# ACCESS-coupled N48 for deep paleo
**URL:** https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529
**Category:** Earth System
**Tags:** palaeogeography
**Created:** [3 March 2023 00:32 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529 "2023-03-03T00:32:54Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@Dietmar\_Dommenget](https://forum.access-hive.org.au/u/Dietmar_Dommenget)
#### Post date: [3 March 2023 00:32 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/1 "2023-03-03T00:32:54Z")
The project aims at running the ACCESS-N48 coupled ocean-atmosphere model in Eocene topographic and orographic configuration.
Our current problem is that we cannot change the ancillary files in any way.
As a starting we would like to run the ACCESS-N48 with a change in moving Australia to a different location, to test that we can run the model. This is likely to involve ancillary files of both atmosphere and ocean model.
@abhik @atteggiani
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### Author:  [@Aidan](https://forum.access-hive.org.au/u/Aidan)
#### Post date: [6 March 2023 05:10 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/3 "2023-03-06T05:10:06Z")
> [@Dietmar\_Dommenget](#):
>
> As a starting we would like to run the ACCESS-N48 with a change in moving Australia to a different location, to test that we can run the model. This is likely to involve ancillary files of both atmosphere and ocean model.
The need for this was discussed in [today’s panel discussion](https://www.eventbrite.com/e/modelling-earths-past-and-future-climate-practices-and-possibilities-tickets-531269841397). This was a focus in particular for [Nicky Wright](https://www.sydney.edu.au/science/about/our-people/academic-staff/nicky-wright.html). I’ll see if she wants to join in the discussion here.
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### Author:  [@nickywright](https://forum.access-hive.org.au/u/nickywright)
#### Post date: [7 March 2023 05:18 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/4 "2023-03-07T05:18:32Z")
Thanks Aidan!
Happy to help where I can, though I don’t have much successful experience in actually setting up a deep-time run.
I’m guessing you’re starting with the Early Eocene setup from [here?](https://gmd.copernicus.org/articles/10/889/2017/)
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### Author:  [@Dietmar\_Dommenget](https://forum.access-hive.org.au/u/Dietmar_Dommenget)
#### Post date: [7 March 2023 21:41 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/5 "2023-03-07T21:41:05Z")
Well, we thought of starting with just a simple test case in which we shift Australia to new location. this should test all elements we would need to do any kind of deep paleo configuration.
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### Author:  [@JulieA](https://forum.access-hive.org.au/u/JulieA)
#### Post date: [7 March 2023 23:26 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/6 "2023-03-07T23:26:39Z")
Yes having this capability with ACCESS will open up many scientific opportunities and additional ways to test the model which (at least in the US CESM2 example I [gave](https://doi.org/10.1038/s41558-020-0764-6)) fed into constraining its future projections. Hopefully the ancillary file issue is something easy to fix, @atteggiani @MartinDix
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### Author:  [@atteggiani](https://forum.access-hive.org.au/u/atteggiani)
#### Post date: [8 March 2023 00:39 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/7 "2023-03-08T00:39:25Z")
For the UM ancillary files, in the library we are building there are still a couple of things that need to be addressed, such as the consistency with land-mask file and the sensibility of some values (e.g. negative temperatures or concentrations, fractional land \< 0 or \> 0, etc.). This for the regridding tool.
The ancillary modifier tool (to modify ancillaries starting from NetCDF files) instead, is ready and should work with any UM ancillary.
We are waiting for all the issues with the regridding tool to be fixed to release all in a single library.
However, if you have ancillary files to modify using netCDF file relative to the Eocene period in your experiment, please let me know the respective directories and I’ll be happy to test the ancillary modifier tool on those files. @abhik @Dietmar_Dommenget
For changing/regridding the Ocean input files, instead, there are a few more problems and I have no experience with Ocean files. I am checking what’s already available and it is under discussion if our library should/can include also the possibility to modify Ocean files.
Some COSIMA people might be able to tell you (us!) more about this. Maybe @aekiss @navidcy @rmholmes?
Cheers
Davide
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### Author:  [@rmholmes](https://forum.access-hive.org.au/u/rmholmes)
#### Post date: [8 March 2023 01:05 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/8 "2023-03-08T01:05:18Z")
> [@atteggiani](#):
>
> For changing/regridding the Ocean input files, instead, there are a few more problems and I have no experience with Ocean files. I am checking what’s already available and it is under discussion if our library should/can include also the possibility to modify Ocean files.
> Some COSIMA people might be able to tell you (us!) more about this. Maybe @aekiss @navidcy @rmholmes?
