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The SSH (Secure Shell) utility is used to establish remote connections using the command-line. Simply connect to one of the interactive Linux machines using the name "". Replace "jdoe" with your user account name. First time around the system will ask you to accept the remote computer into the list of known hosts. You should compare the fingerprint presented to you with the fingerprint shown on our InteractiveMachines page, before you accept it as a trustworthy computer from GSI by typing "yes" followed by pressing enter (return, here represented by the "↵" symbol):

» ssh↵
The authenticity of host ' (' can't be established.
RSA key fingerprint is 96:15:0e:e7:70:09:60:9a:c4:f6:89:05:be:ed:be:c6.
Are you sure you want to continue connecting (yes/no)? yes↵
Warning: Permanently added '' (RSA) to the list of known hosts.'s password:↵
jdoe@lxi050: exit↵

You will be prompted to type in your password before you can login. Next time you login, ssh will check if you connect is authentic (and alerts you if the remote host cannot be trusted anymore). Type exit to logout from the remote computer and end the ssh session. Enable support for tunneling of graphical user interface applications via ssh with the -X option:

» ssh -X↵

Very often this is called enabling X11 forwarding. Continue reading to learn about more sophisticated use-cases of ssh.

Default Account Name for GSI

Many people don't use the same account name on their local computer as they have received from GSI. In this case we recommend to create a general definition in the ssh client configuration file $HOME/.ssh/config for all hosts in GSI:

### Default user for GSI
Host *
  User jdoe
  ForwardX11 yes

It is possible to enable X11 forwarding by default with "ForwardX11 yes".

Create a Key Pair for Authentication

Generate an ssh public/private key pair on your local computer (unless you have one) with the ssh-keygen utility. The public portion of this key pair will reside on the servers you want to connect to, while the private portion needs to remain in $HOME/.ssh/id_rsa on your local machine.

ssh-keygen -q -f ~/.ssh/id_rsa -t rsa

The counterpart of your private key, the public key will be located in $HOME/.ssh/ It is recommend utilizing an ssh-agent to unlock your private key once for all connections.

The password of your private key can be changed with:

ssh-keygen -f ~/.ssh/id_rsa -p

ALERT! We strongly recommend to protect your private key with a non-trivial password!

Use a Public Key for Login

Install your public key manually to a remote machine using the ssh-copy-id program:


If you work on a computer missing this program you can alternatively add your public key to the file $HOME/.ssh/authorized_keyson the remote computer. Upload the file to the remote computer:
scp ~/.ssh/

Login to the remote computer and append the public key to the authorized keys file:
$ cat ~/ >> ~/.ssh/authorized_keys
$ chmod 700 ~/.ssh
$ chmod 600 ~/.ssh/authorized_keys

In case the authorized key file has not been present before, you may need to make sure that the file system permission are set correctly.

Use Key Agents

The ssh-agent is a small daemon started at login time (for GUI sessions eg. KDE logins). It stores your ssh private key and hands it out to ssh processes for authentication. Therefore you only have to introduce your private key to your ssh-agent once for each session and are able to login password-less afterwards.

User can start an ssh-agent on the command-line, also. Private keys are added with ssh-add:

» eval $(ssh-agent)
Agent pid 2157
» ssh-add ~/.ssh/id_rsa 
Enter passphrase for /home/jdoe/.ssh/id_rsa:
Identity added: /home/jdoe/.ssh/id_rsa (/home/jdoe/.ssh/id_rsa)
» ssh-add -l 
2048 2b:c5:77:23:c1:34:ab:23:79:e6:34:71:7a:65:70:ce .ssh/id_rsa (RSA)
4096 2b:c5:77:23:c1:34:ab:23:79:e6:34:71:7a:65:70:cd project/id_rsa (RSA)

The script ssh-agent-session helps to use a single ssh-agent session in multiple shells. It will start a new agent and store the connection information to ~/.ssh/agent-session.

