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INTRODUCTION TO COMPUTING IN THE DEPARTMENT OF ATMOSPHERIC & OCEANIC SCIENCES AT UCLA

This section of the XEP introduction manual is a short guide to the Department’s computing facilities and resources. In it, the following items will be discussed:



[UPDATE: Summer 2005 -- e-mail dated 26 July]

Dear All,

The computer committee and the department's IT staff have been working
on developing new policies and capacities for the department's IT
infrastructure. Several changes being planned for this summer may
significantly impact how you use the department's network.

The most profound change will be a new security model for the
department. The target date for implementation is October 1. Its
most obvious effect will be to force all remote access to department
computers through a gateway server using either one time passwords or
public keys (similar to what is necessary to get on the wireless).
More details on this policy and the motivation behind it can be found
here: http://www.atmos.ucla.edu/security_policy.pdf

Another important change will be the configuration of a new
departmental email server
(mail.atmos.ucla.edu, which will replace
cloud.atmos.ucla.edu) at the beginning of the fall quarter. This
server will not allow users to directly log on to read their email. As
such we will all be forced to access our mail using encrypted POP or
IMAP (i.e., POPS/IMAPS which are common tools to almost all email
clients) or through UCLA's webmail server. As we get closer to
implementing the new server a number of announcements and tutorials
will be available to help you understand its impact and how you can
continue to receive your mail in an efficient manner.

The switchover to the Gigabit network should be completed by the end of this
week. With sufficiently fast network cards and some tuning this network
will greatly increase our networking capabilities; transfer rates of as much
as 100 Gbytes/half hour are conceivable. If you have occasion to use
this bandwidth please see Matt Uller for help.

Lastly, other minor changes should be evident. From planned new displays in
the downstairs window to a new data server (perhaps coming on line this
summer) and back up servers. We will continue to try and keep you
posted of developments, and should you have questions, please don't
hesitate to ask any of us.

Your computer committee,

Nicolas Gruber, Rob Fovell, Kayo Ide, Brian Medeiros, Matthias Munnich,
Bjorn Stevens, Matt Uller, and Jeanne Ladner (ex-officio)


1. Available Servers & Accessibility

The Department supports a variety of network servers made available for all faculty, researchers, students and staff of the Department. These include the following:

  • Solar

  • Micro

  • Polar

  • Rainbow

  • Halo

  • Cloud **UPDATE: cloud will not exist any longer starting in Fall 2005, see email above.

Accessibility to the servers begins after first setting up an account and password via the computer IT staff. Most passwords will expire after 120 days and must be updated with a unique character string within the same year. All passwords must consist of a minimum of 6 characters, one that is not a letter. For security reasons, passwords may not be based upon any common name or dictionary word (even if the word is spelled in a language other than English). The IT staff will provide all needed support for accessing and maintaining your computer account. A disk quota [type 'quota -v' at the command prompt to see your quota] will also be set up for you at the beginning and may be changed to accommodate any special requirements that you might have pertaining to coursework, research etc.

Cloud is the only server on which e-mail can be accessed. It is POP enabled, meaning common programs for reading e-mail, such as Netscape and Eudora can be configured for use. E-mails can also be retrieved via the UNIX mail commands, MailX, ELM and PINE. **UPDATE: see email above; only encrypted POP/IMAP are allowed now.

More will be said about these commands in the section titled, “Brief Introduction to UNIX: Getting started”. Cloud is a restrictive machine, however and must only be used for e-mail; no other jobs are permitted. Other restricted servers requiring special permission privileges include the following:

  • Cisk **UPDATE: cisk is no longer functional

  • Typhoon (Weather data ingestion)

  • Webster **UPDATE: webster may not be functional much longer, use sparingly!

  • Glory

Further questions about accessing the Department servers and/or regarding account set-up and passwords should be directed to the computer IT staff. Refer to the last section, “Information Technology (IT) Staff – Who to talk to when having problems” for contact information.

UPDATE: The best way to access departmental computers now is by going through our gateway machine using one-time passwords. The machine is called 'gate1,' see IT staff for login information.


2. Where are the Computer Labs?

The Department maintains two computer labs containing general access machines, reserved users in the Department. One is the Synoptic Meteorology Lab, in MS 7101, and the other is the Terminal Room, in MS 7964.

The public access machines in the two computer labs are not to be used for running large jobs and have certain restrictions for use. Below is a short description of the two labs.

a. The Synoptic Meteorology Lab:

The lab has around 20 Sun Workstations, which can be used freely when there are no classes in session (typically AS 2 and AS 3 labs are conducted here during the school year). Usage times are generally from 8-5pm. If after-hour access is required, a pass code will be needed to enter the lab. This can be obtained at the Department front office. Please note that several computers in the lab are on the restricted list. The IT staff can provide more information this.

