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Connecting via SSH on Windows

Hint

Connecting from within MDC/Charite Network

Click on Session.

Click on SSH.

In Basic SSH settings, enter a hostname (hpc-login-X.cubi.bihealth.org, where X is 1 or 2), check Specify username and enter your username in the textfield. Select the tab Advanced SSH settings, check Use private key and select your private SSH key file (possible choices described with the next to figures).

Select the id_rsa file generated in Linux OR

select the id_rsa.ppk file generated in Windows with MobaXterm.

Afterwards hit the OK button and MobaXterm will connect.

The session will be stored automatically and you can establish new connections later on, or also multiple ones at the same time, if you like.

Mounting the FS from within the MDC/Charite Network

Once WinSshFS is started, an icon will be added to your taskbar:

Left-clicking that icon will bring up a window. If not, right click the taskbar icon, select Show Manager and click Add in the menu.

Fill out the marked fields:

  • Drive Name: Name that will show up in the windows explorer
  • Host: hpc-transfer-1.cubi.bihealth.org
  • Username: Your cluster username
  • Authentication method: PrivateKey. Select the id_rsa private key, not the .ppk format that is provided by PuTTY. Enter the password that you used to secure your key with.
  • Directory: Cluster directory that will be mounted, you can choose any directory you have access to on the cluster.

Then click Save and then Mount.

Open the explorer. A new drive with the name you gave should show up:

Finished!

Connecting via MDC Jail Node

  • This requires an active MDC account!

  • Additional to the steps above, click on the tab Network settings.

  • Check Connect through SSH gateway (jump host) and in the text field Gateway SSH server enter ssh1.mdc-berlin.de and in the field User your MDC username.
  • Check Use private key and select the SSH key that you uploaded to the MDC persdb (this might differ from your cluster key!).
  • Click OK

X11

Do you really need to run a graphical application on the cluster?

Please note that running more complex Java applications, such as IGV may be not very efficient because of the connection speed. In most cases you can run them on your local workstation by mounting them via SSHFS.

Start MobaXterm, it should automatically fetch your saved Putty sessions as you can see on screen below:

Connect to one of the login nodes, by double-click on saved profile, and then use srun --pty --x11 bash command to start X11 session to one of the nodes:

Finally, start X11 application (below example of starting Visual Terminal):

Last update: February 7, 2023