The Secure Shell Protocol

To access different machines and minimize the risk of getting hacked while doing it, we use the Secure Shell protocol. There are two main commands: ssh and scp.

To log into a different machine, type
    ssh username@machineid
For example,
    ssh jkua@10.120.108.45
gets me into the machine with IP address 10.120.108.45 (provided I have a user account)
and if I wanted to log into saber2, I could type
    ssh jkua@saber3.sandiego.edu

Some machines can only be accessed via a particular port number, you will need to specify the port number when you use ssh. You do this by
    ssh -p portnumber username@machineid

To copy files from one machine to another, you need to know the full path of both the machine name and the directory tree. For example, if I was sitting at my laptop and I wanted to copy over a file from my home directory on saber3, I could for example type:
scp jkua@saber3.sandiego.edu:/home/jkua/mymolecule .
Remember that last dot (.) means to copy to the current directory you're in just like for the regular cp command in Unix. Note that you use a capital P to specify for the port number for scp but you use a lower case p for ssh.

Or if you wanted to copy a file from your machine to saber3, and assuming you are currently in the directory where your file mymolecule is located...
scp mymolecule username@saber3.sandiego.edu:/home/username/

If you don't want to deal with scp on the command line, there's a free program called Cyberduck that allows you to drag and drop files. I can show you how to use it after you download it to your laptop (Windows or Mac).
https://cyberduck.io/download/

If you are off-campus (or not behind the USD firewall), you will need VPN access to ssh in or use scp. You won't be able to pull up any graphics in any case, because it will be too slow to run from off-campus. But you can open a Terminal Window and use text.