Physics 329 - Fall 1996

Physics 329: Unix Notes

Please report all errors/typos. etc to matt@infeld.ph.utexas.edu

Index

Introduction and motivation
Files and Directories
Commands Overview
Basic Commands
More on the C-shell

INTRODUCTION AND MOTIVATION

The main purpose of this introduction is to get you familiar with the interactive use of Unix for day-to-day organizational and programming tasks. First, recall that Unix is an operating system which we can loosely define as a collection of programs (often called processes) which manage the resources of a computer for one or more users. These resources include the CPU, network facilities, terminals, file systems, disk drives and other mass-storage devices, printers, and many more. During the course, the most common way you will use Unix is through a command-line interface; you will type commands to create and manipulate files and directories, start up applications such as text-editors or plotting packages, send, compile and run C and Fortran programs, etc. etc. As many of you are probably aware, various Unix vendors have written GUIs (graphical user interfaces) for their particular versions of Unix. As with similar systems on Macs and PCs, these GUIs largely eliminate the need to issue commands by providing intuitive visual metaphors for most common tasks. However, the command-line approach is still well worth mastering for a variety of reasons, including:

Portability: All Unix systems support the command-line approach, and by sticking with standard features, what you learn on the Linux and SGI machines will be applicable on virtually all Unix systems
Speed: Command-line interfaces minimize the amount of information which needs to be passed from machine to machine when working remotely. If you just want to accomplish a few quick tasks, nothing is more annoying that a sluggish GUI.
Power: Commands can be extended and combined in a straightforward way. Defining new commands using shell programming facilities, or via C and Fortran is also relatively easy.

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. I recommend that you use the ``C-shell'' (csh) or the ``tC-shell'' (tcsh) for interactive use. Your Linux and SGI accounts are currently set up so that tcsh is your default interactive shell. Everything which is described below as being a C-shell feature should work equally as well in tcsh. Note that a significant enhancement of tcsh versus csh is the availability of command-history recall and editing 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. In the following, I assume you have at least one active shell on each system in which to type sample commands, and I will often refer to a window in which as shell is executing as the terminal.

In the following, commands which you type to the shell, as well as the output from the commands and the shell prompt (denoted "% ") will appear in typewriter font. Here's an example

% pwd
/usr2/people/matt
% date
Mon Sep  2 20:45:57 CDT 1996
%

FILES AND DIRECTORIES

I assume you are familiar with the notion of a hierarchical organization (tree structure) of files and directories which many modern operating systems employ. If you are not, refer to one of the Unix references or on-line tutorials which I have suggested. There are essentially only two types of files in Unix:

Plain files: which contain specific information such as plain text, C or Fortran source code, object code, executable code, postscript code, a Maple worksheet etc.
Directories: special files which are essentially containers for other files (including other directories)

Absolute and relative pathnames, working directory: All Unix filesystems are rooted in the special directory called '/'. All files within the filesystem have absolute pathnames which begin with '/' and which describe the path down the file tree to the file in question. Thus

/u4/phy329/junk

refers to a file named 'junk' which resides in a directory with absolute pathname

/u4/phy329

which itself lives in directory

/u4

which 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:

% pwd
/usr/people/matt
%

If you refer to a filename such as

foo

or a pathname such as

dir1/dir2/foo

so 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

/usr/people/matt

the two previous relative pathnames are identical to the absolute pathnames

/usr/people/matt/foo
/usr/people/dir1/dir2/foo

Note that although these files have the same filename 'foo', they have different absolute pathnames, and hence are distinct files.

Home directories: Each user of a Unix system typically has a single directory called his/her home directory which 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 Linux machines you should see something like this

% cd
% pwd
/u2/choptuik

while on the SGIs it will be something like

/usr2/people/phy329

/d/einstein/usr2/people/phy329

When using the C-shell, you may refer to your home directory using a tilde ('~'). Thus, assuming my home directory is

/usr/people/matt

then

% cd ~

and

% cd ~/dir1/dir2

are identical to

% cd /usr/people/matt

and

% cd /usr/people/matt/dir1/dir2

respectively. The C-shell 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 phy329's home directory,

% cd ~phy329

will 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 ~phy329i/hw1
% pwd
/usr2/people/phy329i/hw1
% cd ..
% pwd
/usr2/people/phy329i
% cd .
% pwd
/usr2/people/phy329i

Note that

% cd .

does nothing---the working directory remains the same. However, the '.' notation is often used when copying or moving files into the working directory. See below.

