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https://github.com/gaelforget/eccov4_flt_offline
tools to use MITgcm/pkg/flt
https://github.com/gaelforget/eccov4_flt_offline
Last synced: 22 days ago
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tools to use MITgcm/pkg/flt
- Host: GitHub
- URL: https://github.com/gaelforget/eccov4_flt_offline
- Owner: gaelforget
- Created: 2019-03-21T18:38:47.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-11-02T14:22:27.000Z (about 4 years ago)
- Last Synced: 2024-10-10T11:38:54.863Z (about 1 month ago)
- Language: Fortran
- Size: 51.8 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# ECCOv4_flt_offline
[](https://zenodo.org/badge/latestdoi/177004362)
**Content:** This repo provides tools to use `MITgcm/pkg/flt/` and/or `MITgcm/pkg/offline/` with global grids that often rely on `pkg/exch2/` and `ECCOv4` in particular (Forget et al 2015). This `README.md` provides user directions plus bits of documentation. All contents should be regarded as work in progress. This setup served as the basis for `Rousselet et al 2020` and subsequent studies.
- Campin, et al, MITgcm/MITgcm: mid 2020 version (Version checkpoint67s). Zenodo.
- Forget, et al., ECCO version 4: an integrated framework for non-linear inverse modeling and global ocean state estimation. Geosci. Model. Dev. 8, 3071–3104 (2015)
- Rousselet, Cessi, Forget, Routes of the upper branch of the Atlantic Meridional Overturning Circulation according to an ocean state estimate. Geophys. Res. Lett. 47, (2020)
**Author:** `[email protected]`
**Date:** `2019/03/12`
## 1) Repo Folders
- `code_flt/` and `code_off/` contain compile time options / settings plus a few modified function files which would eventually be merged into the main `MITgcm` repo.
- `input_flt/` and `input_off/` contain run time options / settings.
- `tools/` contains tools to prepare model input and analyze model output.
- `201702files/` contains initial testing stuff from 2017/02 (see below).
## 2) How To -- Use `pkg/flt` In ECCO
To run the model and pkg/flt concurrently (i.e., in online mode) proceed as follows.
- [Download the setup](https://eccov4.readthedocs.io/en/latest/downloads.html)
- Go to `MITgcm/mysetups/ECCOv4/` and download `code_flt/` + `input_flt/` as follows:
```
cd MITgcm/mysetups/ECCOv4/
git clone https://github.com/gaelforget/MITgcm_flt
```
- [Compile the model](https://eccov4.readthedocs.io/en/latest/runs.html) but with `-mods="../MITgcm_flt/code_flt ../code"`. If you are using gfortran for example you want to use the `linux_amd64_gfortran` option file:
```
cd MITgcm/mysetups/ECCOv4/build
../../../tools/genmake2 -mods="../MITgcm_flt/code_flt ../code" -optfile \
../../../tools/build_options/linux_amd64_gfortran -mpi
make depend
make -j 4
cd ..
```
- Prepare the run directory using the following sequence where it is assumed that `init_flt/` contains initial conditions provided by user (e.g., see **How To -- Initialize `pkg/flt`**).
```
mkdir run
cd run
ln -s ../build/mitgcmuv .
ln -s ../MITgcm_flt/input_flt/* .
ln -s ../input/* .
ln -s ../inputs_baseline2/input*/* .
ln -s ../forcing_baseline2 .
ln -s ../init_flt/* .
```
- [Run the model](https://eccov4.readthedocs.io/en/latest/runs.html) using your favorite computer and shell script.
- Plot output as needed using your favorite software (e.g., see **How To -- Plot Trajectory Output**).
### 2.1) Notes on "How To -- Use `pkg/flt` in ECCO"
The included, preliminary setup may need to be modified depending on the application; in particular:
- Once all variables needed to setup `pkf/offline` have been generated using the full model then one should be able to run `pkf/flt` in offline mode (see **How To -- Use `pkg/offline` In ECCO**).
- The preliminary `pkf/flt` setup provided here is for a simple 2D problem where particles drift at the surface using uVel, vVel, wVel. Dealing with 3D problems may require including bolus and diffusivity components or modifying the fortran code.
### 2.2) How To -- Initialize `pkg/flt`
Download [gcmfaces](https://gcmfaces.readthedocs.io/en/latest/) to use it along with `MITgcm_flt/tools/`.
```
cd MITgcm/mysetups/ECCOv4/
git clone https://github.com/gaelforget/gcmfaces
```
Open `Matlab` and go to `MITgcm/mysetups/ECCOv4/` and execute `create_init_flt.m`.
```
cd MITgcm/mysetups/ECCOv4/
addpath(genpath([pwd '/gcmfaces/']));
addpath(genpath([pwd '/MITgcm_flt/tools/']));
create_init_flt;
```
### 2.3) How To -- Plot Trajectory Output
After having completed a model run, it's time to plot and analyze results. In `Matlab` for example, one can use `read_flt_traj.m` and `plot_flt_traj.m` as shown below [^read_flt_traj].
