Frequently asked questions on computing

Where do I submit jobs?
Use our clusters elektra and hera. See usage instructions for the PBS queueing system. Alternatively, use the desktop machines: there is a separate queue that makes these machines available (option -q normal in your PBS script). Make certain that "/opt/pbs/bin" is in your PATH.
Where do I temporarily store large amounts of data?
Not in your home directory! Every user has a separate scratch directory (typically 500GB) for these purposes. Furthermore, there is 340GB of shared scratch space (/scratch). Like your own scratch partition, this is not backed up, but at least you have the security that it is located on the RAID and hence relatively well protected against hardware failure.
How do I get an overview of changes in installed software, etc.?
See the separate page with Computing News.
Which web browser should I use?
Both Mozilla and Opera are available on all machines and kept up to date.
How do I quickly see how busy the different machines are?
On the command line, type load to get information about all desktop machines. Use qstat -n to see queue information. The same two commands can also be used on elektra and hera. Finally, if you type queues, you see a compact overview of the status of all queues.
Note that the load command only works if you have set up password-less login (see next question).
How do I log in on these machines?
Use ssh, protocol version 2. It is convenient (and required for queue jobs) to set up password-less login within all group machines. Here are the instructions. If you wish to access a machine from a Windows client, see these instructions.
Where do I use Mathematica?
Mathematica 6 is available on all desktop machines. Mathematica 5.2 can still be invoked via "mathematica52".
How do I use RevTeX?
Add the following line to your .bashrc file:
export TEXINPUTS=/usr/local/share/tex//:
If TEXINPUTS is already defined in your .bashrc file, make sure that you change the definition so that it also includes the above directory. RevTeX documentation is available on the Links and Documentation page. Furthermore, adjust your BibTeX environment as indicated in the next question.
How do I use BibTeX style files?
Add the following line to your .bashrc file:
export BSTINPUTS=/usr/local/share/tex/bibstyles:
How do I check the spelling and syntax of LaTeX files?
Use ispell and lacheck. View the corresponding documentation with man ispell and man lacheck.
How do I write CD's or DVD's?
CD writers are available on orestes and niobe. If you haven't done this before, use the program xcdroast on Linux 2.4 or k3b on Linux 2.6. Experienced users may prefer cdrecord (note: under SuSE 9.2 the additional option "dev=ATA" appears necessary). DVD writers are available on apollo, odysseus and theseus; they can write the DVD+R, DVD-R, DVD+RW, DVD-RW formats. See DVD writing instructions.
Which compiler should I use?
Generally, the fastest code is produced by the Intel compilers; the latest version is available on all machines. The C/C++ compiler is invoked via icc. The Fortran 77/Fortran 90 compiler is invoked via ifc. See these instructions to learn how to set up your environment. The recommended compiler options are: -O3 -tpp6 -xK for Athlon machines and -O3 -tpp7 -xW for Xeon machines.
In addition, an up-to-date version of GCC/G++/G77 is available on all machines.
How can I access e-mail on my student/staff account from a local e-mail program?
This works via IMAP, which is supported both by pine and by mozilla. Instructions for pine. Instructions for Mozilla follow soon.
How do I ensure that I have access to all globally installed software?
Make sure that the directory /usr/local/bin appears in your PATH environment variable, before any system directories.
How do I debug my programs?
The Data Display Debugger (ddd) is strongly recommended. Extensive help is available.
How do I watch MPEG movies that I created for my simulations?
Use vlc.
How do I improve the contrast in xdvi, to make my screen previews more readable?
Use the option "-gamma". For example: xdvi -gamma 1.75 paper.dvi
If you find a setting you wish to make the default, consider setting it in ~/.Xdefaults. Add the following line to this file (replace 1.75 by the value of your choice):
xdvi*gamma: 1.75
As always, this change won't take effect until the next time you log in. This can be circumvented by issuing the following command:
xrdb -merge ~/.Xdefaults
Now "xdvi paper.dvi" should work as desired.
How do I print single-sided, double-sided (duplex), 2-up, etc.?
If you are printing from a program such as Acrobat or Mozilla, it is easiest to use the kprinter printer interface. In the kprinter window, simply click on the "Properties" button to select all desired printing options. (In SuSE 8.0, qtcups was used instead.)
In Acrobat, the kprinter interface can be invoked by selecting "Print". In the "Printer Command" box, delete "/usr/bin/lpr" and enter "kprinter".
In Mozilla, the kprinter interface can be activated by putting this file in the directory "~/.mozilla/YOURNAME/XXXX/user.js". Here "XXXX" is some string that is different for every user (the directory will contain all your profile settings). Restart Mozilla and things should be working.
If you are printing from the command-line (using "lpr"), please note that duplex printing is the default setting. In order to select single-sided printing, use
lpr -Pps -o sides=one-sided
If you need this to print on letterhead paper, put the paper into the top tray (pull open) and select this tray via
lpr -Pps -o media=upper -o sides=one-sided
For further options, see the CUPS manual.
How do I use Rasmol?
The proper binary for 32-bit displays is rasmol_32bit. If you define an alias (alias rasmol='rasmol_32bit') in your ~/.bashrc file, you can simply use rasmol. In addition, you need to specify the location of the Rasmol help file. Add this line to your ~/.bashrc file:
export RASMOLPATH=/usr/local/share/rasmol
Further documentation can be found on the Links and Documentation page.
How do I use AUCTeX? (And preview-latex?)
AUCTeX is a package for GNU Emacs that facilitates writing LaTeX files. Documentation is available here. You enable this package by adding the following lines to your ~/.emacs file:
(setq load-path (cons "/usr/local/share/emacs/site-lisp" load-path))
(require 'tex-site)
If you desire preview-latex, also add the following line to ~/.emacs:
(load "preview-latex.el" nil t t)
How do I download via BitTorrent?
Use azureus. This program is installed on ariadne only. Log in to ariadne, start azureus and open the .torrent file corresponding to your download.
Which machines have a large amount of memory installed?
Apollo (3GB), Athena (2GB), Odysseus (2GB). Niobe has 1.5GB. Orestes and Theseus each have 1GB. All other machines have 512MB per CPU.
Where do I find the icons to associate with applications on my desktop?
For convenience, several of them have been collected in /usr/local/share/icons.

How do I obtain Emacs for Windows?
See this webpage. In brief, after downloading the package emacs-XX.X-fullbin-i386.tar.gz (where "XX.X" is currently "21.3") from ftp.gnu.org, unpack it in an appropriate place (e.g., "C:\Program Files"). Note that the aforementioned webpage provides information on unpacking tar.gz files under Windows. You can then invoke Emacs right away by starting "C:\Program Files\emacs-XX.X\bin\runemacs.exe". You may wish to create a shortcut to this program.
How do I print to the HP2300 or HP2420 from my laptop?
First, download the printer driver (HP2300 or HP2420) and unpack it somewhere on your laptop. Next, follow the steps described in the print server manual, starting halfway on page 5 (i.e., at "For Windows XP"). On page 7, use the IP address and port name provided here.
Is there a list with all IP addresses that are in use within our group?
See this list. Note that laptops always should use DHCP.

This page was last updated on August 18, 2008.