FAQs Category


Last modified 9 years ago Last modified on 03/05/13 12:16:45

How do I restart my ssh agent? 

Normally your ssh agent persists even when you log out of puma. However, from time to time it can vanish.

If you are prompted for your passphrase, this means the ssh agent has stopped for some reason. The agent should have been re-initialised when you logged into puma, but you will need to re-associate your ssh keys to the agent.

To do so, run the following command:

puma$ ssh-add

How do I tidy up old ssh keys? 

If you have forgotten your passphrase you will need to regenerate your ssh keys. Before doing so, you will need to tidy up the old keys otherwise the ssh agent can get itself confused.

Go to your ~/.ssh directory, and look at the files, you should see something like:

puma$ ls ~/.ssh
environment.puma  id_rsa  known_hosts  ssh-setup

Delete the public and private keys. These will normally be named id_rsa and, or id_dsa and

You should also delete the environment.puma file.

Next check if you have an agent running:

puma$ ps -flu <puma-username> | grep ssh-agent

If an agent is running, one or more lines like the following will be returned:

15658 ?        00:00:00 ssh-agent

The number in the first column is the process-id, pass this to the kill command to stop the process, for example:

puma$ kill -9 15658

What files can I safely delete on PUMA? 

There is limited disk space available on PUMA, so all users need to clear up files in their home directories regularly to stay within their quota.

Extract directories:

Submission of UM jobs via the UMUI and UM suites through Rose/Cylc, generate lots of files which mount up quickly and can be safely deleted as follows:

For the UMUI:

Job extract directories usually under ~/um/um_extracts or ~/FCM_extracts can be deleted. They will be recreated as required.

For Rose suites:

The extract directory ~/cylc-run/<suite-id>/share/fcm_make_um/.fcm_make can be deleted safely. If you are running a coupled suite there will also be a corresponding extract directory for the NEMO build (e.g. ~/cylc-run/<suite-id>/share/fcm_make_ocean/.fcm_make)

Cylc-run directories:

Once you are finished running a suite you should delete the cylc-run directory for that suite. (E.g. ~/cylc-run/u-ag137)

Working copies of branches:

Once all local changes to a branch have been committed you should delete the working copy and reference the branch in your job/suite by its repository URL. (e.g fcm:um.xm-br/dev/marcstringer/vn10.6_fix_OpenMP_nice_use)

`ssh-add` gives error message: `Could not open a connection to your authentication agent.` 

This is because your ssh-agent has stopped running for some reason and is unable to restart automatically. Try removing the following file on PUMA:

puma$ rm ~/.ssh/environment.puma

Then log out of PUMA and back in again. You should then see a message similar to:

Initialising new SSH agent...

And you should then be able to run ssh-add successfully.