at least one 'a' and one 'b'. (Note the use of the pipe to stream the stdout from the first grep into the stdin of the second.)
% grep -v '^#' input > outputextracts all lines from file input that do not have a '#' in the first column and writes them to file output.
Pattern matching (searching for strings) using regular expressions is a powerful concept, but one that can be made even more useful with certain extensions. Many of these extensions are implemented in a relative of grep known as egrep. See the man page for egrep if you are interested.
Using Quotes (' ', " ", and ` `): Most shells, including bash, use the three different types of quotes found on a standard keyboard
' ' -> Known as forward quotes, single quotes, quotesfor distinct purposes.
" " -> Known as double quotes
` ` -> Known as backward quotes, backquotes, backticks
Forward quotes: ' ' We have already encountered several examples of the use of forward quotes that inhibit shell evaluation of any and all special characters and/or constructs. Here's an example:
% a=100Note how in the final assignment, b='$a', the $a is protected from evaluation by the single quotes. Single quotes are commonly used to assign a shell variable a value that contains whitespace, or to protect command arguments that contain characters special to the shell (see the discussion of grep for an example).
% echo $a
100
% b=$a
% echo $b
100
% b='$a'
% echo $b
$a
Double quotes: " " Double quotes function in much the same way as forward quotes, except that the shell "looks inside" them and evaluates (1) any references to the values of shell variables, and (2) anything within backquotes (see below). Example:
% a=100
% echo $a
100
% string="The value of a is $a"
% echo $string
The value of a is 100
Backward quotes (backquotes, backticks): ` ` The shell uses backquotes to provide a powerful mechanism for capturing the standard output of a Unix command (or, more generally, a sequence of Unix commands) as a string that can then be assigned to a shell variable or used as an argument to another command. Specifically, when the shell encounters a string enclosed in back-quotes, it attempts to evaluate the string as a Unix command, precisely as if the string had been entered at a shell prompt, and returns the standard output of the command as a string. In effect, the output of the command is substituted for the string and the enclosing back-quotes. Here are a few simple examples:
% dateNote that the file command attempts to guess what type of contents its arguments (which should be files) contain and which reports full path names for commands that are supplied as arguments. Observe that in the last example, multiple back-quoting constructs are used on a single command line.
Mon Sep 1 17:08:59 PDT 2014
% thedate=`date`
% echo $thedate
Mon Sep 1 17:09:18 PDT 2014
% which true
/bin/true
% file `which true`
/bin/true: ELF 64-bit LSB executable, x86-64, ...
% file `which true` `which false`
/bin/true: ELF 64-bit LSB executable, x86-64, ...
/bin/false: ELF 64-bit LSB executable, x86-64, ...
Finally, here's an example illustrating that back-quote substitution is enabled for strings within double quotes, but disabled for strings within single quotes:
% var1="The current date is `date`"
% echo $var1
The current date is Mon Sep 1 17:10:37 PDT 2014
% var2='The current date is `date`'
% echo $var2
The current date is `date`
Job Control: Unix is a multi-tasking operating system: at any given time, the system is effectively running many distinct processes (commands) simultaneously (of course, if the machine only has one CPU (core), only one process can run at a specific time, so this simultaneity is often somewhat of an illusion). Even within a single shell, it is possible to run several different commands at the same time. Job control refers to the shell facilities for managing how these different processes are run. It should be noted that job control is arguably less important in the current age of windowing systems than it used to be, since one can now simply use multiple shell windows to manage several concurrently running tasks.
Commands issued from the command-line normally run in the foreground. This generally means that the command "takes over" standard input and standard output (the terminal), and, in particular, the command must complete before you can type additional commands to the shell. If, however, the command line is terminated with an ampersand: &, the job is run in the background and you can immediately type new commands while the command executes. Example:
% grep the huge_file > grep_output &In this example, the shell responds with a '[1]' that identifies the task at the shell level, and a '1299' (the process id) that identifies the task at the system level. You can continue to type commands while the grep job runs in the background. At some point grep will finish, and the next time you type 'Enter' (or 'Return'), the shell will inform you that the job has completed:
[1] 1299
[1]+ Done grep the huge_file > grep_outputThe following sequence illustrates another way to run the same job in the background:
% grep the huge_file > grep_outputHere, typing ^Z while the command is running in the foreground stops (suspends) the job, the shell command bg restarts it in the background. You can see which jobs are running or stopped by using the shell jobs command.
