MARBL-DART

[robin-armstrong]

Description:

Contains model-mods for data assimilation with the Marine Biogeochemistry Library (MARBL/MOM6).

also fixes #614

Testing Datasets:

A test package for MARBL_joint_estimation can be found at /glade/u/home/rarmstrong/DART_test_package.

[hkershaw-brown]

Thanks for this Robin!

For reviewers, summary of July 11th 2024 meeting as todo list:

model mom6-marbl:

• [ ] MARBL_joint_estimation is the version of the model directory that should be released. (rename to something sensible)
• [ ] remove other MARBL_ model directories
  • [ ] MARBL_param_estimation
  • [ ] MARBL_state_estimation
• [ ] documentation
  • [ ] options to set in marbl-mom6 to do DA.
  • [ ] what is available (parameter estimation?) models/MARBL_param_estimation has metadata.txt is this needed?
• [ ] model_mod name

observation converter(s):

• [ ] check the difference between these:
  • [ ] BATS
  • [ ] BATS_clim
  • [ ] documentation
  • [ ] observations/obs_converters/BATS_clim/bats_climatology.py
  • [ ] converter documentation .rst

General git tidiness:

• [x] remove netcdf files (may remove from history if they are large)
• [x] remove binary files (may remove from history if they are large)
• [x] revert mpi/fix system changes
• [x] update to main
• [x] rewrite history so Robin's commits are credited to his github account
• [x] .gitignores dotted around, remove or move to root/.gitignore

Other:

• [ ] Fix for https://github.com/NCAR/DART/issues/614

Testing:

• [ ] test case /glade/work/hkershaw/DART/marbl/DART_test_package (copy of /glade/u/home/rarmstrong/DART_test_package edit: without symlinks).
  /glade/u/home/rarmstrong/DART_test_package.robin is the original with symlinks (watch out for links INPUT->INPUT)
• [ ] netcdf dimension fix

backup of this branch since we're rewriting history: https://github.com/hkershaw-brown/DART/tree/marbl-dart

[hkershaw-brown]

note for test package, I switched to inflation not read from file

hkershaw@dec1004:/glade/work/hkershaw/DART/marbl/DART_test_package/test/DART$ diff input.nml input.nml.robin 
1,6d0
< &probit_transform_nml
< /
< 
< &algorithm_info_nml
< /
< 
73,74c67,68
<    inf_initial_from_restart    = .false.,                 .false.,
<    inf_sd_initial_from_restart = .false.,                  .false.,
---
>    inf_initial_from_restart    = .true.,                 .false.,
>    inf_sd_initial_from_restart = .true.,                  .false.,
108a103
>    filter_kind                     = 1,

[mgharamti]

I checked out the code and I was not able to run any of the DART executables. Here is the error that I was getting:

ERROR FROM:
  source : ensemble_manager_mod.f90
  routine: set_up_ens_distribution
  message: not enough MPI tasks for the model size, suggest at least ***** tasks

So, it turns out the length of the state vector is 7036994676854122!! I realize the issue is in computing the variable model_size. Right now, the function get_model_size in the model_mod is computing it using local variables. When someone calls get_model_size() outside the model_mod, this fails. So, the correct approach is to compute model_size inside static_init_model as I outlined in my previous review and then get_model_size should simply look like this:

function get_model_size()
integer(i8) :: get_model_size
get_model_size = model_size 
end function get_model_size

With this change, I can now run model_mod_check and the model_size is now correctly computed as 3434. It's still puzzling to me that this version of the code was running during Robin's internship. Could it be that we have a different version?

[hkershaw-brown]

pushed robins branch to https://github.com/NCAR/DART/tree/marbl-dart