Scratch Partition and its directory structures

As shown in chapter 6.1.1 the VM surf is divided into two partitions: the disk /dev/sda "mounted" in the root directory / and the disk /dev/sdb "mounted" in the directory /scratch. The scratch partition contains all the SURF packages and follows the directory structure as shown in figure B.1: The up-to-date version release is structured as follow:

• 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.

We describe here 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 it is located in the directory /scratch/surf/surf_install. The folder surf_install_1.00 has the directory structure as in figure B.1:

• The folder scripts/ containing the bash scripts to install (install.sh) and to create (dorelease.sh) packages release.
• The text file ChangeLog.txt containing documentation of all notable changes to the 'surf_install' package.
• The text file ReadMe.txt describing of the contents of the 'surf_install' package.
• The bash file vertion.sh containing the version number of the 'surf_install' package. This number is displayed in the upper-right corner of 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 directory structure as in figure B.1:

• The folder nemo/ contains the source code of the NEMO ocean model (v3.6).
• The folder scripts/ contains the scripts for the pre- and post-processing needed to execute the relocatable SURF model.
• The folder utilities/ contains the source code of several utility functions used for specific tasks in the pre-/post-processing.
• The json file setParFree.json of the template configuration file for the case study experiment.
• The text file ChangeLog.txt containing the documentation of all notable changes to the 'surf_nemo' package.
• The text file ReadMe.txt describing of the contents of the 'surf_nemo' package.
• The text file Licence.txt containing the product licensing information.
• The bash file vertion.sh containing the version number of the 'surf_nemo' package. This number is displayed in the upper-right corner of VM desktop.

The surf_datasets directory structure

Once installed (see section xx), the SURF-DATASETS package is located in the directory /scratch/surf/surf_datasets. The folder surf_datasets_1.00 has the directory structure as in figure B.1:

• The folder bathymetry/ contains the GEBCO Bathymetric datasets at 30 arc seconds resolution.
• The folder coastline/ contains the GSHHG coastline datasets provided by the NOAA National Geophysical Data Center (NGDC).
• The folder meshmask/ contains the meshmask files of the parent ocean model and atmosphere source.
• The folder experiments_regrid/ used when you want execute the SURF platform operationally. It contains the weight files for remapping ocean and atmospheric input data, the meshmask and bathymetry remapped on the child grid.
• The text file ChangeLog.txt containing the documentation of all notable changes to the 'surf_datasets' package.
• The text file ReadMe.txt describing of the contents of the 'surf_datasets' package.
• The bash file vertion.sh containing the version number of the 'surf_datasets' package. This number is displayed in the upper-right corner of VM desktop.

The experiments directory

Once the experiment is executed (i.e. expID), it is located in the directory /scratch/surf/experiments/. The folder expID has the directory structure as in figure B.1:

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