Configuration files¶

Overview¶

There are several configuration files in ESMValCore:

config-user.yml: sets a number of user-specific options like desired graphical output format, root paths to data, etc.;
config-developer.yml: sets a number of standardized file-naming and paths to data formatting;
config-logging.yml: stores information on logging.

and one configuration file which is distributed with ESMValTool:

config-references.yml: stores information on diagnostic and recipe authors and scientific journals references;

User configuration file¶

The config-user.yml configuration file contains all the global level information needed by ESMValTool. It can be reused as many times the user needs to before changing any of the options stored in it. This file is essentially the gateway between the user and the machine-specific instructions to esmvaltool. By default, esmvaltool looks for it in the home directory, inside the .esmvaltool folder.

Users can get a copy of this file with default values by running

esmvaltool config get-config-user --path=${TARGET_FOLDER}

If the option --path is omitted, the file will be created in ${HOME}/.esmvaltool

The following shows the default settings from the config-user.yml file with explanations in a commented line above each option:

# Diagnostics create plots? [true]/false
# turning it off will turn off graphical output from diagnostic
write_plots: true

# Diagnostics write NetCDF files? [true]/false
# turning it off will turn off netCDF output from diagnostic
write_netcdf: true

# Set the console log level debug, [info], warning, error
# for much more information printed to screen set log_level: debug
log_level: info

# Exit on warning (only for NCL diagnostic scripts)? true/[false]
exit_on_warning: false

# Plot file format? [png]/pdf/ps/eps/epsi
output_file_type: png

# Destination directory where all output will be written
# including log files and performance stats
output_dir: ./esmvaltool_output

# Auxiliary data directory (used for some additional datasets)
# this is where e.g. files can be downloaded to by a download
# script embedded in the diagnostic
auxiliary_data_dir: ./auxiliary_data

# Use netCDF compression true/[false]
compress_netcdf: false

# Save intermediary cubes in the preprocessor true/[false]
# set to true will save the output cube from each preprocessing step
# these files are numbered according to the preprocessing order
save_intermediary_cubes: false

# Remove the preproc dir if all fine
# if this option is set to "true", ALL preprocessor files will be removed
# CAUTION when using: if you need those files, set it to false
remove_preproc_dir: true

# Run at most this many tasks in parallel [null]/1/2/3/4/..
# Set to null to use the number of available CPUs.
# If you run out of memory, try setting max_parallel_tasks to 1 and check the
# amount of memory you need for that by inspecting the file
# run/resource_usage.txt in the output directory. Using the number there you
# can increase the number of parallel tasks again to a reasonable number for
# the amount of memory available in your system.
max_parallel_tasks: null

# Path to custom config-developer file, to customise project configurations.
# See config-developer.yml for an example. Set to None to use the default
config_developer_file: null

# Use a profiling tool for the diagnostic run [false]/true
# A profiler tells you which functions in your code take most time to run.
# For this purpose we use vprof, see below for notes
# Only available for Python diagnostics
profile_diagnostic: false

# Rootpaths to the data from different projects (lists are also possible)
rootpath:
  CMIP5: [~/cmip5_inputpath1, ~/cmip5_inputpath2]
  OBS: ~/obs_inputpath
  default: ~/default_inputpath

# Directory structure for input data: [default]/BADC/DKRZ/ETHZ/etc
# See config-developer.yml for definitions.
drs:
  CMIP5: default

Most of these settings are fairly self-explanatory, e.g.:

# Diagnostics create plots? [true]/false
write_plots: true
# Diagnostics write NetCDF files? [true]/false
write_netcdf: true

The write_plots setting is used to inform ESMValTool diagnostics about your preference for creating figures. Similarly, the write_netcdf setting is a boolean which turns on or off the writing of netCDF files by the diagnostic scripts.

# Auxiliary data directory (used for some additional datasets)
auxiliary_data_dir: ~/auxiliary_data

The auxiliary_data_dir setting is the path to place any required additional auxiliary data files. This is necessary because certain Python toolkits, such as cartopy, will attempt to download data files at run time, typically geographic data files such as coastlines or land surface maps. This can fail if the machine does not have access to the wider internet. This location allows the user to specify where to find such files if they can not be downloaded at runtime.

Warning

This setting is not for model or observational datasets, rather it is for data files used in plotting such as coastline descriptions and so on.

The profile_diagnostic setting triggers profiling of Python diagnostics, this will tell you which functions in the diagnostic took most time to run. For this purpose we use vprof. For each diagnostic script in the recipe, the profiler writes a .json file that can be used to plot a flame graph of the profiling information by running

vprof --input-file esmvaltool_output/recipe_output/run/diagnostic/script/profile.json

Note that it is also possible to use vprof to understand other resources used while running the diagnostic, including execution time of different code blocks and memory usage.

