From ad2fe18db4c7027d36860b1ede15521fdaabb906 Mon Sep 17 00:00:00 2001 From: yuchengt900 Date: Tue, 27 Feb 2024 16:25:00 -0500 Subject: [PATCH] Adressed ACR's comments --- docs/source/BuildMOM6.rst | 4 ++-- docs/source/ContainerQuickstart.rst | 19 ++++++++++--------- docs/source/InputsOutputs.rst | 10 ++++++++-- docs/source/RunNWA12.rst | 8 ++++++++ 4 files changed, 28 insertions(+), 13 deletions(-) diff --git a/docs/source/BuildMOM6.rst b/docs/source/BuildMOM6.rst index a8c952082..431fa4e74 100644 --- a/docs/source/BuildMOM6.rst +++ b/docs/source/BuildMOM6.rst @@ -90,7 +90,7 @@ After download the source code, users can navigate to the ``builds`` directory a .. code-block:: console - cd CEFI-regional-MOM6\builds + cd CEFI-regional-MOM6/builds mkdir YOUR_MACHINE_DIRECTORY cd YOUR_MACHINE_DIRECTORY @@ -116,7 +116,7 @@ Once the two files are created, use the following command to build the model (Ma .. code-block:: console - cd CEFI-regional-MOM6\builds + cd CEFI-regional-MOM6/builds ./linux-build.bash -m YOUR_MACHINE_DIRECTORY -p NAME_OF_YOUR_mk_FILE -t repro -f mom6sis2 If the build completes successfully, you should be able to find the executable here: ``builds/build/YOUR_MACHINE_DIRECTORY-NAME_OF_YOUR_mk_FILE/ocean_ice/repro/MOM6SIS2`` diff --git a/docs/source/ContainerQuickstart.rst b/docs/source/ContainerQuickstart.rst index 5bab72483..1da956d1d 100644 --- a/docs/source/ContainerQuickstart.rst +++ b/docs/source/ContainerQuickstart.rst @@ -29,15 +29,16 @@ To build and run the MOM6-COBALT using a Singularity/Apptainer container, first Build and run 1-D example using Docker ----------------------------------------- User can follow the following steps to build and run MOM6-SIS2-COBALT 1-D case within a Docker container. + .. code-block:: - #Assume user is under /USER_HOME_PATH + #Assume user is under $HOME docker pull clouden90/1d_mom6_cobalt:base #This will pull docker image to your local machine git clone https://github.com/NOAA-GFDL/CEFI-regional-MOM6.git --recursive #git clone CEFI-regional-MOM6 repo - cd USER_HOME_PATH/CEFI-regional-MOM6/exps + cd $HOME/CEFI-regional-MOM6/exps wget https://gfdl-med.s3.amazonaws.com/OceanBGC_dataset/1d_datasets.tar.gz && tar -zxvf 1d_datasets.tar.gz && rm -rf 1d_datasets.tar.gz - cd USER_HOME_PATH - docker run --rm -v /USER_HOME_PATH:/work -it clouden90/1d_mom6_cobalt:v0.1 bash --login # run docker container interactively + cd $HOME + docker run --rm -v $HOME:/work -it clouden90/1d_mom6_cobalt:v0.1 bash --login # run docker container interactively cd /work/CEFI-regional-MOM6/builds ./linux-build.bash -m docker -p linux-gnu -t repro -f mom6sis2 #build MOM6-SIS2-COBALT cd /work/CEFI-regional-MOM6/exps @@ -59,14 +60,14 @@ where ``/absolute/path/to/writable/directory/`` refers to a writable directory ( Then User can follow the following steps to build and run MOM6-SIS2-COBALT 1-D case within a Singularity/Apptainer container. .. code-block:: - #Assume user is under /USER_HOME_PATH - cd /USER_HOME_PATH + #Assume user is under $HOME + cd $HOME singularity pull 1d_mom6_cobalt.sif docker://clouden90/1d_mom6_cobalt:base #pull docker image and convert to sif git clone https://github.com/NOAA-GFDL/CEFI-regional-MOM6.git --recursive #git clone CEFI-regional-MOM6 repo - cd USER_HOME_PATH/CEFI-regional-MOM6/exps + cd $HOME/CEFI-regional-MOM6/exps wget https://gfdl-med.s3.amazonaws.com/OceanBGC_dataset/1d_datasets.tar.gz && tar -zxvf 1d_datasets.tar.gz && rm -rf 1d_datasets.tar.gz - cd USER_HOME_PATH - singularity shell -B /USER_HOME_PATH:/work -e /USER_HOME_PATH/1d_mom6_cobalt.sif # start singularity/apptainer container interactively + cd $HOME + singularity shell -B $HOME:/work -e $HOME/1d_mom6_cobalt.sif # start singularity/apptainer container interactively cd /work/CEFI-regional-MOM6/builds ./linux-build.bash -m docker -p linux-gnu -t repro -f mom6sis2 #build MOM6-SIS2-COBALT cd /work/CEFI-regional-MOM6/exps diff --git a/docs/source/InputsOutputs.rst b/docs/source/InputsOutputs.rst index 17467435a..ade1d0f70 100644 --- a/docs/source/InputsOutputs.rst +++ b/docs/source/InputsOutputs.rst @@ -79,7 +79,7 @@ Users are referred to this `link `. +The model configuration files for regional MOM6-SIS2-COBALT configurations are listed and described in :numref:`Table %s `. .. _ModelConfig: @@ -170,6 +170,12 @@ Example Format: "ATM", "t_bot", "t2m", "./INPUT/2t_ERA5.nc", "bilinear", 1.0 +Users can also set a constant value by entering empty quotes for ``fieldname_file`` and ``file_name`` and setting ``interpol_method`` to ``none``. Below is an example of setting a constant atmospheric oxygen value: + +.. code-block:: console + + "ATM", "o2_flux_pcair_atm", "", "", "none", 0.214 + ============= Outputs ============= diff --git a/docs/source/RunNWA12.rst b/docs/source/RunNWA12.rst index 63874f912..e3d8939c6 100644 --- a/docs/source/RunNWA12.rst +++ b/docs/source/RunNWA12.rst @@ -59,3 +59,11 @@ Users may need to modify the run script according to their HPC machine configura #override LAYOUT = 20,20 Also, please ensure to modify your run script according to the changes in the model layout. + +here `__ + +Users can also use the `FRE-NCtools `__ to create their own mask_table to avoid wasting a lot of computational resources. The command for a 20x20 mask would be like the following: + +.. code-block:: console + + check_mask --grid_file ocean_mosaic.nc --ocean_topog ocean_topog.nc --layout 20,20