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Getting Started on ARSC's Linux Workstations

Contents

 

Getting Started

Introduction

The Arctic Region Supercomputing Center (ARSC) maintains a number of workstations running Fedora Core Linux. As one component of ARSC's computational environment, these machines are available to any ARSC user as local workstations.

Your User Account

To obtain an account for the Linux workstations, you must request resources from ARSC. Workstation accounts are subject to the same policies and restrictions as other ARSC accounts.

Security is another responsibility to be assumed (and shared with the rest of ARSC's community) by accepting your account. If someone else, either with or without your compliance, gains access to ARSC computational resources via your user id and password, you will be held responsible for their actions. The best way to protect our network (and yourself) is to choose a good password and change it regularly. User Support can provide you with some ideas, either online or by request.

Logging On and Off

All ARSC users will receive a user id, kerberos password, SecurID Card, and PIN number for their SecurID Card when they obtain an account.

Once issued an account, there are several ways to connect. One approach is to sit down at a workstation in one of the ARSC access labs, and log directly onto the desktop. To do this, move the mouse around to awaken the screen-saver. It will present you with a dialog box similar to this:

                  --------------------
                 |   WARNING BANNER   |
                 | .................. |
                 | .................. |
                 | .................. |
                 | .................. |
                 |--------------------|
                 | Login name:        |
                 | Principal:         |
                 | Password:          |
                  --------------------

Respond as follows:

'Login:'     Enter your standard ARSC UserID.
'Principle:' Leave this blank. It is only needed if you are authenticating 
             with a remote server (for example: joe@WES.HPC.MIL).
'Password:'  Enter your Kerberos passphrase.
'Passcode:'  After you have entered your Kerberos passphrase, this
             prompt will appear.  Obtain your 6-digit passcode by entering your 
             4-digit PIN into your SecurID card, pressing the diamond shaped key,
             and then read the passcode from the card display.

Please read our Kerberos/SecurID Login Procedures for detailed information about logging onto other ARSC hosts.

To disconnect, use the mouse to select Desktop -> Log Out from the menu bar.

 

Policies

Accounts and Passwords

All of your ARSC accounts have the same account login name and kerberos password (or "pass-phrase"). To change your kerberos passphrase by using the kpasswd command from a Linux/Unix client or invoke the "Change Passphrase" utility contained within the Macintosh or PC Kerberos5 client. You will be prompted once for your old kerberos passphrase, once for a SecurID Card passcode, and twice for your new kerberos passphrase.

The kerberos passphrase may be up to 255 characters long and must be at least 8 characters in length including at least two character classes, such as:

i love miss.ISS.ipp1

or

p0lar beer #17 RATS!!!

If someone obtains your passphrase, PIN, SecurID card, and accesses your account, you are responsible for the use or misuse of ARSC resources. Please review ARSC's personal password protection policy.

NOTE: Your initial passphrase must be changed within 30 days of the creation of your account.

Rebooting Workstations

Pressing the reset button or power switch on a Linux workstation is considered an abuse of the system. Any time power is lost to a Linux/Unix workstation, the filesystem may be damaged. If there is a problem, check with the lab assistant, or contact User Support. Continued abuse will result in the loss of your access laboratory privileges.

Running Background Jobs

The primary purpose of the Linux workstations is to provide interactive console use and data processing services. Background processes are permitted on these systems, however long background jobs without checkpointing are vulnerable to data loss, and urgent system administration tasks may require termination of background jobs with little or no notice.

Game Playing

Playing computer games on ARSC systems is considered an inappropriate use of ARSC resources.

Screen Locking

ARSC requires users to lock their screens during all absences from a workstation. This is a necessary precaution to prevent anybody else with physical access to the machine from using your account inappropriately. To manually lock the screen, type xlock.

No locking for over 15 minutes! Screen locking is intended for short absences, not to allow a user to monopolize a system. Please help maintain an atmosphere of mutual support and cooperation by leaving a terminal for no more than 15 minutes. If screen locking is abused, let us know, and we will address the issue with the user.

 

Operating System / Shells

The following shells are available on the Linux workstations:

If you would like to have your login shell changed, please contact User Support.

 

System News & Status

System news is available via the news when logged onto a Linux workstation. System status and news items are available on the web.