A detailed explanation of the data finding-related sections of the config-user.yml (rootpath and drs) is presented in the Data retrieval section. This section relates directly to the data finding capabilities of ESMValTool and are very important to be understood by the user.

Note

You can choose your config-user.yml file at run time, so you could have several of them available with different purposes. One for a formalised run, another for debugging, etc. You can even provide any config user value as a run flag --argument_name argument_value

Developer configuration file¶

Most users and diagnostic developers will not need to change this file, but it may be useful to understand its content. It will be installed along with ESMValCore and can also be viewed on GitHub: esmvalcore/config-developer.yml. This configuration file describes the file system structure and CMOR tables for several key projects (CMIP6, CMIP5, obs4mips, OBS6, OBS) on several key machines (e.g. BADC, CP4CDS, DKRZ, ETHZ, SMHI, BSC). CMIP data is stored as part of the Earth System Grid Federation (ESGF) and the standards for file naming and paths to files are set out by CMOR and DRS. For a detailed description of these standards and their adoption in ESMValCore, we refer the user to CMIP data - CMOR Data Reference Syntax (DRS) and the ESGF section where we relate these standards to the data retrieval mechanism of the ESMValCore.

By default, esmvaltool looks for it in the home directory, inside the ‘.esmvaltool’ folder.

Users can get a copy of this file with default values by running

esmvaltool config get-config-developer --path=${TARGET_FOLDER}

If the option --path is omitted, the file will be created in `${HOME}/.esmvaltool.

Note

Remember to change your config-user file if you want to use a custom config-developer.

Example of the CMIP6 project configuration:

CMIP6:
  input_dir:
    default: '/'
    BADC: '{activity}/{institute}/{dataset}/{exp}/{ensemble}/{mip}/{short_name}/{grid}/{latestversion}'
    DKRZ: '{activity}/{institute}/{dataset}/{exp}/{ensemble}/{mip}/{short_name}/{grid}/{latestversion}'
    ETHZ: '{exp}/{mip}/{short_name}/{dataset}/{ensemble}/{grid}/'
  input_file: '{short_name}_{mip}_{dataset}_{exp}_{ensemble}_{grid}*.nc'
  output_file: '{project}_{dataset}_{mip}_{exp}_{ensemble}_{short_name}'
  cmor_type: 'CMIP6'
  cmor_strict: true

Input file paths¶

When looking for input files, the esmvaltool command provided by ESMValCore replaces the placeholders [item] in input_dir and input_file with the values supplied in the recipe. ESMValCore will try to automatically fill in the values for institute, frequency, and modeling_realm based on the information provided in the CMOR tables and/or config-developer.yml when reading the recipe. If this fails for some reason, these values can be provided in the recipe too.

The data directory structure of the CMIP projects is set up differently at each site. As an example, the CMIP6 directory path on BADC would be:

'{activity}/{institute}/{dataset}/{exp}/{ensemble}/{mip}/{short_name}/{grid}/{latestversion}'

The resulting directory path would look something like this:

CMIP/MOHC/HadGEM3-GC31-LL/historical/r1i1p1f3/Omon/tos/gn/latest

For a more in-depth description of how to configure ESMValCore so it can find your data please see CMIP data - CMOR Data Reference Syntax (DRS) and the ESGF.

Preprocessor output files¶

The filename to use for preprocessed data is configured in a similar manner using output_file. Note that the extension .nc (and if applicable, a start and end time) will automatically be appended to the filename.

CMOR table configuration¶

ESMValCore comes bundled with several CMOR tables, which are stored in the directory esmvalcore/cmor/tables. These are copies of the tables available from PCMDI.

There are four settings related to CMOR tables available:

cmor_type: can be CMIP5 if the CMOR table is in the same format as the CMIP5 table or CMIP6 if the table is in the same format as the CMIP6 table.
cmor_strict: if this is set to false, the CMOR table will be extended with variables from the esmvalcore/cmor/tables/custom directory and it is possible to use variables with a mip which is different from the MIP table in which they are defined.
cmor_path: path to the CMOR table. Defaults to the value provided in cmor_type written in lower case.
cmor_default_table_prefix: defaults to the value provided in cmor_type.

References configuration file¶

The config-references.yml file contains the list of ESMValTool diagnostic and recipe authors, references and projects. Each author, project and reference referred to in the documentation section of a recipe needs to be in this file in the relevant section.

For instance, the recipe recipe_ocean_example.yml file contains the following documentation section:

documentation:
  authors:
    - demo_le

  maintainer:
    - demo_le

  references:
    - demora2018gmd

  projects:
    - ukesm

These four items here are named people, references and projects listed in the config-references.yml file.

Logging configuration file¶

Warning

Section to be added