Scientific Computing Laboratory Handbook

1. INTRODUCTION
• Convention
• Help and Enquires
• User Accounts
• Scientific Computing Laboratory R735 Opening Hours
• Staff-in-charge Schedule
• Policy and Regulations for Scientific Computing Laboratory R735
• Hardware
• Licensed Software
• Public Domain Software
2. UNIX ENVIRONMENT
• Introduction to UNIX
• Log on
• AIXwindows (Graphical User Interface)
• Logging Out
• Shells
• User Password
• Password Guidelines
• User and System Information
• Current Date and Time
• Display Manual Pages Online (A Help Service)
• Pathname
• Commands Overview
3. PRINTING
4. EDITOR
• vi
5. ELECTRONIC MAIL SERVICES
• Read Mail
• Send Mail
• Send internal mail
• E-mail to Internet
• E-mail from other domains
• Send a file
• Read message headers
• Reply mail
• Finish Mail Service
• Redirect Mails from IBM to other machines
• A summary of mail Commands
• Other e-mail software
6. C PROGRAMMING
7. FORTRAN
8. FTP (FILE TRANSFER PROTOCOL)
9. MODEM
10. TERMINAL SETTINGS
• Terminal Types Description
• Change Terminal Settings

1. Introduction

The Scientific Computing Laboratory is located at R735 Sir Run Run Shaw Building, Ho Sin Hang Campus, Hong Kong Baptist University. An UNIX computer system is in service. This laboratory is mainly dedicated for MSc students in Scientific Computing, but also serves Science Faculty staff, postgraduate students and authorized third year undergraduate project students of the Science Faculty.

This handbook is written for the users who are working in the S cientific Computing Laboratory. The purpose is to help users to get familiar with the laboratory, to learn AIX (IBM UNIX operating system) and to use the facilities provided by the system.

Convention

Throughout this handbook, the following conventions have been adopted:

• Bold letters represent command words.
• Italic letters represent user entries.
• Underlined letters represent variables.
• [] indicates options.

Help and Enquires

User Accounts

Applicants can get application forms in R734 or R735. Applications should be approved by the laboratory co-managers.

User should set their password as soon as they log into their accounts at the first time (see page 5). They should change their password periodically for security purpose.

Users can work in the laboratory or remotely log on the system from other computers, which have been connected to University network system. Users can also access the machines through modem supported by ITSC.

Scientific Computing Laboratory R735 Opening Hours

Staff-in-charge Schedule

R734 - Staff-in-charge could be contacted at R734.
*R734 - Staff-in-charge could be contacted at R734 when there is a laboratory class.

Policy and Regulations for Scientific Computing Laboratory R735

• R735 is for students of MSc in Scientific Computing, staff, postgraduate students and authorized third year undergraduate project students in Science Faculty.
• Users at R735 may be requested to show their student or staff ID card by laboratory co-managers or staff-incharge.
• All equipment must be checked before use. Any malfunction or missing items must be reported to technicians in R734 immediately or by e-mail to system administrator (sysadm).
• Each user may only occupy one workstation any one time. MSc students in Scientific Computing have the highest priority to use the computer facilities in this laboratory.
• Remember your user name and password, and keep your password secret. Send an e-mail for help to sysadm by yourself or through other classmates if you have any problem.
• User must log out his account before leave.
• User must not power off any computer or any equipment in the laboratory.
• No relocation of equipment is allowed.
• Resources are limited. Please keep discipline in sharing computer resources.
• User must not take out any manuals from R735. User must not cause any damages to the manuals. All manuals should be returned to the original place after use.
• Smoking, drinking, eating and playing in R735 are strictly prohibited. No games are allowed.
• The room must be kept clean, tidy and quiet.
• Trying to log on other user's account or break into system administrator's account is strongly prohibited.
• Violation of any of the regulations will be warned. We reserve the right to revoke your authority to use any facilities provided in R735.
• Please report to system administrator if you find anyone breaking the rules or intrude the system.