Filenames: There are relatively few restrictions on filenames in Unix. On most systems (including the Linux and SGI machines), 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 which 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 in other operating systems, the period is often used to separate the ``body'' of a filename from an ``extension'' as in:

program.c  (extension .c)
paper.tex  (extension .tex)
the.longextension (extension .longextension)
noextension (no extension)

Note that unlike 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:

this_is_a_long_file_name
this-is-another-long-file-name

The system makes it difficult for you to create a filename which starts with a minus. It is equally difficult 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'
% mv 'file_name_with_an_embedded_*_asterisk' sane_name

Note that the single quotes in this example are forward-quotes: (') Backward quotes have a completely different meaning to the shell.

COMMANDS OVERVIEW

General Structure: The general structure of Unix commands is given schematically by

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 -l
% cp -R ...
% man -k ...

Arguments are typically names of files or directories or other text strings which do not start with '-'. Individual arguments are separated by white space (one or more spaces or tabs):

% cp file1 file2  
% grep 'a string' file1

There are two arguments in both of the above examples; note the use of single quotes to supply the grep command with an argument which contains a space. The command

% grep a string file1

which 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 which 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 the C-shell, the current list of directories which constitute your path is maintained in the shell variable, 'path'. To display the contents of this variable, type:

% echo $path

(Note that the '$' mechanism is the standard way of evaluating shell variables and environment variables alike.) On the SGIs, the resulting output should look something like

. /usr/sbin /usr/bsd /sbin /usr/bin /bin /usr/bin/X11 /usr/local/bin

Note that the '.' in the output indicates that the working directory is in your path. The order in which path-components (First '.', then '/usr/sbin', then '/sbin', etc.) appear in your path is important. When you invoke a command without using an absolute pathname as in

% ls

the 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:

% helpme
helpme: Command not found.

The path variable is typically set in your '~/.login' file and/or (preferably) your '~/.cshrc' file. Examine the file '~/.cshrc' in your SGI account. You should see a line like

set path=($path /usr/local/bin $HOME/bin)

which adds '/usr/local/bin' and '$HOME/bin' to the previous (system default) value of 'path'. Also note the use of parentheses to assign a value containing whitespace to the shell variable. 'HOME' is an environment variable which stores the name of your home directory. Thus

set path=($path /usr/local/bin ~/bin)

will produce the same effect.

Control Characters: The following control characters typically have the following special meaning or uses within the C-shell. (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

% ^Z

for example, means depress the z-key (upper or lower case) while holding down the Control key.

^D: End-of-file (EOF). Type ^D to signal end of input when interacting with a program (such as Mail) which is reading input from the terminal. Here's an example using Mail:
```
% Mail -s "test message" matt@einstein.ph.utexas.edu
This is a one line message.
^D
EOT
% 
```
If 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 is gracious enough to echo the characters EOT (end-of-transmission) when you type ^D, but other commands, such as cat, will not echo anything. In almost all cases, however, you should be presented with a csh prompt. Also, by default, a C-shell exits when it encounters EOF, so if you type ^D at a csh prompt, you may find that you are logged out. If you don't like this behaviour (I don't), put the following line in '~/.cshrc':
```
set ignoreeof
```
^C: Interrupt. Type ^C to kill (stop in a non-restartable fashion) commands (processes) which you have started from the command-line. This is particularly useful for commands which are taking much longer to execute or producing much more output to the terminal than you had anticipated. Many commands `catch' interrupts and you may sometimes have to type more than one to get out. Here's an example, again from Mail
```
% Mail -s "a message which I decide not to send" matt@einstein.ph.utexas.edu
This is a one line message.
^C
(Interrupt -- one more to kill letter)
^C
%
```
Once more, if you try this example, you should notice that the control sequences are not explicitly echoed by the shell
^Z: Suspend. Type ^Z to suspend (stop in a restartable fashion) commands which you have started from the shell. It is often convenient to temporarily halt execution of a command as I will briefly discus in job control below.

Special Files: The following files, all of which reside in your home directory, have special purposes and you should become familiar with what they contain on the systems you work with:

~/.cshrc
Commands in this file are executed each time a new C-shell is started.
~/.login
Commands in this file are executed after those in '~/.cshrc' and only for login shells. The existence of separate '~/.cshrc' and '~/.login' files was more useful in the days when interaction with Unix was typically via a single screen (dumb ASCII terminal) and machines were slower so start-up time of shells was an issue. When interacting with Unix via a windowing system, it is easy to start an interactive shell which is not a login shell, but for which you presumably want the same initialization procedure. Consequently, your '~/.login' should be probably be kept as brief as possible and you should put start-up commands in '~/.cshrc' instead.
~/.rhosts
This file controls access to your account from remote machines. Its format will be illustrated in the discussion of rlogin below.

