CSL: Linux/Unix FAQ

The CS department is now using Intel-based PCs running Linux as the trusted operating environment. This document describes some of the issues that may be encountered in Linux on the desktop.
Trusted Linux

Based on preferences expressed by the C.S. user community, the department has gradually transitioned to workstations running Linux for desktop use. These workstations are Intel (x86) PCs, and can run any of various operating systems, including those supported by the Lab Staff and connected to the trusted network, and those installed and supported by the user and connected to the untrusted network. This document will only discuss the trusted Linux distribution which is installed and maintained by the Lab staff and connected to the trusted network.

We are currently using the Ubuntu distribution, to take advantage of its faster release schedule and broader application support. For more information, please see:

Window managers

A window manager is a complex set of programs that organize, manage, and decorate the various programs and windows associated with the display on your workstation. You can only run one window manager at a time, and configuration changes you make will only effect that window manager.

On Linux, Gnome and KDE are the primary window managers. Both work well, with some differences in style, appearance, and utilities. Deciding which to use is mostly a matter of personal preference.

Before logging into the desktop, you can click the Session tab at the bottom of the screen to select which window manager to use.

CD Audio
While the audio does work on the Linux machines, you need to make sure that the the audio is not muted (using the Volume control to unmute the PCM sound control, and to raise the volume). On the Linux machines, there is no cable that goes between the CD player, and the motherboard (apparently this is a common manufacturing technique). This means that the audio application has to decode the information on the CD using the CPU on the machine. This can't be done using the standard players, but we have installed a program called alsaplayer that will work. In order to access the CD:
	Open alsaplayer
	Click on the icon that looks like a page of written text
	Select CDDA
That should work.
Account configuration files (aka, dot files)

A user's account contains configuration data usually referred to as dot files, since the name of each file typically starts with a period. Many accounts have dot files that were originally designed for Solaris (and prior OSs), and which don't always work well with Linux. Please see the Linux/Unix Account Configuration FAQ for information on configuring these.

Software availability

If you are running a trusted Linux desktop and you need to use a program that is not available, please consider some combination of these options:

  • Open a terminal window on a login server, and run the program from there. If you have a problem with X-server access, check that your DISPLAY environment variable is set correctly.
  • Send a request to request, along with any details, so we can look into it.
  • Learn to use a functionally equivalent program available on Linux.
  • Process scheduling with cron

cron is background system process that will run scheduled commands without user intervention. Virtually any program or script which can be run manually can be run as a "cron" job. For more information, please see the CS Crontabs FAQ page.


Nothing on the Linux desktops is backed up at this time. If you have important data that is stored locally on the system (eg, in /var/tmp/), please be sure to maintain a copy elsewhere. If you use programs such as crontab which store data locally, please make sure to copy anything that you would not want to lose. For more information about backups, please see the various CSL Backup FAQ pages.


The automounter supports a browsability feature. This allows all of the potential filesystem mount points to be visible, whether or not they are mounted. So, on Linux, you might see:

% ls /usr/project
ai              csed            dna             misc2           tune2
ari1            csed2           dnanano         msdnaa          vision
ari_scratch1    csed3           edels           news            visiontemp
ari_scratch2    csed4           frontiers       packages        voice
ari_scratch3    csed5           ft              parr            web-docs
atmp            csed6           ftp             projects        xiaobai
biogeo0         csedtmp         geodata         robocup         xlang5
cgc             csem            httpd           services        xtmp
cgc1            cvpr2005        jsv             spider1
cgi             cwd             kamesh          support
coursearchive   cyberchair      kedem           sysarch_papers
courses         datacomp        misc            tocs

Thus, TAB-key autocompletion and wildcard matches won't work for these directory names on Linux until the mount is induced; you will have to type out the entire directory name, possibly followed by a slash (/), depending on the circumstance. This is similar to the behavior of the .snapshot feature available on filesystems residing on a Network Appliance Filer.

Mounting USB devices

You should be able to mount a USB device using the following command on the linux machines:

mount /mnt/usbkey

The files should then appear under the /mnt/usbkey directory. Please remember to unmount the file system using the command:

umount /mnt/usbkey