RHIT Math Department Computing - Compute Servers HowTo Page

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Items to be updated or in transition are in red italics

Contents

• Purpose of this page
• Linux compute servers - clive and derek
• Network Resources, Accounts and AFS
• Available Software
• SSH, SFTP and Xwindows Sessions on Servers
• Starting Applications
• File and Process Management
• Getting Help
• More on AFS
  • AFS access and file sharing
  • AFS token limits

Purpose of this page

This document, and its companion document the Theorodrome Howto Page, are intended to enable new Linux users to use basic applications, manage files, and use basic network resources on HP Linux servers in the Mathematics Department. In this document we describe the servers, login procedures, accounts and network file spaces, using applications, 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.

Compute Servers - Clive and Derek

The compute servers, clive and derek, are dual-processor HP Linux based servers. The servers and their configurations are:

clive, derek
Hardware: HP DL140, with dual Intel Xeon Processor 3.20GHz/533MHz-1MB, 4GB ECC RAM, 2x80GB ATA-100 IDE disk drives, Integrated Dual Broadcom 10/100/1000 NICs, and CD-ROM.
OS : Redhat Enterprise Linux

The compute servers are accessible by through SSH terminal window sessions, SFTP file transfer sessions, or an Xwindows session. From the Linux workstations this is fairly transparent. From a faculty or student laptop you must use SecureCRT (SSH), SecureFX (secure file transfer) or Xwin32 (Xwindows session). All these programs are either pre-installed or available available from Tibia. See the software section of the IAIT site. When using the server through an X-windows session form a workstation, everything works works more or less as described in Theorodrome Howto Page.

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 In addition to the global AFS file system the local file system of server will be occasionally be of importance, especially the /home and /work directories. The local file system on the server should only be used for disk intensive tasks or long computations where the time limitations of the AFS system tokens cause problems (longer that 10 hours). To solve this problem, each user may have a personal directory on the local server in the /work directory (only if needed, see Mike Mcleish to set one up). Files should eventually be moved to the AFS system where there is more space and a backup policy. The /work directories are never backed up. This is described below.

Available Software

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

tr>

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

SSH, SFTP and Xwindows Sessions on Servers

A server can be accessed through either a text-only terminal window through an SSH session, and SFTP secure file transfer session, or a graphical session using an Xwindows.

Note: To access any of the math department servers or workstations form off campus you must connect to the Rose network using the off-campus VPN. See this IAIT webpage for details.

Get help from Mike Mcleish if you are having trouble.

SSH sessions

• From Math Linux workstation: Open a terminal window and type in one of
  • ssh clive.cs.rose-hulman.edu
  • ssh derek.cs.rose-hulman.edu
  • then type in your Kerberos username and/or password as prompted.
• From a Windows laptop/desktop: Use SecureCRT a session with these parameters:
  • protocol: ssh2
  • hostname: clive.cs.rose-hulman.edu or derek.cs.rose-hulman.edu
  • port: 22
  • authentication primary: password

SFTP sessions

• From Math Linux workstation: Use the file browser or gftp on the Application > Internet menu section .
• From a Windows laptop/desktop: Use a SecureFX session with these parameters :
  • protocol: sftp
  • hostname: clive.cs.rose-hulman.edu or derek.cs.rose-hulman.edu
  • port: 22
  • authentication primary: password

Xwindows Session

• From Math Linux workstation: Log into the server as follows:
  • at the top graphical login dialog box click on Actions
  • click on XDMPC chooser
  • if needed, add the host name
  • click on connect and then log in .
• From a Windows laptop/desktop: Use an Xwin32 session with these parameters :
  • XDMCP mode: Query
  • hostname: clive.cs.rose-hulman.edu or derek.cs.rose-hulman.edu

Starting Applications

Application commands: To start a text only session for an application open up an SSH session on the appropriate server as above. To start a graphical session for an application start an Xwindows session on the appropriate server and type in the appropriate command in a terminal window or select a program form the Applications menu.

software title	hosts	Text session command	Xwin session command
Cplex	clive, derek	installed summer 2006	installed summer 2006
Femlab	clive,derek	installed soon	installed soon
Maple	clive, derek	maple	xmaple
Maple 9 (classic worksheet)	clive, derek		maple -cw
Matlab		matlab	matlab
Matlab no jvm but figures	clive, derek		matlab -nojvm
Magma	clive, derek	magma
Mathematica	clive, derek		mathematica
SAS	derek	sas	sas
Splus	clive	Splus

Long computations: To start an long term application that continues running after logging out do the following:

1. Log into a terminal window on the server
2. change to a directory on the server where you may write files and where your input files are located.
3. type in a command of the following type
nohup app inputfileinfostring outputfileinfostring &
4. where
• app = application command
• inputfileinfostring = string of information to supply commands to the application
• outputfileinfostring = string of information to supply commands to the application
  
• the nohup at the beginning of the command line tells linux not to kill the process when you log out. the & at the end the command line indicate that the process should run in the background.
5. logout and check the progress of the application periodically by logging in and using top or some other command.

For some applications the output files may be designated in the input file. Normally the input file needs to have some form of a quit command at the end.

Here are some examples.

• nohup matlab <test.m >results.txt &
• nohup matlab <test.m & (embed a diary or save command in test.m)
• nohup magma -s test.mgm & (embed file writes or log file commands in test.mgm)
• nohup maple test.mpl > rez.txt &
• nohup maple -q test.mpl & (embed file writes in test.mpl)

File and Process Management

Normally navigating the local file system on a server or AFS file system is most easily accomplished using graphical interface such as the file browser on a workstation or SecureFX or Xwin32 from a laptop/desktop. The AFS system is also navigable with Windows Explorer from a laptop/desktop. If required, one may also use linux file management commands from a terminal window. In addition, there are commands for sharing file spaces and managing processes. You may get help for these commands through man pages as described the getting help section.

Command	Operation
pwd	show current directory
cd	change directory
dir, ls	directory contents
cp	copy
mkdir	make a directory
rm	delete a file
rmdir	remove an empty directory
mv	move or rename a file
fs listacl	list AFS acl
fs setacl	set AFS acl
fs command	file system command
ps	show processes
kill	kill a process
top	show top processes

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 UNIX 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 

And you will 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 department people. As IAIT  support is mainly for AFS maintenance, accounts and system wide software, they may redirect your request to the Math Dept.

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