^Z
[1}+ Stopped grep the huge_file > grep_output
% bg
[1]+ grep the huge_file > grep_output &
% jobsUse
[1] + Stopped grep the huge_file > grep_output
[2] Running other_command
% fg %1to have the job labeled '[1]' (that may either be stopped or running in the background), run in the foreground. You can kill (terminate) a job using its job number (%1, %2, etc.)
% kill %1You can also kill a job using its process ID (PID), which you can obtain using the Unix ps command. See the man pages for ps and kill for more details.
[1] Terminated grep the huge_file > grep_output
On many Unix systems, including Linux, there is a killall command, which allows you to kill processes by name. Finally, the shell will complain if you try to logout or exit the shell when one or more jobs are stopped. Either explicitly kill the jobs (or let them finish up if that's appropriate) or type logout or exit again to ignore the warning, kill all stopped jobs, and exit.
Another useful, though Linux-specific, command is pstree, which shows processes currently running on the host machine in the form of a tree. If you want to limit the output to your own processes (and not, for example, root's), use
% pstree -u your_userid
Time constraints preclude anything but a basic overview of bash programming; if you wish
to become a wizard of this particular craft, you might want to
consult the classic text, The UNIX Programming Environment,
by Kernighan and Pike, cited in the following as reference [1]. In
addition, there is plenty of information to be found about the
subject online (see the representative links at the end of this
document, for example. which are also available via the Course Resources page). Finally,
should you find yourself in need of complex scripts, you
may wish to consider learning/using perl,
which is an extremely powerful scripting language that has become
very popular in the Unix community over the past couple of decades
(the python
language is another good choice in this regard).
We start with a very simple example. Consider the problem of "swapping" the names of two files, which arises more often in practice than one might expect, and which cannot be accomplished with a standard Unix command. Assuming that no file t exists in the working directory, the command sequence
% mv a twill exchange the names of files a and b. Building on this sequence, here's a script called swap that, naturally enough, "swaps" the names of an arbitrary pair of files:
% mv b a
% mv t b
#! /bin/bashThe first line of the script
# Bare-bones script to swap names of two files
# Usage: swap file1 file2
mv $1 t
mv $2 $1
mv t $2
#! /bin/bashis an important bit of Unix magic that tells the shell that when the name of the file containing the script is used as a command, the shell should start up a new shell (in this case another bash) and execute the remaining contents of the script in the context of that new shell. Every bash script that you write should start with this incantation.
Continuing with our dissection of the script, lines that begin with a hash ("number sign") # (excluding the magic first line) such as
# Bare-bones script to swap names of two filesare comments, and are ignored by the shell.
# Usage: swap file1 file2
The final three lines of the script
mv $1 tdo all the work. The constructs $1 and $2 evaluate to the first and second arguments, respectively, which are supplied to the script. In general, one can access the first nine arguments of a script using $1, $2, ..., $9, and, if more than nine arguments need to be parsed (!), using ${10}, ${11}, etc. If a specific argument is missing, the corresponding construct will evaluate to the null string, i.e. to "nothing".
mv $2 $1
mv t $2
Having created a file called swap containing the above lines, I set execute permission on the file with the chmod command
% chmod a+x swapand the script is ready to use:
% ls -l swap
-rwxr-xr-x 1 phys210 public 116 2009-09-07 16:32 swap*
% ls
f1 f2 swap*
% cat f1
This is the first file.
% cat f2
This is the second file.
% swap f1 f2
% cat f1
This is the second file.
% cat f2
This is the first file.
When developing and debugging a shell program, it is often very useful to enable "tracing" of the script. This is done by adding the -x option to the header line:
#! /bin/bash -xHaving made this modification, I now see the following output when I invoke swap a second time:
% swap f1 f2Note how each command in the script is echoed to standard error (with a + prepended) as it is executed. Again, observe that the mv command used in this instance is the "bare bones" version since any aliases that I have defined via ~/.bashrc for an interactive bash will not be in effect while the script executes.
+ mv f1 t
+ mv f2 f1
+ mv t f2
Although swap as coded above is reasonably functional, it is not very robust and can potentially generate undesired "side-effects" if used incorrectly. Observe, for example, what happens when the script is invoked without any arguments (tracing has now been disabled by removing the -x option in the header)
% swapor, worse, with one argument
mv: missing file argument
Try `mv --help' for more information.
mv: missing file arguments
Try `mv --help' for more information.
mv: missing file argument
Try `mv --help' for more information.
% swap f1Here's a second version of swap that fixes several of the shortcomings of the naive version, and that also illustrates many additional shell programming features:
mv: missing file argument
Try `mv --help' for more information.
mv: missing file argument
Try `mv --help' for more information.