Note that files whose name begins with a period ('.') are called hidden since they do not normally show up in the listing produced by the 'ls' command. Use

% cd; ls -a

for 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 should 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 of interactive use, particularly by novices. The C-shell provides a mechanism called aliasing which allows you to easily remedy these deficiencies in many cases. The basic syntax for aliasing is

% alias name definition

where '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 'definition' tells the shell what to do when you type 'name' as if it was a command. The following examples should give you basic idea; see the csh documentation (man csh) for more complete information:

% alias ls 'ls -FC'

provides an alias for the ls command which 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 white-space.

% alias rm 'rm -i'
% alias cp 'cp -i'
% alias mv 'mv -i'

Define aliases for rm, cp and mv (see below) which will not clobber files without first asking you for explicit confirmation. Highly recommended for novices and experts alike.

% alias RM '/bin/rm'
% alias CP '/bin/cp'
% alias MV '/bin/mv'

Define aliases RM, CP, and MV which act like the ``bare'' Unix commands rm, cp and mv (i.e. which are not cautious). Use when you are sure you are about to do the correct thing: the presumption being that you have to think a little more to type the upper-case command. To see a list of all your current aliases, simply type

% aliases

Note that all of the preceding aliases (and a few more) are defined in a file '~/.aliases' in your SGI accounts. As configured, these aliases will be available in all interactive shells you start since

% source ~/.aliases

is in your '~/.cshrc'. (The 'source' command tells the shell to execute the commands in the file supplied as an argument). Although this is not a ``standardized'' approach, I commend it to you as a means of keeping your '~/.cshrc' relatively uncluttered if you end up defining a lot of aliases.

BASIC COMMANDS

The following list is by no means exhaustive, but rather represents what I consider an essential base set of Unix commands (organized roughly by topic) with which you should familiarize yourself as soon as possible. Refer to the man pages, or one of the suggested Unix references for additional information.

Getting Help or Information:

man

Use man (short for 'manual') to print information about a specific Unix command or to print a list of commands which have something to do with a specified topic (-k option, for keyword). It is difficult to overemphasize how important it is for you to become familiar with this command. 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. Typical usage examples include:

% man man

to get detailed information on the man command itself,

% man cp

for information on cp and

% man -k 'working directory'

to get a list of commands having something to do with the topic 'working directory'. The command apropos, found on most Unix systems, is essentially an alias for man -k

Communicating with Other Machines:

rlogin

Use rlogin to login into another (remote) machine. Typical usage is

% rlogin einstein.ph.utexas.edu -l matt

which will initiate a remote-login for user 'matt' on machine 'einstein.ph.utexas.edu'. Assume that I typed this command from 'linux1.ph.utexas.edu' as user 'choptuik'. Then, if on 'einstein', the file '~matt/.rhosts' exists and contains a line with the information,

linux1.ph.utexas.edu   choptuik

then I will not be prompted for a password. The structure of '~/.rhosts' files sometimes confuses the uninitiated: remember that if you want to be able to login to a given machine (the target) from some other machine (the source) without being prompted for a password, then in your '~/.rhosts' on the target machine there must be an entry identifying the source machine as well as your account name on the source machine. Confusion can be minimized by (1) maintaining (on some machine) a single master .rhosts file which contains lines for every machine/user combination you use and (2) distributing that file (via ftp or rcp) to all other machines whenever you modify it. Also note that many installations consider the use of the .rhosts mechanism a major security risk and will have disabled it. In such a case you'll have to resort to telnet. If you want to exit in a hurry from a session you've established via rlogin, type '~.' (tilde-dot).

telnet

Use telnet to establish a connection with another system (not necessarily Unix). Typical usage is

% telnet einstein.ph.utexas.edu
Connected to einstein.ph.utexas.edu.
Escape character is '^]'.


IRIX System V.4 (einstein)

login:

at which point you login as usual. If a session established this way ``hangs'' on you, or you otherwise appear to have lost control of your terminal, try typing

% ^]

(i.e. 'Control-]') at which point you should get a

telnet>

prompt. Type quit at the the prompt to exit telnet.

ftp

Use ftp to establish a connection to another machine for the express purpose of copying files between the two machines. Here's an example illustrating how I might copy my '~/.rhosts' file from my SGI account to my Linux account.

