This is an old revision of the document!
Set of bash functions called through the ocean_pp.bash script allowing the user to perform a series of diagnostics.
The bash script ocean_pp.bash performs diagnostics on monthly or daily ocean model outputs. It relies on a set of functions included in common_ocean_post.txt that can also be used within the Ec-Earth and NEMO post templates when using autosubmit. Many of the functions included in common_ocean_post.txt have been built based on Hui Du's post-processing scripts.
The outputs of ocean_pp.bash are of 3 types :
If you post-process daily or monthly means the output directory is daily_mean or monthly_mean.
Some more specifications:
ocean_pp.bash handles any range of leadtimes instead of complete years only. However, the max_moc diagnostic can not be computed if you do not have complete years since it is a diagnostic computed from annual means.
ocean_pp.bash also post-processes daily means, instead of only monthly means. You only need to specify as output directory daily_mean instead of monthly_mean because the number of time steps and dates are read from the output. It has been tested with NEMO only simulations but this required some changes in the NEMO templates so that some changes in the EcEarth templates might be needed also before using this option for EcEarth simulations.
This package needs cdftools 2.1, cdo and nco.
To perform the postprocessing of the files, you must run ./ocean_pp.bash with a configuration file (config_file-ocean_pp.bash) available in the git project. Through this configuration file, you can specify which diagnostics you want to run, which variables to extract, the dates and members, etc… Everything is detailed in the configuration file.
If “default” option is specified, it will treat only a set of variables (sosstsst, sosaline and somxl010 for ocean, isnowthi, iicethic, ileadfra, iicetemp, ice_pres for sea ice). If nothing is specified, it will extract all the 2D variables present in the input files. Otherwise, it will treat exclusively the variables listed.
A README file describes the various diagnostics which are available as options through the listpost argument.
The link to the GIT repository is https://earth.bsc.es/gitlab/es/ocean_diagnostics.git
The coordinator of this project are Pierre-Antoine Bretonnière firstname.lastname@example.org and Javier Vegas email@example.com. In case of bugs, you can also ask Virginie Guemas firstname.lastname@example.org.
If you want to include a new diagnostic. Look for the @ signs in the common_ocean_post.txt then ocean_pp.bash and you'll find the locations where you have to include lines of code and some additional instructions so that everything works fine. Feel free to ask if something is not clear. To facilitate testing of new functions or of new options in existing functions, you can use the script named setup_development_oriol.bash in any working directory.
If you want to make available the post-processing tools for new grids, you need to choose a flag for this new grid (such as Ec2.3_O1L42), and then prepare all the configuration files such as done here : /esnas/autosubmit/con_files/ for example for any other flags. Namely you need to prepare the files :
Download the repository folder to your computer ( git clone https://earth.bsc.es/gitlab/es/ocean_diagnostics.git <local_folder> ) and check-out to the branch you want to develop in. You can find GIT help here: https://earth.bsc.es/wiki/doku.php?id=library:git
See the following page to check the current branching scheme used within the GIT project 'Ocean postprocessing': Git branching scheme
You can check the style guide for the ocean_diagnostics package here