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;

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. If only certain values are allowed for an option, these are listed after ---. The option in square brackets is the default value, i.e., the one that is used if this option is omitted in the file.

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

# Auxiliary data directory
# Used by some recipes to look for additional datasets.
auxiliary_data_dir: ~/auxiliary_data

# Automatic data download from ESGF --- [never]/when_missing/always
# Use automatic download of missing CMIP3, CMIP5, CMIP6, CORDEX, and obs4MIPs
# data from ESGF. ``never`` disables this feature, which is useful if you are
# working on a computer without an internet connection, or if you have limited
# disk space. ``when_missing`` enables the automatic download for files that
# are not available locally. ``always`` will always check ESGF for the latest
# version of a file, and will only use local files if they correspond to that
# latest version.
search_esgf: never

# Directory for storing downloaded climate data
# Make sure to use a directory where you can store multiple GBs of data. Your
# home directory on a HPC is usually not suited for this purpose, so please
# change the default value in this case!
download_dir: ~/climate_data

# Rootpaths to the data from different projects
# This default setting will work if files have been downloaded by ESMValTool
# via ``search_esgf``. Lists are also possible. For site-specific entries,
# see the default ``config-user.yml`` file that can be installed with the
# command ``esmvaltool config get_config_user``. For each project, this can
# be either a single path or a list of paths. Comment out these when using a
# site-specific path.
rootpath:
  default: ~/climate_data

# Directory structure for input data --- [default]/ESGF/BADC/DKRZ/ETHZ/etc.
# This default setting will work if files have been downloaded by ESMValTool
# via ``search_esgf``. See ``config-developer.yml`` for definitions. Comment
# out/replace as per needed.
drs:
  CMIP3: ESGF
  CMIP5: ESGF
  CMIP6: ESGF
  CORDEX: ESGF
  obs4MIPs: ESGF

# 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

# Log level of the console --- debug/[info]/warning/error
# For much more information printed to screen set log_level to ``debug``.
log_level: info

# Exit on warning --- true/[false]
# Only used in NCL diagnostic scripts.
exit_on_warning: false

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

# Remove the ``preproc`` directory if the run was successful --- [true]/false
# By default this option is set to ``true``, so all preprocessor output files
# will be removed after a successful run. Set to ``false`` if you need those files.
remove_preproc_dir: true

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

# Save intermediary cubes in the preprocessor --- true/[false]
# Setting this to ``true`` will save the output cube from each preprocessing
# step. These files are numbered according to the preprocessing order.
save_intermediary_cubes: false

# 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

# Path to custom ``config-developer.yml`` file
# This can be used to customise project configurations. See
# ``config-developer.yml`` for an example. Set to ``null`` to use the default.
config_developer_file: null

The search_esgf setting can be used to disable or enable automatic downloads from ESGF. If search_esgf is set to never, the tool does not download any data from the ESGF. If search_esgf is set to when_missing, the tool will download any CMIP3, CMIP5, CMIP6, CORDEX, and obs4MIPs data that is required to run a recipe but not available locally and store it in download_dir using the ESGF directory structure defined in the Developer configuration file. If search_esgf is set to always, the tool will first check the ESGF for the needed data, regardless of any local data availability; if the data found on ESGF is newer than the local data (if any) or the user specifies a version of the data that is available only from the ESGF, then that data will be downloaded; otherwise, local data will be used.

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. The example user configuration file already contains two valid locations for auxiliary_data_dir directories on CEDA-JASMIN and DKRZ, and a number of such maps and shapefiles (used by current diagnostics) are already there. You will need esmeval group workspace membership to access the JASMIN one (see instructions how to gain access to the group workspace.

Warning

This setting is not for model or observational datasets, rather it is for extra data files such as shapefiles or other data sources needed by the diagnostics.

