This guide explains how to run the MITgcm ocean plastic model. The example used in this guide is located at `/data3/home/xlwang/MITgcm/verification/global_microp_igsm` and is based on personal understanding of the model.
Contents:
1. Introduction
2. Research Overview
3. Code Overview
4. Build
5. Code
6. Run
7. Running Tutorial
—
1. Introduction
This guide is based on the code found at `/data3/home/xlwang/MITgcm/verification/global_microp_igsm`. The instructions are designed to explain how to simulate the spatial and temporal evolution of global ocean plastic from 1950 to 2018.
—
2. Research Overview
The model simulates the distribution and movement of ocean plastics over time, from 1950 to 2018.
—
3. Code Overview
In your working directory, the important folders include `build`, `code`, and `run`, which are described below:
—
4. Build
The `build` directory contains the compiled code. Relevant code files are located in the `pkg` directory (path: `/data3/home/xlwang/MITgcm/pkg`) and in the `code` directory. Most of the code related to ocean plastic simulation is located in `code`.
—
5. Code
Some key files that may require modification during the research process include:
– Header Files (Global Variables):
– `PTRACERS_SIZE.h`: Sets the number of plastic tracers.
– `SIZE.h`: Configures the number of CPU cores for running the model. The values `nPx * nPy` set the number of cores, while `sNx * nPx = 144` and `sNy * nPy = 90` configure the grid resolution.
– Run Code Files:
– `Microp_fields_load.F`: Reads plastic input data and environmental variables.
– `Microp_forcing.F`: Distributes input plastics by particle size.
– `Microp_surfforcing*.F`: Calculates the surface concentration of plastics in the ocean.
– `Microp_readparms.F`: Initializes and reads the plastic parameter settings.
– `Microp_process.F`: Main program defining plastic tracers, including density and radius.
– `Microp_p_beaching.F`: Simulates plastic beaching.
– `Microp_p_biofouling.F`: Simulates biofouling on plastics.
– `Microp_p_degradablement.F`: Simulates plastic degradation.
– `Microp_p_sediment.F`: Simulates the sinking of plastics.
—
6. Run
– Key Files for Running the Model:
– `data.ptracer` and `data.diagnostics*`: Describe the attributes of plastic tracers.
– `data.microp`: Provides file paths and parameter settings for input data.
– `data`: Sets the model’s time steps and other parameters.
– `run.microp`: This file is used for running the model. You must specify the run file, the available server nodes, and the number of nodes to use before starting the simulation.
– The `diags` folder contains the model’s output data, including beached plastics, etc.
– The `input*` folder contains input data needed by the model.
—
7. Running Tutorial
1. Create a Working Directory:
First, copy all the necessary files into your working directory:
cp -r /data3/home/xlwang/MITgcm ./
2. Set Alias for Compilation:
In your `.bashrc` file, set up an alias for the `premake` command:
alias premake='../../../tools/genmake2 -mpi -mods=../code -optfile=../../../tools/build_options/linux_ifort_impi'
3. Source Code Compilation:
Navigate to the `build` directory:
cd ~/MITgcm/verification/global_microp_igsm/build
In the `build` folder, run the following commands:
premake
4. Compile and Link:
Once the build files are generated, use these commands to compile the model:
make depend make
After compilation, copy the executable file to the `run` folder:
cp ./mitgcmuv ../run/mitgcmuv
5. Run the Model:
Navigate to the `run` directory and submit the job:
cd ~/MITgcm/verification/global_microp_igsm/run bsub <run.microp
This will start the simulation for the ocean plastic model.
Recent Comments