Computing in the Special Research Centre for the Subatomic Structure of Matter
and National Institute for Theoretical Physics
Welcome to the Special Research Centre for the Subatomic Structure of Matter Computing Facilities. This document gives an outline of what computing facilities are available to you and recommended usage policies.
Problems, Questions and Suggestions
When you log in you should see a row of buttons running down the left side of your screen, a clock on the top right and a window called "Desktop" on the bottom right. The buttons contain the most common applications you are likely to use. Here is a description of each:
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Manual: |
tkman - An index of manual pages for commands |
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Terminal: |
xterm - Terminal Window. You will type most of your commands from here |
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File Manager: |
xfm - a basic file manager |
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Mail: |
pine - A mail reader. Pine and elm are supported in this department but pine is recommended. |
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Text Editor: |
emacs - the text editor that does everything! Start it and type Ctrl-h t for a tutorial on how to use it. |
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Netscape: |
netscape - The world famous World Wide Web browser. This is what "surfin' the net" is all about. |
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Drawing: |
xfig - a drawing package. This package will produce postscript files and EPS files that you can include in your LaTeX documents |
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GhostView: |
ghostview - a postscript previewer |
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Calculator |
xcalc - a calculator (duh) |
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PicViewer: |
xv - lets you view pictures in gif, jpeg and heaps of other formats. |
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Logout: |
Press this button to logout. BUT PLEASE ensure that you have exited any netscape or emacs windows you may have open to prevent rogue processes remaining on the machine. |
Fvwm is a "Virtual Window" manager. This means that your "desktop" (what you see on the screen) can be bigger than your "window" (the size of the monitor). The default is that your desktop is four windows big (2x2). To go to the next window, move the mouse to the edge of your window. You can also use Control key with the arrow keys to move. In the Desktop window on the bottom right hand corner you will see the current window move to the next one.
Your mouse has three buttons - left, middle and right. Each one has menus bound to it. These menus come up when the mouse is on the desktop (looks like an X). The most important of these is the menu on the right button. This menu gives you access to the other hosts in the department. The first item is called "Local Host". This is the same as the terminal button mentioned above. The other items are cascading menus that list groups of hosts organised by groups. By selecting an item (eg CSSM) and then a sub-item (eg born) you can log into that host. You should be able to log into all hosts listed under 'Departmental Hosts' and also the hosts listed in the group to which you belong.
Your .xinitrc is set up so that to exit you press the Logout button on the left side of your screen. Make sure you have saved any work you are working on as the exit procedure DOES NOT CHECK FOR UNSAVED FILES.
To change your password use:
yppasswd.Your new password won't come into effect immediately. It usually takes 5 - 10 minutes.
When running long jobs type:
nice +10 <command> where <command> is the name of your job. This lets jobs run at a niceness (priority) of 10 so that interactive users are not disadvantaged (the higher the number, the lower the priority). It is departmental policy that any jobs that run for more than 10 CPU minutes must be run at a niceness of 10.If you want to customize your environment the files
.mycshrc and .mylogin are provided instead of .login and .chsrc, a useful example is to set your default printer in .mycshrc, then you don't need to specify it each time you print a file (eg: setenv PRINTER lxk4). To find out more about customizing your environment read the manual page on csh. You do this by typing man csh. This is also a good introduction to UNIX.There are two printers available for general use and a colour one for presentation transparencies. Each queue has a name. The laser queues are called
lxk4, lxk13. The printers are identical Lexmark printers both are set to print A4 double-side and recognise postscript level three.|
lxk4: |
located in Capital building (10 Pulteney St.) on level 4, you can print from both Unix workstations as well as Personal Computers. |
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lxk13: |
located in the same building on level 13 workspace B. |
Yes, they do have strange names! To print from unix use the following command:
lpr -Pqueuename filename
eg: to print a file called
test.txt to the lp queue typelpr -Plxk4 test.txt
Another way of printing text files is to use
a2ps. This compresses text so it prints two pages to a real page. It's very readable and a good way to save paper. To print a text file using a2ps type:a2ps < file.txt | lpr -Pqueuename
To print .dvi files (output from LaTeX) you use the
dvips command. This is explained in detail in the Introduction to Latex document by Rod Crewther.To check the status of any print queue type:
lpq -Pqueuename
to remove a job from a queue type
lprm -Pqueuename jobnumber
If the job is owned by another person this won't work, you must see an administrator in order to be removed.
This is a list of software on machines in CSSM each with a brief (one line) description. More information on software can be found by typing:
man <command>
where
<command> is the command you are interested in. If there isn't a manual page for the command you're interested in, see me or send me a mail message and I'll explain things as best I can.All machines have basically the same software although there may be some small differences in versions.
Below is a list of the most popular software used in the department. This is not comprehensive as the software changes all the time.