Hardware

Licensed Software

• AIXwindows
• C compiler
• C++ compiler
• Fortran compiler
• Mathematica
• MATLAB
• SAS
• Lindo, Lingo, Gino
• NISA (on compute server only)
• ESSL (on compute server only)

Public Domain Software

2. UNIX Environment

Introduction to UNIX

Log on

When users log on to a workstation in the laboratory, they will see a user login prompt. Type the user name and password respectively.

	login: username
	password: 

If login process is not accepted, try again in case of mis-typing.

User may remote log on to the system from other machines by the software TELNET. The fully qualified domain addresses of the machines are

abacus.sci.hkbu.edu.hk	(sc1.sci.hkbu.edu.hk, abacus)	- The compute server
beads.sci.hkbu.edu.hk	(sc3.sci.hkbu.edu.hk, beads)	- The file server
calculus.sci.hkbu.edu.hk	(sc4.sci.hkbu.edu.hk, calculus)	- The file server
www.sci.hkbu.edu.hk	(sc5.sci.hkbu.edu.hk, ftp.sci.hkbu.edu.hk)	- The ftp and WWW server
ada.sci.hkbu.edu.hk	(sc11.sci.hkbu.edu.hk, ada)	- The client machines
babbage.sci.hkbu.edu.hk	(sc12.sci.hkbu.edu.hk, babbage)
cauchy.sci.hkbu.edu.hk	(sc13.sci.hkbu.edu.hk, cauchy)
einstein.sci.hkbu.edu.hk	(sc14.sci.hkbu.edu.hk, einstein)
fourier.sci.hkbu.edu.hk	(sc15.sci.hkbu.edu.hk, fourier)
gauss.sci.hkbu.edu.hk	(sc16.sci.hkbu.edu.hk, gauss)
hilbert.sci.hkbu.edu.hk	(sc17.sci.hkbu.edu.hk, hilbert)
jacobi.sci.hkbu.edu.hk	(sc18.sci.hkbu.edu.hk, jacobi)
kutta.sci.hkbu.edu.hk	(sc19.sci.hkbu.edu.hk, kutta)
laplace.sci.hkbu.edu.hk	(sc20.sci.hkbu.edu.hk, laplace)
markov.sci.hkbu.edu.hk	(sc21.sci.hkbu.edu.hk, markov)
newton.sci.hkbu.edu.hk	(sc22.sci.hkbu.edu.hk, newton)
pascal.sci.hkbu.edu.hk	(sc23.sci.hkbu.edu.hk, pascal)
runge.sci.hkbu.edu.hk	(sc24.sci.hkbu.edu.hk, runge)
stokes.sci.hkbu.edu.hk	(sc25.sci.hkbu.edu.hk, stokes)
turing.sci.hkbu.edu.hk	(sc26.sci.hkbu.edu.hk, turing)

For instance, type telnet ada.sci.hkbu.edu.hk or telnet sc11.sci.hkbu.edu.hk

Common Desktop Environment (CDE) -- a graphical user interface

Logging Out

Shells

The command prompt is different among different shells. % is for C shell. $ is for Bourne shell and Korn shell. The prompt can be set and changed by the system administrator or the user.

User Password

When you firstly log on the UNIX system, you will have either no password or an arbitrary password assigned by the system administrator. Neither of them really offers any security. You should change your password by issuing the command passwd. Type

	passwd
	Type your old password
	Old passwd: 
	Type your new password
	New passwd: 
	Type your new password again for verification
	Verify: 

Password Guidelines

• Do not use words shorter than six characters.
• Do not write passwords down. However, if you must write them down, place them in a physically secure place, such as a locked cabinet.
• Do not use your user ID or components of you name as a password. Do not use it reversed, doubled, or other easily decoded modification of your name.
• Do not use any person's name as your password.
• Do not use words that can be found in the on-line spelling-check dictionary.
• Do use passwords that are easy to remember, so you won't have to write them down.
• Do use passwords that use both letters and numbers and that have both lowercase and uppercase letters.