```
cd MITgcm/mysetups/ECCOv4/
addpath(genpath([pwd '/MITgcm_flt/tools/']));
dirRun=[pwd filesep 'run' filesep];
[flts,data,header]=read_flt_traj([dirRun 'float_trajectories'],4);
plot_flt_traj(flts(1:100:end));
```
## 3) How To -- Use `pkg/offline` In ECCO
First, download ECCO v4r2's [nctiles_climatology/](https://eccov4.readthedocs.io/en/latest/downloads.html) into `MITgcm/mysetups/ECCOv4/` and use e.g. `create_input_offline.m` to generate `input_climatology/`.
```
cd MITgcm/mysetups/ECCOv4/
addpath(genpath([pwd '/MITgcm_flt/tools/']));
create_input_offline;
```
Then, follow the same directions as in **How To -- Use `pkg/flt` In ECCO** but with `code_off`, `input_off`, and `input_climatology` replacing `code_flt`, `input_flt`, and `init_flt`.
Running this `mitgcmuv` should generate monthly output via `pkg/diagnostics` comparable to the original from `nctiles_climatology/` (e.g. see `tools/check_run_offline.m`).
### 3.1) Notes on "Use `pkg/offline` In ECCO"
The included, preliminary setup may need to be re-evaluated depending on the application; in particular:
- the divergent part of the velocity field may need to be subtracted
- the gm component (uvelstar, etc.) may need to be added to the velocity field
If variables are needed that are not available online (i.e., in [nctiles_climatology/](https://eccov4.readthedocs.io/en/latest/downloads.html)) then the full model needs to be re-ran to generate new output (see **How To -- Use `pkg/flt` In ECCO** and [pkg/diagnostics](https://mitgcm.readthedocs.io/en/latest/outp_pkgs/outp_pkgs.html)).
## 4) How To -- Use `pkg/offline` + `pkg/flt` In ECCO
Proceed as before but with a few modifications:
- Uncomment the `#flt` line that in `code_off/packages.conf` .
- Add ` useFLT = .TRUE.,` in `input_off/data.pkg` .
- Compile with:
```
../../../tools/genmake2 -mods="../MITgcm_flt/code_off ../MITgcm_flt/code_flt ../code" \
-optfile ../../../tools/build_options/linux_amd64_gfortran -mpi
```
- Setup the run directory as:
```
mkdir run
cd run
ln -s ../build/mitgcmuv .
ln -s ../MITgcm_flt/input_off/* .
ln -s ../MITgcm_flt/input_flt/* .
ln -s ../input/* .
ln -s ../inputs_baseline2/input*/* .
ln -s ../forcing_baseline2 .
ln -s ../input_climatology/* .
ln -s ../init_flt/* .
```
## Appendix 1) Initial Test Material From 2017/02
The `201702files/` folder contains:
- `pkg_flt_diff` summarizes modifications made to MITgcm/pkg/flt before compiling it
- `FLT_SIZE.h` is a compile time option file
- `data.flt` is a run time option file
- `ini_pos.bin` is an initial condition file
- `prep_ini2.m` was used to prepare `ini_pos.bin`
- `read_flt_traj2.m` is used in `plot_traj2.m` to read in the model output (`float_trajectories.???.001.data`)
- `plot_traj2.m` plots the trajectories (model output) in global projection using m_map and gcmfaces
## Appendix 2) Just in case ...
In case your build option file does not handle the case of multiple `mods` directories as one would expect you can try something like this:
```
mkdir code_flt_online
cp -pi MITgcm_flt/code_flt/* code_flt_online/
cp -pi code/* code_flt_online/
#/bin/cp: overwrite 'code_flt_online/packages.conf'? n
cd ..
mkdir build_flt_online
cd build_flt_online
../../../tools/genmake2 -mods=../code_flt_online \
-optfile ../../../tools/build_options/linux_amd64_gfortran -mpi
cd ..
mkdir run_flt_online
cd run_flt_online
ln -s ../build_flt_online/mitgcmuv .
et cetera ...
```
And this for the offline+flt case:
```
mkdir code_flt_offline
cp -pi MITgcm_flt/code_off/* code_flt_offline/
cp -pi MITgcm_flt/code_flt/* code_flt_offline/
#/bin/cp: overwrite 'code_flt_offline/packages.conf'? n
cp -pi code/* code_flt_offline/
#/bin/cp: overwrite 'code_flt_offline/packages.conf'? n
cd ..
mkdir build_flt_offline
cd build_flt_offline
../../../tools/genmake2 -mods=../code_flt_offline \
-optfile ../../../tools/build_options/linux_amd64_gfortran -mpi
et cetera ...
```
[^read_flt_traj]: The execution of `read_flt_traj` can take a few minutes.