CAMd Summer school 2012

Logging in to the databar terminals

When you log into the databars, you can select various desktop environments. Please choose IceWM, the other choices will cause trouble!

Exercises will make use of terminals. It is important that you open the terminal on one of the Linux servers, not on the Sun server running the graphical user interface, as GPAW will not work on it. Choose Terminal ‣ xterm on Linux from the GBar menu, accessible by right-clicking on the desktop in IceWM. Or press the Terminal icon on the bottom toolbar.

Setting up your UNIX environment

The first time you use the databar computers, you must configure your environment. Run the commands:

$ cd
$ mv .bashrc old.bashrc
$ cp ~jasc/camd.bashrc .bashrc
$ source ~/.bashrc

This will set up the environment for you so that you can use ASE, GPAW, VMD and matplotlib.

Note that the filename .bashrc starts with a period, making it a hidden file in Unix. Also note that the tilde (~) key on the databar computers is in an unusual place: Alt Graph 5

Running GPAW calculations

GPAW calculations are written as Python scripts, which can be run with the command:

$ python filename.py

If the calculation lasts more than a few seconds, submit it to the queue instead of running it directly:

$ gpaw-qsub filename.py

This will allow the script to be executed on a different host, so the jobs will be distributed efficiently even if many users logged on to the same computer. The output from your script will be written to the files filename.py.oNNNNNN and filename.py.eNNNNNN where NNNNNN is a job number. Normal output (stdout) goes to the .oNNNNNN file, whereas error messages (stderr) goes to .eNNNNNN. Unlike some queue systems these files appear when the job starts, so you can follow job progress by looking at them.

You can run jobs in parallel, using more CPUs for increased speed, by specifying e.g. 4 CPUs like this:

$ gpaw-qsub -p 4 filename.py

The qstat or qstat -u USERNAME commands can be used to monitor running jobs, and qdel JOB_ID to delete jobs if necessary. On the joblist from qstat, you can find the JOB_ID. You can also see the status of the jobs, Q means queued, R means running, C means completed (jobs remain on the list for a while after completing).

Notes and hints

  • Editor: Several editors are available including emacs, vim and gedit.
  • Printer: There is a printer in each databar, the name is written on the printer. To use it from a terminal: lp -d printename filename. Read more about printing here.
  • To open a pdf-file: evince filename
  • How to use USB sticks.
  • The normal tilde (~) key combination is not functional on the databar computers. Use Alt Graph + 5 to type a tilde.

Using your own laptop

If you wish to use your own laptop to log into the databar, that is indeed possible. You can either log in via SSH (secure shell) or using the ThinLinc client. Note that most likely we cannot help you getting it to work if something on your laptop causes trouble.

Linux and Mac laptops

You need to open a terminal and log in to login.gbar.dtu.dk. From there, you log onto one of the Linux hosts.

$ ssh -X USERNAME@login.gbar.dtu.dk
  ( ... message of the day is printed ... )
$ linuxsh -X

Windows laptops

As there is no X server running on a windows laptop, you either have to install one, or use a full-screen client such as ThinLinc.

You can download ThinLinc from Cendio’s webpage. Information about how to connect with ThinLinc is available from the DTU databar wiki.

Note that we recommend going into Options, Screen and disable full screen mode. Either set the resolution to Near current screen size, or if that still gives a too large window, set the size manually. When logging in with thinlinc, you need to log in to the host thinlinc.gbar.dtu.dk and proceed as if you logged into a databar terminal.

An more pleasant (but more complicated) alternative to ThinLinc is to install an X server. Help on doing this can be found on the Niflheim wiki.

When loggin in using an X server, you should log in to login.gbar.dtu.dk and proceed to the Linux hosts with the command:

$ linuxsh -X