User and System Information

	whoami

	sysadm

	who am i

	sysadm		pts/0		Nov 11 09:30

To display who is log on, type

	who

	finger

	finger username

	finger surname-of-that-user

	tty

	/dev/hft0

Current Date and Time

	date

Display Manual Pages Online (A Help Service)

	man command      
	man -k command      

For instance, you can type the command man man. Then, the online manual will appear.

To read the next page, press the space bar, type

	man man

	man -k man

Pathname

A pathname that traces the path from the root to a file is called a full pathname. A full pathname provides a complete and unambiguous name for a file.

In a full pathname, the first slash(/) refers to the root of the file system. The last slash separates a file name from the directory names. The other slashes separate the sub-directory names.

Note: The directory separator is denoted by "/" instead of "\" as in DOS.

A single dot "." is used to refer to the current directory (the directory which you are working at).

Double dots ".." are used to refer to the parent directory of the current directory.

"../.." refers to the parent of the parent of the current directory.

Commands Overview

Flags further define the actions of commands. A flag is a modifier used with the command name on the command line, usually preceded by a dash.

List Files and Directories

	ls [ options ] name 

List the contents of the current directory.

		ls

		ls -la

		ls /

		ls /student

		ls ..

Concatenate and Display File Contents

		cat [ options ] file...

		cat > my_file1
		Testing!
		This is my file.
		

		cat my_file1

		cat my_file1 > my_file2

		more file ...

Create Directory

			mkdir directory-name
			mkdir temp
			mkdir demonstration

Copy File and Directory

		cp [ options ] file1 file2
		cp [ options ] file1... directory
		cp [ options ] directory1... directoryn

		cp my_file1 temp_file1
		cp my_file1 demo/my_file1

		cp -R demo demo1

Move (Rename) File or Directory

	mv [options] name1 name2

                mv demonstration demo

		mv my_file3 your_file1

		mv your_file1 demo

Remove File or Directory

		rm [options] name

		rm your_file1

		rm -r temp

Change Current Directory

		cd [options] directory-name

Change the current directory to demo.

		cd demo

		cd

		cd ..

Print Working Directory

		pwd

Locate a Command or Program

	whereis command

	whereis Mail

	Mail:	/bin/Mail	/usr/bin/Mail	/lib/Mail.rc	/usr/ucb/Mail 
			/usr/lib/Mail.rc

		history

		ps

		ps -ef

3. Printing

		lpr [Options] file 
		lpr -Pprintqueue file 

		lpr -Ppcl postscript_file.ps

	lptxt postscript_file.ps

		lpr -Pps postscript_file.ps

	lpps postscript_file.ps

	lpstat

	lprm -Pprintqueue jobnumber

4. Editor

vi

	man vi

	vi filename

If the file has already been created, this message will appear:

	"filename" ? lines, ? characters

	"filename" [new file]

In the input mode, characters entered from the keyboard is interpreted as text input intended to be placed in the current position of the file.

When you run the command vi, you will first be in the command mode. Type i to enter the input mode. Press <Esc> to enter the command mode.

The followings are some useful vi commands:

Text Insertion
a	Append text after the cursor position.
i	Insert text before the cursor position.
o	Open a new line below the current line.
<Esc>	Stop text operation and return to the command mode.
Text Copy
yy	Copy the current line to the file buffer.
2yy	Copy 2 current lines (other number can also be used) to the file buffer.
p	Copy the content of the file buffer to the position after the current line.
P	Copy the content to the position before the current line.
Text Deletion
dw	Delete the current word.
x	Delete the current character.
dd	Delete the current line.
p	Put back the text from the previous delete.
Text Replacement
r<Char>	Replace the current character to a specified character.
R<string><Esc>	Replace string on the current line.
Recover the last change
u	Recover the last change.
Paging
<Ctrl f>	Page forward one screen.
<Ctrl b>	Page back one screen.
<Ctrl d>	Page down half screen.
<Ctrl u>	Page up half screen.
<Ctrl l>	Reprint current screen (screen refresh).
Cursor Positioning
j	Move cursor down one line
k	Move cursor up one line
h	Move cursor one character left.
l	Move cursor one character right.
Read and write file
:r filename	Read a file into the file buffer at the current position.
:w filename	Write the contents to a file.
:1;3w filename	Write line 1 to line 3 to a file.
Exiting vi
:wq	Write changes to the current file and quits the edit session.
:q	Quit if there is no change.
:q!	Force to quit and abandon any change.

