Accessing computers through the terminal

In UNIX, we can access separate computers through the terminal. This allows us to e.g. perform large-scale computations on dedicated servers and then move the results to our laptop to insert the results into the papers we are writing.

Accessing the system remotely: SSH

We can connect to any UNIX computer using ssh, a.k.a. Secure SHell (once we know it’s IP address). The program starts an encrypted connection to a machine of choice idenitified by an IP address or an equivalent set label. To connect from say, our laptop to another machine on a local network, we can run:

$my_terminal$: ssh user@mymachine.localnetwork

This will ask you for your password to enter mymachine.localnetwork as user ; after entering it, the terminal you are working on will effectively be the terminal of the machine you connected to. This means that

you have access to the filesystem of the remote machine
all processes you run from this terminal will use the computational resources of the machine you are connected to

In order to close the ssh connection, type exit or close the terminal window.

Skip writing passwords - SSH keys

Everybody hates to type in passwords and so should you. When accessing a computer, like for most laptops, SSH needs you to type the password of the computer you are connecting to. Fortunately, we can skip entering the passwords for accessing computers and servers using ssh keys. These are configuration files that save and authorise your ssh ID upon login.

The ssh keys are stored in your home folder, in a hidden folder .ssh and are named id_rsa and id_rsa.pub. if you don’t have them, you need to generate your ssh keys first.

On your machine (laptop or office workstation):

$my_terminal$: ssh-keygen

Then, you have to copy them to the server you want to connect to, e.g. proxyserver. By doing this you are telling the remote server that it can trust the passwordless access from your local machine. You can do this 2 ways:

1) automatically

from your local machine, simply type:

$my_terminal$: ssh-copy-id user@proxyserver.localnetwork

2) manually

you have to append the text from your PUBLIC key id_rsa.pub of your local machine to the file .ssh/authorized_keys on the remote machine you want to connect to (proxyserver in our previous examples).

Either way, this will allow your local machine to passwordless access to the remote server.

Connecting to a machine passing trough another one: ssh tunnels

In some cases, you have no direct access to a machine and the only way to connect to it is through another, third machine. This is typically an issue when connecting to intranet networks protected by a proxy.

This can be easily done with ssh using the -J option. In our case, the server we need to go through is proxyserver

$my_terminal$: ssh -J user@proxyserver.localnetwork user@mymachine.localnetwork

This will connect you directly to mymachine.localnetwork.

Copying files over ssh

Now that we can connect to all our favorite servers, we may want to copy files from or to them. We can do this with scp. scp uses the same syntax as cp, but you can add from/to what computer you want to copy.

For example, let’s make an empty file banana.txt, copy it to proxyserver and back to your machine renaming it as banana_comeback.txt:

$my_terminal$: touch banana.txt
$my_terminal$: scp banana.txt user@proxyserver.localnetwork:home/user/.
$my_terminal$: scp user@proxyserver.localnetwork:home/user/banana.txt banana_comeback.txt
$my_terminal$: ls
banana.txt banana_comeback.txt

And if we need to pass through a third machine (see section above):

$my_terminal$: scp -o ProxyJump=user@proxyserver.localnetwork banana.txt user@mymachine.localnetwork:home/user/.

Unfortunately only the most recent versions of scp have the same option -J as ssh, so I suggest the option -o ProxyJump= as above for portability.

Graphics over ssh

If you want to connect to a computer and use a program that has some graphics (for instance, opening an image or pdf or running Matlab in visual mode), using ssh will not suffice. If you are on mac, first you will need to install Xquartz. After that, we can use ssh -X or -Y to view graphics.

In slow connections, the weight of graphics can slow down the process, so I suggest to also always use the -C option to compress slightly the graphics and improve performance.

Let’s copy the image about the file permissions to our remote machine and open it:

$my_terminal$: scp Permissions_explanation.png user@mymachine.localnetwork:home/user/.
$my_terminal$: ssh -Y -C user@mymachine.localnetwork
$my_terminal$: nomacs Permissions_explanation.png

On mac, this will open XQuartz and then show the picture. On Ubuntu the picture should open directly. If your connection is bad, this can take some time, even with the -C option.