Unix Tutorial Eight

8.1 UNIX Variables
                  Variables are a way of passing information from the shell to programs when you run them. Programs look "in the environment" for particular variables and if they are found will use the values stored. Some are set by the system, others by you, yet others by the shell, or any program that loads another program.
                   Standard UNIX variables are split into two categories, environment variables and shell variables. In broad terms, shell variables apply only to the current instance of the shell and are used to set short-term working conditions; environment variables have a farther reaching significance, and those set at login are valid for the duration of the session. By convention, environment variables have UPPER CASE and shell variables have lower case names.

8.2 Environment Variables
                    An example of an environment variable is the OSTYPE variable. The value of this is the current operating system you are using. Type
% echo $OSTYPE

More examples of environment variables are

• USER (your login name)
• HOME (the path name of your home directory)
• HOST (the name of the computer you are using)
• ARCH (the architecture of the computers processor)
• DISPLAY (the name of the computer screen to display X windows)
• PRINTER (the default printer to send print jobs)
• PATH (the directories the shell should search to find a command)

Finding out the current values of these variables.

ENVIRONMENT variables are set using the setenv command, displayed using the printenv or env commands, and unset using the unsetenv command.
To show all values of these variables, type
% printenv | less

8.3 Shell Variables
                  An example of a shell variable is the history variable. The value of this is how many shell commands to save, allow the user to scroll back through all the commands they have previously entered. Type
% echo $history

More examples of shell variables are

• cwd (your current working directory)
• home (the path name of your home directory)
• path (the directories the shell should search to find a command)
• prompt (the text string used to prompt for interactive commands shell your login shell)

Finding out the current values of these variables.
                  SHELL variables are both set and displayed using the set command. They can be unset by using the unset command.
To show all values of these variables, type
% set | less

So what is the difference between PATH and path ?
                  In general, environment and shell variables that have the same name (apart from the case) are distinct and independent, except for possibly having the same initial values. There are, however, exceptions.
                  Each time the shell variables home, user and term are changed, the corresponding environment variables HOME, USER and TERM receive the same values. However, altering the environment variables has no effect on the corresponding shell variables.
                   PATH and path specify directories to search for commands and programs. Both variables always represent the same directory list, and altering either automatically causes the other to be changed.

8.4 Using and setting variables
                   Each time you login to a UNIX host, the system looks in your home directory for initialisation files. Information in these files is used to set up your working environment. The C and TC shells uses two files called .login and .cshrc (note that both file names begin with a dot).
At login the C shell first reads .cshrc followed by .logi

1.      .login is to set conditions which will apply to the whole session and to perform actions that are relevant only at login.
2.      .cshrc is used to set conditions and perform actions specific to the shell and to each invocation of it.

The guidelines are to set ENVIRONMENT variables in the .login file and SHELL variables in the .cshrc file.

WARNING: NEVER put commands that run graphical displays (e.g. a web browser) in your .cshrc or .login file.

8.5 Setting shell variables in the .cshrc file
                   For example, to change the number of shell commands saved in the history list, you need to set the shell variable history. It is set to 100 by default, but you can increase this if you wish.
% set history = 200
Check this has worked by typing
% echo $history
However, this has only set the variable for the lifetime of the current shell. If you open a new xterm window, it will only have the default history value set. To PERMANENTLY set the value of history, you will need to add the set command to the .cshrc file.
First open the .cshrc file in a text editor. An easy, user-friendly editor to use is nedit.
% nedit ~/.cshrc

Add the following line AFTER the list of other commands.
set history = 200

Save the file and force the shell to reread its .cshrc file buy using the shell source command.
% source .cshrc

Check this has worked by typing
% echo $history

8.6 Setting the path
                    When you type a command, your path (or PATH) variable defines in which directories the shell will look to find the command you typed. If the system returns a message saying "command: Command not found", this indicates that either the command doesn't exist at all on the system or it is simply not in your path.
                    For example, to run units, you either need to directly specify the units path (~/units174/bin/units), or you need to have the directory ~/units174/bin in your path.
                     You can add it to the end of your existing path (the $path represents this) by issuing the command:
% set path = ($path ~/units174/bin)

Test that this worked by trying to run units in any directory other that where units is actually located.
% cd; units

HINT: You can run multiple commands on one line by separating them with a semicolon.

To add this path PERMANENTLY, add the following line to your .cshrc AFTER the list of other commands.
set path = ($path ~/units174/bin)



M.Stonebank@surrey.ac.uk October 2001

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Unix Tutorial Seven

7.1 Compiling UNIX software packages
               We have many public domain and commercial software packages installed on our systems, which are available to all users. However, students are allowed to download and install small software packages in their own home directory, software usually only useful to them personally.
There are a number of steps needed to install the software.

