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How do I use SSH to access HPC systems?

Secure Shell (SSH) is the standard network protocol for connecting to iSolutions HPC services on Linux, indeed for the Iridis and Lyceum clusters this is the only allowed method. Telnet, rlogin and rsh are not allowed as there are many security concerns with these protocols. If you wish to display a GUI back to your local Windows PC you will also need the Exceed software package to display "X windows".

SSH and Exceed are installed on iSolutions workstations. If you need to install either of them on your own Windows PC, they are available from our software download server (but first check whether they are available from "Add/Remove Programs on your PC). If you are running Linux, or on a Mac, then you will probably have the ssh & X packages available already.

You should connect using your iSolutions username and password,

Logging in to a remote HPC service Using SSH Secure Shell From iSolutions workstations

  1. Open SSH using: Start -> Programs-> Internet and network access -> SSH Secure Shell-> Secure Shell Client 
  2. In the Connect to Remote Host dialog box, type the host name, for example,, and your iSolutions username. A variety of authentication methods are possible, choose Password unless you have good reason to use another method.
  3. Press Enter or click Connect.
  4. If this is the first time you've used SSH Secure Shell to connect to this remote host, SSH will show you the host's public key and ask you: "Do you want to save the new host key to the local database?" If you believe this is the right host, click Yes to save it.
  5. The Enter Password dialog box opens. Type your password in the Password: box, and press Enter or click OK
  6. To save the settings for the connection to the machine, type a "profile name", eg. Solaris, into the AddProfile window that appears briefly after after you login (or do this later from the AddProfile menu option of Profiles). Then press the "Save settings" option from the file menu. The next time you want to login, just select the appropriate profile name from the Profiles menu.

 Transferring files to/from a remote host with sFTP

SSH also supports protocols to exchange files between your local compute and a remote host. On Unix/Linux systems use the scp or sftp commands . On Windows you can use the sFTP file transfer Window that is installed with the SSH software. This can either be started directly, eg. on ISolutions Workstations:

Start -> Programs -> Internet and network access -> SSH Secure Shell -> Secure File Transfer Client

or if you already logged in with a Secure Shell Client simply click the file transfer icon, a file folder with a quarter circle of blue dots over it, to open a File transfer window without the need to login again.

An alternative to the windows SSH client is an application called putty, although this is perhaps not so convenient to use. However, it is readily available from the internet (and should also be available from Add/Remove Programs on iSolutions windows installations).

Displaying a GUI from a remote machine to your local computer

Application GUIs are displayed on Unix/Linux systems using the X-windows software. An application GUI running on a remote computer can be displayed back to your local computer. If your local machine is running Windows, you will need to have an X-windows server installed and running on your local machine before you attempt to start the GUI on the remote machine. On iSolutions workstations the Exceed package is available as an X-server and can be started from the "All Programs" menu ("internet and network access -> Hummingbird connectivity -> Exceed").

Exceed can be downloaded from our software download server if you don't have it installed already on your PC and isn't available from "Add/Remove Programs". (You may also want the Exceed 3D add-on which is used by many engineering packages such as Abaqus and StarCCM+ - see the "common problem" note below.) It is recomended that Exceed is configured to use Passive mode and Multiple Windows - these are normally the defaults.

If you are connecting from a Linux/Unix machine use the "-X" flag to the ssh command to ensure that X-forwarding is enabled, eg.

ssh -X

(note that Mac users need to use "-Y" rather than "-X"

As a quick check on whether X-windows can be displayed correctly back to your local host, type the command xclock & on the remote machine (after ensuring that you have an X-server such as Exceed running locally). A clock window should be displayed locally.

Common Problems with X

  1. Error: Can't open display: - When using SSH from Windows, check that "X-tunneling" is enabled. To do this open the SSH "Settings" window from the icon with two cogs, or from the Edit profiles menu for the connection. Select the Tunneling tab and then check the Tunnel X Windows box. Save the Settings so that this is remembered next time you use SSH for this connection. You will need to disconnect from the remote machine and log back in again before any changes to Tunneling take effect.
  2. .Error: Can't open display: somemachine:0 - This may mean that you have the environment variable DISPLAY set inappropriately. The DISPLAY variable used to be required with older connection methods, such as telnet, but with SSH it should not be set by the user if tunneling is enabled. The command printenv DISPLAY will reveal if this variable has been set. The problem is often caused by out-of-date settings in shell initialisation files such as .login, .cshrc or .tcshrc., and so references to the DISPLAY variable in these files may need to be removed.
  3. The keys you press on the keyboard don't produce the correct symbols, eg. you get " instead of @ and vice versa. - This maybe due to an incorrect keyboard mapping in the Exceed configuration. 
    One way to change the Exceed configuration is to start Exceed, right-click on it's toolbar icon and select: tools -> configuration ...
    This should bring up the configuration window. The keyboard mapping probably needs to be set uk102.kbf (it may be configured with us.kbf as default). You may have to restart Exceed before the change in keyboard mapping is effective.
  4. Xlib: extension "GLX" missing on display "localhost:14.0" - This probably means that the GUI uses the "OpenGL" 3D libraries and there is no support for these on your local machine. OpenGL functionality can be provided by the Exceed 3D add-on to Exceed which is also available from our software download server. If you don't have Exceed 3D installed some application GUI's will just revert to a slower rendering method, eg. Gambit. Others, such as Starccm+, may fail unless you specify an alternative method when you start the GUI, eg. "starccm+ -mesa"
  5. Running out of filestore quota - When you first login you may see a message like: “/usr/X11R6/bin/xauth: error in locking authority file /home/fred/.Xauthority” - This most often means that you have exceeded your home filestore quota and as a result cannot modify the .Xauthority file in your home filestore. This file is used to control access to X-Windows and if there is a problem with it you won't be able to run X applications. The first thing to do is to check your filestore usage (on Lyceum use quota -s. The command on Iridis is more complicated - see the "Getting_Started" page on the Iridis wiki). If you are close to your quota limit (or have been recently) then you will need to clean up your filestore first, so that there is space for the .Xauthority file to be updated next time you login. Sometimes the .Xauthority file becomes corrupted when there is a problem with space, so it may be necessary to delete this file and logout(it will then be recreated when you log back in again).

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