-
Notifications
You must be signed in to change notification settings - Fork 144
Create your own repository of experiments
In other documentation we describe how to clone the MOM6-examples repository of experiment configurations. Here we describe how to construct your own independent experiment repository in which you can keep your own configurations.
These steps will create a repository with a structure as follows:
$ tree -L 2 My_experiments My_experiments ├── expt1 │ ├── diag_table │ ├── input.nml │ └── MOM_input └── src ├── FMS ├── mkmf └── MOM6
You can choose to put expt1 under "ocean_only" if you want to mimic the structure in MOM6-examples and maintain different classes of experiments, such as "ocean_only" or "coupled".
First create a new folder and initialize git. This folder will be what you get after a git clone
and has the equivalent role that MOM6-examples has for GFDL experiments. We recommend naming the folder with the name of the repository you intend to use:
mkdir My_experiments
cd My_experiments
git init
By default git will use branch "master". If you want to develop on a different branch then you can change the branch now:
git checkout -b my_dev_branch
Now add the software and source code needed to build an ocean-only model:
git submodule init
git submodule add https://github.com/mom-ocean/mkmf.git src/mkmf
git submodule add https://github.com/NOAA-GFDL/FMS.git src/FMS
git submodule add [email protected]:my_github_account_name/MOM6.git src/MOM6
git submodule update --init --recursive
Note that we used the "https" transfer protocol for repositories which we never expect to need to fork and push to (i.e. read-only). For the MOM6 repository we used the git transfer protocol and pointed to your fork (replace "my_github_account_name" with your GitHub account name). If you don't have or want your own fork of MOM6, then replace the url with "https://github.com/NOAA-GFDL/MOM6.git".
This is what your directory will look like
% tree -L 2 . . `-- src |-- FMS |-- mkmf `-- MOM6 3 directories, 0 files
and git status
reports:
% git status On branch dev/master
Initial commit
Changes to be committed: (use "git rm --cached ..." to unstage)
new file: .gitmodules new file: src/FMS new file: src/MOM6 new file: src/mkmf
Let's commit this before adding an experiment:
git commit -m "Added source needed for ocean-only experiments"
If you plan to use the sea-ice model with your ocean then we need some other components:
git submodule add https://github.com/NOAA-GFDL/SIS2.git src/SIS2
git submodule add https://github.com/NOAA-GFDL/atmos_null.git src/atmos_null
git submodule add https://github.com/NOAA-GFDL/coupler.git src/coupler
git submodule add https://github.com/NOAA-GFDL/land_null.git src/land_null
git submodule add https://github.com/NOAA-GFDL/icebergs.git src/icebergs
git submodule add https://github.com/NOAA-GFDL/ice_param.git src/ice_param
Let's commit these additions:
git add .
git commit -m "Added components needed for ice-ocean experiments"
From the "My_experiments" directory, first name your experiment and create a directory (here we use "expt1"):
mkdir expt1
cd expt1
The bare minimum of input files you need are input.nml, MOM_input, diag_table. Create input.nml with
cat << EOFA > input.nml
&MOM_input_nml
output_directory = './',
input_filename = 'n'
restart_input_dir = 'INPUT/',
restart_output_dir = 'RESTART/',
parameter_filename = 'MOM_input' /
&diag_manager_nml
/
&fms_nml
domains_stack_size = 955296
stack_size =0 /
EOFA
Note that if you like to use the MOM_override model of perturbation parameters change parameter_filename = 'MOM_input','MOM_override'
.
Grab a working MOM_input
wget -o/dev/null -O- https://github.com/NOAA-GFDL/MOM6-examples/archive/dev/master.tar.gz | tar -zxv --strip-components=3 -f - MOM6-examples-dev-master/ocean_only/benchmark/MOM_input
Create a simple diag_table with:
cat << EOFA > diag_table
"Experiment expt1"
1 1 1 0 0 0
"output", 1,"days",1,"days","time",
#This is the field section of the diag_table.
# Prognostic Ocean fields:
#=========================
"ocean_model","u","u","output","all",.false.,"none",2
"ocean_model","v","v","output","all",.false.,"none",2
"ocean_model","h","h","output","all",.false.,"none",1
"ocean_model","e","e","output","all",.false.,"none",2
"ocean_model","temp","temp","output","all",.false.,"none",2
EOFA
Add the experiment to your repository
cd ../ # Back to top level
git add expt1
git commit -m "Added ocean-only experiment expt1 (based on benchmark from MOM6-examples)"
Having followed the above steps you now have a working directory under version control with git. To collaborate, or even just backup your work, you can push it up to GitHub:
- Create a new repository on GitHub by going to your account and clicking on the "+" icon "Create new..." (top-right of GitHub page once you are logged in).
- Enter a name for the repository (we recommend using the same name for the folder you created and the repository but it is not mandatory)
- Do not check "Initialize this repository with a README" nor add license or README files. You want a blank repository to push to since you already created a history in the steps above.
- Create the blank respository by clicking "Create repository"
- On the next page you will be given instructions for pushing, under the title "…or push an existing repository from the command line", which will be something like:
git remote add origin https://github.com/<my_github_account>/My_experiments
git push -u origin my_dev_branch
where the "my_dev_branch" is whatever you decided to use as the first branch (e.g. "master" by default).