% ls
f2 swap* t
#! /bin/bash
# Improved version of script to swap names of two files
# Set shell variable 'P' to name of script
P=`basename $0`
# Set shell variable 't' to name of temporary file
t=.swap.tempfile.3141
# Usage function
usage () {
cat << END
usage: $P file1 file2
Swaps filenames of file1 and file2
END
exit 1
}
# Function that is invoked if temporary file already exists
t_exists () {
cat << END
$P: Temporary file '$t' exists.
$P: Remove it explicitly before executing this script.
/bin/rm -f $t
END
exit 1
}
# Function that checks that its (first) argument is an
# existing file
check_file () {
if [ ! -f $1 ]; then
echo "$P: File '$1' does not exist"
error="yes"
fi
}
# Argument parsing---script requires exactly 2 arguments
case $# in
2) file1=$1; file2=$2 ;;
*) usage;;
esac
# Check that the arguments refer to existing files
check_file $1
check_file $2
# Bail out if either or both arguments are invalid
test "X${error}" = X || exit 1
# Ensure that temporary file doesn't already exist
test -f $t && t_exists
# Do the swap
mv $file1 $t
mv $file2 $file1
mv $t $file2
# Normal exit, return 'success' exit status
exit 0
Let us examine this new version of swap in detail.
As the comment indicates, the command
# Set shell variable 'P' to name of scriptsets the shell variable P to the filename of the script, i.e. to swap in this case. This happens as follows. First, $0 is a special shell-script variable that always evaluates to the invocation name of the script---i.e. what the user actually typed in order to execute the script. Second, as man tells us, the basename command deletes any prefix ending in / from its argument and prints the result on the standard output. Third, the backquotes around the basename invocation capture the standard output of the command, which is then assigned to the shell variable P via the assignment statement.
P=`basename $0`
We use basename here so that if someone invokes our script using its full path name, perhaps
% /home/phys210/shellpgm/ex2/swap f1 f2the shell variable P will still be assigned the value swap. The value of P is subsequently used in diagnostic messages, to make the origin of the messages clear to the user. Use of this mechanism can save some typing if one is writing a script that prints many such messages. In addition, if the script is subsequently used as a basis for a new shell program, a minimum of changes (perhaps none) are necessary in order that the new script output the "correct" diagnostics.
The next assignment sets the shell variable t to the name of a temporary file that, under normal circumstances, should never exist in the directory in which swap is executed. This isn't the most bullet-proof of strategies, but it's better than using t itself for the name for the temporary file!
# Set shell variable 't' to name of temporary file
t=.swap.tempfile.3141
The next section of code defines a shell function, called usage, which can be invoked from anywhere in the script. When called, the function will print a message to standard output informing the user of the proper usage of the command, and then exit (stop execution of the script).
# Usage functionThe general form of a function definition is
usage () {
cat << END
usage: $P file1 file2
Swaps filenames of file1 and file2
END
exit 1
}
routinename () {
command
command
...
}
The parentheses pair after routinename tells the shell that
a function is being defined, while the braces enclose the body of
the function.
Within the usage routine appears the construct
cat << ENDknown as a "here document". Here documents can be used anywhere in a script to provide "in-place" input for the standard input of a command. You can refer to the man page on bash for full details, but the basic idea and mechanics are quite simple. To provide "in-place" input to an arbitrary command, append << END after the command name, any arguments to the command, and any output redirection directives. There can be whitespace before and after the token END. Subsequent lines are then the standard input to the command. A line that exactly matches the string END (i.e. grep '^END$' succeeds) signals end-of-file (i.e. the end of the here document), so be sure you have such a line in your script!.
...
END
An interesting and useful feature of here-documents is that they are partially interpreted by the shell before being fed into their destination command. In particular, shell-variable-evaluations
$varare executed, as are
`command [arguments]`constructs. Thus, when the usage function is executed, the message
usage: swap file1 file2will appear on standard output, after which the execution of
Swaps filenames of file1 and file2
exit 1will return control to the invoking shell. Here, the argument to the exit command is an exit code indicating a completion status for the script. Since there is generally only one way for a command to succeed, but often many ways it can fail, a exit status of 0 indicates success in Unix, while any non-zero value (1 in this case), indicates failure.
All Unix commands return such codes (scripts that terminate without an explicit exit, implicitly return success to the invoking shell) and they can be used in the context of shell-control structures such as if, while and until statements.
The function t_exists is very similar in construction to usage, and is used in the unlikely event that a file named .swap.tempfile.3141 does exist in the directory in which the script is invoked.
