Merge pull request #254 from NOAA-GFDL/fix/remove-yct-contact-info

uwagura · web-flow · commit 0b4447dd8f08 · 2026-01-16T11:55:35.000-05:00
Update documentation to include latest contact info and data sources
diff --git a/diagnostics/README.md b/diagnostics/README.md
@@ -1,8 +1,8 @@
 # diagnostics
 This folder provides scripts, that can be utilized for analyzing model results.
-Please contact the code manager Yi-Cheng Teng (Contact: yi-cheng.teng@noaa.gov) if you have any queations.
+Please contact us at oar.gfdl.cefi-support AT noaa DOT gov if you have any queations.
 
 ## Prerequisite
 The majority of the scripts are written in Python. One can follow the instructions (README.md under tools folder) to create a Python virtual environment on NOAA R&D HPCs or GFDL Analysis.
 
-The Python scripts that read model data are written to take advantage of the `hsmget` command for faster reading and caching of data from the archive filesystem. When using GFDL Analysis, it is recommended to load the hsm module (`module load hsm/1.3.0`) before running any of the diagnostic scripts. 
+The Python scripts that read model data are written to take advantage of the `hsmget` command for faster reading and caching of data from the archive filesystem. When using GFDL Analysis, it is recommended to load the hsm module (`module load hsm/1.3.0`) before running any of the diagnostic scripts.
diff --git a/docs/source/BuildMOM6.rst b/docs/source/BuildMOM6.rst
@@ -12,7 +12,7 @@ To build the MOM6-SIS2-COBALT, users will complete the following steps:
 
 .. _StackInfo:
 
-Install the Prerequisite Softwares 
+Install the Prerequisite Softwares
 ==========================================
 
 .. note::
@@ -23,7 +23,7 @@ Users on any sufficiently up-to-date machine with a UNIX-based operating system
 
 .. code-block:: console
 
-   # Linux system such as Ubuntu 
+   # Linux system such as Ubuntu
    sudo apt update
    sudo apt install make gfortran git git-lfs tcsh netcdf-bin libnetcdf-dev libnetcdff-dev openmpi-bin libopenmpi-dev
 
@@ -40,7 +40,7 @@ Users on any sufficiently up-to-date machine with a UNIX-based operating system
 
 For **Windows users**, we recommend installing `WSL <https://learn.microsoft.com/en-us/windows/wsl/install>`__ (Windows Subsystem for Ubuntu and Linux), and following the above steps to install the prerequisite software. Alternatively users can opt for the Docker container approach. See :ref:`Container-Based Quick Start Guide <QuickstartC>` for more details.
 
-After completing installation, continue to the :ref:`next section <DownloadMOM6>` to download the CEFI-regional-MOM6. 
+After completing installation, continue to the :ref:`next section <DownloadMOM6>` to download the CEFI-regional-MOM6.
 
 .. _DownloadMOM6:
 
@@ -50,9 +50,9 @@ The CEFI-regional-MOM6 source code is publicly available on GitHub. To download
 
 .. code-block:: console
 
-   git clone https://github.com/NOAA-GFDL/CEFI-regional-MOM6.git --recursive 
+   git clone https://github.com/NOAA-GFDL/CEFI-regional-MOM6.git --recursive
 
-The cloned repository contains files and sub-directories shown in :numref:`Table %s <FilesAndSubDirs>`. 
+The cloned repository contains files and sub-directories shown in :numref:`Table %s <FilesAndSubDirs>`.
 