• Locate and download the source code (which is usually compressed)
• Unpack the source code
• Compile the code
• Install the resulting executable
• Set paths to the installation directory

Of the above steps, probably the most difficult is the compilation stage

Compiling Source Code
                      All high-level language code must be converted into a form the computer understands. For example, C language source code is converted into a lower-level language called assembly language. The assembly language code made by the previous stage is then converted into object code which are fragments of code which the computer understands directly. The final stage in compiling a program involves linking the object code to code libraries which contain certain built-in functions. This final stage produces an executable program.
                  To do all these steps by hand is complicated and beyond the capability of the ordinary user. A number of utilities and tools have been developed for programmers and end-users to simplify these steps.

make and the Makefile
                  The make command allows programmers to manage large programs or groups of programs. It aids in developing large programs by keeping track of which portions of the entire program have been changed, compiling only those parts of the program which have changed since the last compile.
                   The make program gets its set of compile rules from a text file called Makefile which resides in the same directory as the source files. It contains information on how to compile the software, e.g. the optimisation level, whether to include debugging info in the executable. It also contains information on where to install the finished compiled binaries (executables), manual pages, data files, dependent library files, configuration files, etc.
                   Some packages require you to edit the Makefile by hand to set the final installation directory and any other parameters. However, many packages are now being distributed with the GNU configure utility.

configure
                As the number of UNIX variants increased, it became harder to write programs which could run on all variants. Developers frequently did not have access to every system, and the characteristics of some systems changed from version to version. The GNU configure and build system simplifies the building of programs distributed as source code. All programs are built using a simple, standardised, two step process. The program builder need not install any special tools in order to build the program.
                The configure shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses those values to create a Makefile in each directory of the package.
                The simplest way to compile a package is:

• cd to the directory containing the package's source code.
• Type ./configure to configure the package for your system.
• Type make to compile the package.
• Optionally, type make check to run any self-tests that come with the package.
• Type make install to install the programs and any data files and documentation.
• Optionally, type make clean to remove the program binaries and object files from the source code directory 

          The configure utility supports a wide variety of options. You can usually use the --help option to get a list of interesting options for a particular configure script.
          The only generic options you are likely to use are the --prefix and --exec-prefix options. These options are used to specify the installation directories.
           The directory named by the --prefix option will hold machine independent files such as documentation, data and configuration files.
            The directory named by the --exec-prefix option, (which is normally a subdirectory of the --prefix directory), will hold machine dependent files such as executables.

7.2 Extracting the source code
                 Go into your download directory and list the contents.
% cd download
% ls -l

As you can see, the filename ends in tar.gz. The tar command turns several files and directories into one single tar file. This is then compressed using the gzip command (to create a tar.gz file).
First unzip the file using the gunzip command. This will create a .tar file.
% gunzip units-1.74.tar.gz

Then extract the contents of the tar file.
% tar -xvf units-1.74.tar

Again, list the contents of the download directory, then go to the units-1.74 sub-directory.
% cd units-1.74

7.3 Configuring and creating the Makefile
                    The first thing to do is carefully read the README and INSTALL text files (use the less command). These contain important information on how to compile and run the software.
                     The units package uses the GNU configure system to compile the source code. We will need to specify the installation directory, since the default will be the main system area which you will not have write permissions for. We need to create an install directory in your home directory.
% mkdir ~/units174
 
Then run the configure utility setting the installation path to this.
% ./configure --prefix=$HOME/units174

NOTE:
The $HOME variable is an example of an environment variable.
The value of $HOME is the path to your home directory. Just type
% echo $HOME
to show the contents of this variable. We will learn more about environment variables in a later chapter.

If configure has run correctly, it will have created a Makefile with all necessary options. You can view the Makefile if you wish (use the less command), but do not edit the contents of this.

7.4 Building the package
                 Now you can go ahead and build the package by running the make command.
% make

After a minute or two (depending on the speed of the computer), the executables will be created. You can check to see everything compiled successfully by typing
% make check

If everything is okay, you can now install the package.
% make install

This will install the files into the ~/units174 directory you created earlier.

