Scratch Partition and its directory structures

As mentioned in Chapter 6.1.1, the VM-SURF is divided into two partitions: the disk /dev/sda "mounted" at the root directory /, and the disk /dev/sdb "mounted" at /scratch. The scratch partition contains all the SURF packages and follows the directory structure illustrated in Figure B.1. The latest version of the release is structured as follows:

• The directory surf_install/ contains the utilities necessary to manage all the operations of creation and installation of each package of the SURF platform.
• The directory surf_datasets/ contains a list of static input datasets needed to run the SURF_NEMO package. With 'static' we mean here datasets which do not depend on the selected simulation period; i.e. bathymetry, coastline, parent meshmask, weight for remapping, meshmask and bathymetry remapped on the child grid.
• The directory surf_nemo/ contains the sources code of the SURF-NEMO package.
• The directory experiments/ contains all the experiments you have executed.

Below is a detailed description of the contents of these directories.

Fig. B.1 SURF package directories tree.

The surf_install Directory Structure

The SURF-INSTALL package is pre-installed in the SURF platform and is located in the directory /scratch/surf/surf_install. The folder surf_install_1.00 has the following structure:

• The folder scripts/ contains bash scripts to install (install.sh) and create (dorelease.sh) package releases.
• The ChangeLog.txt file documents all notable changes to the 'surf_install' package.
• The ReadMe.txt file provides an overview of the contents of the 'surf_install' package.
• The vertion.sh bash file displays the version number of the 'surf_install' package, shown in the upper-right corner of the VM desktop.

The surf_nemo Directory Structure

Once installed (see Section 6.2), the SURF-NEMO package is located in the directory /scratch/surf/surf_nemo/. The folder surf_nemo_1.00 has the following structure:

• The folder nemo/ contains the source code of the NEMO ocean model (v3.6).
• The folder scripts/ holds pre- and post-processing scripts required to run the relocatable SURF model.
• The folder utilities/ contains utility functions for specific pre-/post-processing tasks.
• The setParFree.json file is a template configuration file for case study experiments.
• The ChangeLog.txt file documents all notable changes to the 'surf_nemo' package.
• The ReadMe.txt file describes the contents of the 'surf_nemo' package.
• The Licence.txt file contains licensing information for the product.
• The vertion.sh bash file displays the version number of the 'surf_nemo' package, shown in the upper-right corner of the VM desktop.

The surf_datasets Directory Structure

Once installed (see Section 6.2), the SURF-DATASETS package is located in the directory /scratch/surf/surf_datasets. The folder surf_datasets_1.00 is structured as follows:

• The bathymetry/ folder contains the GEBCO Bathymetric datasets with 30 arc-second resolution.
• The coastline/ folder includes GSHHG coastline datasets, provided by NOAA’s National Geophysical Data Center (NGDC).
• The meshmask/ folder stores meshmask files for the parent ocean model and atmospheric sources.
• The experiments_regrid/ folder holds weight files for remapping ocean and atmospheric input data, along with meshmask and bathymetry files remapped onto the child grid. This is used when executing the SURF platform operationally.
• The ChangeLog.txt file documents all notable changes to the 'surf_datasets' package.
• The ReadMe.txt file describes the contents of the 'surf_datasets' package.
• The vertion.sh bash file shows the version number of the 'surf_datasets' package, displayed in the upper-right corner of the VM desktop.

The experiments directory

Once an experiment (e.g., expID) is executed, it is located in the directory /scratch/surf/experiments/. The folder expID has the following structure:

• A copy of the configuration file setParFree.json (from the directory surf/from_GUI/expID/).
• The code/ folder contains a copy of the source code (from surf/surf_nemo/current/) used for the simulation.
• The data/ folder stores all data used in the experiment:
  • Source input data (data/indata/),
  • Extrapolated data (data/extrapoldata/),
  • Regridded data (data/regriddata/),
  • Output data (data/outdata/).
  The input datasets are downloaded from local or web repositories for the selected simulation period.
• The figure/ folder contains plots of:
  • Source input data (figure/indata/),
  • Extrapolated data (figure/extrapoldata/),
  • Regridded data (figure/regriddata/),
  • Output data (figure/outdata/),
  • Comparisons between child and parent (coarse resolution) data.