There are some instructions for changing topography and land masks in the ocean for these kinds of things in the wiki at [Tutorials · COSIMA/access-om2 Wiki · GitHub](https://github.com/COSIMA/access-om2/wiki/Tutorials#changing-the-bathymetry-land-sea-mask-and-oasis-remapping-weights). A few people have used this, including myself (for closing off the ITF) and some of @LaurieM’s students. If you have any problems let us know!
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### Author:  [@abhik](https://forum.access-hive.org.au/u/abhik)
#### Post date: [8 March 2023 01:17 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/9 "2023-03-08T01:17:34Z")
Thanks, @atteggiani and ACCESS-NRI team.
For testing the ancillary modifier tool, you can use the original Eocene files in /g/data/n69/sza565/ancil-from-uk/JASMIN\_input\_data.tar.gz
These files were built on the JASMIN system in the UK, some tools/libraries may not be readily available on NCI.
However, for the consistent ocean-atmosphere coupled ACCESS ancillary files, the ancillary file creation process should start from a single bathymetry file to generate the land-ocean mask and coupling weights. The same land-ocean mask file should be used to create topography, river routing, and other required ancillary files.
Please follow the Eocene suite setup guideline file for your reference.
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### Author:  [@abhik](https://forum.access-hive.org.au/u/abhik)
#### Post date: [10 March 2023 00:53 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/10 "2023-03-10T00:53:30Z")
@rmholmes Could you please update the input file location at [Tutorials · COSIMA/access-om2 Wiki · GitHub](https://github.com/COSIMA/access-om2/wiki/Tutorials#changing-the-bathymetry-land-sea-mask-and-oasis-remapping-weights)
We wish to generate a new set of ocean bathymetry and land-sea mask following your tutorial for the paleoclimate experiment that @Dietmar_Dommenget mentioned above.
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### Author:  [@LaurieM](https://forum.access-hive.org.au/u/LaurieM)
#### Post date: [10 March 2023 02:30 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/11 "2023-03-10T02:30:47Z")
The N48 coupled model is not supported by ACCESS-NRI, right? If we wanted to run some paleo-simulation could we get access to it? I guess it is quite faster than the ACCESS-ESM, right? That could work well for our planned Pliocene exp.
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### Author:  [@dkhutch](https://forum.access-hive.org.au/u/dkhutch)
#### Post date: [10 March 2023 02:38 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/12 "2023-03-10T02:38:37Z")
Hi, I am also interested in using an ACCESS coupled model for deep time simulations. My targets are Miocene (15 Ma) and Oligocene (30 Ma), but I have previously simulated Eocene climates using GFDL CM2.1. I had planned to use ACCESS-ESM1.5, but would also be keen to know if it’s possible using the N48 atmosphere. Would be interested to collaborate and/or discuss issues around setting up the boundary conditions for the atmosphere and land models.
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### Author:  [@Dietmar\_Dommenget](https://forum.access-hive.org.au/u/Dietmar_Dommenget)
#### Post date: [10 March 2023 05:59 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/13 "2023-03-10T05:59:36Z")
Well, the idea is that we develop the N48 version, so that people can use it, but we are not quite there yet. And yes, it is much fast and cheaper. It runs about 30yrs per CPU day, potentially it can be faster than that.
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### Author:  [@rmholmes](https://forum.access-hive.org.au/u/rmholmes)
#### Post date: [12 March 2023 22:43 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/14 "2023-03-12T22:43:41Z")
> [@abhik](#):
>
> @rmholmes Could you please update the input file location at [Tutorials · COSIMA/access-om2 Wiki · GitHub](https://github.com/COSIMA/access-om2/wiki/Tutorials#changing-the-bathymetry-land-sea-mask-and-oasis-remapping-weights)
I’ve updated the paths in that tutorial now to something that should work for Gadi (I haven’t tested it). Note the specific paths you use depend on the configuration you’re using (e.g. JRA55 v1.3 vs v1.4 vs. coupled etc., your own `custom_topog_test` directory, the remapping files appropriate for your resolution etc.). If you run into any problems please let me know.
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### Author:  [@abhik](https://forum.access-hive.org.au/u/abhik)
#### Post date: [13 March 2023 23:38 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/15 "2023-03-13T23:38:39Z")
@rmholmes the exe file
/g/data/ik11/inputs/access-om2/bin/fms\_ACCESS-OM\_1c1f23e\_libaccessom2\_b6caeab.x
doesn’t exist. But there are many other similar exe files in the same directory. Can I use any of them alternatively?