% ftp linux1.ph.utexas.edu
Connected to linux1.ph.utexas.edu.
220 linux1 FTP server ... ready.
Name (linux1.ph.utexas.edu:matt): choptuik
331 Password required for choptuik.
Password:
230 User choptuik logged in.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> put .rhosts
local: .rhosts remote: .rhosts
200 PORT command successful.
150 Opening BINARY mode data connection for .rhosts.
226 Transfer complete.
3719 bytes sent in 0.00 seconds (5829.59 Kbytes/s)
ftp> quit
221 Goodbye.

ftp has fairly extensive on-line help. Try

% ftp
ftp> help

as well as

ftp> help bin
ftp> help cd
ftp> help lcd
ftp> help put
ftp> help get
ftp> help prompt
ftp> help mget

to learn the basics. It is usually advisable to use ``BINARY mode'' to transfer files. Some installations support anonymous ftp. This means that anyone can ftp to the site using username 'anonymous'. In such cases you are usually requested to type your full name or e-mail address as your password. In most cases you will only be able to get (and not put) files from such sites.

Mail

I assume most of you will read and send your e-mail from a single machine which may not be one of the Linux or SGI machines. If you do wish to use one of the ``course machines'' for mail, I recommend that you use pine on the Linux machines, which provides a friendlier user interface than Mail which is described briefly here. The advantage of knowing a bit about Mail is that it is almost universally available (pine isn't installed on the SGIs for example) and is good for firing off short messages, particularly if they have been prepared in files beforehand.

Here's a quick example showing how to use Mail to send a message:

% Mail -s "this is the subject" matt@infeld.ph.utexas.edu
This is a one line test message.
^D

Note that multiple recipients can be specified on the command line. Another form involves redirection from a file.

% Mail -s "sending a file as a message" matt@infeld.ph.utexas.edu < message

sends the contents of file 'message'.

If you wish to read mail using Mail, type Mail (when you have mail) then type help to figure out how to continue. The Mail sub-commands:

h to display message headers
p to print the next message
s to save a message
d to delete a message
r to reply to a message
q to quit Mail

should get you going. Finally note that I advocate using the alias

% alias mail Mail

so that you never invoke the unfriendly ``bare'' mail command. Your accounts were initially set up so that this alias was automatically defined.

.forward

Whatever mailer you use, you should make sure that on every distinct home directory you own (recall that you have one home directory on the Linux machines and one on the SGIs), there is a file called '.forward' which contains an e-mail address. That way, mail sent to your username at any machine will be automatically forwarded to the specified address. You can verify for yourself that my .forward on both the Linux machines ('~choptuik/.forward') and the SGIs ('~matt/.forward') contains

matt@infeld.ph.utexas.edu

Of course, your '~/.forward' should contain your own preferred e-mail address.

Creating, Manipulating and Viewing Files (including Directories):

vi or emacs

It is absolutely crucial that you become facile with one of these standard Unix editors and because each editor itself has many sub-commands I refer you to suitably general texts on Unix, or specific books on vi or emacs for detailed information. Either of these two editors will more than suffice for creation, modification and viewing of text files at the level required for this course.

more

Use more to view the contents of one or more files a page at a time. For example:

% more ~/.cshrc
umask 022

limit -h coredumpsize 0

setenv HOMEMWC       /d/einstein/usr/people/matt
setenv SYSTEM        SGI

setenv PRINTER       lp2

--More--(1%)

In this case I have executed the more command in a shell window containing only a few lines (i.e. my pages are short). The

--More--(1%)

message is actually a prompt: hit the spacebar to see the next page, type b to backup a page, and type q to quit viewing the file. Refer to the man page for the many other features of the command. Note that the output from man is typically piped through more.

lpr

Use lpr to print files. By default, files are sent to the system-default printer, or to the printer specified in your PRINTER environment variable (see below). Typical usage is

lpr file_to_be_printed

On the Linux machines, the enscript command is recommended. Type 'man enscript' on those machines for more information.

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 (note that I use semi-colons to separate distinct Unix commands issued on the same line):

% cd
% pwd
/usr/people/matt
% cd ~; pwd
/usr/people/matt
% cd /tmp: pwd
/tmp
% cd ~phy329i; pwd
/usr2/people/phy329i
% cd ..; pwd
/usr2/people
% cd phy329i; pwd
/usr2/people/phy329i

Recall that '..' refers to the parent directory of the working directory so that

% 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. Recall that I advocate the use of the alias

% alias ls 'ls -FC'

which will cause ls to (1) append special characters (notably '*' for executables and '/' for directories) to the names of certain files (the -F option) and (2) list in columns (the -C option). Example;

% cd ~phy329i
% ls
cmd*  hw1/
%

Note that the file 'cmd' is marked executable while 'hw1' is a directory. To see hidden files, use the -a option:

% cd ~phy329i; ls -a 
./               .cshrc           .login           hw1/
../              .cshrc.O         .profile
.Xauthority      .expertInsight   .rhosts
.aliases         .insightrc       cmd*

and to view the files in ``long'' format, use -l:

% cd ~phy329i; ls -l
total 1
-rwxr-xr-x    1 phy329i  choptuik       0 Sep  3 15:50 cmd*
drwxr-xr-x    4 phy329i  choptuik     512 Aug 29 23:14 hw1/

The 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 which are further subdivided as follows:

first character: file type: '-' for regular file, 'd' for directory.
next nine characters: 3 groups of 3 characters each specifying read (r), write (w), and execute (x) permissions for the user (owner of the file), user's in the owner's group and all other users. A '-' in a permission field indicates that the particular permission is denied.

