CAMd Summer school 2010

When you log into the databars, you can select various desktop environments. We recommend CDE or IceWM, but any will do.

Exercises will make use of terminals. Choose Terminal ‣ Terminal (mrxvt) from the GBar menu, accessible by right-clicking on the desktop in CDE/IceWM.

Setting up your UNIX environment

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

$ mv ~/.bashrc ~/old.bashrc
$ echo source ~ashj/summerschool-env/gbar-gpaw.rc > ~/.bashrc
$ source ~/.bashrc

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

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

$ gpaw-qsub -pe 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.

Notes

  • Editor: Several editors are available including emacs, vim and gedit.
  • Printer: gps1-308. Terminal: lp -d gps1-308 filename. The printer is located in databar 15, the middle of the three databars.
  • 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.