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axe |
Is a simple to use text editor for X that represents a significant improvement over xedit. |
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cc |
C compiler |
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elm |
A text based interface to mail. Just start up elm and follow the menus on the bottom of the screen. |
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emacs |
Emacs is the only text editor with a 300 page manual. It is a very powerful editor though the commands are somewhat counter-intuitive. Emacs' advantage is that it is used on just about every UNIX box in existence. It comes with modes that recognise file formats. For example, you can edit a LaTeX file and emacs will automatically load a LaTeX mode that recognises such entities as chapters, sections, quotes etc. Emacs even comes with its own mail and news reading utilities that you can run from within the editor itself!! Emacs has extensions that run under X. You can have more than one window open with emacs under X at a time. Emacs is programmed in lisp and so are most of the functions. This is the reason for its power but also for its un-user-friendliness. There is a set of menus that can be run under emacs. |
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f77,f90,f95 |
Fortran 77,90,95 compilers |
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gcc |
GNU C compiler |
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ghostview |
Postscript previewer (front end to gs) |
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gs |
Ghostscript (postscript) interpreter |
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idl |
The experimentalist's best friend. IDL stands for Interactive Data Language. It is a number-crunching package that comes with a lot of scientific functions such as Fast Fourier Transforms among others already built in. Type .run demo at the IDL prompt to get an idea of what it does. Manuals are available in my office though they are popular. |
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joe |
Joe is a simple editor that is based on WordStar. It's main advantage is its simplicity and that you can see a complete command summary on your screen by typing Ctrl-K H. It doesn't scroll well on xterms though. |
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kermit |
Kermit File Transfer program. If you run kermit at home to connect via the staff or student modem pool, then this is kermit's alter-ego that you can start up for file transfers |
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latex |
A text formatting language. Although there are heaps of text editors, there are no word processors on the workstations. Thus to write up documents and/or theses you need to use latex. Although somewhat un-user-friendly and definitely not WYSIWYG it is very powerful and is the workstation package that has a comprehensive equation-writing facility. It's also text based so it's used as the common format for exchanging documents. Manuals are available for it. |
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maple |
Another symbolic calculation package. It has a nice X interface. The graphics aren't as good as on mathematica but the calculation side of things is better. |
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mathematica |
The theorist's best friend. It's a symbolic calculation package that comes with nifty functions built in that theoretical physicists use. It also has very good graphics capabilities. Manuals are available from my office. Mathematica3.02 licenses exist on Mercury, Blazar, Vortex and Wave. An old version2.2 is licensed to Pilot. |
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netscape |
World Wide Web Browser This latest version has a lot of bells and whistles including a good mail and news reader. |
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nn |
Text based news reader. This is the only one supported in this department. |
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pine |
Another mail reader - this is a bit easier and more full-featured than elm and is the recommended mail reader for the department. It is the program that starts up when you press the Mail button on your X Desktop |
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sysupdate |
sysupdate is a script that you can use to get the most recent version of the .cshrc, .login, .twmrc, .xinitrc, .Xdefaults, and the introductory files. Type sysupdate to find out what you can do. |
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talk and write |
write user will send what you type to a users terminal. Type Ctrl-D at the end of your message. Talk sets up a two way interactive session where what you type ends up on the recipient's screen and vice versa. Both are good for talking to people logged on other workstations. |
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tex |
LaTeX is a built on TeX. This is a lower level and you most probably won't need to learn this - unless you're a masochist… |
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top |
top is a utility that displays the top 20 (usually - depends on the size of your terminal window) processes. It's good to use when you want to check on the niceness of your job. You can renice jobs from top by typing r pid and kill a process by typing k pid. Top runs on all the suns and Digital 5000/120s |
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xdbx |
X interface to dbx debugger |
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xdvi |
A dvi previewer under X. After you latex your file for the first time type xdvi filename& Every time you latex your file again all you have to do is put the xdvi window in the background and bring it back to the foreground. Then it will show any changes you have made in your latex file. |
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xedit |
Xedit is an X based editor that comes with X windows. It is very simple with is both its advantage and disadvantage. It doesn't have very many functions in it. Just cut and paste. But then, sometimes this is all you need. |
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xfig |
Drawing Package |
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xfm |
File Manager - a little bit like the Windows File Manager |
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xmail |
A tool for using mail in X windows. Has good online help facilities. Pretty easy to use. |
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xv |
Graphics file viewer |
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zoo |
File archiver |
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mesg and biff |
typing biff y means you will get a message on your screen whenever mail arrives. Typing mesg y (this is the default) means you can receive talk and write messages. Typing mesg n means you can't. Good for privacy. These things need only to be typed once when you log in so put them in your .mylogin file. |
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Zmodem utilities |
sz and rz are two commands for sending and receiving Zmodem protocol file transfers over a modem. They are much faster than kermit and seem to be better supported in modem packages that aren't kermit. |
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There are also numerous small utilites on the system such as make and patch. If you feel like exploring look in /usr/local/bin and /usr/bin for other stuff. I will endeavour to keep this file as up to date as possible. Any queries please see me in room 213 in the Oliphant wing or mail to me.