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

ESGF configuration#

The esmvaltool run command can automatically download the files required to run a recipe from ESGF for the projects CMIP3, CMIP5, CMIP6, CORDEX, and obs4MIPs. The downloaded files will be stored in the download_dir specified in the User configuration file. To enable automatic downloads from ESGF, set search_esgf: when_missing or search_esgf: always in the User configuration file, or provide the corresponding command line arguments --search_esgf=when_missing or --search_esgf=always when running the recipe.

Note

When running a recipe that uses many or large datasets on a machine that does not have any data available locally, the amount of data that will be downloaded can be in the range of a few hundred gigabyte to a few terrabyte. See Obtaining input data for advice on getting access to machines with large datasets already available.

A log message will be displayed with the total amount of data that will be downloaded before starting the download. If you see that this is more than you would like to download, stop the tool by pressing the Ctrl and C keys on your keyboard simultaneously several times, edit the recipe so it contains fewer datasets and try again.

For downloading some files (e.g. those produced by the CORDEX project), you need to log in to be able to download the data.

See the ESGF user guide for instructions on how to create an ESGF OpenID account if you do not have one yet. Note that the OpenID account consists of 3 components instead of the usual two, in addition a username and password you also need the hostname of the provider of the ID; for example esgf-data.dkrz.de. Even though the account is issued by a particular host, the same OpenID account can be used to download data from all hosts in the ESGF.

Next, configure your system so the esmvaltool can use your credentials. This can be done using the keyring package or they can be stored in a configuration file.

Storing credentials in keyring#

First install the keyring package. Note that this requires a supported backend that may not be available on compute clusters, see the keyring documentation for more information.

pip install keyring

Next, set your username and password by running the commands:

keyring set ESGF hostname
keyring set ESGF username
keyring set ESGF password

for example, if you created an account on the host esgf-data.dkrz.de with username ‘cookiemonster’ and password ‘Welcome01’, run the command

keyring set ESGF hostname

this will display the text

Password for 'hostname' in 'ESGF':

type esgf-data.dkrz.de (the characters will not be shown) and press Enter. Repeat the same procedure with keyring set ESGF username, type cookiemonster and press Enter and keyring set ESGF password, type Welcome01 and press Enter.

To check that you entered your credentials correctly, run:

keyring get ESGF hostname
keyring get ESGF username
keyring get ESGF password

Configuration file#

An optional configuration file can be created for configuring how the tool uses esgf-pyclient to find and download data. The name of this file is ~/.esmvaltool/esgf-pyclient.yml.

Logon#

In the logon section you can provide arguments that will be passed on to pyesgf.logon.LogonManager.logon(). For example, you can store the hostname, username, and password or your OpenID account in the file like this:

logon:
  hostname: "your-hostname"
  username: "your-username"
  password: "your-password"

for example

logon:
  hostname: "esgf-data.dkrz.de"
  username: "cookiemonster"
  password: "Welcome01"

if you created an account on the host esgf-data.dkrz.de with username ‘cookiemonster’ and password ‘Welcome01’. Alternatively, you can configure an interactive log in:

logon:
  interactive: true

Note that storing your password in plain text in the configuration file is less secure. On shared systems, make sure the permissions of the file are set so only you and administrators can read it, i.e.

ls -l ~/.esmvaltool/esgf-pyclient.yml

shows permissions -rw-------.

Search#

Any arguments to pyesgf.search.connection.SearchConnection can be provided in the section search_connection, for example:

search_connection:
  expire_after: 2592000  # the number of seconds in a month

to keep cached search results for a month.

The default settings are:

urls:
  - 'https://esgf.ceda.ac.uk/esg-search'
  - 'https://esgf-node.llnl.gov/esg-search'
  - 'https://esgf-data.dkrz.de/esg-search'
  - 'https://esgf-node.ipsl.upmc.fr/esg-search'
  - 'https://esg-dn1.nsc.liu.se/esg-search'
  - 'https://esgf.nci.org.au/esg-search'
  - 'https://esgf.nccs.nasa.gov/esg-search'
  - 'https://esgdata.gfdl.noaa.gov/esg-search'
distrib: true
timeout: 120  # seconds
cache: '~/.esmvaltool/cache/pyesgf-search-results'
expire_after: 86400  # cache expires after 1 day

Note that by default the tool will try the ESGF index nodes in the order provided in the configuration file and use the first one that is online. Some ESGF index nodes may return search results faster than others, so you may be able to speed up the search for files by experimenting with placing different index nodes at the top of the list.