# Function that is invoked if temporary file already exists
t_exists () {
cat << END
$P: Temporary file '$t' exists.
$P: Remove it explicitly before executing this script.
/bin/rm -f $t
END
exit 1
}
Function check_file illustrates the use of function arguments, as well as the shell if statement.
# Function that checks that its (first) argument is an
# existing file
check_file () {
if [ ! -f $1 ]; then
echo "$P: File '$1' does not exist"
error="yes"
fi
}
As with arguments to the script itself, function arguments are accessed positionally, via $1, $2, ... . Note, then, that the evaluation of $1, for example, depends crucially on context (or scope): within a function, $1 evaluates to the first argument to the routine, while outside of any function it evaluates to the first argument to the script.
For our purposes, a suitably general form of the shell if statement is
if command a; thenAll clauses apart from the first are optional, as is apparent from the if statement in the check_file routine. The evaluation of the if statement begins with the execution of command a. If this command succeeds (returns exit status 0), then commands 1 are executed (commands must appear on separate lines, or be separated by semicolons) and control then passes to the command following the end of the if statement (i.e. after the fi token). Otherwise, command b is executed; if it succeeds, commands 2 are performed, otherwise command c is executed, and so on.
commands 1
elif command b; then
commands 2
elif command c; then
commands 3
...
else
commands n
fi
The if statement in our check_file routine
if [ ! -f $1 ]; thenuses the Unix test command, for which [ is essentially an alias (the ] is "syntactic-sugar" and does nothing but make the expression "look right"). Thus an equivalent form is
echo "$P: File '$1' does not exist"
error="yes"
fi
if test ! -f $1; thentest accepts a general expression expr as an argument, evaluates expr and, if its value is true, sets a zero exit status (success); otherwise, a non-zero exit status (failure) is set. test accepts many different options for performing a variety of tests on files and directories, and implements a fairly complete set of logical operations such as negation, or, and, tests for string equality/non-equality, integer equal-to, greater-than, less-than etc.; see man test for full details.
echo "$P: File '$1' does not exist"
error="yes"
fi
In the current case, the -f $1 option returns true if the first argument to the routine is an existing regular file (i.e. not a directory or other type of special file). The ! is the negation operator, so the overall test command returns success (true) if the first argument is not an existing regular file.
The next section of code introduces the shell case statement:
# Argument parsing---script requires exactly 2 arguments
case $# in
2) file1=$1; file2=$2 ;;
*) usage;;
esac
A general case statement looks like
case word inStarting from the top, and using essentially the same pattern-matching rules used for filename matching, the case statement compares word to each pattern in turn, until it finds a match. When a match is found, the corresponding commands (and only those commands) are executed, after which control passes to the statement following the end of the case statement (i.e. after the esac token). Note that the commands associated with each case must be terminated with a double semi-colon.
pattern) commands ;;
pattern) commands ;;
...
esac
In our current example, we match on the built-in shell variable $#, which evaluates to the number of arguments that were supplied to the shell. The first set of actions
2) file1=$1; file2=$2 ;;is evaluated if precisely two arguments have been supplied. If the script has been invoked with anything but two arguments, $# is then matched against *, which will always succeed; i.e.
*) usage ;;serves as a "default" case, and the usage function will thus be called if we've used an incorrect number of arguments.
Using the check_file function, the script then ensures that each argument names an existing regular file:
# Check that the arguments refer to existing filesNote that if either or both of the checks fail, then the shell variable error (all variables are global in a shell script unless explicitly declared local, see man bash for more information) will be set to yes. The calls to check_file are followed by a command list that tests whether error has been set, and exits the script if it has:
check_file $file1
check_file $file2
# Bail out if either or both arguments are invalidThe expression
test "X${error}" = X || exit 1
"X${error}" = X
illustrates a little shell trick that tests whether a shell variable
has been defined. If error has been set to yes by check_file,
then "X${error}" evaluates to Xyes; otherwise it
evaluates to X. The binary operator || (double pipe)
can be used between any two Unix commands (or, more generally,
pipelines):
command 1 || command 2and has the following semantics: command 1 is executed, and if and only if the command fails (returns a non-zero exit status), command 2 is executed. Thus, the sequence is equivalent to
if [ ! command 1 ]; then
command 2
fi
Similarly, the next piece of the script
# Ensure that temporary file doesn't already existillustrates the use of the binary operator && (double ampersand), which also can be used between any two commands:
test -f $t && t_exists
command 1 && command 2In this case command 1 is executed, and if and only if the command succeeds (returns a 0 exit status), command 2 is executed. Thus, an equivalent form is
if [ command 1 ]; thenIn the current example, if the temporary file .swap.temp.3141 does exist, the function t_exists is called to print the diagnostic message and exit.
