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Merge pull request #75: update documentation
Generic update after setting up versioning.
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| # Default science configurations | ||
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| A set of science configurations is defined in `benchcab`. This allows for running standardised testing of different version of CABLE. Test results using this default set are required for submission of new code development in CABLE. Occasionally, some code developments might also require test results using a different set of configurations to document their effect on the model results. | ||
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| The science configurations are given as patches to apply to a default namelist file. You can find [the default namelist file](https://github.com/CABLE-LSM/bench_example/blob/dev/namelists/cable.nml) in the `bench_example` repository. | ||
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| Currently, the default science configurations are defined internally by the following data structure: | ||
| ```python | ||
| DEFAULT_SCIENCE_CONFIGURATIONS = { | ||
| "sci0": {"cable": {"cable_user": {"GS_SWITCH": "medlyn"}}}, | ||
| "sci1": {"cable": {"cable_user": {"GS_SWITCH": "leuning"}}}, | ||
| "sci2": {"cable": {"cable_user": {"FWSOIL_SWITCH": "Haverd2013"}}}, | ||
| "sci3": {"cable": {"cable_user": {"FWSOIL_SWITCH": "standard"}}}, | ||
| "sci4": { | ||
| "cable": { | ||
| "cable_user": { | ||
| "GS_SWITCH": "medlyn", | ||
| "FWSOIL_SWITCH": "Haverd2013", | ||
| } | ||
| } | ||
| }, | ||
| "sci5": { | ||
| "cable": { | ||
| "cable_user": { | ||
| "GS_SWITCH": "leuning", | ||
| "FWSOIL_SWITCH": "Haverd2013", | ||
| } | ||
| } | ||
| }, | ||
| "sci6": { | ||
| "cable": { | ||
| "cable_user": { | ||
| "GS_SWITCH": "medlyn", | ||
| "FWSOIL_SWITCH": "standard", | ||
| } | ||
| } | ||
| }, | ||
| "sci7": { | ||
| "cable": { | ||
| "cable_user": { | ||
| "GS_SWITCH": "leuning", | ||
| "FWSOIL_SWITCH": "standard", | ||
| } | ||
| } | ||
| }, | ||
| } | ||
| ``` |
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| # Expected output from benchcab | ||
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| Below you will find examples of the expected output printed by `benchcab` to the screen when running the full workflow, with `benchcab run`. | ||
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| Other sub-commands should print out part of this output. | ||
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| ``` | ||
| $ benchcab run | ||
| Creating src directory: /scratch/tm70/sb8430/bench_example/src | ||
| Checking out repositories... | ||
| Successfully checked out trunk at revision 9550 | ||
| Successfully checked out test-branch at revision 9550 | ||
| Successfully checked out CABLE-AUX at revision 9550 | ||
| Writing revision number info to rev_number-1.log | ||
| Compiling CABLE serially for realisation trunk... | ||
| Successfully compiled CABLE for realisation trunk | ||
| Compiling CABLE serially for realisation test-branch... | ||
| Successfully compiled CABLE for realisation test-branch | ||
| Setting up run directory tree for FLUXNET tests... | ||
| Creating runs/site/logs directory: /scratch/tm70/sb8430/bench_example/runs/site/logs | ||
| Creating runs/site/outputs directory: /scratch/tm70/sb8430/bench_example/runs/site/outputs | ||
| Creating runs/site/tasks directory: /scratch/tm70/sb8430/bench_example/runs/site/tasks | ||
| Creating task directories... | ||
| Setting up tasks... | ||
| Successfully setup FLUXNET tasks | ||
| Creating PBS job script to run FLUXNET tasks on compute nodes: benchmark_cable_qsub.sh | ||
| PBS job submitted: 82479088.gadi-pbs | ||
| The CABLE log file for each task is written to runs/site/logs/<task_name>_log.txt | ||
| The CABLE standard output for each task is written to runs/site/tasks/<task_name>/out.txt | ||
| The NetCDF output for each task is written to runs/site/outputs/<task_name>_out.nc | ||
| ``` | ||
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| The PBS schedule job should print out the following to the job log file: | ||
| ``` | ||
| Running FLUXNET tasks... | ||
| Successfully ran FLUXNET tasks | ||
| ``` |
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