1. Downloads

The following recipes allow users to download CBIOMES-global model output (Section 1.1), tools to manipulate this output (Section 1.2), and the CBIOMES-global model setup (Section 1.3).

1.1. Output

The CBIOMES-global (alpha version) monthly climatology has been interpolated to a \(1/2\times1/2^\circ\) grid (see Interpolate Output) and converted to Netcdf files (see Convert to Netcdf) that can readily be visualized using any Netcdf-enabled software (e.g., Panoply under Windows, Linux, or macOS).

The climatology folder is currently accessed via dropbox. It contains additional documentation – e.g., the solution booklet that extensively depicts CBIOMES-global (alpha version) – and native grid output that allows for accurate computational analyses (see Section 1.2 and Section 2.3).

Note

Please contact us to get access to the dropbox folders – they are not publicly available yet.

1.2. Tools

Accurate computational workflows often require native grid output rather than interpolated output. Manipulation of native grid output, which users may have either downloaded (Section 1.1) or generated themselves (Section 2.2), is facilitated by the gcmfaces toolbox [FCH+15]. This toolbox is available for Matlab (proprietary) and Octave (free); it can be downloaded as follows:

git clone -b nctilesdev https://github.com/gaelforget/gcmfaces

The Section 2.1 and Section 2.3 applications rely on gcmfaces along with CBIOMES-specific codes which can in turn be downloaded as follows:

git clone https://github.com/darwinproject/CBIOMES-Processing.m CBIOMES-tools
git clone https://github.com/gaelforget/CBIOMES CBIOMES-setup

Note

The nctilesdev and Octave branches should soon get merged into the Master branch.

1.3. Model

The Section 2.2 recipes to Compile And Run the ocean model allow users to reproduce CBIOMES-global solutions. This requires the ocean model Code, Setup, And Input (surface boundary conditions, initial conditions, grid, etc.). Provided scripts, dowload_setup.sh and dowload_input.sh, download these various elements along with the Section 1.2 tools and organize directories as expected by the Section 2.2 recipes (Recommended Directory Organization).

Code, Setup, And Input

git clone https://github.com/gaelforget/CBIOMES CBIOMES-setup
bash ./CBIOMES-setup/tools/shell/download_setup.sh
bash ./CBIOMES-setup/tools/shell/download_input.sh

Recommended Directory Organization

MITgcm/
  model/   (MITgcm core code)
  pkg/
    gud/   (bgc + ecosystem modules)
    + other subdirectories
  mysetups/
    CBIOMES/
      code/                 (compile-time settings)
      input/                (run-time settings)
      tools/                (shell and other scripts)
      inputs_drwn3/         (binary model input)
      forcing_baseline2/    (binary model input)
      inputs_baseline2/     (binary model input)
      + other subdirectories
  tools/
    genmake2        (makefile generation script)
    build_options   (various compiler options)
    + other subdirectories
  + other subdirectories

Note

inputs_drwn3/ is not currently installed by dowload_input.sh even though it is needed for the biochemistry and ecology. Please contact us to get access to the corresponding dropbox folder and place its content as shown in Recommended Directory Organization.