Thus, in the above example, 'cmd' is a regular file, with read, write and execute permissions enabled for the owner (user 'phy329i') and read and execute permissions enabled for member's of group 'choptuik' and all other users. 'hw1' is seen a to be a directory with the same permissions. Note that you must have execute (as well as read) permission for a directory in order to be able to cd to it. See chmod below for more information on setting file permissions. Continuing to decipher the long file listing, the next column list the number of links to this file (if you don't know what a link is, don't worry) then comes the name of the user who owns the file and the owner's group. Next comes the size of the file in bytes, then the date and time the file was last modified and finally the name of the file.

If any of the arguments to ls is a directory, then the contents of the directory is listed. Finally, note that the -R option will recursively list sub-directories:

% cd ~phy329i; pwd
/usr2/people/phy329i
% ls -R
cmd*  hw1/

./hw1:
q4/  q5/

./hw1/q4:
input

./hw1/q5:
First.c   first.f

Note how each sub-listing begins with the relative pathname to the directory followed by a colon. For kicks, you might want to try

% cd /
% ls -R

which will list essentially all the files on the system which you can read (have read permission for). Type '^C' when you get bored.

mkdir

Use mkdir to make (create) one or more directories. Sample usage:

% cd ~
% mkdir tempdir
% cd tempdir; pwd
/usr/people/matt/tempdir

If you need to make a 'deep' directory (i.e. a directory for which one or more parents does not exist) use the -p option to automatically create parents when needed:

% cd ~
% mkdir -p a/long/way/down
% cd a/long/way/down; pwd
/usr/people/matt/a/long/way/down

In this case, the mkdir command made the directories

/usr/people/matt/a   /usr/people/matt/a/long    /usr/people/matt/a/long/way

and, finally

/usr/people/matt/a/long/way/down

cp

Use cp to (1) make a copy of a file, or (2) to copy one or more files to a directory, or (3) to duplicate an entire directory structure. The simplest usage is the first, as in:

% cp foo bar

which 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 /tmp

which will create (or overwrite) files

/tmp/foo   /tmp/bar

with contents identical to 'foo' and 'bar' respectively. Finally, use cp with the -r (recursive) option to copy entire hierarchies:

% cd ~phy329i; ls 
cmd*  hw1/
% cd ..; pwd
/usr2/people
% cp -r phy329i /tmp
% cd /tmp/phy329i; ls
cmd*  hw1/

Study the above example carefully to make sure you understand what happened when the command

% cp -r phy329i /tmp

was issued. In brief, the directory '/tmp/phy329i' was created and all contents (including hidden files) of '/usr2/people/phy329i' were recursively copied into that new directory: sub-directories of '/tmp/phy329i' were automatically created when 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

% ls
thisfile
% mv thisfile thatfile
% ls 
thatfile

while the following sequence illustrates how several files might be moved up one level in the directory hierarchy:

% pwd 
/tmp/lev1
% ls
lev2/
% cd lev2
% ls
file1 file2 file3 file4
% mv file1 file2 file3 ..
% ls
file4
% cd ..
% ls
file1 file2 file3 lev1/

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 restore it other than restoring a copy from backup tapes (assuming the system is regularly backed up). Examples include:

% rm thisfile

to remove a single file,

% rm file1 file2 file3

to remove several files at once, and

% rm -r thisdir

to remove all contents of directory 'thisdir', including the directory itself. Be particular careful with this form of the command and note that

% rm thisdir

will 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'). When you create a new file, the system sets the permissions (or mode) of a file to default values which you can modify using the

% umask

command. (See man umask for more information). On the Linux and SGI 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 which should be useful to you include:

% chmod go-rwx file_or_directory_to_hide

which removes all permissions from 'group' and 'others', effectively hiding the file/directory,

% chmod a+x executable_file

to make a file executable by everyone ('a' stands for all and is the union of user, group and other) and

% chmod u-w file_to_write_protect

to remove the user's (your) write permission to a file to prevent accidental modification of particularly valuable information. Note that permissions are added with a '+' and removed with a '-'.

