RHIT Math Department Computing - Theorodrome HowTo Page

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Items to be updated or in transition are in red italics

Contents

• Purpose of this page
• Linux/XP Workstations in the Theorodrome
• Network Resources, Accounts and AFS
• Available Software
• Starting Applications and Terminal Windows
• Using Windows XP
• Printing, Email and Sound
• Getting Help
• More on AFS
  • AFS access and file sharing
  • AFS token limits

Purpose of this page

This document, and its companion document the Compute Servers Howto Page, are intended to enable new Linux users to use basic applications, manage files, and use basic network resources on the HP Linux/XP workstations and HP Linux servers in the Mathematics Department, particularly in the Theorodrome. These workstations, servers, and the companion cluster provide a Linux based computational environment beyond the standard student or faculty laptop. In this document we describe the workstations, login procedures, accounts and network file systems, using applications, printing, email and getting help. Both documents only consider standard configurations on the lab workstations and servers. Tips on specific applications are on the software tips page.

Linux/XP Workstations in the Theorodrome

The Theorodrome contains ten HP Linux/XP workstations. A number of math faculty have similarly configured workstations. The workstations and their configurations are:

moe, shemp, larry, curly, dean, jerry, stan, oliver, lou, bud
Hardware: HP dc7600, 3.4Ghz processor, 2.5Gbyte RAM, 4M cache, 80Gbyte local disk space, DVD-ROM, 21" monitor,
OS: Redhat Enterprise Linux as base OS, with Windows XP as a host OS using VMware

The workstations are configured to boot up in Redhat Linux with the Gnome windows manager. This windows system has a look and feel similar to Windows XP, especially the start menu. Using VMware the workstation can also support Windows XP giving access to some Microsoft programs. This will be implemented in the future.

Network Resources, Accounts, and AFS

Network Resources and Accounts All campus computing facilities (workstations, servers, file systems, and printers) are locally interconnected by 100 megabit subnets and which in turn are connected to a 1-gigabit backbone. These resources are generally accessible for users with a valid AFS account by means of their Kerberos username and password. All users with an AFS account automatically have access to all mathematics department public workstations and servers, and through them, any of the network resources. The login username and password for any mathematics workstation or server is your Kerberos username and password. To change your password simply go to this website: https://passwd.rose-hulman.edu.

Home Directories The UNIX based AFS (Andrews Files System) file system contains all user home directories, software applications, numerous shared filespaces, and web file systems. The files resulting from all non-laptop computing is ultimately stored in AFS, generally in the user's home directory. This includes data files, user configuration files, and application specific data files such as email header files. Using the home directory concept the user's files are available from every workstations and the applications will work the same way from every workstation. Access rights are important to understand for home directories for more information see the AFS file sharing entry below

Configuration Applications are configured by first reading system configuration information form a central location and then adding user specified configuration information from the user's home directory. This information is typically set through the preferences menu of the given application

Local file issues and navigation In some cases for performance and time considerations it is necessary to store files on the local hard drives of workstations and servers, though this is usually only done for server or cluster based computing. This is described below.

On the workstations the AFS network file system is usually navigated via a file browser by clicking folders on the desktop or using the file browser on the application menu. If needed, the file system of the local machine and other mounted file systems may also be navigated through the file browser. The file browser works in a similar fashion to Windows explorer.

Available Software

The following software is available on the workstations and servers in the various modes.

 

software title	Workstation Linux	Workstation XP not installed yet	Servers/ssh	Servers/xwin
Mathematical Applications
Cplex	to be installed summer 2006		to be installed summer 2006	to be installed summer 2006
Femlab	X		X	X
Maple 9 (will be updated to Maple 10 in summer 2006)	X		text maple only	X
Matlab	X		text matlab only	X
Magma	certain hosts		X	X
Mathematica	yes			X
SAS	via ssh/xwin to derek		derek only	derek only
Splus	via ssh/xwin to clive		clive only	clive only
Typesetting and Productivity Applications
TeX	X		X no preview	X
LaTeX	X		X no preview	X
LaTeX2HTML	X		X no preview	X
openoffice.org	X
MS Office
PDF creation	X		X	X
Compilers and Development
GNU compilers and utilities C, C++ and Fortran 77	X		X	X
Java DK	X		X	X
Perl	X		X
Web and Email
Acrobat Reader	X			X
Firefox	X			X
Internet Explorer
Thunderbird	X			X
Graphics Software:
no information at this point

Starting Applications and Terminal Windows

If you are using the workstation in its standard Linux configuration almost every program can be started from an item on the application menu. The mathematics applications are in Math folder on the application menu. In certain cases you will need to bring up a terminal window and type in a specific command.