UPDATE: Many of the machines in the Synoptic Lab have been upgraded to SunBlade 150s and 1500s, while a few Sun Ultra 10s remain. Some of the SunBlades have names like: flash, swirl, heat, fropa, swell, garnet, surge, nami, vapor, lidar, ridge, and fog. The older machines include sapphire, jade, merced, ivory, ruby, and peridot. These machines are not currently available for remote access except through the gateway machine, gate1.

ALSO: A tentative plan to purchase Linux-based machines and form a small cluster has been formed. Details to come.

b. The Terminal Room:

Access to the Terminal Room will require a pass code. This can be obtained at the Department front office. The current [August 2005] configuration of the terminal room includes: 2 Macintosh computers named termg4 and termg4b, which are PowerPC G4s running OS X (10.2), 2 Dell PCs running Windows XP, and 1 Sun Ultra1 workstation named squall. There are 3 scanners (2 on Macs and 1 on a PC), and three large laser printers also. These computers are for academic use only with class and TA related work given priority. If you’re using a computer for research or non-class related topics and a Professor, TA or student requires that computer, you must yield your workstation.

Details on the various computer peripherals (i.e. printers, scanners, back-up devices etc) used in the Department will be addressed in the section titled, “Printers, Scanners, Back-up Tape Drives”.


3. How to access your E-mail

IMPORTANT UPDATE: this section is now obsolete, as cloud is being replaced with mail.atmos.ucla.edu, which will not allow SSH sessions. Instructions for setting up a POP/IMAP enabled e-mail client will be posted eventually. For now, see IT staff for instructions.

As identified in section 1, e-mail can only be accessed via the server, cloud. After you have been assigned your e-mail username (e.g. user_name@atmos.ucla.edu) and default password from the IT staff, you will then be able to log directly into cloud. If you are logged into another server, you can SSH into cloud via the secure network protocol open SSH (compliant version 2 of SSH). This network protocol is a more secure version of services such as FTP and Telnet of which the Department no longer supports. For example, if you were working from within Polar and wish to check your email, you would enter the following at the command line prompt:

Polar {username}: SSH cloud

Username@Cloud’s password: enter password

Cloud {username}:

To return back to Polar when you are done with email, simply type “logout” at the command line prompt:

Cloud {username}: logout

Polar {username}:

SSH should be used at ALL times, including when accessing the Department’s resources from your home computer. A copy of this program can be obtained from the Department’s System Administrator, either via CD or e-mail.

When you have logged into Cloud, you have several options in which to access your mail. As mentioned earlier, you can use the UNIX mail commands, MailX, ELM or PINE. Detailed information on how to use these mail programs can be found in any standard UNIX book or can also be found on the Web. Some good reference books are listed in section 3, Brief Introduction to Unix:

ELM and PINE are typically used the most. To access either one of these programs, enter “elm” or “pine” at the command line prompt.

Cloud {username}: elm (or pine)

The screen will clear and will be replaced with an interactive menu from which you can access your mailboxes. You might see something like the following in your inbox:

1. Dec 8 name of sender (message size) “message 1 title”

2. Dec 7 name of sender (message size) “message 2 title”

3. Dec 7 name of sender (message size) “message 3 title”

4. Dec 6 name of sender (message size) “message 4 title”

You can use any of the following commands by pressing the first character

d)elete or u)ndelete mail, m)ail a message, r)eply or f)orward,

q)uit, To read a message, press <return>. J = move down, k=move up,

?=help

Command: __

ELM requires being familiar with the vi editor when reading and creating messages, whereas PINE does not and therefore is easier to use. The alternative way to access your mail is by using either Eudora or Netscape. To start Netscape for example, type in the following at the command line prompt:

Polar {username}: Netscape &

The ampersand symbol (&) tells UNIX that you want to run Netscape while still being able to run and access other programs in the background. Once Netscape begins, your mailboxes can be accessed. Remember to frequently clean your inbox and outbox folders as these can get quite large and will sometimes cause you to exceed your disk quota. If this occurs, you will not be able to log in to the system. Contact a member of the IT staff if this happens.


4. Brief Introduction to Unix

Getting started

Listed below are some useful reference books on Unix. In addition to these, you may also want to check the World Wide Web for more information on getting started with the Unix operating system. We've included links to Amazon.com in case you want to get more information about these books.

  1. Teach Yourself® UNIX® 4th Edition
    Author: Kelvin Reichard
    Publisher: MIS Press
    Comments: This book has a good appendix of basic commands and a nice glossary. It also has a good section on the vi editor and covers some advanced topics.

  2. More Unix for Dummies
    Author: Levine and Young
    Publisher: IDG Books
    Comments: Great for learning basics but it doesn’t have an appendix or glossary of commands.