The Physics Department has the following machines available for general use by all staff and students of the department:
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NAME |
TYPE |
USE |
WHERE |
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adephi |
DEC Alpha 255/233 |
Departmental Server, you are not able to log into this machine but it is quite important just the same. |
122 |
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bragg |
DEC Alpha AXP 3000/600 |
Workstation, most of the licensed software's running on this machine. |
122 |
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mercury |
DEC Alpha 255/233 |
Workstation |
123 |
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aurora |
DECstation 5000/120 |
Workstation |
123 |
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corona |
DEC AlphaStation 200 4/100 |
Workstation |
123 |
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flare |
Sun SPARC IPC |
Workstation |
123 |
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photon |
DEC AlphaStation 200 4/100 |
Workstation |
123 |
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pilot |
Sun SS10-30 |
Workstation |
123 |
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plasma |
Sun SS1+ |
Workstation |
123 |
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spectrum |
DEC AlphaStation 200 4/100 |
Workstation |
123 |
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teles |
DEC AlphaStation 200 4/100 |
Workstation |
213 |
The following machines are available to members of the Theoretical Physics group only:
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NAME |
TYPE |
USE |
WHERE |
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anduril |
DEC Alpha 255/233 |
Workstation |
level 13 |
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wilson |
DEC Alpha 255/233 |
Workstation |
level 13 |
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bethe |
DEC Alpha 3000 |
Workstation |
127 in Physics |
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dirac |
Sun SS10-30 |
Workstation |
125 in Physics |
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gurrai |
DEC Alpha AXP 3000/700 |
Workstation |
level 13 |
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parton | ^M
Sun SPARC SLC |
Workstation |
121 in Physics |
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parton |
Sony News 3410 |
Workstation |
122 in Physics |
The following machines are available to members of the Institute for Theoretical Physics group only:
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NAME |
TYPE |
USE |
WHERE |
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bose |
DEC AlphaStation 200 4/100 |
Workstation |
level 13 |
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faraday |
DEC AlphaStation 200 4/100 |
Workstation |
level 4 |
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gibbs |
DEC AlphaStation 200 4/100 |
Workstation |
level 13 |
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lagrange |
DEC AlphaStation 200 4/100 |
Workstation |
level 4 |
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maxwell |
DEC AlphaStation 200 4/100 |
Workstation |
level 4 |
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tomonaga |
DEC AlphaStation 200 4/100 |
Workstation |
level 4 |
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yukawa |
DEC AlphaStation 200 4/100 |
Workstation |
level 4 |
The following machines are available to members of the CSSM group only:
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NAME |
TYPE |
USE |
WHERE |
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biedenharn |
DEC Alpha 500au |
SERVER for CSSM not for general purpose logins |
level 4 |
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blatt |
DEC Alpha 500au |
Workstation |
level |
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born |
DEC Alpha 500au |
Workstation |
level 13 |
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darwin |
DEC Alpha 500au |
Workstation |
level 4 |
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fock |
DEC Alpha 500au |
Workstation |
level 4 |
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foldy |
DEC Alpha 500au |
Workstation |
level 4 |
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hartree |
DEC Alpha 500au |
Workstation |
level 4 |
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lamb |
DEC Alpha 500au |
Workstation |
level 4 |
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landau |
DEC Alpha 500au |
Workstation |
level 4 |
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majorana |
DEC Alpha 500au |
Workstation |
level 4 |
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primakoff |
DEC Alpha 500au |
Workstation |
level 13 |
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schwinger |
DEC Alpha 500au |
Workstation |
level 13 |
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thompson |
DEC Alpha 500au |
Workstation |
level 13 |
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wigner |
DEC Alpha 500au |
Workstation |
level 4 |
The workstations listed above that are in staff members' offices.
You should have accounts on every machine that your group has use of plus all of the machines available for general use. If you don't, come and see me and I'll set you up with an account on that machine.
