Getting Set Up (Leeds Training Course)

Warning

You MUST have PUMA2, ARCHER2 and MOSRS accounts setup before starting this section.

Warning

These instructions are for use on the UM Training Course held on 28th-30th November 2023. If you are using them for self-study please contact NCAS-CMS for instructions.

Set up your ARCHER2 connection

To use the UM Introduction Tutorials you will first need to ensure you can connect from your local desktop to ARCHER2.

SSH key files

Before you try and connect to ARCHER2, you need to make sure that you have the ssh-keys available on your computer. In these instructions, we’ve assumed the keys are called id_rsa_archer2 and id_rsa_archer2.pub. Replace with the name of your keys as appropriate.

Hopefully you remembered to bring your ARCHER2 ssh-key with you on a USB stick. Please talk to a course tutor if you have forgotten it.

Copy your ssh-key from the USB stick to the ~/.ssh directory.

Connecting via a Terminal (GNU/Linux & macOS)

Connecting via a terminal with an X11 connection (XQuartz is also required when using macOS)

Login to ARCHER2:

ssh -Y -i ~/.ssh/id_rsa_archer2 <archer2-username>@login.archer2.ac.uk

To simplify the login process, you can define a ~/.ssh/config file entry containing the necessary information. For example:

Host archer2
Hostname login.archer2.ac.uk
User <archer2_username>
IdentityFile ~/.ssh/id_rsa_archer2
ForwardX11 yes
ForwardX11Trusted yes

so that you can connect using just the command:

ssh archer2

Set up your ARCHER2 environment

Login to ARCHER2 from your local desktop, copy the following profile to your home directory.

archer2$ cp /work/y07/shared/umshared/um-training/rose-profile ~/.profile

Change the permissions on your /home and /work directories to enable the NCAS-CMS team to help with any queries:

chmod -R g+rX /home/n02/n02/<your-username>
chmod -R g+rX /work/n02/n02/<your-username>

Set up your PUMA2 connection

PUMA2 is accessed from the ARCHER2 login nodes, and you will use the same username and password.

From an ARCHER2 terminal type:

archer2$ ssh -Y puma2

and type your ARCHER2 password when prompted.

You should now be logged into PUMA2. To go back to the ARCHER2 login nodes, type exit.

Set up passwordless access to PUMA2

You can set up a passphrase-less ssh-key to allow you to connect to PUMA2 without typing a password or passphrase.

Note

We would never normally advise using an ssh-key without a passphrase, but in this case it is safe to do so since we are already authenticated within the ARCHER2 system.

From the ARCHER2 login nodes, type:

archer2$ ssh-keygen -t rsa -f ~/.ssh/id_rsa_puma2

At the prompt, press enter for an empty passphrase.

Copy the key over to PUMA2:

archer2$ ssh-copy-id -i ~/.ssh/id_rsa_puma2 puma2

Type in your ARCHER2 password when prompted.

Next, create a file called ~/.ssh/config (if it doesn’t already exist), and add the following lines:

Host puma2
IdentityFile ~/.ssh/id_rsa_puma2
ForwardX11 yes

Test it works by typing:

archer2$ ssh puma2

You should not be prompted for your password. Note that this should have set up X11 forwarding, so you no longer need the -Y option.

Warning

You should never use a passphrase-less key to access the ARCHER2 login nodes, as this is a serious security risk.

Set up your PUMA2 environment

Copy our standard .profile and .bashrc files:

puma2$ cd
puma2$ cp ~um1/um-training/puma2/.bash_profile .
puma2$ cp ~um1/um-training/puma2/.bashrc .

Logout of PUMA2 and back in again to pick up these changes.

You will get a warning about not being able to find ~/.ssh/ssh-setup. This can be ignored and will be resolved in the next step.

You should also be prompted for your Met Office Science Repository Service password, then username. Note that it asks for your password first. Remember your MOSRS username is one word; usually firstnamelastname, all in lowercase.

If the password caching works, you should see:

Subversion password cached
Rosie password cached

This means you can now access the code and roses suites stored in the Met Office respositories.

Note

The cached password is configured to expire after 12 hours. Simply run the command mosrs-cache-password to re-cache it if this happens. Also if you know you won’t need access to the repositories during a login session then just press return when asked for your MOSRS password.

Finally, change the permission on your PUMA2 /home space:

chmod -R g+rX /home/n02/n02/<your-username>

Set up your ssh-agent

In order to submit jobs to ARCHER2 from PUMA2, you will need to set up an ssh-agent and use it to cache the passphrase to your ARCHER2 key.

i. Copy your ARCHER2 ssh-key pair to PUMA2

Your ARCHER2 key is the one that you use to ssh into the ARCHER2 login nodes. You need to copy both the public and private keys into your .ssh/ directory on PUMA2.

Open a new terminal from wherever you originally connected to ARCHER2 in Set up your ARCHER2 connection, and run the following command

scp ~/.ssh/id_rsa_archer2* <archer2-username>@login.archer2.ac.uk:/home/n02/n02-puma/<archer2-username>/.ssh

ii. Start up your ssh-agent

First copy the ssh-setup script to your .ssh/ directory.

puma2$ cp ~um1/um-training/setup/ssh-setup ~/.ssh

Next log out of PUMA2 and back in again to start up the ssh-agent process. You should see the following message

Initialising new SSH agent...

iii. Add your ARCHER2 key

Add your ARCHER2 key to the ssh-agent, by running

puma2$ ssh-add ~/.ssh/id_rsa_archer2

Enter your passphrase when prompted. If the passphrase has been cached successfully you should see a message like this:

Identity added: /home/n02/n02/<archer2-username>/.ssh/id_rsa_archer2

The ssh-agent will continue to run even when you log out of PUMA2. However, it may stop from time to time, for example if PUMA2 is rebooted. For instructions on what to do in this situation see Restarting your ssh agent in the Appendix.

iv. Configure access to the ARCHER2 login nodes

Create a file ~/.ssh/config (if it doesn’t already exist), and add the following lines:

# ARCHER2 login nodes
Host ln*
IdentityFile ~/.ssh/id_rsa_archer2

iv. Verify the setup is correct

To test this is all working correctly, run:

puma2$ rose host-select archer2

This should return one of the login nodes, e.g. ln01. If it returns a message like [WARN] ln03: (ssh failed) then something has gone wrong with the ssh setup.

You are now ready to try running a UM suite!