 .. _FilesAndSubDirs:
 
@@ -62,12 +62,12 @@ The cloned repository contains files and sub-directories shown in :numref:`Table
 
    * - File/Directory Name
      - Description
-   * - LICENSE.md 
+   * - LICENSE.md
      - A copy of the Gnu lesser general public license, version 3
    * - README.md
      - This file with basic pointers to more information
    * - src
-     - Contains the source code for MOM6-SIS2-COBALT model 
+     - Contains the source code for MOM6-SIS2-COBALT model
    * - builds
      - Contains build script to build MOM6-SIS2-COBALT
    * - diagnostics
@@ -77,14 +77,14 @@ The cloned repository contains files and sub-directories shown in :numref:`Table
    * - tools
      - Contains preprocessing scripts that can be used to generate model input files
    * - xmls
-     - Contains FRE xml files designed for running the CEFI-regional-MOM6 workflow on Gaea   
+     - Contains FRE xml files designed for running the CEFI-regional-MOM6 workflow on Gaea
    * - docs
      - Contains release notes, documentation, and User's Guide
 
 .. _BuildExecutables:
 
 Set Up the Environment and Build the Executables
-=================================================== 
+===================================================
 
 After download the source code, users can navigate to the ``builds`` directory and create a folder for your machine configurations:
 
@@ -112,19 +112,19 @@ The NAME_OF_YOUR_mk_FILE.mk file may be different depends on your system configu
    | Ubuntu (GNU)           | mkmf/templates/linux-ubuntu-trusty-gnu.mk                                       |
    +------------------------+---------------------------------------------------------------------------------+
 
-Once the two files are created, use the following command to build the model (Make sure to use correct names that are consistent with both your machine folder and your mk/env files):  
+Once the two files are created, use the following command to build the model (Make sure to use correct names that are consistent with both your machine folder and your mk/env files):
 
 .. code-block:: console
 
    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``  
+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``
 
 Run an Experiment
 =====================
 
-To test your ``MOM6SIS2``, first navigate to the ``exps`` folder: 
+To test your ``MOM6SIS2``, first navigate to the ``exps`` folder:
 
 .. code-block:: console
 
@@ -134,16 +134,16 @@ Download the model input files:
 
 .. code-block:: console
 
-   wget ftp.gfdl.noaa.gov:/pub/Yi-cheng.Teng/1d_ci_datasets.tar.gz && tar -zxvf 1d_ci_datasets.tar.gz && rm -rf 1d_ci_datasets.tar.gz
+   wget ftp://nomads.gfdl.noaa.gov/1/users/cefi/OM4.single_column.COBALT/data/1d_ci_datasets.tar.gz && tar -zxvf 1d_ci_datasets.tar.gz && rm -rf 1d_ci_datasets.tar.gz
 
 Navigate to the 1-D example:
 
 .. code-block:: console
 
    cd OM4.single_column.COBALT
 
-Use the following command to run the 1-D example:    
+Use the following command to run the 1-D example:
 
 .. code-block:: console
- 
+
    mpirun -np 1 ../../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
@@ -4,18 +4,18 @@
 Container-Based Quick Start Guide
 ====================================
 
-This Container-Based Quick Start Guide will help users build and run the 1D case for the MOM6-SIS2-COBALT System using a `Singularity/Apptainer <https://apptainer.org/docs/user/1.2/introduction.html>`__ container. The :term:`container` approach provides a uniform enviroment in which to build and run the MOM6-SIS2-COBALT. Normally, the details of building and running the MOM6-COBALT vary from system to system due to the many possible combinations of operating systems, compilers, :term:`MPIs <MPI>`, and package versions available. Installation via container reduces this variability and allows for a smoother MOM6-SIS2-COBALT build experience. 
+This Container-Based Quick Start Guide will help users build and run the 1D case for the MOM6-SIS2-COBALT System using a `Singularity/Apptainer <https://apptainer.org/docs/user/1.2/introduction.html>`__ container. The :term:`container` approach provides a uniform enviroment in which to build and run the MOM6-SIS2-COBALT. Normally, the details of building and running the MOM6-COBALT vary from system to system due to the many possible combinations of operating systems, compilers, :term:`MPIs <MPI>`, and package versions available. Installation via container reduces this variability and allows for a smoother MOM6-SIS2-COBALT build experience.
 