command 2
fi
Finally, if we've made it past all of the error-checking, it's time to actually swap the filenames, and have the script return a "success" exit status to the invoking environment:
# Do the swap
mv $file1 $t
mv $file2 $file1
mv $t $file2
# Normal exit, return 'success' code
exit 0
We can now test our improved version of swap, exercising in particular all of the error-checking features that have been incorporated. Here again is a contents-listing of the directory containing the script:
% ls
f1 f2 swap*
% more f1 f2
::::::::::::::
f1
::::::::::::::
This is the first file.
::::::::::::::
f2
::::::::::::::
This is the second file.
We start with a no-argument invocation:
% swapfollowed by single-argument execution:
usage: swap file1 file2
Swaps filenames of file1 and file2
% swap f1In both cases swap dutifully prints the usage message to standard output as desired.
usage: swap file1 file2
Swaps filenames of file1 and file2
We now invoke swap in a "normal" fashion, and verify that it is working properly:
% swap f1 f2
% more f1 f2
::::::::::::::
f1
::::::::::::::
This is the second file.
::::::::::::::
f2
::::::::::::::
This is the first file.
Supplying swap with two arguments that are not names of files in the working directory results in appropriate error messages:
% swap a1 a2as does an invocation where one of the arguments is invalid:
swap: File 'a1' does not exist
swap: File 'a2' does not exist
% swap a1 f2
swap: File 'a1' does not exist
Finally, after (perversely) creating .swap.tempfile.3141 using the touch command (touch filename creates the (empty) file filename if it does not exist, and changes its time of last modification to the current time if it does),
% touch .swap.tempfile.3141execution of swap with valid arguments triggers the t_exists routine:
swap: Temporary file '.swap.tempfile.3141' exists.Removing the file as instructed, the script once again silently performs its job:
swap: Remove it explicitly before executing this script.
/bin/rm -f .swap.tempfile.3141
% /bin/rm -f .swap.tempfile.3141
% swap f1 f2
We will conclude our whirlwind tour of shell programming with a description of a few more control structures, some additional niceties concerning shell variable evaluation, and a glimpse at a command useful for writing scripts that "interact" with the user.
The shell provides three structures for looping. The first is a for loop:
for var in word list; doHere, for each word (token) in word list, the commands in the body of the loop are executed, with the shell variable var being set to each word in turn. As usual, an example makes the semantics clear:
commands
done
% cat for-exampleNote that a "word" can contain whitespace if it has been quoted, as is the case for 'foo bar '
#! /bin/bash
# Illustrates shell 'for' loop
for i in foo bar 'foo bar '; do
echo "i -> $i"
done
% for-example
i -> foo
i -> bar
i -> foo bar
In many instances, a for loop in a script will loop over all of the arguments supplied to the script. The built-in shell variable $* evaluates to the argument list, so we can write
for i in $*; dobut the shell also has a shorthand for this particular case, namely:
commands
done
for i; do
commands
done
In addition to for iterations, there are also while loops:
while command; doand until loops:
commands
done
until command; doFor these iterations, the body of the loop is repetitively executed as long as command succeeds or fails, respectively.
commands
done
The following table summarizes some built-in shell variables that are particularly useful for script writing [1]:
| Variable | Evaluates to |
|---|---|
| $# | number of arguments |
| $* | all arguments |
| $? | return value of last command |
| $$ | process-id of the script |
Also observe that, as intimated above in the discussion of environment variables, a bash script inherits all of the environment variables (such as $HOME, $PATH, ...) that have been set in the invoking shell.
As shown in the next table [1], we can also use some tricks in the evaluation of shell variables to make writing scripts a little easier at times:
| Expression | Evaluates to |
|---|---|
| $var | value of var, nothing if var undefined |
| ${var} | same as above; useful if alphanumerics follow variable name |
| ${var-thing} | value of var if defined; otherwise thing; $var unchanged. |
| ${var=thing} | value of var if defined; otherwise thing; if undefined $var set to thing |
| ${var+thing} | thing if var defined; otherwise nothing |
| ${var?message} | if defined, $var; otherwise print message and exit shell. |
Finally, the read command can be used to interactively provide input to a script. Here's an example
% cat read-example
#! /bin/bash
echo "Hello there! Please type in your name:"
read name
echo "Pleased to meet you, $name"
% read-example
Hello there! Please type in your name
Matthew Choptuik
Pleased to meet you, Matthew Choptuik