Lfric_apps rose stem with cylc vip on archer2 from PUMA2

Rose/Cylc and FCM
1

Hello I am following the UKMO guidance on workflows with git and possibly they are not appropriate for puma2. However, I will lodge the query anyway:

Using a branch on a git clone of a fork of lfric_apps (as per guidance)

/home/n02/n02/mricha/Branches/AppsLFRic/archer2_glomap_transmute

I wanted to try a simple check:

cylc vip -z group=lfric_atm_nwp_quick --set-file=~/archer2_lfric_setfile.txt -n atm_git_01 ./rose-stem

Fails on code extraction (4 attempts) ; the setfile has the HPC_USER, HPC_ACCOUNT, HPC_QUEUE and SITE values

to confirm authorization:

git -T git@github.com works from PUMA (I created a dedicated SSH keypair)

The latter also works from archer2 lnXX login nodes but htat maybe my original github handshake and not the PUMA2 handshake.

I am wondering if I need to adjust the .gitconfig on archer2 $HOME or similar? It maybe a feature of hte separation of source and build.

Any guidance appreciated,

Mark

2

I think it might be to do with the fact that PUMA2 home dir is “/home4/home”. the git command (running on archer2 login I think) is trying to work with a path that starts with home4.

Not sure where to inform the cylc process that from a login node puma looks like

/home/n02/n02-puma/mricha/Branches/AppsLFRic/archer2_glomap_transmute/dependencies.yaml

and NOT

/home4/home/n02-puma/mricha/Branches/AppsLFRic/archer2_glomap_transmute

which is what it looks like from PUMA2 shells.

“home4” appears in the “job” explicitly against the lfric_apps sources.

3

So the actual error message is in /home/n02/n02/mricha/cylc-run/atm_git_01/run1/log/job/1/export-source/01

RuntimeError: [FAIL] Issue found running command [‘git’, ‘-C’, ‘/home/n02/n02/mricha/cylc-run/atm_git_01/run1/share/source/casim’, ‘fetch’, ‘origin’, ‘2025.12.1’]

git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.

so my thoughts on home4 might be a red herring as I probably misunderstand the workflow and where processes are working. I’ll continue investigating.

Mark

4

I think that you are possibly in need of using token based authentication. The MO have guidance here:

5

I will look into that Dave, but that seems specific to MonSOON3.

In the meantime I just got further up until JULES and then:

RuntimeError: [FAIL] Issue found running command [‘git’, ‘-C’, ‘/home/n02/n02/mricha/cylc-run/atm_git_01/run3/share/source/jules’, ‘fetch’, ‘origin’, ‘2025.12.1’]

ERROR: The ‘MetOffice’ organization has enabled or enforced SAML SSO.
To access this repository, you must use the HTTPS remote with a personal access token or SSH with an SSH key and passphrase that has been authorized for this organization.
Visit Authenticating with single sign-on - GitHub Enterprise Cloud Docs for more information.

fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

I had to correct the permissions on ~/.ssh not sure why they went to group readable.

Maybe I cannot use JULES repo. more later…

6

Okay so I had missed step 3 of this setting up of SSH on the working practices.

so progressed past the extracting, the sources are appearingon puma2 disk space.

7

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