bios_testing

This repository contains CABLE test configurations for BIOS3 development (see CABLE-LSM/CABLE#276).

How to run a configuration (Gadi):

1. Clone the repository into scratch space (READ ONLY):

git clone https://github.com/CABLE-LSM/bios_testing.git /scratch/$PROJECT/$USER/bios_testing

If you want to make changes and push these changes to the remote repository, then clone via SSH:

git clone git@github.com:CABLE-LSM/bios_testing.git /scratch/$PROJECT/$USER/bios_testing

2. Checkout a configuration branch. E.g. act9test:

git checkout act9test

Configurations in this repository exist as git branches. To see all available configurations, run:

git branch -a

3. Edit the configuration shell script (config.sh) and set EXE to the absolute path of the CABLE executable.

4. Submit the run.sh PBS job script.

qsub run.sh

Run directory structure:

Here is the directory structure produced for the act9test run:

.
├── bios_act9test.o117989865
├── bios.nml
├── blaze.nml
├── cable-mpi -> /home/189/sb8430/cable/offline/cable-mpi
├── cable.nml
├── clean.sh
├── config.sh
├── input
│   ├── bios_cable_rst.nc -> /g/data/rp23/experiments/2024-04-17_BIOS3-merge/sb8430/bios_act9test/restart_1700_1899/bios_cable_rst.nc
│   ├── bios_casa_rst.nc -> /g/data/rp23/experiments/2024-04-17_BIOS3-merge/sb8430/bios_act9test/restart_1700_1899/bios_casa_rst.nc
│   ├── bios_climate_rst.nc -> /g/data/rp23/experiments/2024-04-17_BIOS3-merge/sb8430/bios_act9test/restart_1700_1899/bios_climate_rst.nc
│   ├── def_soil_params.txt -> /g/data/rp23/experiments/2024-04-17_BIOS3-merge/sb8430/params_bios/def_soil_params.txt
│   ├── def_veg_params.txt -> /g/data/rp23/experiments/2024-04-17_BIOS3-merge/sb8430/params_bios/def_veg_params.txt
│   ├── pftlookup.csv -> /g/data/rp23/experiments/2024-04-17_BIOS3-merge/sb8430/params_bios/pftlookup.csv
│   └── pop_bios_ini.nc -> /g/data/rp23/experiments/2024-04-17_BIOS3-merge/sb8430/bios_act9test/restart_1700_1899/pop_bios_ini.nc
├── logs
│   ├── log_cable.txt
│   └── log_out_cable.txt
├── LUC.nml
├── outputs
│   ├── bios_out_cable.nc
│   ├── bios_out_casa.nc
│   └── cnpfluxOut.csv
├── README.md
├── restart
│   ├── bios_cable_rst.nc
│   ├── bios_casa_rst.nc
│   ├── bios_climate_rst.nc
│   └── pop_bios_ini.nc
├── run.sh
└── setup.sh

bios_act9test.o117989865: PBS log file

bios.nml: BIOS namelist

blaze.nml: BLAZE namelist

cable-mpi -> /home/189/sb8430/cable/offline/cable-mpi: Symlinked CABLE MPI executable

cable.nml: CABLE namelist

clean.sh: Cleanup script (resets the run directory to original state)

config.sh: Configuration script

input: Input directory

logs: Directory containing CABLE log files

LUC.nml: LUC namelist

outputs: Directory containing CABLE output files

README.md: README file

restart: Directory containing CABLE restart files

run.sh: run script (PBS job script)

setup.sh: setup script (always runs prior to executing CABLE)