Running NorESM on Olivia

[oyvindseland]

I am trying to setting up and hopefully running NorESM. The issue #343
does not give much information about the settings. Are there any issue with documentation. For now I can not even set up the code properly.
When I try to run /cluster/projects/nn9560k/oyvinds/noresmbeta11/NorESM]$ ./bin/git-fleximod update hen I get an error message.
Python 3.7 or later is required.

I try to load a more or less random version
First I need to do
module load NRIS/CPU

Due to MODULEPATH changes, the following have been reloaded:

1. EasyBuild/5.2.1

[oyvinds@uan02.olivia /cluster/projects/nn9560k/oyvinds/noresmbeta11/NorESM]$ module load NRIS/GPU

Due to MODULEPATH changes, the following have been reloaded:

1. EasyBuild/5.2.1

The following have been reloaded with a version change:

1. NRIS/CPU => NRIS/GPU

I tried then the two most recent Python versions, e.g.

/cluster/projects/nn9560k/oyvinds/noresmbeta11/NorESM]$ module load Python/3.13.1-GCCcore-14.2.0

The following have been reloaded with a version change:

1. GCCcore/14.3.0 => GCCcore/14.2.0
2. Python/3.13.5-GCCcore-14.3.0 => Python/3.13.1-GCCcore-14.2.0
3. SQLite/3.50.1-GCCcore-14.3.0 => SQLite/3.47.2-GCCcore-14.2.0
4. Tcl/9.0.1-GCCcore-14.3.0 => Tcl/8.6.16-GCCcore-14.2.0
5. XZ/5.8.1-GCCcore-14.3.0 => XZ/5.6.3-GCCcore-14.2.0
6. binutils/2.44-GCCcore-14.3.0 => binutils/2.42-GCCcore-14.2.0
7. bzip2/1.0.8-GCCcore-14.3.0 => bzip2/1.0.8-GCCcore-14.2.0
8. libffi/3.5.1-GCCcore-14.3.0 => libffi/3.4.5-GCCcore-14.2.0
9. libreadline/8.2-GCCcore-14.3.0 => libreadline/8.2-GCCcore-14.2.0
10. ncurses/6.5-GCCcore-14.3.0 => ncurses/6.5-GCCcore-14.2.0
11. zlib/1.3.1-GCCcore-14.3.0 => zlib/1.3.1-GCCcore-14.2.0

but I can still not get flexmid to work

/cluster/projects/nn9560k/oyvinds/noresmbeta11/NorESM]$ ./bin/git-fleximod update
/cluster/software/NRIS/neoverse_v2/software/Python/3.13.1-GCCcore-14.2.0/bin/python3: /cluster/software/NRIS/neoverse_v2/software/Python/3.13.1-GCCcore-14.2.0/bin/python3: cannot execute binary file

@monsieuralok @TomasTorsvik

[TomasTorsvik]

@oyvindseland - For the modules, you can load

NRIS/CPU
Python/3.12.3-GCCcore-13.3.0

Since olivia operates with at least 3 different sets of module lists, I think it is better not to have any module settings in .bashrc or similar. Note that NRIS/CPU gives you access to the Python module (among others) that you can load.

Personally, I have the following setup

module purge
module load NRIS/CPU
module load Python/3.12.3-GCCcore-13.3.0
module save mod_noresm

and then I do

module r mod_noresm

to restore the modules needed ("mod_noresm" is a name I selected, you can call it what you want). You can have several saved lists of modules and do module savelist to list them. It requires an extra step to load the modules each time, but it's probably the safer option (or does anyone have a better suggestion?)

[TomasTorsvik]

@oyvindseland - the slurm partitions on olivia changed after the latest maintenance break, so we had to update config_batch.xml to match the new system. This should become available by default in noresm3_0_beta12 but until this is merged, you may need to include the latest ccs_config tag manually, e.g. modify the .gitmodules file to include ccs_config_noresm0.0.57.

[oyvindseland]

Fleximod works now thank you.
With regards to Olivia. Looks like it is better to wait then even though Betzy is then back again on-line next week. (Fingers crossed) I hope that beta12 can be available early next week in case the Betzy update is slower than expected.

[TomasTorsvik]

Great that it's working!
I have been able to run some short tests with fully coupled compsets. Currently I'm trying to get an OMIP-style run going. It could be interesting to look at performance and cmpare Betzy and Olivia. Preliminary testing suggest that we might have slightly better performance on Olivia.

[TomasTorsvik]

I have started to collect some information about running NorESM on Olivia on the wiki page here:

https://github.com/NorESMhub/noresm3_dev_simulations/wiki/Running-NorESM-on-Olivia

Please expand on this wiki page if you come across further relevant information.

[gold2718]

I am having trouble with inputdata on Olivia. Some files are missing (as has been discussed extensively on email and is being fixed), however, I also am seeing non-writeable directories like this:

$ ls -las /cluster/work/projects/nn9560k/inputdata/atm/cam/dst
total 8
4 drwxr-xr-x  2 agu002 agu002 4096 feb.  23 03:08 .
4 drwxrwxrwx 15 agu002 agu002 4096 jan.  20 14:01 ..

Can we find a way to make this area writable, say by changing to the noresm group?
@monsieuralok

[DirkOlivie]

Hi @TomasTorsvik , when I am logged in on Olivia, I find myself reasonably fast (after 10 minutes sometimes) with a blocked window when I am not actively using it. I don't have this issue with Betzy. Do you have the same experience? Any suggestion how I might change this?

[adagj]

@DirkOlivie I have not encountered this problem, and I have been using Olivia a lot lately

[TomasTorsvik]

Hi @DirkOlivie , I have not had problems with blocked window on Olivia. I haven't been active on Olivia this week, so if it is very recent, I may have missed it.

[DirkOlivie]

Thanks, no it is not very recent. I have had it for more than two weeks, I think.

[TomasTorsvik]

Then I think it is more likely related to your setup or account. Probably best to contact Sigma2 support in that case.

[gold2718]

@DirkOlivie, since it seems to be happening to you and not others (including myself), this may be your local machine not keeping the connection open. Betzy and Olivia seem to behave quite differently when implementing session keepalive probes with Olivia sending them much more often.

If your machine ever goes to sleep, Olivia will notice quite quickly and terminate your window (which often shows up as a frozen window on your local machine). Other than that, if your machine has not been rebooted in a while, that can affect keepalive response (check with the uptime terminal command).

Finally, many of us are using the tmux command to not lose running commands or session state of we get disconnected. On Olivia, I have to run tmux without modules loaded. I then load modules inside the tmux session.

[DirkOlivie]

Hi @alok @TomasTorsvik, I am wondering whether the compression of output files is working well on Olivia. I see that all archived files have the same size after compression, whereas on Betzy the file size will vary a bit between the files.

When I do ncdump -k <file> for a simulation done on Betzy, I get netCDF-4.
When I do ncdump -k <file> for a simulation done on Olivia, I get cdf5.

An example of a simulation run on Olivia (transferred to nird):
/datalake/NS9560K/noresm3/cases/n1850.ne16pg3_tn14.noresm3_0_beta19.Run15-C.Olivia.2026-06-15/atm/hist

[monsieuralok]

@DirkOlivie I can confirm it is not working and I will check it and update what is the issue

[monsieuralok]

@DirkOlivie @TomasTorsvik I send pull request in ccs_config repo; it is very minor change you can implement in yours repo ; so we have more tests.