CLI Commands

initialize_adcirc

initialize_adcirc creates JSON Configurations from initial parameters of a model run (model start and end times, forcing files, storm track ID, etc.). These JSON files provide a portable encapsulation of the entire model run, including model configurations in fort.15 and NEMS couplings. The files are read by generate_adcirc to generate the actual model configuration; generate_adcirc must be run again every time the JSON files change to keep the configuration up to date.

[2024-08-08 14:08:01,521] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/bin/initialize_adcirc", line 5, in <module>
    from coupledmodeldriver.client.initialize_adcirc import main
  File "/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/client/initialize_adcirc.py", line 9, in <module>
    from adcircpy import TidalSource
ModuleNotFoundError: No module named 'adcircpy'

ADCIRC run options that are not exposed by this command, such as runs or gwce_solution_scheme, can be specified by directly modifying the JSON files.

The following command creates JSON files for coupling (ATMESH + WW3DATA) -> ADCIRC over a small Shinnecock Inlet mesh:

initialize_adcirc \
    --platform HERA \
    --mesh-directory /scratch2/COASTAL/coastal/save/shared/models/meshes/shinnecock/v1.0 \
    --output-directory hera_shinnecock_ike_spinup_tidal_atmesh_ww3data \
    --modeled-start-time 20080823 \
    --modeled-duration 14:06:00:00 \
    --modeled-timestep 00:00:02 \
    --nems-interval 01:00:00 \
    --adcirc-executable /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ALLBIN_INSTALL/NEMS-adcirc-atmesh-ww3data.x \
    --adcirc-processors 40
    --adcprep-executable /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ALLBIN_INSTALL/adcprep \
    --modulefile /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/modulefiles/envmodules_intel.hera \
    --forcings tidal,atmesh,ww3data \
    --tidal-source TPXO \
    --tidal-path /scratch2/COASTAL/coastal/save/shared/models/forcings/tides/h_tpxo9.v1.nc \
    --tidal-spinup-duration 12:06:00:00 \
    --atmesh-path /scratch2/COASTAL/coastal/save/shared/models/forcings/shinnecock/ike/wind_atm_fin_ch_time_vec.nc \
    --ww3data-path /scratch2/COASTAL/coastal/save/shared/models/forcings/shinnecock/ike/ww3.Constant.20151214_sxy_ike_date.nc

This will create the directory hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/ with the following JSON configuration files:

πŸ“‚ hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/
┣ πŸ“œ configure_adcirc.json
┣ πŸ“œ configure_atmesh.json
┣ πŸ“œ configure_modeldriver.json
┣ πŸ“œ configure_nems.json
┣ πŸ“œ configure_slurm.json
┣ πŸ“œ configure_tidal_forcing.json
β”— πŸ“œ configure_ww3data.json

These files contain relevant configuration values for an ADCIRC run. You will likely wish to change these values to alter the resulting run, before generating the actual model configuration. For instance, NEMS connections and the run sequence need to be manually specified in configure_nems.json.

generate_adcirc

generate_adcirc reads JSON files (created by initialize_adcirc) and creates a set of ADCIRC configurations (fort.14, fort.15, etc.), as well as a script with which to submit the model run to a job manager such as Slurm.

[2024-08-08 14:08:01,569] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/pyschism/forcing/hycom/gofs.py:8: UserWarning: The seawater library is deprecated! Please use gsw instead.
  import seawater as sw
[2024-08-08 14:08:04,383] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
[2024-08-08 14:08:04,385] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
[2024-08-08 14:08:04,386] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/bin/generate_adcirc", line 5, in <module>
    from coupledmodeldriver.client.generate_adcirc import main
  File "/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/client/generate_adcirc.py", line 6, in <module>
    from coupledmodeldriver.generate import generate_adcirc_configuration
ImportError: cannot import name 'generate_adcirc_configuration' from 'coupledmodeldriver.generate' (/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/generate/__init__.py)

The following command will read the JSON files created in the example above and generate the following files:

cd hera_shinnecock_ike_spinup_tidal_atmesh_ww3data
generate_adcirc

πŸ“‚ hera_shinnecock_ike_spinup_tidal_atmesh_ww3data/
┣ πŸ“œ configure_adcirc.json
┣ πŸ“œ configure_atmesh.json
┣ πŸ“œ configure_modeldriver.json
┣ πŸ“œ configure_nems.json
┣ πŸ“œ configure_slurm.json
┣ πŸ“œ configure_tidal_forcing.json
┣ πŸ“œ configure_ww3data.json
┣ πŸ“‚ spinup/
┃  ┣ πŸ“œ fort.13
┃  ┣ πŸ”— fort.14 -> ../fort.14
┃  ┣ πŸ“œ fort.15
┃  ┣ πŸ“œ nems.configure
┃  ┣ πŸ“œ model_configure
┃  ┣ πŸ”— atm_namelist.rc -> ./model_configure
┃  ┣ πŸ“œ config.rc
┃  ┣ πŸ“œ setup.job
┃  β”— πŸ“œ adcirc.job
┣ πŸ“‚ runs/
┃  β”— πŸ“‚ unperturbed/
┃    ┣ πŸ“œ fort.13
┃    ┣ πŸ”— fort.14 -> ../../fort.14
┃    ┣ πŸ“œ fort.15
┃    ┣ πŸ”— fort.67.nc -> ../../spinup/fort.67.nc
┃    ┣ πŸ”— fort.68.nc -> ../../spinup/fort.68.nc
┃    ┣ πŸ“œ nems.configure
┃    ┣ πŸ“œ model_configure
┃    ┣ πŸ”— atm_namelist.rc -> ./model_configure
┃    ┣ πŸ“œ config.rc
┃    ┣ πŸ“œ setup.job
┃    β”— πŸ“œ adcirc.job
┣ πŸ“œ fort.14
┣ πŸ“œ cleanup.sh
β”— πŸ“œ run_hera.sh

check_completion

check_completion checks the completion status of a running model directory.

