This repository serves as a template for multi-stage CABLE configurations both through (Payu)[https://github.com/payu-org/payu] and through a stand-alone CABLE runner (to come).
The payu configuration in config.yaml remains identical (see the full documentation on payu configurations (here)[https://payu.readthedocs.io/en/latest/config.html]). The additions for CABLE configurations are the stage_config.yaml file and the stage namelist directories. The stage_config.yaml prescribes the stages (and how many times they run), that form the CABLE configuration in order and the locations of the namelists which define the actions of each stage. The branches of this repository contain example configurations.
Once the laboratory is configured, invoke payu run to execute the CABLE configuration. Note that if CABLE exits with a non-success exit code, invoking payu run again will by default restart from the stage that failed (after a payu sweep). To begin from the start, remove the configuration_log.yaml file with rm configuration_log.yaml.
Namelists for each stage are modified by having "patch" namelists for each stage. A directory in the laboratory for each stage specified in stage_config.yaml is required, which contains the patch namelists that will be applied to the top level namelist before running the stage e.g. when running a stage named climate_spinup, a directory named climate_spinup must exist, and it may contain cable.nml, luc.nml and cru.nml (note that it doesn't need to contain all the namelists). These namelists are patched into to the respective top level namelists. Options specified in the stage namelist take precedence. If the directory does not contain a given namelist, the top level namelist will be taken as is.
The point of these multi-stage configurations is to spin-up various physical processes to a quasi-equilibrium, for use in later simulations. As such, we want to capture outputs or restarts from a previous stage and use them as inputs to the next stage. This is achieved by symlinking the contents of the restart directories from the previous stages to the working directory for the current stage. The most recent version of a given restart file will be taken in the instance of multiple stages generating the same file.
The progress of the configuration is monitored by the configuration_log.yaml file, which lists the queued and completed stages, and the stage that is currently running. Once a stage is finished running, it is stored in archive/output{id:%03d}/, where id is the number of the current stage (starting at 0). A copy of the configuration log, snapshotted at the point the stage began, is stored in the output directory to assist interpretation of results.