The Secure Shell network protocol allows you to connect to remote computers through a an encrypted channel. SSH is the standard tool used by computational scientists to interact with computer clusters and supercomputers around the world.

During the four weeks of the tutorial, you have the possibility to access a remote computer (16-core Xeon E5-2690 CPU with 2.9 GHz clock frequency, 256 GB RAM).

Once you have a user name on the remote computer (ask your teaching assistant), you can connect to it:

ssh -X username@pcihopt3.uzh.ch       # Connect to host pcihopt3.uzh.ch with X11 forwarding 

The -X flag ensures that when you run a program with a graphical user interface on the remote computer (such as VMD), the graphical user interface will be forwarded to your local machine.

After connecting to the remote computer, you start in your personal home directory. Since you are connecting to the machine for the first time, this directory will be basically empty.

Let's fill it with some useful data: Copy the intro directory from your local machine to the remote computer by using the scp program:

pwd                                                         # print your home directory
exit                                                        # exit ssh connection
scp -r intro exer01@pcihopt3.uzh.ch:/path/to/home/directory # copy directory 'intro' to remote computer

Later, you may want to copy back some data from the remote machine to your local computer for closer inspection. This works just analogously:

scp -r exer01@pcihopt3.uzh.ch:/path/to/directory . # copy directory from remote computer to working directory