If you experience errors while searching, it sometimes helps to delete the cached results.

Download statistics#

The tool will maintain statistics of how fast data can be downloaded from what host in the file ~/.esmvaltool/cache/esgf-hosts.yml and automatically select hosts that are faster. There is no need to manually edit this file, though it can be useful to delete it if you move your computer to a location that is very different from the place where you previously downloaded data. An entry in the file might look like this:

esgf2.dkrz.de:
  duration (s): 8
  error: false
  size (bytes): 69067460
  speed (MB/s): 7.9

The tool only uses the duration and size to determine the download speed, the speed shown in the file is not used. If error is set to true, the most recent download request to that host failed and the tool will automatically try this host only as a last resort.

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), and for native output data for some models (ICON, IPSL, … see Configuring datasets in native format). 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 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}/{version}'
    DKRZ: '{activity}/{institute}/{dataset}/{exp}/{ensemble}/{mip}/{short_name}/{grid}/{version}'
    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 extra_facets 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}/{version}'

The resulting directory path would look something like this:

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

Please, bear in mind that input_dirs can also be a list for those cases in which may be needed:

- '{exp}/{ensemble}/original/{mip}/{short_name}/{grid}/{version}'
- '{exp}/{ensemble}/computed/{mip}/{short_name}/{grid}/{version}'

In that case, the resultant directories will be:

historical/r1i1p1f3/original/Omon/tos/gn/latest
historical/r1i1p1f3/computed/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.

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.

Project 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.

For every project that can be used in the recipe, there are four settings related to CMOR table settings 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 Custom CMOR tables (by default loaded 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. Relative paths are with respect to esmvalcore/cmor/tables. Defaults to the value provided in cmor_type written in lower case.
cmor_default_table_prefix: Prefix that needs to be added to the mip to get the name of the file containing the mip table. Defaults to the value provided in cmor_type.

Custom CMOR tables#

As mentioned in the previous section, the CMOR tables of projects that use cmor_strict: false will be extended with custom CMOR tables. By default, these are loaded from esmvalcore/cmor/tables/custom. However, by using the special project custom in the config-developer.yml file with the option cmor_path, a custom location for these custom CMOR tables can be specified:

custom:
  cmor_path: ~/my/own/custom_tables

This path can be given as relative path (relative to esmvalcore/cmor/tables) or as absolute path. Other options given for this special table will be ignored.

Custom tables in this directory need to follow the naming convention CMOR_{short_name}.dat and need to be given in CMIP5 format.

Example for the file CMOR_asr.dat:

SOURCE: CMIP5
!============
variable_entry:    asr
!============
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:
units:             W m-2
cell_methods:      time: mean
cell_measures:     area: areacella
long_name:         Absorbed shortwave radiation
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time
type:              real
positive:          down
!----------------------------------
!

It is also possible to use a special coordinates file CMOR_coordinates.dat. If this is not present in the custom directory, the one from the default directory (esmvalcore/cmor/tables/custom/CMOR_coordinates.dat) is used.

Filter preprocessor warnings#

It is possible to ignore specific warnings of the preprocessor for a given project. This is particularly useful for native datasets which do not follow the CMOR standard by default and consequently produce a lot of warnings when handled by Iris. This can be configured in the config-developer.yml file for some steps of the preprocessing chain.

