For windows users

Follow the instruction on the link below until (but not including) the section "Getting access to the software".

https://wiki.fysik.dtu.dk/gpaw/summerschools/summerschool18/setupwin.html

MacOS users

Follow the instruction on the link below until (but not including) the section "Log into the databar".

https://wiki.fysik.dtu.dk/gpaw/summerschools/summerschool18/setuplinmac.html

How to log in to the databar

You use the ssh (Secure SHell) command to create a secure (encrypted) connection to the databar computers. In the terminal, write:

ssh -XY USERNAME@login.gbar.dtu.dk

where USERNAME is your DTU user name (external participants got it in their registration material). Note the -XY option, it is a minus followed by a capital X and a capital Y, it tells ssh to let the remote computer open windows on your screen.

Note that when you write your DTU password, you cannot see what you type (not even stars or similar!).

You now have a command-line window on the DTU login-computer. This computer (gbarlogin a.k.a. login.gbar.dtu.dk) may not be used for calculations, as it would be overloaded. You therefore need to log in to the least loaded interactive computer by writing the command:

linuxsh -X

You now have a command-line window on an interactive compute node, as shown below. (If you want to increase the font size of the terminal you can open a relevant menu with: ctrl+rightclick.)

How to edit files in the terminal

There are many text editors built in to your terminal and some of them are quite advanced. We recommend that you use the "gedit" text editor for editing files and encourage you to make the following tweak to the gedit editor:

- open gedit by entering "gedit" on the command line. This should open a new window with gedit.

- Go to menu -> preferences -> editor. Check "insert spaces instead of tabs" and set tab width to 4. These are the standard settings in the Python community.

Getting the software

(You only have to do this once) We have preinstalled all software for you (ASE and GPAW). To get the sofware open the special initialization file ".bashrc" with gedit on the command line:

gedit ~/.bashrc

and append the line

source ~jjmo/es2020.sh

to the end of the file. Now log out and log in again.

Submitting jobs to the databar computer cluster

Many of the calculations you are going to run will be able to run directly in the terminal. However, you can run in to a situation where the resources required for the calculation are too great and you would then have to submit the job to the databar computer cluster. We have developed a tool that makes this jobs fairly easy (after some initial setup). The tool is called "MyQueue" (link to docs) and can be called using "mq" on the command line.

First the setup: Execute the following commands to set up myqueue:

mq -h

cp ~jjmo/.myqueue/config.py ~/.myqueue/

Now myqueue should be working.

Here is a small crash course in using MyQueue (see the documentation for more usage examples): Assume you have a file name script.py. This can then be submitted using MyQueue on 8 cores for 2 hours using the following command:

mq submit script.py -R 8:2h

To view the status of the submitted jobs execute

mq ls