  3. UNIX System V: A Practical Guide (3rd Edition)
    Author: Mark Sobell
    Publisher: Addison-Wesley
    Comments: This is a more advanced topics book but it does cover some of the basics. It also has good coverage of the vi and emacs editors.

  4. Unix for the Impatient, CD-ROM Version (2nd Edition)
    Author: Abrahams and Larson
    Publisher: Addison-Wesley
    Comments: Has a great summary of UNIX commands. Contains a mix of basic and advanced topics and it also covers the vi and emacs editors.

  5. Sams Teach Yourself UNIX in 24 Hours...
    Author: Dave Taylor
    Publisher: Sams Publishing
    Comments: Provides a good overview of the basic UNIX commands. These comments are actually based on the 2nd edition.

  6. Harley Hahn's Student Guide To Unix
    Author: Harley Hahn
    Publisher: McGraw-Hill Science/Engineering/Math; 2nd edition (May 1, 1996)
    Comments: This books starts from essentially no knowledge of computers, and teaches the very basics in a clear way.

Some useful commands for getting around

cd change to a new directory (or home if no directory is specified, i.e., just type 'cd' at the prompt and press enter)
pwd identifies current path of the working directory, which can be remembered mnemonically as 'present working directory' if it helps
ls list files and directories in the current or specified location. The three key flags: -a shows hidden files; -l provides a long format listing; and –F distinguishes between directories, executables, and symbolic links. There are other options, which you can read about by typing 'man ls' at the prompt.
quota –v shows available memory space
mkdir create a new directory
rmdir removes a directory from the system (files must be removed first)
mv moves files between directories (move oldfile to newfile)
rm removes specified file/directory (Use with caution ! This is irreversible)
cp copies files (e.g., 'cp oldpicture.jpg newpicture.jpg' makes a copy of oldpicture.jpg called newpicture.jpg)
more display contents of file on screen but pausing between each screen. A common alternative is 'less,' which is not always available.
man display the help page of a command, example: '$> man more' will display the instructions for more.

A useful feature for obtaining help on any one of the Unix commands is to simply enter the word “man” + command at the command line prompt. For example, if you need help with the cp command, you would do the following:


Polar {user name} man cp


You will then notice the following at the top of the page:

*****************************************

Reformatting page. Please Wait... done


User Commands cp(1)


NAME

cp - copy files


SYNOPSIS

/usr/bin/cp [-fip] source_file target_file

/usr/bin/cp [-fip] source_file... target

/usr/bin/cp -r|-R [-fip] source_dir... target


/usr/xpg4/bin/cp [-fip] source_file target_file

/usr/xpg4/bin/cp [-fip] source_file... target

/usr/xpg4/bin/cp -r|-R [-fip] source_dir... target

******************************************

This, for example, will display useful information regarding the cp command.

Aliases – How to set up / Making life much simpler

Command aliases can be thought of as mapping a particular command or command sequence to your own assigned name so that you can easily remember them, or for having certain flags added by default. For example, say if you have your most frequently accessed working directory located on the server polar. Maybe the data you need is contained in a nested subdirectory, i.e. /home/last name/field campaigns/safari/ground data/lidar. Instead of having to use the “cd” command repeatedly until you arrive at the lidar subdirectory, you can create an alias as follows:

alias lidar ‘/home/last name/field campaigns/safari/ground data/lidar’

By typing in the word “lidar” at the command line prompt in your home directory, you will be taken to the lidar subdirectory automatically. Command aliases, like the one above, are inputted into your. cshrc file, which is without going into detail, your start-up file that is read in every time you open up a new shell. This sets up your working environment each time you begin a new session. Refer to any Unix reference book for more information on creating aliases and how to modify your. cshrc file.

Vi Editor – What is it

Various text editors are usually included in the Unix system, including vi and an alternative editor called emacs. These editors allow you to peer inside files and to make needed changes as well as creating new files. The following briefly describes on getting around using the vi editor. Consult a Unix reference book or the World Wide Web for more detailed information on specific tools and techniques.

The first thing you need to know about vi, unlike emacs, is that it is a modal editor. This means that different modes in vi interpret the same key differently. “Insert mode”, for example, interprets the “a” key differently than does the “command mode”. If you’re in “insert mode”, typing an “a” adds the letter “a” to the text. However, if you’re in “command mode”, typing an “a” is the key abbreviation for the append command. This puts you in inset mode and positions the cursor at the end of the current line. Command mode allows you to manage your file, which includes adding and removing text, while insert mode is what you must be in to add text to your document from the keyboard.

To start up vi, and begin editing a file you have already created, enter “vi” and the name of the file at the command line prompt:

Polar {user name}: vi Filename

The screen will open as shown below with the first character of each blank line containing a tilde (~) symbol. The cursor will be positioned at the upper left hand corner awaiting for further instruction. Note the file name, and the number of lines and characters in the file on the bottom left.