As mentioned above, Netscape is the department's preferred Web browser and it has a button allocated to it on your button row on the left side of your screen. By default Netscape is not configured properly and you will need to do this yourself. Follow these instructions:
In the Options menu, select the General Preferences... item. In the window that you see, select Home Page Location and in the box next to it type
http://www.physics.adelaide.edu.au. Select Pictures and Text from Toolbars and then Press OK.To use netscape as your mailer, in the Options menu, select the Mail and News Preferences... item. Select the Compose Tab and then press the Mime-compliant button. Press the Servers tab. Set the SMTP server to be
adelphi and the News server to be news.adelaide.edu.au. Press the Identity Tab. Type in your name and your email address if it isn't there already. Set the Organisation to be Dept Physics, Adelaide University.In the Options menu, select the Network Preferences... item. Press the Proxies tab. Select Automatic Proxy Configuration and type in
http://www.adelaide.edu.au/proxy.pac Your Netscape should now be ready to run! Press Home and away you go!The department makes use of the World Wide Web for a number of purposes. Our home page is
http://www.physics.adelaide.edu.au. All notices about the departmental computer systems are displayed on the Physics Notice Board. This is a WWW notice board that can be accessed through our home page (Click on Notice Boards and the Physics Notice Board) or directy via http://www.physics.adelaide.edu.au/noticeboards/pnb. This page is a facility primarily used for posting system message (You will notice that 90% of the postings come from me). It is, however also available for general use. Anyone can post notices by simply clicking on the Post Article text and filling out the form. As I mentioned before, all system notices are posted here and NOWHERE ELSE. This includes information about system and network downtime and software upgrades. It is a good habit to check this area each time you log in.For those people familiar with html documents, all notices are html documents with the content of the posting enclosed by preformatted text commands (
<pre></pre>). Thus it is possible to embed html commands such as url's and formatting in your posting. Also it is possible to escape the pre-formatted text by typing </pre> in your post. Please then conclude your post with a <pre> command.When you log in from an X terminal or workstation, X is started up for you by default. You have a file in your home directory called
.xsession which calls another script called .xinitrc. This is the script you use to customise your environment.When you log in the X server looks for a file called
.xinitrc in your home directory. You need to have at least one application in this file. The X server sources this file and runs until all the programs in this file have been executed. This means that all the applications listed in .xinitrc have to be run in the background except for the last one. To quit X you exit out of that last application. Here is an example of a .xinitrc:# Sample .xinitrc
# A # at the beginning of the line means this is a comment and
# it isn't read by the X server
# It's an xterm that grabs all the console messages.
# the & means run in the background
xterm -C -geometry +0+80 &
# Run a clock. Specify where to put it
dclock -geometry +0-1 &
# The last application - must be run in the foreground
# Run a window manager
fvwm
# End of sample.
So to exit the X server running with this file means you have to exit the window manager (this is done by selecting exit in one of the menus or the logout button on the standard setup).
A window manager lets you control the various windows you have in your X session. There are several window managers around. The one we choose to use here is called
fvwm. There are others called awm, uwm, twm and olwm. All these window managers have manual pages. The window manager is what lets you move windows around with a mouse. It also controls all the properties of the title bars of the windows, the menus you get when you press the mouse buttons and whether you want icons displayed or not. All this is controlled in a file in your home directory called .fvwmrc. If you were running uwm you would have a file called .uwmrc and if you were running awm you would have a file called .awmrc. olwm has several files to configure it. Have a look at your .fvwmrc in your home directory. It has a lot of instructions in it about how to customise it. Fvwm allows you to resize your window by dragging the mouse when the pointer is on one of the corners of the window. You can make your window an icon (called iconifying or minimising) by clicking once on the box at the top right that has the small dot. You can de-iconify the icon by double-clicking on it using the left mouse button.You may want to have some applications displayed in a certain colour or placed in a certain position on the screen or use a particular font. Instead of having to type all the details out on the command line each time you start an application, you can set this up in a file in your home directory called
.Xdefaults. This file is easy to get around in so have a browse. It's in your home directory.One of the biggest advantages of X is that you can run an application on another workstation but have it display on your workstation ie: you can run run IDL on anduril but have it display its output on faraday's console. All X-terminals work like this. There is a command in your
.xinitrc called xhost that enables access and an environment variable called DISPLAY that is set whenever you start an application.The three files you can customise are
.xinitrc, .fvwmrc and .Xdefaults. Have a look at the ones you have been given. There are a number of comments in them to help you customise.There are a number of X applications available to you. Most of them are in
/usr/local/bin or /usr/bin/X11 on the sonys. Have a look at the Software section of this document.Modem access is provided by Camtech who are located in the Capita Building, 10 Pulteny Street. The details of what's on offer and prices are available from
http://www.camtech.net.au/uniserv.htmlAs you have an account you automatically have an email address. This address is your login name followed by:
@physics.adelaide.edu.au eg: Mike Shorthose's, email address is mshortho@physics.adelaide.edu.auSpecial Research Centre for the Subatomic Structure of Matter has a Computing Officer. Her name is Ramona Adorjan. She lives in room 213 Oliphant Wing, Physics Building and phone number 33548. Her email address is radorjan@physics.adelaide.edu.au.
If you have logged in for the first time this notice is the first thing you should see. It will re-appear each time you log in. To get rid of this you need to edit your .xsession file and get rid of the line that starts with
netscape http://www.physics.adelaide.edu.au/computing/
Then it won't appear any more.