Getting Started with MOM6: A Step-by-Step Guide for Running the Model on Ubuntu Linux

Introduction to MOM6

The Modular Ocean Model version 6 (MOM6) is a flexible and powerful ocean general circulation model widely used in the geosciences and oceanography. It provides advanced capabilities for simulating and studying various aspects of the ocean, including ocean currents, temperature, salinity, and biogeochemical processes. If you are interested in working with MOM6 on your Ubuntu Linux machine, this article will guide you through the process of getting started.

Before diving into the installation and configuration steps, it’s important to note that MOM6 is a complex model that requires a solid understanding of earth science principles and programming. Familiarity with the Linux command line and basic programming concepts will be beneficial to effectively work with MOM6.

Installation requirements

The first step in getting started with MOM6 is to install the necessary prerequisites on your Ubuntu Linux machine. MOM6 relies on several external libraries and tools to function properly. To install these prerequisites, open a terminal and follow the steps below:

1. Update your package list by running sudo apt update.
2. Install the required packages by running: sudo apt install gfortran netcdf-bin libnetcdf-dev libnetcdff-dev. This will install the GNU Fortran compiler, the NetCDF libraries and their development files.
3. Verify the installations by running nc-config –all. This should display the NetCDF configuration information without errors.

Once the prerequisites are installed, you can proceed to the next step of downloading and setting up MOM6 on your Ubuntu Linux machine.

Downloading and Setting Up MOM6

To download and set up MOM6 on your Ubuntu Linux machine, follow these steps

1. Open a terminal and navigate to the directory where you want to download MOM6.
2. Clone the MOM6 source code repository from GitHub by running the command: git clone https://github.com/NOAA-GFDL/MOM6. This will create a local copy of the MOM6 source code on your computer.
3. Navigate to the MOM6 directory by issuing the command: cd MOM6.
4. Configure the MOM6 build options by running the command: ./configure. This will prompt you to select the desired build options and paths. The default options should work for most users, but you can customize them to suit your specific needs.
5. Build MOM6 by issuing the command: make. This will compile the source code and generate the MOM6 executable.

Once the build process has completed successfully, you will have a working MOM6 installation on your Ubuntu Linux machine. The MOM6 executable will be located in the “MOM6/exec” directory within the MOM6 source directory.

Running MOM6 simulations

With MOM6 successfully installed on your Ubuntu Linux machine, you are now ready to start running ocean simulations. MOM6 provides a flexible framework for configuring and running simulations tailored to your specific research goals. To run a MOM6 simulation, follow these steps

1. Prepare the necessary input data for your simulation, including initial conditions, boundary conditions, and forcing data.
2. Create a run directory for your simulation and copy the necessary input data into it.
3. Edit the runtime configuration file, typically named “input.nml” or similar, to specify the simulation parameters and file paths.
4. Open a terminal, navigate to the run directory and start the MOM6 executable by executing the command ../exec/mom6.
5. Monitor the simulation progress and analyze the output data using appropriate post-processing tools and visualization software.

It’s important to note that running MOM6 simulations can be computationally intensive, especially for large and long-running simulations. It’s recommended to run MOM6 on a high performance computing (HPC) cluster or a machine with sufficient computing resources to ensure optimal performance.

FAQs

How do I start with Modular Ocean Model version 6 i.e. MOM6 on my Ubuntu Linux machine?

To start working with MOM6 on your Ubuntu Linux machine, you can follow these steps:

What are the system requirements for running MOM6 on Ubuntu Linux?

Before installing MOM6, ensure that your Ubuntu Linux machine meets the following system requirements:

• An x86-64 processor
• At least 4 GB of RAM (8 GB or more recommended)
• Several gigabytes of free disk space
• Ubuntu Linux 18.04 or a later version

What are the prerequisites for running MOM6 on Ubuntu Linux?

Prior to installing MOM6, you’ll need to have the following software installed on your Ubuntu Linux machine:

• Fortran compiler (e.g., gfortran)
• C compiler (e.g., gcc)
• NetCDF library and development files
• Python (optional, but recommended for post-processing)

You can install these dependencies using the package manager (e.g., apt-get) or by downloading them from their respective websites.

How do I download and install MOM6 on Ubuntu Linux?

Here are the steps to download and install MOM6 on your Ubuntu Linux machine:

1. Open a terminal on your Ubuntu Linux machine.
2. Clone the MOM6 source code repository from the official GitHub repository using the following command:

   git clone https://github.com/NOAA-GFDL/MOM6

3. Change into the MOM6 directory using the following command:

   cd MOM6

4. Build MOM6 by running the build script:

   ./MOM6/om/build.sh -j

5. Once the build is complete, you can proceed to configure and run MOM6 according to your specific needs. Detailed instructions can be found in the MOM6 documentation.

How do I run MOM6 on Ubuntu Linux?

After building MOM6, you can run it by following these steps:

1. Ensure that you are in the MOM6 directory.
2. Run the model using the provided run script:

   ./MOM6/examples/ice_ocean_SIS2/execute_this_program.py

3. The run script will execute the MOM6 model with the specified configuration. You can modify the configuration files according to your requirements.

Where can I find more documentation and resources for working with MOM6?

If you need more information about MOM6, you can refer to the official MOM6 documentation available on the GitHub repository. The documentation provides detailed instructions on building, configuring, and running MOM6. Additionally, you can join the MOM6 community forums or mailing lists to seek assistance and interact with other users.