rcp

Use rcp (whose syntax is an extension of cp) to copy files or hierarchies from one Unix system to another. In order to use this command you must have your '~/.rhosts' file set up properly as described above in the discussion of rlogin. Then, for example, assuming I am logged into one of the SGI machines, the command

% rcp ~/.cshrc choptuik@linux1:~

will copy my '~/.cshrc' file into my home directory on 'linux1'. Note the

user@remotehost:filename

construction to specify a file or directory on the remote machine. Similarly, the command

% rcp choptuik@linux1:~/.cshrc .

will copy my '~/.cshrc' file from 'linux1' to my working directory on the SGI machine. Be very careful using rcp, particularly since there is no -i (cautious) option. Also note that there is a -r option for remote-copying entire hierarchies. Finally, if a suitable entry in the '~/.rhosts' file on the remote machine is not found, the rcp command will tell you:

Permission denied.

MORE ON THE C-SHELL

Shell Variables: The shell maintains a list of local variables, some of which, such as 'path', 'term' and 'shell' are always defined and serve specific purposes within the shell. Other variables, such as 'filec' and 'ignoreeof' are optionally defined and frequently control details of shell operation. Finally, you are free to define you own shell variables as you see fit (but beware of redefining existing variables). By convention, shell variables have all-lowercase names. To see a list of all currently defined shell variables, simply type

% set

To print the value of a particular variable, use the Unix echo command plus the fact that a '$' in front of a variable name, causes the evaluation of that variable:

% echo $path

To set the value of a shell variable use one of the two forms:

% set thisvar=thisvalue
% echo $thisvar
thisvalue

% set thisvarlist=(value1 value2 value3)
% echo $thisvarlist
value1 value2 value3

Shell variables may be defined without being associated a specific value. For example:

% set somevar
% echo $somevar

The shell frequently uses this `defined' mechanism to control enabling of certain features. To ``undefine'' a shell variable use unset as in

% unset somevar
% echo $somevar
somevar - Undefined variable

Following is a list of some of the main shell variables (predefined and optional) and their functions:

path: Stores the current path for resolving commands. See discussion above.
prompt: The current shell prompt---what the shell displays when it's expecting input.
cwd: Contains the name of the (current) working directory.
term: Defines the terminal type. If your terminal is acting strangely
```
	% set term=vt100; resize
```
often provides a quick fix.
noclobber: When set, prevents existing files from being overwritten via output redirection (see below)
filec: When set, enables file-completion. Partially typing a file name (using an initial sequence which is unique among files in the working directory), then typing 'TAB' will result in the system doing the rest of the typing of the file-name for you.
shell: Which particular shell you're using
ignoreeof: When set, will disable shell 'logout' when ^D is typed.

Environment Variables: Unix uses another type of variable---called an environment variable---which is often used for communication between the shell (not necessarily a C-shell) and other processes. By convention, environment variables have all uppercase names. In the C-shell, you can display the value of all currently defined environment variables using

% env

Some environment variables, such as 'PATH' are automatically derived from shell variables. Others have their values set (typically in '~/.cshrc' or '~/.login' ) using the syntax:

% setenv VARNAME value

Note that, unlike the case of shell variables and set, there is no '=' sign in the assignment. The values of individual environment variables may be displayed using printenv or echo:

% printenv HOME
/usr/people/matt
% echo $HOME
/usr/people/matt

Observe that, as with shell variables, the dollar sign causes evaluation of an environment variable. It is particularly notable that the values of environment variables defined in one shell are inherited by commands (including C and Fortran programs, and other shells) which are initiated from that shell. For this reason, environment variables are widely used to communicate information to Unix commands (applications). The DISPLAY environment variable, which every X-application checks to see which display it should use for output s a canonical example.

Following is a list of some of standard environment variables with their functions:

DISPLAY: Tells X-applications which display (screen) to use for output. Typically set on remote machines so that output appears on the local screen. For example, assuming I am remote logged into 'einstein' from the console of 'linux1'. Then, at my 'einstein' prompt, I can type:
```
setenv DISPLAY linux1.ph.utexas.edu:0.0
```
after which all X-applications started on 'einstein' will display on the 'linux1' console. If you encounter problems displaying windows from a remote application on your local console, try typing xhost + at any shell prompt on the local machine. See man xhost for more information
HOME: Stores home directory;
```
cd $HOME/dir1
```
is equivalent to
```
cd ~/dir1
```
PRINTER: Defines default printer for use with lpr, enscript, netscape etc. Check your '~/.cshrc' files on both the SGI and Linux machines for lines which set this variable.