Create a testing file my_file4.

	vi my_file4
	i
	    - Go to the text mode.  Insert text to the new file.
	This is my file.
	This is the second line.
	<Esc>
	    - Go to the command mode.
	:wq
	    - Save and quit vi.

	cat my_file4

	vi my_file4
	j
	j
	  - Move cursor 2 lines down.
	a
	   - Go to the text mode.  Append text to the current position.
	This is the third line.
	<Esc>
	   - Go to the command mode.
	:wq
	   - Save and quit vi.

	cat my_file4

5. Electronic Mail Services

	You have new mail!!!

Read Mail

	mail
	   ...
	   messages
	   ...
	&

	& h

	& 1

Send Mail

	mail person1 ... 
	mail person1@machine-name ... 
	mail person1@address ... 

Send internal mail

What follows is an example to send an e-mail to a student c0000001. Type the subject heading. Type the message body. Press to finish the mail and send a copy to another student c0000002.

	mail c0000001
	Subject:  testing
	It is a test on the mail service.
	 ...
	
	Cc: c0000002

E-mail to Internet

Send an e-mail to a person in Yale University.

	mail username@yale.edu

E-mail from other domains

If someone wants to send an e-mail to you, he should type

	mail username@sci.hkbu.edu.hk

Send a file

	mail person1 ... < file

Read message headers

		& h
	  

Reply mail

		& r 1

Finish Mail Service

	& q

	vi .forward
	i
	username%bc750.bitnet@yale.edu
	
	:wq

	vi .forward
	i
	username@math.hkbu.edu.hk
	
	:wq

	vi .forward
	i
	username@comp.hkbu.edu.hk
	
	:wq

	+              	Print the next message                     
	        	Print the next message                     
	-              	Print the previous message                 
	#              	Print the number of the current message    
	d              	Delete message                             
	dp             	Delete message & print the next one        
	dq             	Delete message & quit                      
	exit 		Exit the mail system and abandon the changing
	h              	Display headers of the current messages 
	m person       	Mail this message to person                
	p              	Print the current message again            
	q or <Ctrl d> 	Put undeleted mail back to /var/spool/mail 
	u N            	Undelete message N (N is the message no.)  
	r users        	Reply to users; then delete the message    
	s file         	Save the message to a file                 
	?              	Print summary of mail commands

	elm
	pine

	cc [ options ] source-file...
	xlc [ options ] source-file...

	cc 

	xlc 

	man cc
	man xlc

 
	vi source.c
	a
	  - Remember a is to append a file.
	#include 
	main()
	{
		printf("\nHello!\n"); 	
	}
	
	:wq

	cc source.c

	a.out

  	cc -o hello source.c

	hello

	f77 [ options ] source-file...
	xlf [ options ] source-file...

	f77

	xlf 

	man f77
	man xlf

  
	ftp somewhere.domain
	ftp ada.sci.hkbu.edu.hk
or	ftp sc11.sci.hkbu.edu.hk

ftp> dir
	List current directory.

ftp> cd remote-directory
	Change remote working directory.

ftp> lcd local-directory
	Change local working directory.

ftp> get remote-file local-file
	Get a file from a remote computer to the local computer.

ftp> mget r*
	Get all files starting with "r", from remote to local. 

ftp> put local-file remote-file
	Put a file from the local computer to a remote computer.

ftp> mput l*
	Put all files starting with "l", from local to remote.

ftp> ascii
	Set file transfer to ASCII mode (default mode).  Only ASCII 
	characters will be transferred.

ftp> binary
	Set file transfer to binary.  All characters will be passed.

ftp> quit
	Exit from ftp service.

      3411 4933   

	stty erase <Backspace>

	stty werase <Del>