/doc/summerschools/summerschool16.rst
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- .. _summerschool16:
- =======================
- CAMd Summer School 2016
- =======================
- Announcement:
- http://www.fysik.dtu.dk/english/Research/CAMD/Events/Summer-school-2016
- .. highlight:: bash
- Logging in to the databar
- =========================
- The software (mainly Python, ASE and GPAW) that you need for the
- computer exercises are available in the databar. You are expected to
- access the databar from your own laptops. There are essentially two
- ways for doing that: ThinLinc and Secure Shell. ThinLinc will give
- you a Linux desktop, Secure Shell will open windows on your normal
- desktop.
- :Linux and Mac users:
- We recommend using Secure Shell.
- :Windows users:
- ThinLinc is easier to install, many find that Secure Shell is nicer
- to work with.
- Using Secure Shell on Linux and Mac computers
- ---------------------------------------------
- ..
- **Mac users**: You need to install the semi-official X-server for
- MacOS: http://xquartz.macosforge.org/
- To log in, open a Terminal window. On Ubuntu Linux click on the Dash Home
- and search for Terminal - we recommend dragging it to the dock. In Mac OS X,
- find it in Spotlight, again we suggest dragging it to the dock.
- In the terminal window, type::
- $ ssh -X login.gbar.dtu.dk
- and once you are logged in, proceed to log in to one of the Linux machines
- with::
- $ linuxsh -X
- Note that first you log in to a login server that cannot run our
- software, the second command then logs you on to one of the least
- loaded Linux servers where the software is expected to
- work. **Forgetting to run the ``linuxsh -X`` command every time you
- login is the most common source of errors!**
- You now need to read `Setting up your UNIX environment`_.
- Installing and using Secure Shell on Windows computers
- ------------------------------------------------------
- To log in to the databar and display the applications on your Windows
- desktop, you need to install an X11 server on your Windows machine.
- We recommend installing `MobaXterm <http://mobaxterm.mobatek.net/>`_.
- See also :ref:`mobaxterm`.
- The server name is login.gbar.dtu.dk
- Once you have an xterm terminal window open on the gbar login server, type::
- $ linuxsh -X
- to proceed to one of the Linux servers, where the course software is installed.
- You now need to read `Setting up your UNIX environment`_.
- Installing and using ThinLinc
- -----------------------------
- **This is an alternative way to access the computers from Macs and
- Windows machines, if for some reasons you do not wish to use SSH.**
- Information on how to install and use ThinLinc is available here:
- http://gbar.dtu.dk/index.php/faq/43-thinlinc
- Set the server name to thinlinc.gbar.dtu.dk. User name and password is
- your DTU login. When loggin in, you are asked to choose between
- different desktops, we recommend choosing Xfce (some of the other
- choices will cause trouble).
- You need to open a terminal window to use gpaw. Click on the
- Applications Menu, then on Terminal Emulator.
- *Hint*: Before you log in the first time, click on Options, choose the
- Screen tab, and select "Work area (maximized)". Then thinlinc will
- open a window filling the whole screen, but will not go into
- full-screen mode which many people find annoying to get out of again.
- Setting up your UNIX environment
- ================================
- The first time you use the databar computers, you must configure your
- environment. Add the following line to the very end of your
- ``.bashrc`` file::
- source ~mikst/camd2016.bashrc
- This will set up the environment for you so that you can use ASE, GPAW and
- matplotlib.
- Note that the file ``.bashrc`` starts with a period, making it a hidden file in Unix.
- If you would like to setup the text editors ``nedit`` and ``vim`` in a python
- friendly way you can execute the command::
- $ sh ~mikst/python_friendly.sh
- This may take about a minute or so.
- Running GPAW calculations
- =========================
- **Warning** do not use spaces in the directory/file names!
- 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 :samp:`filename.py.oNNNNNN` and :samp:`filename.py.eNNNNNN`
- where :samp:`NNNNNN` is a job number. Normal output (stdout) goes to
- the :samp:`.oNNNNNN` file, whereas error messages (stderr) goes to
- :samp:`.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 :samp:`qstat -u {USERNAME}` commands can be used to
- monitor running jobs, and :samp:`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).
- Exercises and Tutorials
- =======================
- You are now ready to embark on the :ref:`exercises` and :ref:`tutorials`.
- Have fun.
- Accessing databar files on your laptop
- ======================================
- The databar has its own file system, separate from your laptop
- (obviously). If you want to keep your scripts and/or results, the
- files should be transferred to your own computer.
- * If you use MobaXTerm on Windows, you can access your databar files
- by dragging and dropping in the file window to the left.
- * If you use ssh to log in, and are familiar with the scp command, you
- can use it to copy files back and forth::
- scp camd16XXX@login.gbar.dtu.dk:myfolder/myfile .
- scp localfile camd16XXX@login.gbar.dtu.dk:myfolder
- * You can map your databar home folder as a network drive:
- - **On a MAC**: From Finder select Go / Connect to Server (⌘K) and
- enter the following as the Server Address::
- smb://home.cc.dtu.dk/camd16XXX
- - **On Windows**: Tools | Map Network drive
- And select any unused drive letter and enter the following as path::
- \\home.cc.dtu.dk\camd16XXX
- - **On Linux**: It depends on the Linux distribution and on what
- software is installed. If you have samba installed, you should be
- able to mount the drive using the smb protocol, use the same
- address as on a Mac (see above).
- Another option that may work is the sshfs command. Create an empty
- directory, and mount the remove file system there::
- mkdir databar
- sshfs camd16XXX@transfer.gbar.dtu.dk: databar
- If you fumble, you may leave the folder in a half-mounted state,
- and get a "Device or resource not ready" or "Transport endpoint is
- not connected" error when you try again. In those case, either create a new folder
- with a new name, or reboot your linux machine.
- Cannot open new windows after 20 minutes
- ========================================
- If you use SSH to log in from a Mac (and from *some* Linux
- distributions), an over-zealous security measure prevents the databar
- computer from opening new windows if it is more than 20 minutes since
- you logged in.
- To fix it, edit the file /etc/ssh/ssh_config as the super-user, and
- add a magic line to it::
- cd /etc/ssh
- sudo nano ssh_config
- This opens a primitive editor. Use the arrow keys to go to the end of
- the file, and add this line::
- ForwardX11Timeout 36000
- (it is case sensitive, so use copy-paste).
- Save the file and exit (Control-X). This increases the time-out to 36000 seconds, i.e. ten hours.
- 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: :samp:`lp -d {printename}
- {filename}`. Read more about printing `here
- <http://www.gbar.dtu.dk/wiki/Printing>`_.
- * To open a pdf-file: :samp:`evince {filename.pdf}`
- * The normal tilde (~) key combination is not functional on the
- databar computers. Use :kbd:`Alt Graph + 5` to type a tilde.
- .. * How to `use USB sticks <http://www.gbar.dtu.dk/wiki/USB_Access>`_.