7.6 Running the software
                   You are now ready to run the software (assuming everything worked).
% cd ~/units174

If you list the contents of the units directory, you will see a number of subdirectories.
bin                        The binary executables
info                       GNU info formatted documentation
man                      Man pages
share                    Shared data files

To run the program, change to the bin directory and type
% ./units

As an example, convert 6 feet to metres.
You have: 6 feet
You want: metres

* 1.8288

If you get the answer 1.8288, congratulations, it worked.
To view what units it can convert between, view the data file in the share directory (the list is quite comprehensive).
To read the full documentation, change into the info directory and type
% info --file=units.info

7.7 Stripping unnecessary code
                   When a piece of software is being developed, it is useful for the programmer to include debugging information into the resulting executable. This way, if there are problems encountered when running the executable, the programmer can load the executable into a debugging software package and track down any software bugs.
                    This is useful for the programmer, but unnecessary for the user. We can assume that the package, once finished and available for download has already been tested and debugged. However, when we compiled the software above, debugging information was still compiled into the final executable. Since it is unlikey that we are going to need this debugging information, we can strip it out of the final executable. One of the advantages of this is a much smaller executable, which should run slightly faster.
                    What we are going to do is look at the before and after size of the binary file. First change into the bin directory of the units installation directory.
% cd ~/units174/bin

% ls -l

As you can see, the file is over 100 kbytes in size. You can get more information on the type of file by using the filecommand.
% file units

units: ELF 32-bit LSB executable, Intel 80386, version 1, dynamically linked (uses shared libs), not stripped
To strip all the debug and line numbering information out of the binary file, use the strip command
% strip units

% ls -l
As you can see, the file is now 36 kbytes - a third of its original size. Two thirds of the binary file was debug code !!!
Check the file information again.
% file units

units: ELF 32-bit LSB executable, Intel 80386, version 1, dynamically linked (uses shared libs), stripped

HINT: You can use the make command to install pre-stripped copies of all the binary files when you install the package.

Instead of typing make install, simply type make install-strip





M.Stonebank@surrey.ac.uk, © October 2001

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Unix Tutorial Six

Other useful UNIX commands
quota
               All students are allocated a certain amount of disk space on the file system for their personal files, usually about 100Mb. If you go over your quota, you are given 7 days to remove excess files.
To check your current quota and how much of it you have used, type
% quota -v

df
                The df command reports on the space left on the file system. For example, to find out how much space is left on the fileserver, type
% df .

du
                The du command outputs the number of kilobyes used by each subdirectory. Useful if you have gone over quota and you want to find out which directory has the most files. In your home-directory, type
% du

compress
                 This reduces the size of a file, thus freeing valuable disk space. For example, type
% ls -l science.txt
and note the size of the file. Then to compress science.txt, type
% compress science.txt

This will compress the file and place it in a file called science.txt.Z
To see the change in size, type ls -l again.
To uncomress the file, use the uncompress command.
% uncompress science.txt.Z

gzip
                   This also compresses a file, and is more efficient than compress. For example, to zip science.txt, type
% gzip science.txt

This will zip the file and place it in a file called science.txt.gz
To unzip the file, use the gunzip command.
% gunzip science.txt.gz

file
                     file classifies the named files according to the type of data they contain, for example ascii (text), pictures, compressed data, etc.. To report on all files in your home directory, type
% file *

history
                    The C shell keeps an ordered list of all the commands that you have entered. Each command is given a number according to the order it was entered.
% history (show command history list)

If you are using the C shell, you can use the exclamation character (!) to recall commands easily.

% !! (recall last command)

% !-3 (recall third most recent command)

% !5 (recall 5th command in list)

% !grep (recall last command starting with grep)

You can increase the size of the history buffer by typing

% set history=100





M.Stonebank@surrey.ac.uk, © 24th August 2001

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Unix Tutorial Five

5.1 File system security (access rights)
           In your unixstuff directory, type

% ls -l (l for long listing!)

           You will see that you now get lots of details about the contents of your directory, similar to the example below.

            Each file (and directory) has associated access rights, which may be found by typing ls -l. Also, ls -lg gives additional information as to which group owns the file (beng95 in the following example):

-rwxrw-r-- 1 ee51ab beng95 2450 Sept29 11:52 file1

In the left-hand column is a 10 symbol string consisting of the symbols d, r, w, x, -, and, occasionally, s or S. If d is present, it will be at the left hand end of the string, and indicates a directory: otherwise - will be the starting symbol of the string.
The 9 remaining symbols indicate the permissions, or access rights, and are taken as three groups of 3.

• The left group of 3 gives the file permissions for the user that owns the file (or directory) (ee51ab in the above example); 
• the middle group gives the permissions for the group of people to whom the file (or directory) belongs (eebeng95 in the above example);
• the rightmost group gives the permissions for all others.

The symbols r, w, etc., have slightly different meanings depending on whether they refer to a simple file or to a directory.

Access rights on files.

• r (or -), indicates read permission (or otherwise), that is, the presence or absence of permission to read and copy the file 
• w (or -), indicates write permission (or otherwise), that is, the permission (or otherwise) to change a file 
• x (or -), indicates execution permission (or otherwise), that is, the permission to execute a file, where appropriate

Access rights on directories.

