Introduction to Unix
CONTENTS
INTRODUCTION
This document is intended to help the new user of computers that run a version of the Unix operating system. It is primarily aimed at users of the ITC clusters, which run a version of Unix called Linux.
The command interpreter described in this document is the bash shell, which acts as an interface between the user and the Unix system. Bash is standard on Linux systems, but currently many users use the Korn shell (ksh). Users may change shell on Blue, but the commands typed at the command line are nearly identical for ksh and bash; the main difference is in support for features such as filename completion and history.
THINGS TO REMEMBER
The Unix operating system is case-sensitive; i.e., a command in lower-case letters is interpreted differently from one in capital letters. Make sure your caps-lock key is not engaged. Enter all commands in lower-case letters unless otherwise instructed.
Be sure to end everything that you type with a carriage return (marked Return). The Return key is shown as
<CR>in this document.
GETTING STARTED
Connecting to a Unix Computer
To connect to a remote Unix machine, you must install a client for Secure Shell (ssh) on your local computer. For Windows we recommend SecureCRT, available for UVa affiliates through Software Central. Mac OSX has ssh built in; start the Terminal application and type ssh mst3k@hostname.itc.virginia.edu. Replace the examples with your own information, of course.
Logging In and Changing Your Password
If you wish to change your password, log on to blue.unix.virginia.edu and type passwd. It will ask for your old password and after verifying it, will ask for your new choice. Enter a new password with six to eight characters including at least one numeric or special character. The system will let you know if the password does not meet our security requirements. You will be asked to enter the password twice for confirmation.
Choosing a password that provides system security is important, not only to protect your files, but also to protect the entire system from being accessed by the mischievous or unscrupulous. Do not use your name or initials or any word that can be found in the dictionary. Putting a number in the place of a letter (the digit 1 for the letter l, for instance) is not by itself not secure, nor is putting a digit at the beginning or end of a word or name. It is safer to use a sequence that is meaningful only to you, or to use the first letters of a phrase you can remember, with digits and special characters added and/or substituting for letters.
Terminating and Pausing a Command, Halting Screen Output and Logging Out
Terminating and Pausing a Command
If you want to stop a command before it completes execution, press the control and c keys simultaneously (usually denoted by ^C or control-c). This should return you to your initial prompt.
To pause a process, type control-z. To resume it, type fg (foreground). To send it to the background, i.e. to have it continue to run but to regain the prompt, type bg.
To run any Unix command in the background so that you can continue other work at your terminal, append an ampersand (&) to the command. You will immediately be returned to the system prompt so that you can issue other commands. The command jobs will show you the status of your background jobs.
Halting Screen Output
If you want to temporarily halt output to your screen without terminating the execution of the command, enter Ctrl-s. Start output again by entering Ctrl-q.
Logging Out
When you are ready to log out, type exit.
Tutorial
We strongly recommend that beginners go through the tutorials, especially the first four.
FILES
The File System
Unix uses a hierarchical (or tree-structured) directory system to store files. A diagram of a portion of a file tree is shown below, with the directory /, called the "root" directory, at the top of the tree.
In the Unix system, all the commands you type, as well as peripheral devices such as disk, can be specified as a path to a file. A path name can be absolute, meaning it begins with /, or relative to the directory where you are attached, called the current or working directory. Directory names are separated by additional slashes (e.g., /etc/passwd). In the figure above, some of the directories shown are:
|
Name |
Directory Contents |
Name |
Directory Contents |
|
/bin |
Unix utilities, such as |
/etc |
administrative files |
|
/usr |
additional utilities |
/lib |
libraries, such as C |
|
/tmp |
temporary files; this |
/dev |
peripheral devices, |
|
/home |
user directories |
/uva |
locally installed utilities |
You will be assigned a directory with your login ID as its name when you are given an account. The user accounts reside in the /home directory. When you complete the login process, you will be attached at the directory /home/your-login-id in the file tree. Your login directory is called your HOME directory, where $HOME is one of the Unix system's environment variables. Environment variables are a type of shell variable that apply to the user's current shell and all subshells.
You can create other directories and files below your HOME directory as you need them. For instance, if your login ID is "mst3k," you may be assigned a HOME directory with the name /home/mst3k. If you create a subdirectory named "docs", you could put all the chapters of your thesis in that directory. Then the full path of a file named "chap1.thesis" would be
/home/mst3k/docs/chap1.thesis
Unix Command Syntax
The typical syntax of a Unix command is
command arguments files
where the command options, also called arguments, are usually preceded by a hyphen (-). More than one file name may sometimes be given. In our notation, optional arguments will be surrounded by square brackets ([ ]) in the documentation on each command.