[2024-08-08 14:08:04,705] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/pyschism/forcing/hycom/gofs.py:8: UserWarning: The seawater library is deprecated! Please use gsw instead.
  import seawater as sw
[2024-08-08 14:08:07,517] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
[2024-08-08 14:08:07,519] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
[2024-08-08 14:08:07,521] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
usage: check_completion [-h] [--model MODEL] [--verbose] [directory ...]

positional arguments:
  directory      directory containing model run configuration

options:
  -h, --help     show this help message and exit
  --model MODEL  model that is running, one of: `ADCIRC`, `SCHISM`
  --verbose      list all errors and problems with runs

check_completion

{
    "hera_shinnecock_ike_spinup_tidal_atmesh_ww3data": {
        "spinup": "running - 15%",
        "runs": "not_started - 0%"
    }
}

you can also pass a specific directory (or several directories):

check_completion spinup

{
    "spinup": "running - 27%"
}

cd run_20211027_florence_besttrack_250msubset_quadrature
check_completion runs/*_13

{
    "vortex_4_variable_perturbation_13": "completed - 100.0%",
    "vortex_4_variable_quadrature_13": "not_started - 0%"
}

if a run has an error, you can pass –verbose to see detailed logs:

check_completion spinup

{
    "spinup": "error - 0%"
}

check_completion spinup --verbose

{
    "spinup": {
        "status": "error",
        "progress": "0%",
        "error": {
            "ADCIRC_SETUP_SPINUP.err.log": [
                "forrtl: severe (24): end-of-file during read, unit -4, file /proc/92195/fd/0\n",
                "Image              PC                Routine            Line        Source             \n",
                "adcprep            000000000069A72E  Unknown               Unknown  Unknown\n",
                "adcprep            00000000006CBAAF  Unknown               Unknown  Unknown\n",
                "adcprep            000000000050A5CB  openprepfiles_           6996  prep.F\n",
                "adcprep            0000000000507F22  prep13_                   753  prep.F\n",
                "adcprep            000000000042E2E9  prepinput_                717  adcprep.F\n",
                "adcprep            000000000042BCDB  MAIN__                    239  adcprep.F\n",
                "adcprep            000000000040B65E  Unknown               Unknown  Unknown\n",
                "libc-2.17.so       00002AAEC02EB555  __libc_start_main     Unknown  Unknown\n",
                "adcprep            000000000040B569  Unknown               Unknown  Unknown\n",
                "srun: error: h24c51: task 0: Exited with exit code 24\n",
                "srun: launch/slurm: _step_signal: Terminating StepId=25366266.1\n"
            ]
        }
    }
}

check_completion runs

{
    "spinup": "failed - 0%"
}

check_completion runs --verbose

{
    "runs": {
        "status": "failed",
        "progress": "0%",
        "failed": {
            "fort.16": "ADCIRC output file `fort.16` not found"
        },
        "error": {
            "ADCIRC_SETUP_unperturbed.err.log": [
                "slurmstepd: error: execve(): /scratch2/COASTAL/coastal/save/shared/repositories/CoastalApp/ADCIRC/ALLBIN_INSTALL/adcprep: No such file or directory\n",
                "srun: error: h18c49: task 0: Exited with exit code 2\n",
                "srun: launch/slurm: _step_signal: Terminating StepId=25366268.0\n"
            ]
        }
    }
}

unqueued_runs

unqueued_runs finds and optionally submits runs that haven’t been queued to a job manager.

[2024-08-08 14:08:07,837] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/pyschism/forcing/hycom/gofs.py:8: UserWarning: The seawater library is deprecated! Please use gsw instead.
  import seawater as sw
[2024-08-08 14:08:10,647] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
[2024-08-08 14:08:10,648] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
[2024-08-08 14:08:10,651] /home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/_depend.py WARNING : can't find the 'adcircpy' module
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/bin/unqueued_runs", line 5, in <module>
    from coupledmodeldriver.client.unqueued_runs import main
  File "/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/client/unqueued_runs.py", line 7, in <module>
    from coupledmodeldriver.client.check_completion import (
ImportError: cannot import name 'MODELS' from 'coupledmodeldriver.client.check_completion' (/home/docs/checkouts/readthedocs.org/user_builds/coupledmodeldriver/envs/stable/lib/python3.10/site-packages/coupledmodeldriver/client/check_completion.py)

corresponding Python functions

coupledmodeldriver.client.check_completion.check_completion(directory: PathLike | None = None, verbose: bool = False, model: Model | None = None) → Dict[str, Any]

check the completion status of a running model

Parameters:

  • directory – directory containing model run configuration

  • verbose – list all errors and problems with runs

  • model – model that is running, one of: ADCIRC, SCHISM

Returns:

JSON output of completion status