ESM Runscripts

Running a Model/Setup

ESM-Runscripts is the ESM-Tools package that allows the user to run the experiments. ESM-Runscripts reads the runscript (either a bash or yaml file), applies the required changes to the namelists and configuration files, submits the runs of the experiment to the compute nodes, and handles and organizes restart, output and log files. The command to run a runscript is:

esm_runscripts <runscript.yaml/.run> -e <experiment_ID>

The runscript.yaml/.run should contain all the information regarding the experiment paths, and particular configurations of the experiment (see the Runscripts section for more information about the syntax of yaml runscripts). The experiment_ID is used to identify the experiment in the scheduler and to name the experiment’s directory (see Experiment Directory Structure).

ESM-Runscript allows to run an experiment check by adding the -c flag to the previous command. This check performs all the system operations related to the experiment that would take place on a normal run (creates the experiment directory and subdirectories, copies the binaries and the necessary restart/forcing files, edits the namelists, …) but stops before submitting the run to the compute nodes. We strongly recommend running first a check before submitting an experiment to the compute nodes, as the check outputs contains already valuable information to understand whether the experiment will work correctly or not (we strongly encourage users to pay particular attention to the Namelists and the Missing files sections of the check’s output).

Job Phases

The following table summarizes the job phases of ESM-Runscripts and gives a brief description. …

Running only part of a job

It’s possible to run only part of a job. This is particularly interesting for development work; when you might only want to test a specific phase without having to run a whole simulation.

As an example; let’s say you only want to run the tidy phase of a particular job; which will move things from the particular run folder to the overall experiment tree. In this example; the experiment will be called test001:

$ esm_runscripts ${PATH_TO_USER_CONFIG} -t tidy_and_resubmit

Experiment Directory Structure

All the files related to a given experiment are saved in the Experiment Directory. This includes among others model binaries, libraries, namelists, configuration files, outputs, restarts, etc. The idea behind this approach is that all the necessary files for running an experiment are contained in this folder (the user can always control through the runscript or configuration files whether the large forcing and mesh files also go into this folder), so that the experiment can be reproduced again, for example, even if there were changes into one of the model’s binaries or in the original runscript.

The path of the Experiment Directory is composed by the general.base_dir path specified in the runscript (see Runscripts syntax) followed by the given experiment_ID during the esm_runscripts call:


The main experiment folder contains the subfolders indicated in the table below. Each of these subfolders contains a folder for each component in the experiment (i.e. for an AWI-CM experiment the outdata folder will contain the subfolders echam, fesom, hdmodel, jsbach, oasis3mct).

Subfolder Files Description
analysis user’s files Results of user’s “by-hand” analysis can be placed here.
bin component binaries Model binaries needed for the experiment.
  • <experiment_ID>_ finished_config.yaml
  • namelists
  • other configuration files
Configuration files for the experiment including namelists and other files specified in the component’s configuration files (<PATH>/esm_tools/configs/<component>/<component>.yaml, see File Dictionaries). The file <experiment_ID>_finished_config.yaml is located at the base of the config folder and contains the whole ESM-Tools variable space for the experiment, resulting from combining the variables of the runscript, setup and component configuration files, and the machine environment file.
couple coupling related files Necessary files for model couplings.
forcing forcing files Forcing files for the experiment. Only copied here when specified by the user in the runscript or in the configuration files (File Dictionaries).
input input files Input files for the experiment. Only copied here when specified by the user in the runscript or in the configuration files (File Dictionaries).
  • <experiment_ID>_ <setup_name>.log
  • component log files
Experiment log files. The component specific log files are placed in their respective subfolder. The general log file <experiment_ID>_<setup_name>.log reports on the ESM-Runscripts Job Phases and is located at the base of the log folder. Log file names and copying instructions should be included in the configuration files of components (File Dictionaries).
mon user’s files Monitoring scripts created by the user can be placed here.
outdata outdata files Outdata files are placed here. Outdata file names and copying instructions should be included in the configuration files of components (File Dictionaries).
restart restart files Restart files are placed here. Restart file names and copying instructions should be included in the configuration files of components (File Dictionaries).
run_YYYYMMDD-YYYYMMDD run files Run folder containing all the files for a given run. Folders contained here have the same names as the ones contained in the general experiment folder (analysis, bin, config, etc). Once the run is finished files the run files are copied to the general experiment folder.
  • esm_tools folder containing:

    • all namelists
    • all functions
  • <experiment_ID>_ compute_YYYYMMDD- YYYYMMDD.sad>

  • <experiment_ID>_ compute_YYYYMMDD- YYYYMMDD_<JobID>.log

  • <experiment_ID>_ <setup_name>.date

  • original runscript

  • file.log

  • hostfile_srun

Contains all the scripts needed for the experiment. A subfolder esm_tools includes all the config files and namelists of ESM-Tools (a copy of the configs and namelists folders in the esm_tools installation folder). It also contains the .sad files to be submitted to slurm. The file <experiment_ID>_compute_YYYYMMDD_YYYYMMDD_<JobID>.log is the log file for the experiment run. The <experiment_ID>_<setup_name>.date indicates the finishing date of the last run.
unknown   Folder where all the unknown files should be copied.
viz user’s files Aimed for user’s visualization scripts.
  • component files
  • output files before copied to the output folder
  • restart files before copied to the restart folder
The work folder inside the run_YYYYMMDD_YYYYMMDD folder is the main directory where the components are executed. Output and restart files are generated here before being copied to their respective folders.

If one file was to be copied in a directory containing a file with the same name, both files get renamed by the addition of their start date and end dates at the end of their names (i.e. fesom.clock_YYYYMMDD-YYYYMMDD).

The structure of the run_YYYYMMDD-YYYYMMDD directory replicates that of the general experiment folder. Run directories are created before each new run and they are useful to debug and restart experiments that have crashed.


Having a general and several run subfolders means that files are duplicated and, when models consist of several runs, the general directory can end up looking very untidy. Run folders were created with the idea that they will be deleted once all files have been transferred to their respective folders in the general experiment directory. Currently, that is not the case due to potential issues when there is a need for restarting a crashed simulation: a faulty tidy-up (i.e. due to a run crash, some run files are updated but others not) will lead to a faulty restart. In the the near future the user will have control on whether keeping the run folders or deleting them, through a variable in the runscript.

Debugging an Experiment

To debug an experiment we recommend checking the following files that you will find, either in the general experiment directory or in the run subdirectory:

  • The ESM-Tools variable space file config/<experiment_ID>_finished_config.yaml.
  • The run log file run_YYYYMMDD-YYYYMMDD/<experiment_ID>_compute_YYYYMMDD-YYYYMMDD_<JobID>.log`.