Using C-shell Pattern Matching: The C-shell provides facilities which 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

 
?       Matches any single character
*       Matches any string of characters
[a-z]   (Example) Matches any single character contained in the 
        specified range (the match set)---in this case lower-case 'a' 
        through lower-case 'z'
[^a-z]  (Example) Matches any single character not contained 
        in the specified range

Match sets may also be specified explicitly, as in

[02468]

Examples:

ls ??

lists all regular (not hidden) files and directories whose names contain precisely two characters.

cp a* /tmp

copies all files whose name begins with 'a' to the temporary directory '/tmp'.

mv *.f ../newdir

moves all files whose names end with '.f' to directory '../newdir'. Note that the command

mv *.f *.for

will not rename all files ending with '.f' to files with the same prefixes, but ending in '.for', as is the case on some other operating systems. 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 *.f

which is not at all what was intended.

Using the C-shell History and Event Mechanisms: The C-shell maintains a numbered history of previously entered command lines. Because each line may consist of more than one distinct command (separated by ';'), the lines are called events rather simply commands. Type

% history

after entering a few commands to view the history. Although tcsh (which I assume you are using) allows you to work back through the command history using the up-arrow and down-arrow keys, the following event designators for recalling and modifying events are still useful, particularly if the event number forms part of the shell prompt as it does for your initial set-ups on the Linux and Sgi machines:

!!       Repeat the previous command line
!21      (Example) Repeat command line number 21
!a       (Example) Repeat most recently issued command line which started
         with an 'a'.  Use an initial sub-string of length > 1 for 
         more specificity.
!?b      (Example) Repeat most recently issued command line which contains
         'b'; any string of characters can be used after the '?'

(Note that Unix users often refer to an exclamation point ('!') as ``bang''.) The following constructs are useful for recycling command arguments:

!*       Evaluates to all of the arguments supplied to the previous 
         command
!$       Evaluates to the last argument supplied to the previous command

Finally, the following construct is useful for correcting small typos in command lines:

^old_string^new_string

This changes the first occurrence of old_string in the previous command to new_string then executes the modified command. Example:

% cp foo /usr2/poeple/matt
Cannot create /usr2/poeple/matt
No such file or directory
% ^oe^eo
cp foo /usr2/people/matt

Note that whenever any of the above constructs are used, the shell echoes the effective command before it is executed.

Standard Input, Standard Output and Standard Error: A typical Unix command (process, program) 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 which read and write their input and output from ``standard'' locations. Thus, Unix defines the notions of

standard input: default source of input
standard output: default destination of output
standard error: default destination for error messages and diagnostics

Many Unix commands are designed so that, unless specified otherwise, input is taken from standard input (or stdin), and output is written on standard output (or stdout). Normally, both stdin and stdout are attached to the terminal. The cat command with no arguments provides a canonical example (see man cat if you can't understand the example):

% cat 
foo
foo
bar
bar
^D

Here, 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 which reads from stdin and writes to stdout is known as a filter.

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 which are implemented in the C-shell. 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 which is followed by the name of a file from which the input is to be extracted. Thus the command-line

% cat < input_to_cat

causes 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_cat

has been entered

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_cat

will 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 which will happen in the above example is that the file 'output_from_cat' will be clobbered. If the shell variable 'noclobber' is set (recommended for novices), then output will not be allowed to be redirected to an existing file. Thus, in the above example, if 'output_from_cat' already existed, the shell would respond as follows:

% cat > output_from_cat
output_from_cat: File exists

and the command would be aborted.

The standard output from a command can also be appended to a file using the two-character sequence '>>' (no intervening spaces). Thus

% cat >> existing_file

will 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' which is ideally suited for this purpose. Output redirection to this file, as in:

verbose_command > /dev/null

will 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 which produces output such as:

% pgm_wrong
Time = 0.0 seconds  Force = 6.0 Newtons
Time = 1.0 seconds  Force = 6.1 Newtons
Time = 2.0 seconds  Force = 6.2 Newtons

we write one which produces

% pgm_right
0.0   6.0
1.0   6.1
2.0   6.2

The 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 output 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:

% ls -1 | wc
10     10     82

The -1 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) which appears on the standard output is simply the number of regular files and directories in the current directory.

Pipelines can be made as long as desired, and once you know a few Unix commands and have mastered the basics of the C-shell history mechanism, you can easily accomplish some fairly sophisticated tasks by building up multi-stage pipelines.