 The basic "1D" case described here builds a MOM6-COBALT for the Bermuda Atlantic Time-series Study (BATS) with OM4 single column configuration as well as COBALTV3.0.
 
-Prerequisites 
+Prerequisites
 -------------------
 
 Users must have either Docker (recommended for personal Windows/macOS systems) or Singularity/Apptainer (recommended for users working on Linux, NOAA Cloud, or HPC systems).
 
 Install Docker on Windows/macOS
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-To build and run the MOM6-SIS2-COBALT using a Docker container, first install the software according to the `Docker Installation Guide for Windows <https://docs.docker.com/desktop/install/windows-install/>`__ or `Docker Installation Guide for macOS <https://docs.docker.com/desktop/install/mac-install/>`__. 
+To build and run the MOM6-SIS2-COBALT using a Docker container, first install the software according to the `Docker Installation Guide for Windows <https://docs.docker.com/desktop/install/windows-install/>`__ or `Docker Installation Guide for macOS <https://docs.docker.com/desktop/install/mac-install/>`__.
 
 Install Singularity/Apptainer
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -26,17 +26,17 @@ Install Singularity/Apptainer
 
 To build and run the MOM6-COBALT using a Singularity/Apptainer container, first install the software according to the `Apptainer Installation Guide <https://apptainer.org/docs/admin/1.2/installation.html>`__. This will include the installation of all dependencies.
 
-Build and run 1-D example using Docker 
+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 $HOME 
+   #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 $HOME/CEFI-regional-MOM6/exps
-   wget ftp.gfdl.noaa.gov:/pub/Yi-cheng.Teng/1d_ci_datasets.tar.gz && tar -zxvf 1d_ci_datasets.tar.gz && rm -rf 1d_ci_datasets.tar.gz
+   wget ftp://nomads.gfdl.noaa.gov/1/users/cefi/OM4.single_column.COBALT/data/1d_ci_datasets.tar.gz && tar -zxvf 1d_ci_datasets.tar.gz && rm -rf 1d_ci_datasets.tar.gz
    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
@@ -50,7 +50,7 @@ Build and run 1-D example using Singularity/Apptainer container
 -----------------------------------------
 For users working on systems with limited disk space in their ``/home`` directory, it is recommended to set the ``SINGULARITY_CACHEDIR`` and ``SINGULARITY_TMPDIR`` environment variables to point to a location with adequate disk space. For example:
 
-.. code-block:: 
+.. code-block::
 
    export SINGULARITY_CACHEDIR=/absolute/path/to/writable/directory/cache
    export SINGULARITY_TMPDIR=/absolute/path/to/writable/directory/tmp
@@ -60,13 +60,13 @@ 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 $HOME 
-   cd $HOME 
+   #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 
+   git clone https://github.com/NOAA-GFDL/CEFI-regional-MOM6.git --recursive #git clone CEFI-regional-MOM6 repo
    cd $HOME/CEFI-regional-MOM6/exps
-   wget ftp.gfdl.noaa.gov:/pub/Yi-cheng.Teng/1d_ci_datasets.tar.gz && tar -zxvf 1d_ci_datasets.tar.gz && rm -rf 1d_ci_datasets.tar.gz
-   cd $HOME 
+   wget ftp://nomads.gfdl.noaa.gov/1/users/cefi/OM4.single_column.COBALT/data/1d_ci_datasets.tar.gz && tar -zxvf 1d_ci_datasets.tar.gz && rm -rf 1d_ci_datasets.tar.gz
+   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
diff --git a/docs/source/Diagnostics.rst b/docs/source/Diagnostics.rst
@@ -4,8 +4,8 @@
 Analysis output
 ====================================
 
-The ``CEFI-regional-MOM6/diagnostics`` folder contains python scripts that can be used to analyze modeled physical and biogeochemical results. 
-Please contact the code manager `Yi-cheng.Teng <yi-cheng.teng@noaa.gov>`_ if you have any queations.
+The ``CEFI-regional-MOM6/diagnostics`` folder contains python scripts that can be used to analyze modeled physical and biogeochemical results.
+Please contact us at `oar.gfdl.cefi-support@noaa.gov`_ if you have any queations.
 