» source ssh-agent-session
ssh-agent started, session in /home/jdoe/.ssh/agent-session
» ssh-add ~/.ssh/id_rsa 

Another shell can bind to the same agent:

» source ssh-agent-session
ssh-agent running with process ID 19264
» ssh-add -l 

It is convenient to source this script within the shell profile, in order to bind all shells to a single ssh-agent instance.

» echo "source /path/to/ssh-agent-session"  >> ~/.bashrc

Proxy Connections

Proxied ssh-connections give you the same convenience as Key Forwarding, without the bad security implications. To proxy an ssh-connection to over can put the following in ~/.ssh/config
Host lxpool                                         # <-- lxpool is an arbitrary name, choose what suits you
   User $USER_AT_GSI                                # <-- must be your account at gsi
   ForwardAgent no
   HostName                           # <-- must be the real name of lxpool
Host kronos                                         # <-- again, arbitrary
   User $USER_AT_GSI
   ProxyCommand ssh lxpool nc 22  # <-- lxpool here must be the arbirtary name chosen above
                                                    #     for the connection to lxpool.

If setup like that, you should be able to connect to kronos by just typing ssh kronos, using the arbitrary for the kronos-connection. The same works for lxpool.

Key Forwarding

Ssh agent forwarding moves keys stored in the local ssh-agent along to the remote machines you logon to. To enable agent forwarding, add the -A option when you run ssh, or add the line "ForwardAgent yes" to the ssh config file, ~/.ssh/config.

»  ssh -A -t ssh

Since agent forwarding exposes your unprotected key to the host you forward it to, you should only enable agent forwarding to trustworthy servers!

Managing Fingerprints

When connecting to remote computer using SSH for the first time you'll be prompted to accept its host fingerprint. Once accepted, this fingerprint will be stored in $HOME/.ssh/known_hosts. A List of all known host fingerprints can be displayed with.

ssh-keygen -lv -f $HOME/.ssh/known_hosts

Removing all fingerprints belonging to a host:
ssh-keygen -R

Show the fingerprint of a host (and optionally append it to the list of known hosts) with ssh-keyscan:

» ssh-keyscan -t rsa,dsa
» ssh-keyscan >> $HOME/.ssh/known_hosts

Search for a host in your known host file file:

ssh-keygen -H -F

Avoid Host IP Checking on Login Pools

Connecting to the InteractiveMachines at GSI using one of the alias names like will send you to a different host at each reconnect. All hosts part of the same pool of login machines have the same host key for authentication with your client connection.

You may see a warning that the host IP address has changed, but login will be possible nevertheless. It is possible to disable this warning message by adding to your personal SSH configuration (in the file $HOME/.ssh/config) the following to lines:

    CheckHostIP no

Replace the (DNS) name with any other pool of login machine like for example.

Moving Data with Secure Copy

SCP stands for secure copy, and is used to copy files across ssh connections. Following example copies an entire directory /local/path/ to the users home-directory on one of GSIs InteractiveMachines:

scp -r /local/path/

The option -r ensures that all file in the directory tree are copied recursively. The next example copies file from the InteractiveMachine to the local computer:

scp -r*.pdf /local/path

In both cases your define first what to copy, and second where to copy. Source and/or destination can be located on a remote computer. In case you plan to transfer a signification amount of data you can increase the speed by using an alternative encryption method. Define the a faster cipher algorithm like Blowfish (default is AES 128) with the option =-c=:

scp -c blowfish -r*.root /local/path/to/data

Private Network Tunnel over SSH

Shuttle helps to comfortably access GSI network resources from home transparently. Install the shuttle package on Debian (>=7) and Ubuntu (>= 11.10):

» sudo apt-get install sshuttle

Connect to the GSI network (first the Sudo password is prompted, next the SSH login password):

» sshuttle --dns --remote $ --daemon --pidfile=/tmp/ 0/0

This will route all your traffic (including DNS requests) transparently through SSH. Disconnect with:

» kill $(cat /tmp/

The script ssh-tunnel simplifies this process:

» ssh-tunnel help
» ssh-tunnel connect
[local sudo] Password:'s password: 
» ssh-tunnel status
Sshuttle running with PID 15083.
» ssh-tunnel disconnect
» ssh-tunnel status
Sshuttle not connected.