Regular Expressions and grep: Regular expressions may be formally defined as those character strings which 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 (or regexps for short) as specifications for rather general patterns which we will wish to detect, usually in the contents of files. Although there are similarities in the Unix specification of regexps to C-shell wildcards (see above), there are important differences as well, so be careful. We begin with regular expressions which match a single character:

a         (Example) Matches 'a', any character other than 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)
.         Matches ANY single character.
[abc]     (Example) Matches any one of 'a', 'b' or 'c'.
[^abc]    (Example) Matches any character which 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.

Multiple-character regexps may then be built up as follows:

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.

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 the

will read lines from stdin (normally the terminal) and echo only those lines which contain the string 'the'. If one or more file arguments are supplied along with the regexp, then grep will search those files for lines matching the regexp, 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 which 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 text

will print all lines of the file 'text' which contain 'the' or 'The' or 'tHe' etc. Second, the -v option instructs grep to print all lines which do not match the pattern; thus

% grep -v the text

will print all lines of text which 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 text

will print, with line numbers, all lines of the file 'text' which 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.

Here are a few slightly more complicated examples. Note that when supplying a regexp which contains characters such as '*', '?', '[', '!' ..., which are special to the shell, the regexp 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 regexp in single quotes.

% grep '^.....$' file1

prints all lines of 'file1' which contain exactly 5 characters.

% grep 'a' file1 | grep 'b'

prints all lines of 'file1' which 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 > output

extracts all lines from file 'input' which 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 which 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 the csh and the Bourne-shell, use the three different types of quotes found on a standard keyboard

    ' ' ->  Known as forward quotes, single quotes, quotes 
    " " ->  Known as double quotes
    ` ` ->  Known as backward quotes, back-quotes

for distinct purposes.

Forward quotes: ' ' We have already encountered several examples of the use of forward quotes which inhibit shell evaluation of any and all special characters and/or constructs. Here's an example:

% set a=100
% echo $a
100

% set b=$a
% echo $b
100

% set b='$a'
% echo $b
$a

Note how in the final assignment, set b='$a', the $a is protected from evaluation by the single quotes. Single quotes are commonly used to assign a shell variable a value which contains whitespace, or to protect command arguments which contain characters special to the shell (see the discussion of grep for an example).

Double quotes: " " Double quotes function in much the same way as forward quotes, except that the shell ``looks inside'' them and evaluates (a) any references to the values of shell variables, and (b) anything within back-quotes (see below). Example:

% set a=100
% echo $a
100

% set string="The value of a is $a"
% echo $string
The value of a is 10

Backward quotes: ' ' The shell uses back-quotes 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 which 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:

% date
Wed Jan 22 13:52:03 CST 1997

% set thedate=`date`
% echo $thedate
Wed Jan 22 13:52:27 CST 1997

% which true
/bin/true

% file `which true`
/bin/true:      /sbin/sh script text

% more `which true`
#!/sbin/sh
#Tag 0x00000f00
#       Copyright (c) 1984, 1986, 1987, 1988, 1989 AT&T
#         All Rights Reserved

#       THIS IS UNPUBLISHED PROPRIETARY SOURCE CODE OF AT&T
#       The copyright notice above does not evidence any
#       actual or intended publication of such source code.

#ident  "@(#)true:true.sh       1.4"
#ident  "$Revision: 1.6 $"

% file `which true` `which false`
/bin/true:      /sbin/sh script text
/bin/false:      /bin/sh script text

Note that the file command attempts to guess what type of contents its file arguments contain and which reports full path names for commands which are supplied as arguments. Observe that in the last example, multiple back-quoting constructs are used on a single command line.

Finally, here's an example illustrating that back-quote substitution is enabled for strings within double quotes, but disabled for strings within single quotes:

% set var1="The current date is `date`"
% echo $var1
The current date is Thu Jan 23 15:12:57 CST 1997

% set 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, only one process can run at a specific time, so this simultaneity is 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 &
[1] 1299

In this example, the shell responds with a '[1]' which identifies the task at the shell level, and a '1299' (the process id) which 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]    Done   grep the huge_file > grep_output

The following sequence illustrates another way to run the same job in the background:

% grep the huge_file > grep_output 
^Z  
Stopped
% bg
[1] grep the huge_file > grep_output &

Here, typing '^Z' while the command is running in the foreground stops (suspends) the job, the shell command bg restarts it in the foreground. You can see which jobs are running or stopped by using the shell jobs command.

% jobs
[1] + Stopped    grep the huge_file > grep_output
[2]   Running    other_command

Use

% fg %1

to make run the job labeled '[1]' (which may either be stopped or running in the background), run in the foreground. You can kill a job using its job number (%1, %2, etc.)

% kill %1
[1]  Terminated    grep the huge_file > grep_output

You 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. 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.