If you have been allocated a guest account on the Crop Diversity HPC system the method you need to use to connect is a slightly different from a normal user account. Guest accounts are temporary accounts created to give limited access to the system for training or similar purposes. You will have access to your own home folder and scratch folder locations but not to the shared project folders. For running jobs you’ll have access to compute servers on the
debug queue of the SLURM job management system only.
As with a normal user account you must log in to the main login server called
gruffalo using the Secure Shell (SSH) protocol.
If using Linux or macOS, then you’ll already have an SSH client installed that you can access via a local terminal. If using Windows, then you’ll have to install one or more new programs in order to connect, good options include MobaXterm, WSL (Windows 10+ only), Cygwin/mintty or PuTTY.
We require guest accounts to authenticate using an SSH private key we will send to you. This is a special file giving you permission to login. We’ll send two versions of this private key, due to the putty program requiring a different format than all the other programs, to allow you to use putty if you wish. The private key files will be called guestxxx_key (generic format) and guestxxx_key_putty.ppk (putty format), where xxx is replaced by the number of you specific guest account. Both private key files are protected by a passphrase (a type of password) that you must type in when connecting, which we’ll also provide to you.
It is vital that you keep the private key files and the passphrase safe while you guest account is active, as otherwise hackers could use them to gain unauthorised access to the system. Only store the key files in a secure location on your computer, and never on a shared network drive accessible to others. Do not save the passphrase in a file on the same computer as the private key file.
Once your guest account expires, such as after the training sessions are finished, all the files created on the system will be wiped and the private key will be revoked so that it no longer grants access.
Connecting using the SSH command
On a Mac or Linux computer, or on Windows using WSL, Cygwin, Mobaxterm etc you have access to a command line environment providing the
ssh command which will allow you to connect to Crop Diversity using the provided private key file. The command required to connect is:
ssh -i path/to/guestxxx_key firstname.lastname@example.org
where you must replace
path/to/guestxxx_key with the full path to the location you saved the generic private key file. On Mac or Linux make sure only your user has permissions to read the private key file or the command will refuse to run. You can fix this using the command
chmod og-wrx guestxxx_key.
The first time you connect you may be asked to confirm you trust the identity of the remote server, by checking its finger print. See here for the correct finger print values.
You will then be prompted to enter the passphrase which you will have been provided with separately.
Connecting using MobaXterm
MobaXterm also allows you to connect using a graphical interface without having to type in the
ssh command manually. Do this as following:
Session -> SSH -> Basic SSH settings: Remote host: gruffalo.cropdiversity.ac.uk Specify username: guestxxx Advanced SSH settings: Use private key: browse and select guestxxx_key
Where xxx is replaced by the number of your guest account. Make sure you use guestxxx_key and not guestxxx_key_putty.ppk. As with the command line method you may be asked to verify the server’s fingerprint (see here). You’ll also have to enter the passphrase you’ll be provided you.
Connecting using PuTTY
Similarly PuTTY allows you to connect using a graphical interface:
Session: Hostname: gruffalo.cropdiversity.ac.uk Connection -> SSH -> Auth Private key file for authentication: browse and select guestxxx_key_putty.ppk
Where xxx is replaced by the number of your guest account. Make sure you use guestxxx_key_putty.ppk and not guestxxx_key. As with the command line method you may be asked to verify the server’s fingerprint (see here). You’ll also have to enter the passphrase you’ll be provided with.