The table below gives some commands and selected options that are useful for manipulating files and moving around in the file system, including how to list the contents of a directory (ls), the contents of a file (cat or more) and how to move from directory to directory (cd). To get complete information on each command and all its options, use man command to view the on-line documentation. The syntax is:
man command
|
Command |
Meaning |
Result |
|
cat filename(s) |
catenate |
list contents of filename(s) to the screen, |
|
cd directory |
change directory |
change working directory to directory; |
|
cp file1 file2 |
copy |
make a new copy of file1 called file2 |
|
diff file1 file2 |
difference |
list the differences between file1 and |
|
find dir -name file -print |
find |
find files beginning search at directory |
|
grep [-i] string file(s) |
global regular |
search file(s) for string and list |
|
head filename(s) |
|
list first ten lines of filename(s) |
|
ls [-AlpsCF] |
list |
return a list of the files in -A all entries, including files beginning with period
(.) |
|
mkdir dir |
make directory |
create a new directory named dir |
|
more filename(s) |
|
list contents of filename(s) a |
|
mv name1 name2 |
move |
rename file name1 to become |
|
page filename(s) |
|
same as more |
|
pwd |
print working directory |
list the pathname of the working |
|
rm [-i] |
remove |
delete a file; the -i option queries |
|
rmdir directory |
remove directory |
delete directory; |
|
tail filename(s) |
|
list last ten lines of filename(s) |
|
tee filename(s) |
|
input to tee is sent to both |
|
wc filename(s) |
word count |
list the number of lines, words |
The ls Command
Sample output from the command ls -Al is shown below with column numbers at the top for reference with the explanation following.
1 2 3 4 5 6 7 8 _________________________________________________________________________ -rm-r--r-- 1 mst3k usr 4193 Jun 10 10:11 .history -rw-r--r-- 1 mst3k usr 626 Jun 6 12:08 .kshrc -rw-r--r-- 1 mst3k usr 338 Mar 17 16:43 .mailrc -rw-r--r-- 1 mst3k usr 9156 Nov 9 13:06 .newsrc -rw-r--r-- 1 mst3k usr 800 Jun 6 14:28 .profile -rw-r--r-- 1 mst3k usr 1424 Jun 6 14:28 .variables.ksh drwxr-xr-x 2 mst3k usr 144 Jun 9 16:21 News drwxr-xr-x 4 mst3k usr 144 Apr 16 14:34 docs drwxr-xr-x 2 mst3k usr 64 Jun 3 10:34 fortran_progs -rw-r--r-- 1 mst3k usr 3289 Nov 9 10:09 junk
|
Column 1: |
Ten characters giving file information; first character (-, l or d) is type of file; remaining nine are permissions. The first entry will generally be one of the following: d = directory The next nine characters specify the file permissions given to user mst3k (first three characters), the group to which mst3k belongs (next three), and the other users on the system (last three). At UVa, the group to which the user belongs will generally be the same as all other users. The permission characters are as follows: r for read If all permissions are given for a file, these entries would be rwxrwxrwx which gives the user, group and other read, write and execute permissions. For more information, see the section "Setting File Permissions with chmod." |
|
Column 2: |
links; for a file, this is the number of links to the file (see the man page on ln to read more about links); for a directory, it is the number of directories it is in (its parent and itself) plus the directories under it. |
|
Column 3: |
owner of file. |
|
Column 4: |
group to which owner belongs. |
|
Column 5: |
number of bytes (characters) in the file. |
|
Column 6: |
date file was last modified. |
|
Column 7: |
time file was last modified. |
|
Column 8: |
file name. |
Setting File Permissions with chmod
One way to set the permissions on files and directories is with the chmod command. The command syntax is as follows:
chmod mode filename
where
mode is a string of users and permissions and filename is the name of the file whose permissions are to be changed.
The example shown below gives mode as a string defined to be who_permission where who is
u = user (mst3k in the example above)
g = group (usr in the example above)
o = other
a = all (default)and
+ = gives permission
- = denies permissionand permission is
r = read
w = write
x = execute
|
Example 1: |
You want to remove read permission on a file named "personal" from everyone except you. Use the command: chmod go-r personal |
|
Example 2: |
You want to make a command file called "printit" readable and executable by everyone. Use the commands: chmod ugo+rx printit chmod a+rx printit |
Some Special Characters
Some characters have special meaning to the Unix system's shell interpreter. These can be used so that you do not need to type long names of directories and files, or they can be used to "wildcard" (match more than one) directory and file name. Some of these characters are defined below.
|
File Expansion Characters |
Explanation |
|
. |
Current directory |
|
.. |
Parent of current directory |
|
~/ |
The system
will expand ~ before / to |
|
~login_ID |
The system
will expand ~ before a login_ID to |
|
* |
Matches 0
or more characters; does not |
|
? |
Matches any single character |
|
[...] |
Matches
one character in a specification where |
INPUT/OUTPUT AND REDIRECTION
Every Unix process has three files that are normally associated with the console (in modern usage, the user's terminal); these files are called standard input (the keyboard, file descriptor 0), standard output (the screen, file descriptor 1), and standard error (file descriptor 2). One of the features provided by the Unix shell is the ability to redirect these "invisible" files to named disk files. Some of the characters used for redirection by the bash shell are:
|
Redirection Character |
Use |
|
> |
Write output from a command to a file |
|
>> |
Append output from a command to a file |
|
< |
Read input to a command from a file |
|
| |
Send ("pipe") output from one |
The pipe is an example of how Unix commands can be chained together to accomplish very complex tasks in a single line.