• r allows users to list files in the directory;
• w means that users may delete files from the directory or move files into it;
• x means the right to access files in the directory. This implies that you may read files in the directory provided you have read permission on the individual files.

So, in order to read a file, you must have execute permission on the directory containing that file, and hence on any directory containing that directory as a subdirectory, and so on, up the tree.

Some examples

-rwxrwxrwx            a file that everyone can read, write 

                                     and execute (and delete).
-rw-------                  a file that only the owner can read and write - no-one else
                                     can read or write and no-one has execution rights (e.g. your
                                     mailbox file).

5.2 Changing access rights

chmod (changing a file mode)

Only the owner of a file can use chmod to change the permissions of a file. The options of chmod are as follows
SymbolMeaning

u                               user
g                                group
o                                other
a                                all
r                                read
w                               write (and delete)
x                                execute (and access directory)
+                               add permission
-                                 take away permission

For example, to remove read write and execute permissions on the file biglist for the group and others, type

% chmod go-rwx biglist

This will leave the other permissions unaffected.
To give read and write permissions on the file biglist to all,

% chmod a+rw biglist

Exercise 5a

Try changing access permissions on the file science.txt and on the directory backups
Use ls -l to check that the permissions have changed.

5.3 Processes and Jobs

A process is an executing program identified by a unique PID (process identifier). To see information about your processes, with their associated PID and status, type

% ps

A process may be in the foreground, in the background, or be suspended. In general the shell does not return the UNIX prompt until the current process has finished executing.
Some processes take a long time to run and hold up the terminal. Backgrounding a long process has the effect that the UNIX prompt is returned immediately, and other tasks can be carried out while the original process continues executing.
Running background processes
               To background a process, type an & at the end of the command line. For example, the command sleep waits a given number of seconds before continuing. Type

% sleep 10

This will wait 10 seconds before returning the command prompt %. Until the command prompt is returned, you can do nothing except wait.
To run sleep in the background, type

% sleep 10 &

[1] 6259

The & runs the job in the background and returns the prompt straight away, allowing you do run other programs while waiting for that one to finish.
The first line in the above example is typed in by the user; the next line, indicating job number and PID, is returned by the machine. The user is be notified of a job number (numbered from 1) enclosed in square brackets, together with a PID and is notified when a background process is finished. Backgrounding is useful for jobs which will take a long time to complete.
Backgrounding a current foreground process
At the prompt, type

% sleep 100

You can suspend the process running in the foreground by holding down the [control] key and typing [z] (written as ^Z) Then to put it in the background, type

% bg

Note: do not background programs that require user interaction e.g. pine

5.4 Listing suspended and background processes
                 When a process is running, backgrounded or suspended, it will be entered onto a list along with a job number. To examine this list, type

% jobs

An example of a job list could be

[1] Suspended sleep 100
[2] Running netscape
[3] Running nedit

To restart (foreground) a suspended processes, type

% fg %jobnumber

For example, to restart sleep 100, type

% fg %1

Typing fg with no job number foregrounds the last suspended process.

5.5 Killing a process

kill (terminate or signal a process)

It is sometimes necessary to kill a process (for example, when an executing program is in an infinite loop)
To kill a job running in the foreground, type ^C (control c). For example, run

% sleep 100
^C

To kill a suspended or background process, type

% kill %jobnumber

For example, run

% sleep 100 &
% jobs

If it is job number 4, type

% kill %4

To check whether this has worked, examine the job list again to see if the process has been removed.

ps (process status)
                      Alternatively, processes can be killed by finding their process numbers (PIDs) and using kill PID_number

% sleep 100 &
% ps

PID TT S TIME COMMAND
20077 pts/5 S 0:05 sleep 100
21563 pts/5 T 0:00 netscape
21873 pts/5 S 0:25 nedit

To kill off the process sleep 100, type

% kill 20077

and then type ps again to see if it has been removed from the list.

If a process refuses to be killed, uses the -9 option, i.e. type

% kill -9 20077

Note: It is not possible to kill off other users' processes !!!

Summary

ls -lag                                          list access rights for all files
chmod [options] file            change access rights for named file
command &                              run command in background
^C                                                 kill the job running in the foreground
^Z                                                 suspend the job running in the foreground
bg                                                  background the suspended job
jobs                                              list current jobs
fg %1                                            foreground job number 1
kill %1                                         kill job number 1
ps                                                  list current processes
kill 26152                                  kill process number 26152






M.Stonebank@surrey.ac.uk, 9th October 2000

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