***********************************

Angle correction routines and sample data

~

~

~

~

~

~"File name" 1 line, 42 characters

***********************************

You are automatically put into command mode, so to begin editing the document, you must first switch to insert mode. By pressing the letter “i” on the keyboard, you’ll be put into insert mode and you can begin typing at the current cursor location which in the sample file above would be just before the letter “A” in Angle. If, instead, you want to begin a new line, press the letter “o” and begin typing. If you want to append new text to the end of the current line, press (shift key $) to position the cursor on the last letter of the line (2nd “a” in data), and then press the letter “a” for append, then begin typing. Some useful vi commands for getting around the document are as follows:

  • (j) - move down one line
  • (k) - move up one line
  • (l)- move right one character
  • (h) move left one character
  • (x) deletes a single character
  • (d) deletes word
  • (dd) deletes sentence
  • (U) Undo – restore current line if changed

When you are ready to save your document, press shift and the colon key to position the cursor at the bottom left-hand corner. Then press w to save. To exit the document, press shift and the colon key once again and then enter q to return back to the Unix command line prompt.


5. Printers, Scanners and Back-up Tape Drives

The department supports a number of peripheral devices for printing and scanning in documents, as well as backing up data.

5a. Printers

The department has the following printers available for use. Listed are the printers and where they can be located.

      1. HP laser-jet 8100DN black and white (MS 7964)
        HP color laser-jet 4550DN (MS 7964)
        HP laser-jet 8150-series, black and white (MS 7964)
        HP laser-jet 4000N black and white (MS 7101)
        HP laser-jet 4300N (MS 7101)
        HP laser-jet 5M black and white (MS 7150)
        There is an Okidata printers in MS 7150 as well. Details coming.

5b. Scanners

The department has three scanners in the Terminal Room (MS 7964).

5c. Back-up Devices

The Terminal room's Macs have ZIP drives (100/250 MB). One Mac and the PCs have CD burning capabilities. There is an 8 mm tape drive on workstation 'ivory' in MS 7101 (Exabyte Mammoth 8mm Cartridge - 170m AME). The department only backs up crucial directories (/home and /webdisk).

A 'data server' is currently being implemented, which will have significant hard drive storage for backing up additional resources. Please see IT staff for further details.


6. Available Hardware/Software and Operating Systems

The department currently supports the latest version of the following products:

Hardware, PC platforms – Dell and Gateway

Hardware, Apple platforms – PowerMac

Hardware, Unix platforms – Sun and Compaq/DEC

Operating systems, PC platforms – Windows XP, NT4, and 2000 (Windows 95,98 and ME will be supported in limited applications, like data-collection laptops when approved by IT staff)

Operating systems, Unix platforms – IRIX, Linux (Mandrake is the supported distribution), Solaris

Software packages – Eudora, Microsoft Explorer, Netscape, Adobe Acrobat Reader, Office 97, Office 2000 and Office XP (Access, Word, Excel, and PowerPoint), UCLA’s anti-virus package, Xwin32, and ssh/sftp.

Other software available to the Department is as follows:

  • Sun forte compilers (Fortran 77/90/95, C, C++, Java)
  • Python (version 1.5.2)
  • Perl (version 5.004_04)
  • GEMPAK (version 5.4)
  • IDL (version 5.5): Version 5.6 ready to go (have 10 licenses)
  • Matlab (version 6.0)
  • Mathematica (version 3.0)
  • Staroffice (version 6.0)
  • NCAR graphics (NCL)
  • ImageMagick (version 5.1.1)
  • GraDS (version 1.7beta9)
  • PCFileViewer (Solaris)

More information regarding available Department software can be found in the Department web site (atmos access only). See below

The paths to these software packages are not included in your resource files by default.


7. Department Web Sites – How to pages

Please consult the Department web site at: http://www.atmos.ucla.edu for all Department related information. Useful links related to computing resources can be found by selecting “info” at the top of the home page and then entering” Computing Information” (HERE)

**UPDATE: For questions and comments, please visit the department computing forums!


8. Information Technology Staff (IT) – Who to talk to when having problems

The Department IT staff is available for computer support and all related questions. The following personnel are the IT Staff Members:

Matt Uller (Systems Administrator)
(310) 825-2418
MS 7101A
uller@atmos.ucla.edu

Kerry Murphy (Web Programmer, PC/Mac Support Staff)
(310) 825-1659
MS 7115
kerry@atmos.ucla.edu

James Murakami (UNIX Support Staff & Dept. Meteorologist)
(310) 825-2418
MS 7101A
tenki@atmos.ucla.edu



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