 .. note::
 
@@ -43,7 +43,7 @@ The :numref:`Table %s <Diagsphytable>` below provides short descriptions for scr
 
    * - File Name
      - Description
-   * - sst_eval.py 
+   * - sst_eval.py
      - Compare model SST with 1993--2019 data from OISST and GLORYS
    * - sst_trends.py
      - Compare the model 2005-2019 SST trends from OISST and GLORYS
@@ -52,15 +52,15 @@ The :numref:`Table %s <Diagsphytable>` below provides short descriptions for scr
    * - ssh_eval.py
      - Compare model SSH with 1993--2019 data from GLORYS
    * - mld_eval.py
-     - Compare model MLD with climatologies from Holte et al. 2017 and de Boyer 2022     
+     - Compare model MLD with climatologies from Holte et al. 2017 and de Boyer 2022
    * - compute_tides_job.sh
      - Compare modeled tidal amplitude and phase with TPXO9 data
    * - NWA12/coldpool.py
-     - Compare bottom temperature from the model and du Pontavice et al.(2022) in the cold-pool region averaged over June-September  
+     - Compare bottom temperature from the model and du Pontavice et al.(2022) in the cold-pool region averaged over June-September
    * - NWA12/nechannel.py
      - Plot model-data comparison for Northeast Channel temperature and salinity
    * - NWA12/seaice.py
-     - Compare monthly climatology of sea ice concentration from the model and a satellite observation dataset    
+     - Compare monthly climatology of sea ice concentration from the model and a satellite observation dataset
    * - NWA12/tbot_epu.py
      - Compare annual average bottom-temperature anomalies in four different northeast US ecological production units from model,
        reanalysis, and observed data
@@ -92,8 +92,8 @@ The :numref:`Table %s <Diagsbiogeotable>` below provides short descriptions for
      - Comparison of model seasonal mean surface phosphate and nitrate with the World Ocean Atlas data
    * - oa_metrics.py
      - Compare Mean surface alkalinity, dissolved inorganic carbon, and aragonite saturation statee between the model and the
-       observation-derived climatology   
+       observation-derived climatology
    * - zooplankton.py
      - Compare the 0-200 m average mesozooplankton biomass climatology between model and Observations from the COPEPOD dataset
    * - NWA12/hypoxic_area.py
-     - Compare monthly climatologies of hypoxic area over the LA-TX Shelf between the model and geostatistical estimates from Matli et al. (2020) 
+     - Compare monthly climatologies of hypoxic area over the LA-TX Shelf between the model and geostatistical estimates from Matli et al. (2020)
diff --git a/docs/source/RunNWA12.rst b/docs/source/RunNWA12.rst
@@ -21,37 +21,38 @@ Download the model input dataset
 
 The dataset for the MOM6-COBALT-NWA12 (retrospective run from year 1993) is publicly available. Follow the steps below to download the dataset:
 
+
 .. code-block:: console
 
    cd CEFI-regional-MOM6/exps
-   wget ftp.gfdl.noaa.gov:/pub/Yi-cheng.Teng/nwa12_datasets.tar.gz
+   wget ftp://nomads.gfdl.noaa.gov/1/users/cefi/OM4.single_column.COBALT/data/1d_ci_datasets.tar.gz
    tar -zxvf nwa12_datasets.tar.gz
 
 This dataset contains all the necessary model input files (e.g. grid files, ICs, BCs, atmospheric forcings, river dischages, BGC fluxes from atmosphere). Most of these input files can be generated using the tools under ``CEFI-regional/MOM6/tools``. Please be aware that this dataset is quite large (51 GB), so please be patient while downloading it.
 