To bring up a terminal window right click on the desktop or go to SystemTools > Terminal on the start menu. Here is a short list of commands you might want to use within a terminal window.

Command	Application or Use
maple	text version of Maple
maple -cw	classic worksheet version of Maple 9
matlab -nojvm	Matlab in terminal mode but figures will appear in windows
magma	Magma 2.11
ssh	start a secure session on another host
various commands see below	TeX, LaTeX

Printing and Email

Printing: This can usually be done through the application menu. You can print to the Crapo 2 printer, Faculty can print to departmental computers.

Email: The simplest thing to do is use firefox to access webmail https://exch-gw.ms.rose-hulman.edu/exchange/ Alternatively, Thunderbird can be configured to work with the exchange email server or another server. See the sotware tips page and the IAIT website email setup section for details.

Sound: From the application menu click on the Sound and Video entry and then volume control. Go to the Mono column and unclick mute.

Using Windows XP

This will be supplied later.

Getting Help

Most work can be done through applications or the file manager, which have help systems. If you need help on basic system management functions using Linux commands at a terminal window  you can usually get help from the manual page. For instance if you needed help on the copy command you would type:

man cp

Press the space bar to look at additional pages, press the Q key to quit.

Alternatively type

cp --help 

You can get help on most commands by using the --help option for a command.

If the help you need seems beyond this, say login problems, AFS system problems, or printing problems, you should seek help from the helpdesk or math system administrator. As IAIT  support is mainly for AFS maintenance, accounts and system wide software, they may redirect your request to the Math Dept. Here is how to get in touch with these folks.

Person/Org	Title	Email Address	Webpages	Phone
TSC Helpdesk		helpdesk@rose-hulman.edu	http://www.rose-hulman.edu/TSC/	x8989
Mike Mcleish	Math SysAdmin	mcleish@rose-hulman.edu		x8415

More on AFS

AFS access and file sharing

In general, data files should be stored in the Private subfolder of the home directory in order to guarantee privacy. By setting the access rights of the Desktop folder to the user only, files can also be safely stored on the desktop. Correspondingly, files intended to be shared with everyone should be stored in the Public folder. If several users need to share files you may wish to give this group access to the files in question. The files should be stored in a separate folder and then access to this folder given to this group only.

The method to accomplish the forgoing is by modifying AFS permissions on folders. The methods for doing this from the laptop or from a workstation are documented on the IAIT FAQ page. In order to change the permission from a workstation open up a terminal window and follow the steps given on the IAIT FAQ page.

AFS Limits when Working with Long Computations

When you log into a workstation or server the default working directory is your home directory and the AFS file system server provides you with an AFS token which allows you to access the file system. This token is valid only for logins of limited duration and special workarounds are needed for lengthy calculations. Here are some workarounds courtesy of Steve Jones in IAIT. The third option is recommended.

AFS tokens are good for up to ten hours, and must be renewed before they expire. It doesn't matter what type of file you're working on, a valid token must exist before access (read, write, or whatever) is granted. Given that, there are three ways to ensure your files are saved on AFS.

1. One is to make sure the application completes before the AFS token expires.
2. Option two is to use renewal tickets and run "kinit -R" and "aklog" automatically (via cron or at, depending on the user and the system). Neither of these applications will require a password, so they may be executed automatically, but the tickets must be renewed before they expire, and the ticket lifetime must be long enough to support the application.
3. The easiest option is not to use AFS filespace for files that must be accessed for a length of time greater than 10 hours. When doing computations that are this long it is best to log into one of the remote servers clive or derek and use a subfolder of the /work directories on those servers to store temporary files. You will need to contact Mike McLeish to set up a folder in the work directory for yourself.