Examples
To send all the Fortran compiler error messages to a file called "compile.out" rather than have them come to the screen:
gfortran myprog.f >& compile.out
To join "file1" and "file2", send the output to the sort command and then put the sorted output into a file called "sorted.big.file":
cat file1 file2 | sort >sorted.big.file
Special Files
It is possible to customize your Unix environment by editing the appropriate files. You can change the names of commands as well as specify which command options are selected.
When you log in, the system reads .profile (ksh, bash) or .bash_profile (bash), or .login (tcsh) to set your environment. All subsequent non-login shells read .kshrc (ksh), .bashrc (bash), or .tcshrc (tcsh).
The following are some of the reconfiguration files you may see when you issue the ls -A command.
|
.profile |
used by the Korn shell to set the user's environment at login |
|
.variables.ksh |
used by ITC to set values for certain shell variables |
|
.kshrc |
sets user's command aliases, if specified |
|
.history |
stores commands you have issued |
Default .profile, .variables.ksh, and .kshrc files exist, but you can create your own versions of these files to set your initialization preferences. You can look at and modify any of these files, though you should not normally modify .bash_history, which holds a list of your previous commands.
Shell Variables
The shell sets up some special variables, called shell variables, that are read by Unix commands. One way that the Unix environment can be tailored is to change the values of these variables. A complete list of the shell variables set up by the Korn shell can be found on the ksh man page.
An an environment variable is a shell variable that is exported to child shells. It is conventionally written in upper-case letters (remember that Unix is case-sensitive) and its value is often a path to a directory or file. Envirionment variables are usually set in the .profile, .bash_profile, or .login files since children of the login shell will inherit them. (Note that Unix distinguishes between login and non-login shells.) Ordinary shell variables apply only to a given shell and are conventionally set in the .kshrc, .bashrc, or .[t]cshrc file.
Some shell variables are described below.
|
EDITOR |
name of editor you use |
|
ENV |
specifies file to be executed at shell invocation; |
|
HISTSIZE |
number of commands stored (default is 128) |
|
HOME |
default is current directory when you log in; e.g., /home/abc3f |
|
PATH |
search path used to find executable files (commands) |
|
PS1 |
prompt |
The PATH environment variable has special importance since it names the directories (separated by colons) that the system will search for commands you type. The directories are searched in order from left to right. For example, if you invoke the ls command by typing the complete path /bin/ls, the value of PATH would not be used since there is a / in the command. However, if you type ls, the system searches the directories given in the PATH variable. The first executable file named "ls" found in one of the PATH directories will be executed. If no file is found, the error message command not found will appear.
To see the current value of the PATH, issue the command:
printenv $PATH
The directory specified by "." represents the current directory.
If you create your own executable command files (e.g., C programs or Unix shell scripts), you could put them in a "bin" directory in your HOME directory. To get the system to search that directory, set your PATH value to
PATH=${HOME}/bin:${PATH}
which will cause the system to search your bin directory before searching other directories.
To see the current values of all environment variables, issue the command printenv (bash or tcsh) or (ksh or bash) env.
The shell provides the user with command aliasing, which is a way to rename a command along with your favorite options to a name of your choice. To see the current aliases, issue the command alias with no parameters. The default ITC startup scripts define several aliases.
Terminating Runaway Processes
The ps command
The kill-9 processID command terminates process number
processID, which is
determined by issuing the ps
command. Use with discretion.
|
ps [-eflu] or ps [x] |
lists running processes (RS, SGI, Solaris) |
|
ps [-alux] |
lists running processes (SunOS) |
APPENDIX: SOME UTILITY COMMANDS
|
Utility Commands |
Result |
|---|---|
|
cal month year |
return a calendar for month (digit 1-12) |
|
calendar |
read a file named "calendar" in your HOME
|
|
cut (-clist filename | -flist filename) |
return list of columns or fields from filename |
|
date |
return date and time of day |
|
df |
disk free; return available disk space in |
|
du directory |
disk usage; return number of blocks used by directory |
|
expand filename |
replace each tab character in filename with spaces |
|
file filename |
show the type of a file (e.g., ascii, |
|
man [-k] command |
return a copy of the manual page for command; |
|
sort filename |
sort filename in ascending order; |