 

Storage

Storage Variables

On all ARSC systems, three environment variables point to elements of the storage environment and are defined for users. Please use these environment variables:

Name Purpose Quota (*) Purge Policy Back Up Policy
$HOME "dot" and other small files 256MB not purged backed up
$SCRATCH compilation, program execution, storage for active program data files none purged not backed up
$ARCHIVE long-term storage none not purged backed up

* Requests for increased quotas should be sent to User Support

Here are more details, subject to change, on the Linux workstation storage environment.

See http://www.arsc.edu/support/howtos/storage.html for more information on storage policies at ARSC.

Disk Quota Limits

All home directories have a default disk quota limit of 256MB. Requests for larger quotas should be sent to User Support. Using the command qcheck -k allows you to see your disk quota and current use for your home directory. The output from this command will look similar to the following:

                                        Online Limits                Total Limits
               Type    ID    In Use     Soft     Hard    In Use     Soft     Hard
       /export/lnxhome
       Files   user  0000      1034   100000   110000      1034   100000   110000
       Blocks  user  0000    155908   256000   300000    155908   256000   300000
       Grace period                    1w                          1w

Reading the "Blocks" row from left to right, the fourth column "In Use" shows how much disk space your home directory is currently using (measured in KB). The fifth column, labeled "Soft" shows your disk quota. The sixth column, "Hard" shows the maximum amount of disk space your account can use. NOTE: You can exceed the amount shown in the "Soft" column for up to 7 days, but can never exceed the amount shown in the "Hard" column. This allows you to work on large projects (larger than would normally fit into your home directory) for short periods of time. Note also that if you don't reduce your disk usage to the amount shown under "Soft" within 7 days, you will be unable to use any additional disk space in your home directory.

If you would like to be informed about your current disk space usage upon log in, you can add the command "qcheck -k" to the file ".login" in the top level of your home directory if you are using C shell, or ".profile" if you using Bourne or Korn shell.

Burning CDs

All ARSC Linux workstations are equipped with CD burners. Files can be written to CD using the graphical CD/DVD Creator software that comes bundled with Fedora Core. Upon inseration of a blank CD-R, the CD/DVD Creator window will automatically appear. Files and directories can be dragged and dropped into this window. When all desired files have been added to the window, click File -> Write to Disc... to burn the files to a CD. If you have closed the CD/DVD Creator window, or if it failed to appear upon blank CD insertion, it can be invoked by right-clicking the "Blank CD-R Disc" icon on the desktop and selecting "Open".

 

Programming Environment

Development Suites

Tools Portland Group (*) GNU
Fortran compiler pgf77/pgf90/pgf95/pghpf gfortran (f95)
C compiler pgcc gcc (cc)
C++ compiler pgCC g++ (c++)
Debuggers pgdbg gdb
Performance Analysis pgprof gprof

* To use the Portland Group compilers and tools, you must first load the "pgi" module. Please refer to the Modules section of this document for more information.

Scripting Languages

In addition to the Portland Group and GNU compilers and analysis tools, ARSC's Linux workstations include many popular scripting languages, including Perl, Python, and Ruby.

 

Modules

Linux workstations have the "modules" package installed. This tool allows a user to quickly and easily switch between different versions of a package (e.g. compilers). The module package sets common environment variables used by applications such as PATH, LD_LIBRARY_PATH, etc.

Before the modules package can be used, you must first source the modules "init" file corresponding to the shell you are using. For example, if your shell is bash, you would need to type:

       source /usr/local/pkg/modules/init/bash

Once the appropriate "init" file has been sourced, you can use the modules package with the following commands:

Command Example Use Purpose
module avail module avail lists all available modules for the system.
module load pkg module load pgi loads a module file from the environment
module unload pkg module unload pgi unloads a module file from the environment
module list module list displays the modules which are currently loaded.
module switch old new module switch pgi pgi.6.0 replaces the module old with module new in the environment
module purge module purge unload all module settings, restoring the environment to the state before any modules were loaded.

 

Duckering Access Lab

Located in the University of Alaska Fairbanks Duckering Building, room 234, the Duckering Access Laboratory provides computational resources to its users in a convenient location on lower campus. Read the Access Lab Policy for details on gaining access to this lab.

 

More Information

 

Arctic Region Supercomputing Center
PO Box 756020, Fairbanks, AK 99775 | voice: 907-450-8600 | email:

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