Limit tunneling to a range of IP networks:

» ssh-tunnel connect 

Mount Directories over SSH

Use SSHFS to mount a directory on a remote system to a local folder, so you will be able to do any operation on the mounted files with local tools (e.g. to edit a text file).

Install sshfs from the following sources:

  • sshfs package on Debian, Ubuntu, RedHat, CentOS, Fedora, ArchLinux
  • SSHFS bundle on Mac OS X
  • win-sshfs on Windows XP/Vista/7

The command sshfs mounts a remote path with:

» sshfs [user@]host[:port] /mnt/path -C -o reconnect,auto_cache,follow_symlinks
» fusermount -u /mnt/path

The command fusermount is used to unmount the remote system.

The script ssh-fs simplifies this process:

» ssh-fs mount ~/nyx
» ssh-fs list on /my_home_dir/nyx
» ssh-fs umount ~/nyx

Mount Nyx directories when outside the GSI network and sshuttle is not available

When you are located outside the perimeter of the GSI network, a direct connection to the frontend nodes of our cluster ( is not possible. If a proxy like sshuttle is not available on your local machine, there are two possible ways to mount a remote filesystem locally:

In case the /SAT/nyx mount point is not available through lxpool, you can still achieve the same result with the following commands:
1) ssh -f -L -N
2) sshfs -p 3000 user@ /my_local_dir

Get a Mathematica License Over Ssh

Ssh has the capability to tunnel arbitrary network traffic through the SSH connection. This way internal services that are normally blocked by the firewall from remote can be made accessible.

Example: To obtain a GSI Mathematica license from remote (this implies you already have Mathematica installed) use the following command:

ssh -L

This will connect to one of the computers of the central interactive Linux farm while forwarding the Mathematica license server to your local computer. You have to put !localhost in your local mathpass file to tell Mathematica where to find its licenseserver. Then startup Mathematica and it will obtain a GSI floating license.

Trouble Shooting

Password Forgotten

Please contact the UserHelpDesk (SB3 1.247, ☎ 2515).

Session Hangs

In case the computer loses connectivity with the remote host your ssh session could hang, and is not reacting anymore on keyboard input. For these cases use the escape sequence ~. to end the connection even when you have no command prompt. Type return twice (for good measure) and then the tilde followed by a period. This will terminate the ssh connection from the client end instead of the server end.

Note that besides the terminate connection escape sequence you can use ~? to show a list of all available escapes:

Supported escape sequences:
  ~.  - terminate connection (and any multiplexed sessions)
  ~B  - send a BREAK to the remote system
  ~C  - open a command line
  ~R  - Request rekey (SSH protocol 2 only)
  ~^Z - suspend ssh
  ~#  - list forwarded connections
  ~&  - background ssh (when waiting for connections to terminate)
  ~?  - this message
  ~~  - send the escape character by typing it twice
(Note that escapes are only recognized immediately after newline.)

Permission Denied

The permission denied error indicates that the private key authentication has failed.

» ssh -o "PasswordAuthentication no"
Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password)

This can have several reasons:

  1. Your ssh-agent has no private keys loaded.
  2. None of your private keys matches an entry in ~/.ssh/authorized_keys on the target node.
  3. The login account doesn't exist on the remote node.
Topic attachments
I Attachment Action Size Date Who Comment
ssh-agent-sessionEXT ssh-agent-session manage 2.0 K 2014-04-10 - 12:48 VictorPenso Script to share a single ssh-agent across multiple shells.
ssh-fsEXT ssh-fs manage 1.9 K 2014-12-10 - 12:09 VictorPenso Mount a remote directory over SSH
ssh-tunnelEXT ssh-tunnel manage 2.0 K 2014-10-16 - 09:09 VictorPenso Manage SSH network tunnels.
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Topic revision: r38 - 2018-02-22, MatteoDessalvi