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  • How do I connect to a server with ssh?

  • How can I debug if there’s a problem connecting with ssh?

  • Connect to a server via ssh.

  • Copy files from your local computer to the host server.

  • Copy files from your host server to your local computer.

Now back to SSH: When we connect to a server using SSH, it will use the same method of asymmetric encryption to establish the identity of the server. When you connect for the first time, SSH will ask you if you know this computer. If you type for the first time

ssh <username>@<servername>

(again, replace <username> for your collaboration username and <servername> for your collaboration servername), you should see something like

The authenticity of host ' (' can't be established.
RSA key fingerprint is SHA256:WbkI/Ko+FdCbIAVn6ky2odyWxCvCL3+5XqWSZQ6PynE.
Are you sure you want to continue connecting (yes/no)?

This means that ssh doesn’t have the public key of the servername, (in this case), which is called the “host key”. Therefore, it warns that it cannot be sure you connected to the right server. It’s usually fine to just say yes; it will only ask you the first time and remember this decision. After you enter yes, you will get a message like

Warning: Permanently added '' (RSA) to the list of known hosts.

which is perfectly normal. In the next step, the server will ask you for your password and after that, you should see a command line prompt and are now connected.

Once you are connected, the next important step is to disconnect. To do so, just type exit and press return (enter), and your connection will be closed. If you’re very impatient you can also press Ctrl-D as a shortcut.

Warning: Long running jobs

Don’t run long-running and CPU or memory heavy jobs on login nodes like the one you just used. Login nodes are shared resources for all users and it’s not very polite and, mostly, it is also not permitted to occupy them with calculations that could be done on dedicated machines. You probably have access to batch systems to submit resource intensive jobs!


Login to your desired server and verify that the login succeeded with the hostname command and log out again.

One final thing about host keys

After you connected to a server, ssh remembers the host key and will verify it on each connection. So you might see something like this:

Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that a host key has just been changed.
The fingerprint for the RSA key sent by the remote host is
Please contact your system administrator.

This means the host presented a different key than it used to. This can sometimes happen if the server you want to connect to was reinstalled. If you know that the server was reinstalled or upgraded, you can tell ssh to forget the previous host key by running

ssh-keygen -R <servername>

Copying Files

In addition to just connecting to a remote shell we can also ssh to copy files from one computer to another. Very similar to the cp command, there is a scp command, for a “Secure Copy”. To specify a file on a server just precede the filename with the ssh connection string followed by a colon. For example:

scp bastion-message

This will copy the file /etc/motd into the current directory on your local computer as bastion-message. In the same way,

scp bastion-message

will copy the file bastion-message from your local directory into your home directory on the server


Copy a file from your local computer to your server’s home directory


You can use the touch command to create an empty file to copy.


Copy a file from your server’s home directory to you local directory.


Copy a full directory with all files at once either from your local computer to the server or from the server to your local computer.


Try man scp or scp --help to get to know about scp flags that may be of use.


Supply -r to scp to recursively copy the full directory.

However, for more efficient copying of large amount of files you should consider using rsync


If you run into trouble in one of the following sections, it can be very instructive to switch on debugging output to get to know possible issues, by using the -v flag of ssh:

ssh -v <username>@<servername>

Once you have created a configuration file (next section) it can also sometimes be helpful to disable it to rule out this source of error. This can be done by using the -F option to specify a blank config file:

ssh -F /dev/null <username>@<servername>

Key Points

  • simple connection to a server is just done by ssh username@servername

  • scp can be used to copy files from and to remote computers

  • ssh uses host keys to ensure the identity of the server you connect to