We don’t need cice file as our planned experiments will be run in sea-ice-free conditions. Will there be any issue with the output ocean\_mask.nc file if we don’t use the generated kmt.nc file in the experiment?
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### Author:  [@rmholmes](https://forum.access-hive.org.au/u/rmholmes)
#### Post date: [14 March 2023 00:57 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/16 "2023-03-14T00:57:42Z")
> [@abhik](#):
>
> @rmholmes the exe file
> /g/data/ik11/inputs/access-om2/bin/fms\_ACCESS-OM\_1c1f23e\_libaccessom2\_b6caeab.x
> doesn’t exist. But there are many other similar exe files in the same directory. Can I use any of them alternatively?
What are you trying to do exactly? Are you trying to run a version of ACCESS-OM2 to test that your changes to the topography and masking works properly? If so, then I’d suggest working from one of the up-to-date default configurations, which will have all the right paths for you (e.g.
[GitHub - COSIMA/1deg\_jra55\_ryf: 1 degree ACCESS-OM2 experiment with JRA55 RYF atmospheric forcing.](https://github.com/COSIMA/1deg_jra55_ryf/tree/master)).
If instead you’re trying to use the coupled model (without sea ice), then some of the details of how you use the `topog.nc`, `ocean_mask.nc` may be different (depending on whether the coupled model uses `payu`, and thus `config.yaml` to run or not). Also the remapping files will be different because of the coupling. In this case I don’t think you’ll be able to use the ACCESS-OM2 `make_remap_weights.py` script to make your remapping files, although you might be able to adapt it to work. I’d expect that the `topogtools` should be fine still to produce the mask file (and you can probably just ignore the `kmt.nc` file)?
If you are working with the coupled model I’m probably the wrong person to help.
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### Author:  [@abhik](https://forum.access-hive.org.au/u/abhik)
#### Post date: [14 March 2023 01:19 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/17 "2023-03-14T01:19:12Z")
Thanks, @rmholmes. Our experiments will be conducted in O-A coupled N48 framework. Using a given topography file, I could create an ocean\_mask.nc file through topog2mask.py (with minor modifications in the code). However, we perhaps need to adopt a different approach for generating coupling weights as you suggested.
Any help from others on this would be much appreciated.
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### Author:  [@dkhutch](https://forum.access-hive.org.au/u/dkhutch)
#### Post date: [14 March 2023 01:26 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/18 "2023-03-14T01:26:35Z")
Hi Dietmar, could you please provide a rough guide for how many CPUs is required for the N48 coupled model? For the N96 version we have the following numbers:
ACCESS-ESM1.5: CPUs: 384, Model cost 1.1kSU/year, Walltime: 16 years/day
Do you have something similar for N48?
Regards, David
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### Author:  [@Dietmar\_Dommenget](https://forum.access-hive.org.au/u/Dietmar_Dommenget)
#### Post date: [17 March 2023 00:26 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/19 "2023-03-17T00:26:11Z")
Dear ACCESS-NRI,
to make some progress here we currently like to know how we can edit the ancillary files of the ACCESS-N48 coupled model. In particular, we need to know:
1. What ancillary files of the atmos, ocean and coupler to we need to edit to change topography/orography and land-sea mask for atmos and ocean?
2. How can we edit these ancillary files?
3. Is there something else we need to consider in this context?
best regards
Dietmar
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### Author:  [@Dietmar\_Dommenget](https://forum.access-hive.org.au/u/Dietmar_Dommenget)
#### Post date: [17 March 2023 00:27 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/20 "2023-03-17T00:27:41Z")
Dear David,
good point. Abhik would know. As far as I know the model runs 1yrs simulation in 40min wall time.
best regards
Dietmar
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### Author:  [@abhik](https://forum.access-hive.org.au/u/abhik)
#### Post date: [17 March 2023 01:04 UTC](https://forum.access-hive.org.au/t/access-coupled-n48-for-deep-paleo/529/21 "2023-03-17T01:04:19Z")
@dkhutch Our coupled N48 uses 480 CPUs and completes 2 calendar years simulation in 1 hr 40 mins. Therefore, the computational cost is 480x1.67x2 = 1.6 kSU/2yrs or 0.8 kSU/yr.
The N48 suite should complete ~30 yrs/day. However, we merely get 20 yrs/day in reality. Our suite can run ~2 years only in a single job and resubmits another job for the next 2 yrs. This reduces the actual efficiency of the suite as often the jobs wait in the queue.
How can we improve efficiency by running longer than the usual 2 years in a single queued job?
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