This lesson is being piloted (Beta version)

Configuration

Overview

Teaching: 10 min
Exercises: 10 min
Questions
  • What is the user configuration file and how should I use it?

Objectives
  • Understand the contents of the user-config.yml file

  • Prepare a personalized user-config.yml file

  • Configure ESMValTool to use some settings

The configuration file

For the purposes of this tutorial, we will create a directory in our home directory called esmvaltool_tutorial and use that as our working directory. The following steps should do that:

 mkdir esmvaltool_tutorial
 cd esmvaltool_tutorial

The config-user.yml configuration file contains all the global level information needed by ESMValTool to run. This is a YAML file.

You can get the default configuration file by running:

  esmvaltool config get_config_user --path=<target_dir>

The default configuration file will be downloaded to the directory specified with the --path variable. For instance, you can provide the path to your working directory as the target_dir. If this option is not used, the file will be saved to the default location: ~/.esmvaltool/config-user.yml, where ~ is the path to your home directory. Note that files and directories starting with a period are “hidden”, to see the .esmvaltool directory in the terminal use ls -la ~. Note that if a configuration file by that name already exists in the default location, the get_config_user command will not update the file as ESMValTool will not overwrite the file. You will have to move the file first if you want an updated copy of the user configuration file.

We run a text editor called nano to have a look inside the configuration file and then modify it if needed:

  nano ~/.esmvaltool/config-user.yml

This file contains the information for:

Text editor side note

No matter what editor you use, you will need to know where it searches for and saves files. If you start it from the shell, it will (probably) use your current working directory as its default location. We use nano in examples here because it is one of the least complex text editors. Press ctrl + O to save the file, and then ctrl + X to exit nano.

Output settings

The configuration file starts with output settings that inform ESMValTool about your preference for output. You can turn on or off the setting by true or false values. Most of these settings are fairly self-explanatory.

Saving preprocessed data

Later in this tutorial, we will want to look at the contents of the preproc folder. This folder contains preprocessed data and is removed by default when ESMValTool is run. In the configuration file, which settings can be modified to prevent this from happening?

Solution

If the option remove_preproc_dir is set to false, then the preproc/ directory contains all the pre-processed data and the metadata interface files. If the option save_intermediary_cubes is set to true then data will also be saved after each preprocessor step in the folder preproc. Note that saving all intermediate results to file will result in a considerable slowdown, and can quickly fill your disk.

Destination directory

The destination directory is the rootpath where ESMValTool will store its output folders containing e.g. figures, data, logs, etc. With every run, ESMValTool automatically generates a new output folder determined by recipe name, and date and time using the format: YYYYMMDD_HHMMSS.

Set the destination directory

Let’s name our destination directory esmvaltool_output in the working directory. ESMValTool should write the output to this path, so make sure you have the disk space to write output to this directory. How do we set this in the config-user.yml?

Solution

We use output_dir entry in the config-user.yml file as:

output_dir: ./esmvaltool_output

If the esmvaltool_output does not exist, ESMValTool will generate it for you.

Rootpath to input data

ESMValTool uses several categories (in ESMValTool, this is referred to as projects) for input data based on their source. The current categories in the configuration file are mentioned below. For example, CMIP is used for a dataset from the Climate Model Intercomparison Project whereas OBS may be used for an observational dataset. More information about the projects used in ESMValTool is available in the documentation. When using ESMValTool on your own machine, you can create a directory to download climate model data or observation data sets and let the tool use data from there. It is also possible to ask ESMValTool to download climate model data as needed. This can be done by specifying a download directory and by setting the option to download data as shown below.

# Directory for storing downloaded climate data
download_dir: ~/climate_data
offline: false

If you are working offline or do not want to download the data then set the option above to true.

The rootpath specifies the directories where ESMValTool will look for input data. For each category, you can define either one path or several paths as a list. For example:

rootpath:
  CMIP5: [~/cmip5_inputpath1, ~/cmip5_inputpath2]
  OBS: ~/obs_inputpath
  RAWOBS: ~/rawobs_inputpath
  default: ~/climate_data

These are typically available in the default configuration file you downloaded, so simply removing the machine specific lines should be sufficient to access input data.

Set the correct rootpath

In this tutorial, we will work with data from CMIP5 and CMIP6. How can we modify the rootpath to make sure the data path is set correctly for both CMIP5 and CMIP6? Note: to get the data, check the instructions in Setup.

