User Tools

Site Tools


exercises:2016_uzh_cmest:login

This is an old revision of the document!


Your first simulation

In this exercise you will learn how to run your first calculation.

Part I: Login

As mentioned in the lecture, you absolutely need

  • a X11-Server:
    • on Linux: it is enough to be logged-in in a graphical environment (Unity, Gnome, KDE, …)
    • on Mac OS X/OSX/macOS Sierra: you need XQuartz
    • on Microsoft Windows: you need XMing
  • a terminal emulator:
    • on Linux: this can be one of Konsole, Gnome Terminal, Terminal, XTerm, …
    • on Mac OS X/OSX/macOS Sierra: use the X-Windows terminal from XQuartz
    • on Windows: use Putty

optionally you may want:

  • a file transfer tool to copy files from/to the server:
    • on Linux: put sftp:tcopt3.chem.uzh.ch as the address in your file browser and you should be able to login and browser your home directory
    • on Mac OS X/OSX/macOS Sierra: use Cyberduck
    • one Windows: use WinSCP or Cyberduck
  • a plain text editor to edit input files if you are uncomfortable with using vim, nano or emacs via SSH. Please note: It is important that your editor supports Unix line endings. If in doubt, use one of the mentioned editors on the server, or an advanced plain text editor like Atom (plus the line-ending-selector-unix plugin) or Notepad++ on your local machine.

Use the instructions giving in the lecture/available via OLAT to login on the server tcopt3.chem.uzh.ch.

Change the password of your account after your first login, using:
$ passwd

Part II: Loading and running a program

Module loading

Since there are numerous applications with different and possibly conflicting requirements, the module system is used. This means that only basic commands are available until explicitly loaded.

To list all available modules:

$ module avail

while using

$ module list

gives the list of loaded moules.

To load the CP2K module used in this course, use:

$ module load cp2k/r17408_2016_09_19

When you list the loaded modules again at this point (see command above), you will notice that the list has changed.

Now run the following command to verify that the CP2K executable is available:

$ cp2k.popt --help

Which should give you the output

 cp2k.popt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]
           [-i] <input_file>
           [-mpi-mapping|--mpi-mapping] <method>
           [-o] <output_file>
           [-r|-run] [--xml]

 starts the CP2K program, see <https://www.cp2k.org/>

 The easiest way is cp2k.popt <input_file>

 The following options can be used:

  -i <input_file>   : provides an input file name, if it is the last
                      argument, the -i flag is not needed
  -o <output_file>  : provides an output file name [default: screen]

 These switches skip the simulation, unless [-r|-run] is specified:

  --check, -c       : performs a syntax check of the <input_file>
  --echo, -e        : echos the <input_file>, and make all defaults explicit
                      The input is also checked, but only a failure is reported
  --help, -h        : writes this message
  --html-manual     : writes a HTML reference manual of the CP2K input
                      in the current directory. The file index.html is a good
                      starting point for browsing
  --license         : prints the CP2K license
  --mpi-mapping     : applies a given MPI reordering to CP2K
  --run, -r         : forces a CP2K run regardless of other specified flags
  --version, -v     : prints the CP2K version and the SVN revision number
  --xml             : dumps the whole CP2K input structure as a XML file
                      xml2htm generates a HTML manual from this XML file
The module loading is not persistent. You have to reload the modules every time you log back in.
exercises/2016_uzh_cmest/login.1474454442.txt.gz · Last modified: 2016/09/21 10:40 by tmueller