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.. _summerschool08:
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=======================
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CAMd Summer school 2008
=======================

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Databar
=======
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Setting up your UNIX environment
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--------------------------------
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The first time you use the databar computers, you must do this:
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.. highlight:: bash
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::
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  $ ~jjmo/summerschool/setup.sh
  $ source ~/.bashrc
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That will set up the environment for you so that you can use ASE, GPAW, VMD and matlpotlib.
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**Warning** runnig :command:`~jjmo/summerschool/setup.sh` owervrites
users ~/.bashrc ~/.emacs ~/.pythonrc ~/.vmdrc and ~/.matplotlib directory.
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Notes
-----
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* Useful links: Userguides_ FAQ_ Unix_ USB-sticks_
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* Editors: emacs, vim, nedit (MS Windows/Macintosh-like environment). Python syntax
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* Printer: gps1-308. Terminal: lp -d gps1-308 filename
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* E-mail client:
  Thunderbird is the default mail client in the databar and configured  
  with your summer school e-mail (camd0??@student.dtu.dk).
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* To open a pdf-file: acroread filename
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Niflheim
========
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Frontend nodes
--------------
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Log in to niflheim::
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  ssh school1.fysik.dtu.dk
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or::
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  ssh school2.fysik.dtu.dk.
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Same password as handed out for the databar. Please use school1 if the
number in your userid is odd and school2 if it is even.
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Copying files from gbar to niflheim
-----------------------------------
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You can copy files from the Gbar to niflheim with ``scp``. If you are on 
niflheim::
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    scp hald.gbar.dtu.dk:path/filename .
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will copy ``filename`` to your present location. Likewise::

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    scp school1.fysik.dtu.dk:path/filename .
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will copy ``filename`` from Niflheim to your present location at the Gbar.
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GPAW
----
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Use the :command:`gpaw-qsub.py` command to submit GPAW jobs to the queue.
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SIESTA
------

Siesta is installed on Niflheim, so you need to log in to the Niflheim
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front-end nodes as described above in the Niflheim section.
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Furthermore you have to set two environment variables by adding the
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following two lines to your ~/.bashrc file::
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  export SIESTA_PP_PATH=~mvanin/asesiesta
  export SIESTA_SCRIPT=~mvanin/asesiesta/run_siesta.py  

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and source it by typing::
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  $ source ~/.bashrc

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To submit a job to Niflheim, use the ``qsub`` command::

  $ qsub -l nodes=1:ppn=1:switch5 filename.py

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Octopus
-------
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Octopus_ is installed on the 'q' opteron nodes on Niflheim. The way to
run jobs is the following: Create inp file in the working directory as
described in the tutorial_, and then run
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:git:`~doc/tutorialsexercises/unused/octopus_run.py`. To use various octopus utilities such
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as ``oct-cross-section`` and ``oct-broad`` you need to do::
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  source /usr/local/openmpi-1.2.5-pathf90/bin/mpivars-1.2.5.sh
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first. Submitting jobs to the queue is done by::

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  qsub -l nodes=2:ppn=4:switch5 octopus_run.py
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.. _Userguides: http://www.gbar.dtu.dk/index.php/Category:User_Guides
.. _FAQ: http://www.gbar.dtu.dk/index.php/General_use_FAQ
.. _Unix: http://www.gbar.dtu.dk/index.php/UNIX
.. _USB-sticks: http://www.gbar.dtu.dk/index.php/USBsticks
.. _Octopus: http://www.tddft.org/programs/octopus/wiki/index.php/
.. _tutorial: http://www.tddft.org/programs/octopus/wiki/index.php/Tutorial
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