Currently supported preprocessor steps:

load()

Here is an example on how to ignore specific warnings during the preprocessor step load for all datasets of project EMAC (taken from the default config-developer.yml file):

ignore_warnings:
  load:
    - {message: 'Missing CF-netCDF formula term variable .*, referenced by netCDF variable .*', module: iris}
    - {message: 'Ignored formula of unrecognised type: .*', module: iris}

The keyword arguments specified in the list items are directly passed to warnings.filterwarnings() in addition to action=ignore (may be overwritten in config-developer.yml).

Configuring datasets in native format#

ESMValCore can be configured for handling native model output formats and specific reanalysis/observation datasets without preliminary reformatting. These datasets can be either hosted under the native6 project (mostly native reanalysis/observational datasets) or under a dedicated project, e.g., ICON (mostly native models).

Example:

native6:
  cmor_strict: false
  input_dir:
    default: 'Tier{tier}/{dataset}/{version}/{frequency}/{short_name}'
  input_file:
    default: '*.nc'
  output_file: '{project}_{dataset}_{type}_{version}_{mip}_{short_name}'
  cmor_type: 'CMIP6'
  cmor_default_table_prefix: 'CMIP6_'

ICON:
  cmor_strict: false
  input_dir:
    default:
      - '{exp}'
      - '{exp}/outdata'
  input_file:
    default: '{exp}_{var_type}*.nc'
  output_file: '{project}_{dataset}_{exp}_{var_type}_{mip}_{short_name}'
  cmor_type: 'CMIP6'
  cmor_default_table_prefix: 'CMIP6_'

A detailed description on how to add support for further native datasets is given here.

Hint

When using native datasets, it might be helpful to specify a custom location for the Custom CMOR tables. This allows reading arbitrary variables from native datasets. Note that this requires the option cmor_strict: false in the project configuration used for the native model output.

References configuration file#

The esmvaltool/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.

Extra Facets#

It can be useful to automatically add extra key-value pairs to variables or datasets in the recipe. These key-value pairs can be used for finding data or for providing extra information to the functions that fix data before passing it on to the preprocessor.

To support this, we provide the extra facets facilities. Facets are the key-value pairs described in Recipe section: datasets. Extra facets allows for the addition of more details per project, dataset, mip table, and variable name.

More precisely, one can provide this information in an extra yaml file, named {project}-something.yml, where {project} corresponds to the project as used by ESMValTool in Recipe section: datasets and “something” is arbitrary.

Format of the extra facets files#

The extra facets are given in a yaml file, whose file name identifies the project. Inside the file there is a hierarchy of nested dictionaries with the following levels. At the top there is the dataset facet, followed by the mip table, and finally the short_name. The leaf dictionary placed here gives the extra facets that will be made available to data finder and the fix infrastructure. The following example illustrates the concept.

Listing 1 Extra facet example file native6-era5.yml#

ERA5:
  Amon:
    tas: {source_var_name: "t2m", cds_var_name: "2m_temperature"}

The three levels of keys in this mapping can contain Unix shell-style wildcards. The special characters used in shell-style wildcards are:

Pattern	Meaning
`*`	matches everything
`?`	matches any single character
`[seq]`	matches any character in `seq`
`[!seq]`	matches any character not in `seq`

where seq can either be a sequence of characters or just a bunch of characters, for example [A-C] matches the characters A, B, and C, while [AC] matches the characters A and C.

For example, this is used to automatically add product: output1 to any variable of any CMIP5 dataset that does not have a product key yet:

Listing 2 Extra facet example file cmip5-product.yml#

'*':
  '*':
    '*': {product: output1}

Configuration files#

Overview#

User configuration file#

ESGF configuration#

Storing credentials in keyring#

Configuration file#

Logon#

Search#

Download statistics#

Developer configuration file#

Input file paths#

Preprocessor output files#

Project CMOR table configuration#

Custom CMOR tables#

Filter preprocessor warnings#

Configuring datasets in native format#

References configuration file#

Extra Facets#

Format of the extra facets files#

Location of the extra facets files#

Use of extra facets#