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update namelists -- now are consistent again
Julien Palmieri authored
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Name Last commit Last update
medusa_resources update namelists -- now are consistent again
sette forgot to add C1D restarts -- now its all good
nemo @ 51e81985 revert manually to the previous commit -- wrong manip
.gitignore update namelists -- now are consistent again
.gitmodules Rearranged files and added main nemo as a git submodule
README.md Update README.md
add_msa_to_nemo complete the MEDUSA sette tests config and scripts. -- started to test; ORCA2_MEDUSA works, but not yet the others
compare_msa_my_src Added setup scripts and started some documentation
last_patchset Added setup scripts and started some documentation
README.md

MEDUSA for 4.2.x

================

This repository contains the additions and changes needed to add MEDUSA as an optional BGC model in the NEMO system. All the new resources are kept in the medusa_resources subdirectory and maintained through this GitLab service. Cloning this repository will also retrieve the main NEMO source as a submodule. At any point the MEDUSA code should be compatible with the retrieved version of the NEMO trunk but both code sets are kept distinct so that remote changes to NEMO may be tracked.

As well as code only related to MEDUSA, medusa_resources contains some OCE and TOP modules that have been modified to support MEDUSA. These files reside in the medusa_resources/cfgs/SHARED_MEDUSA/MY_SRC directory ready to be symbolically linked from the MY_SRC directory of any new configuration that wishes to use MEDUSA. The script: compare_msa_my_src can be used to obtain a quick overview of the differences compared to the equivalent files in the nemo submodule. This will need to be checked and the SHARED_MEDUSA/MY_SRC files updated, if necessary, when the submodule is updated to later versions of the trunk. The current list of differences is provided in the last_patchset file. This is simply the output of the compare_my_src script run just before the last commit.

The script: add_msa_to_nemo can be used to symbolically include the parts of medusa_resources in the nemo tree so that new configurations using MEDUSA can be built and run. Any added files are listed in ./nemo/.gitignore so that they do not interfere with the main source and good visibility of any changes to NEMO code outside of MEDUSA is maintained. The script adds links to the source code and adds a new reference configuration: ORCA2_MEDUSA which can be used as a basis for new configrations which wish to use MEDUSA.

Since the new reference configuration is part of the medusa_4.2.x repository, it is best not to work directly in this configuration but to create a new configuration that will not be tracked by git. In fact, if you have run the add_msa_to_nemo script, then a wildcard: *MEDUSA* will have be added to the .gitignore file and so anything with MEDUSA in its name will be automatically ignored.

Main MEDUSA (adapted to NEMO-MAIN):

So to get started the recipe is simply:

git clone --recurse-submodules git@git.noc.ac.uk:acc/medusa_4.2.x.git
cd medusa_4.2.x

# put MEDUSA at the right places :
./add_msa_to_nemo

# compile :
cd nemo
./makenemo -r ORCA2_MEDUSA -n MY_NEW_MEDUSA -m x86-64_Anemone -j 8

MEDUSA adapted to NEMO-4.2.1

this version needs a little tweak :

## we don't upload NEMO-submodule strait as we use a different NEMO-git, from the UKMO (we want the GOSI9 branch)
## first get MEDUSA
clone https://git.noc.ac.uk/acc/medusa_4.2.x.git MEDUSA_NEMO4-2-1
cd MEDUSA_NEMO4-2-1/

## switch to the NEMO4.2.1 adapted branch : 
git switch 16-medusa-nemo4-2-1-3 

## check-out NEMO-GOSI9
git submodule init
git submodule update 

# put MEDUSA at the right places :
./add_msa_to_nemo

# compile :
cd nemo
./makenemo -r ORCA2_MEDUSA -n MY_NEW_MEDUSA -m x86-64_Anemone -j 8

Documentation and tutorials

Further documentations on how to compile and run MEDUSA can be found on this git wiki :