 Users interested in the model inputs, outputs, and configurations should refer to :ref:`Data: Input, Model Configuration, and Output Files <InputsOutputs>`.
 
-After downloading the dataset, continue to the :ref:`next section <RunNWA12EXP>` to run the NWA12 example. 
+After downloading the dataset, continue to the :ref:`next section <RunNWA12EXP>` to run the NWA12 example.
 
 .. _RunNWA12EXP:
 
 Run NWA12 Experiment
 =====================
 
-To run the NWA12 example, first navigate to the ``exps/NWA12.COBALT`` folder: 
+To run the NWA12 example, first navigate to the ``exps/NWA12.COBALT`` folder:
 
 .. code-block:: console
 
    cd ../exps/NWA12.COBALT
    cp ./../builds/build/YOUR_MACHINE_DIRECTORY-NAME_OF_YOUR_mk_FILE/ocean_ice/repro/MOM6SIS2 .
 
-Use the following command to run the NWA-12 example on Gaea using SLURM:   
+Use the following command to run the NWA-12 example on Gaea using SLURM:
 
 .. code-block:: console
 
    sbatch run.sub
 
-Users may need to modify the run script according to their HPC machine configurations. The default configuration uses 1646 CPU cores to run the NWA12 example. If users want to change it to their desired number of CPU cores (e.g., 20x20 = 400 cores), they can modify both ``MOM_layout`` and ``SIS_layout`` by removing the mask_table and editing the LAYOUT:   
+Users may need to modify the run script according to their HPC machine configurations. The default configuration uses 1646 CPU cores to run the NWA12 example. If users want to change it to their desired number of CPU cores (e.g., 20x20 = 400 cores), they can modify both ``MOM_layout`` and ``SIS_layout`` by removing the mask_table and editing the LAYOUT:
 
 .. code-block:: console
 
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -6,13 +6,13 @@
 ==============================================
 Welcome to CEFI-regional-MOM6's documentation!
 ==============================================
-**CEFI-regional-MOM6** contains essential tools, XML files, and source codes for collaborators of the Climate, Ecosystems, and Fisheries Initiative (CEFI) to conduct ocean physical-biogeochemical simulations for climate-scale applications, including seasonal predictions (12 months), decadal predictions (10 years), and multi-decadal projections (to the end of the 21st century). 
+**CEFI-regional-MOM6** contains essential tools, XML files, and source codes for collaborators of the Climate, Ecosystems, and Fisheries Initiative (CEFI) to conduct ocean physical-biogeochemical simulations for climate-scale applications, including seasonal predictions (12 months), decadal predictions (10 years), and multi-decadal projections (to the end of the 21st century).
 
 =============
-Code managers
+Contact Info
 =============
 
-* Yi-Cheng Teng - @yichengt900 / yi-cheng.teng@noaa.gov
+* oar.gfdl.cefi-support@noaa.gov
 
 .. toctree::
    :numbered:
diff --git a/tools/README.md b/tools/README.md
@@ -2,7 +2,7 @@
 
 This folder contains tools (mainly written in Python) that can be used to generate initial conditions (ICs), boundary conditions (BCs), and other required inputs for regional MOM6 model runs.
 
-Below we provide instruction for creating a Python virtual environment on NOAA R&D HPCs, specifically configured for the Gaea system. The process outlined here can generally be applied to other clusters within NOAA RDHPCs. The guide has been provided by Yi-Cheng Teng (Contact: yi-cheng.teng@noaa.gov).
+Below we provide instruction for creating a Python virtual environment on NOAA R&D HPCs, specifically configured for the Gaea system. The process outlined here can generally be applied to other clusters within NOAA RDHPCs. If you have any questions, please contact us at oar.gfdl.cefi-support AT noaa DOT gov
 
 ## Install Conda Environment on Gaea
 