Solution

  • Are you working on your own local machine? You need to add the root path of the folder where the data is available to the config-user.yml file as:
  rootpath:
  ...
    CMIP5: ~/esmvaltool_tutorial/data
    CMIP6: ~/esmvaltool_tutorial/data
  • Are you working on your local machine and have downloaded data using ESMValTool? You need to add the root path of the folder where the data has been downloaded to as specified in the download_dir.
rootpath:
...
  CMIP5: ~/climate_data
  CMIP6: ~/climate_data
  • Are you working on a computer cluster like Jasmin or DKRZ? Site-specific path to the data for JASMIN/DKRZ/ETH/IPSL are already listed at the end of the config-user.yml file. You need to uncomment the related lines. For example, on JASMIN:
auxiliary_data_dir: /gws/nopw/j04/esmeval/aux_data/AUX
rootpath: 
 CMIP6: /badc/cmip6/data/CMIP6
 CMIP5: /badc/cmip5/data/cmip5/output1
 OBS: /gws/nopw/j04/esmeval/obsdata-v2
 OBS6: /gws/nopw/j04/esmeval/obsdata-v2
 obs4MIPs: /gws/nopw/j04/esmeval/obsdata-v2
 ana4mips: /gws/nopw/j04/esmeval/obsdata-v2
 default: /gws/nopw/j04/esmeval/obsdata-v2
  • For more information about setting the rootpath, see also the ESMValTool documentation.

Directory structure for the data from different projects

Input data can be from various models, observations and reanalysis data that adhere to the CF/CMOR standard. The drs setting describes the file structure.

The drs setting describes the file structure for several projects (e.g. CMIP6, CMIP5, obs4mips, OBS6, OBS) on several key machines (e.g. BADC, CP4CDS, DKRZ, ETHZ, SMHI, BSC). For more information about drs, you can visit the ESMValTool documentation on Data Reference Syntax (DRS).

Set the correct drs

In this lesson, we will work with data from CMIP5 and CMIP6. How can we set the correct drs?

Solution

  • Are you working on your own local machine? You need to set the drs of the data in the config-user.yml file as:
    drs:
      CMIP5: default
      CMIP6: default
    
  • Are you asking ESMValTool to download the data for use with your diagnostics? You need to set the drs of the data in the config-user.yml file as:
     drs:
       CMIP5: ESGF
       CMIP6: ESGF
       CORDEX: ESGF
       obs4MIPs: ESGF
    
  • Are you working on a computer cluster like Jasmin or DKRZ? Site-specific drs of the data are already listed at the end of the config-user.yml file. You need to uncomment the related lines. For example, on Jasmin:
    # Site-specific entries: Jasmin
    # Uncomment the lines below to locate data on JASMIN
    drs:
      CMIP6: BADC
      CMIP5: BADC
      OBS: default
      OBS6: default
      obs4mips: default
      ana4mips: default
    

Explain the default drs (if working on local machine)

  1. In the previous exercise, we set the drs of CMIP5 data to default. Can you explain why?
  2. Have a look at the directory structure of the OBS data. There is a folder called Tier1. What does it mean?

Solution

  1. drs: default is one way to retrieve data from a ROOT directory that has no DRS-like structure. default indicates that all the files are in a folder without any structure.

  2. Observational data are organized in Tiers depending on their level of public availability. Therefore the default directory must be structured accordingly with sub-directories TierX e.g. Tier1, Tier2 or Tier3, even when drs: default. More details can be found in the documentation.

Other settings

Auxiliary data directory

The auxiliary_data_dir setting is the path where any required additional auxiliary data files are stored. This location allows us to tell the diagnostic script where to find the files if they can not be downloaded at runtime. This option should not be used for model or observational datasets, but for data files (e.g. shape files) used in plotting such as coastline descriptions and if you want to feed some additional data (e.g. shape files) to your recipe.

auxiliary_data_dir: ~/auxiliary_data

See more information in ESMValTool document.

Number of parallel tasks

This option enables you to perform parallel processing. You can choose the number of tasks in parallel as 1/2/3/4/… or you can set it to null. That tells ESMValTool to use the maximum number of available CPUs. For the purpose of the tutorial, please set ESMValTool use only 1 cpu:

max_parallel_tasks: 1

In general, if you run out of memory, try setting max_parallel_tasks to 1. Then, 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.

Make your own configuration file

It is possible to have several configuration files with different purposes, for example: config-user_formalised_runs.yml, config-user_debugging.yml. In this case, you have to pass the path of your own configuration file as a command-line option when running the ESMValTool. We will learn how to do this in the next lesson.

Key Points

  • The config-user.yml tells ESMValTool where to find input data.

  • output_dir defines the destination directory.

  • rootpath defines the root path of the data.

  • drs defines the directory structure of the data.