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noaa-ocs-modeling / CoupledModelDriver

coupled model configuration generation
https://CoupledModelDriver.readthedocs.io
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run `BestTrack` on 120m mesh v2.2 on Hera #77

Closed ghost closed 3 years ago

ghost commented 3 years ago

Set up a BestTrack JSON configuration to run ADCIRC with BestTrack, unperturbed

Jaime has built a makefile system to run besttrack with parameters here: https://github.com/JaimeCalzadaNOAA/coastal-act/blob/updates/tasks/test_Mesh_120m_v22/best_track_storms/Makefile

ghost commented 3 years ago

current BestTrack JSON: https://github.com/noaa-ocs-modeling/CoupledModelDriver/blob/4ff84fa9c9672dd30d5825a209f6c917acf82110/coupledmodeldriver/configure/forcings/base.py#L164-L202

ghost commented 3 years ago

this issue is related to #56

ghost commented 3 years ago

this command should work:

initialize_adcirc \
  --output-directory run_adcirconly_besttrack_hsofs_250m \
  --mesh-directory /scratch2/COASTAL/coastal/save/shared/models/meshes/hsofs/250m/v1.0 \
  --modeled-start-time 20121022T060000 \
  --modeled-duration 04:05:00:00 \
  --modeled-timestep 00:00:02 \
  --tidal-spinup-duration 12:06:00:00 \
  --platform HERA \
  --adcirc-processors 600 \
  --adcirc-executable /scratch2/COASTAL/coastal/save/shared/repositories/ADC-WW3-NWM-NEMS/ADCIRC/work/padcirc \
  --adcprep-executable /scratch2/COASTAL/coastal/save/shared/repositories/ADC-WW3-NWM-NEMS/ADCIRC/work/adcprep \
  --modulefile /scratch2/COASTAL/coastal/save/shared/repositories/ADC-WW3-NWM-NEMS/modulefiles/envmodules_intel.hera \
  --job-duration 06:00:00 \
  --forcings tidal,besttrack \
  --tidal-source TPXO \
  --tidal-path /scratch2/COASTAL/coastal/save/shared/models/forcings/tides/h_tpxo9.v1.nc \
  --besttrack-storm-id sandy2012
ghost commented 3 years ago

the run at /scratch2/COASTAL/coastal/save/shared/working/zach/adcirc/run_20210413_besttrack_hsofs_250m seems to have run successfully, and timed out at hotstart as normal

Here is the code to convert the forcing from a BestTrackForcingJSON into an ADCIRCpy BestTrackForcing object: https://github.com/noaa-ocs-modeling/CoupledModelDriver/blob/4ff84fa9c9672dd30d5825a209f6c917acf82110/coupledmodeldriver/configure/forcings/base.py#L186-L193

Then, add forcings to mesh: https://github.com/noaa-ocs-modeling/CoupledModelDriver/blob/a7bf10e8e7f7fb4b8a9a9e164823335457fd72ea/coupledmodeldriver/configure/models.py#L201-L216

ghost commented 3 years ago

the surface output fort.63.nc seems to have an empty zeta:

fort63_dataset = Dataset('/scratch2/COASTAL/coastal/save/shared/working/zach/adcirc/run_20210413_hsofs_250m_besttrack/runs/run_1/fort.63.nc')
print(fort63_dataset['zeta'].shape)
(0, 1813443)
ghost commented 3 years ago

the surface output fort.63.nc seems to have an empty zeta:

fort63_dataset = Dataset('/scratch2/COASTAL/coastal/save/shared/working/zach/adcirc/run_20210413_hsofs_250m_besttrack/runs/run_1/fort.63.nc')
print(fort63_dataset['zeta'].shape)
(0, 1813443)

Perhaps the output frequency? This should be accessible through driver.set_surface_elevation_output(*args, **kwargs).

ghost commented 3 years ago

updated the code setting the output frequency: https://github.com/noaa-ocs-modeling/CoupledModelDriver/blob/4eea406e35369fbac53682bb8610e2609d8e2b4b/coupledmodeldriver/configure/models.py#L284-L346

120m v2.2 besttrack run outputs w/ stations, 2021-04-14

for the run in

/scratch2/COASTAL/coastal/save/shared/working/zach/adcirc/run_20210414_hsofs_120m_v2.2_besttrack

It looks like fort.61.nc and fort.63.nc have empty zeta arrays:

fort61_dataset = Dataset(COLDSTART_DIRECTORY / 'fort.61.nc')
print({variable_name: variable.shape for variable_name, variable in fort61_dataset.variables.items()})
{'time': (0,), 'station_name': (397, 50), 'x': (397,), 'y': (397,), 'zeta': (0, 397)}
fort63_dataset = Dataset(COLDSTART_DIRECTORY / 'fort.63.nc')
print({variable_name: variable.shape for variable_name, variable in fort63_dataset.variables.items()})
{'time': (0,), 'x': (5792708,), 'y': (5792708,), 'element': (11467160, 3), 'adcirc_mesh': (1,), 'neta': (), 'nvdll': (1,), 'max_nvdll': (), 'ibtypee': (1,), 'nbdv': (273,), 'nvel': (), 'nvell': (513,), 'max_nvell': (), 'ibtype': (513,), 'nbvv': (119521,), 'depth': (5792708,), 'zeta': (0, 5792708)}
ghost commented 3 years ago

From /scratch2/COASTAL/coastal/save/shared/working/zach/adcirc/run_20210414_hsofs_120m_v2.2_besttrack/coldstart/fort.15

NSPOOL**

-5 12.25 12.25 1                                                ! NOUTE TOUTSE TOUTFE NSPOOLE
-5 12.25 12.25 1                                                ! NOUTV TOUTSV TOUTFV NSPOOLV
-5 12.250000 12.250000 1                                        ! NOUTGE TOUTSGE TOUTFGE NSPOOLGE
-5 12.250000 12.250000 1                                        ! NOUTGV TOUTSGV TOUTFGV NSPOOLGV

it looks like the output frequency is still set to 12.25 seconds, even though I wanted 400 seconds for surface. I will look in the code

ghost commented 3 years ago

Check you values for start, end and steps: TOUTS, TOUTFE, NSPOOLE

https://adcirc.org/home/documentation/users-manual-v53/parameter-definitions#TOUTSE

On Thu, Apr 15, 2021 at 8:40 AM Zachary Burnett @.***> wrote:

From /scratch2/COASTAL/coastal/save/shared/working/zach/adcirc/run_20210414_hsofs_120m_v2.2_besttrack/coldstart/fort.15

NSPOOL**

-5 12.25 12.25 1 ! NOUTE TOUTSE TOUTFE NSPOOLE

-5 12.25 12.25 1 ! NOUTV TOUTSV TOUTFV NSPOOLV

-5 12.250000 12.250000 1 ! NOUTGE TOUTSGE TOUTFGE NSPOOLGE -5 12.250000 12.250000 1 ! NOUTGV TOUTSGV TOUTFGV NSPOOLGV

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-- Jaime R. Calzada UCAR Marine Modeling and Analysis Branch National Ocean Service / Office of Coast Survey Development Laboratory National Oceanic and Atmospheric Administration 1315 East West Highway, N/CS13 Silver Spring, MD 20910-3282 phone: (301) 713-2809 x 119 <%28301%29%20713-2809%20x103> mobile: (787) 484-6944 <%28201%29%20539-1679>

ghost commented 3 years ago

blocked by https://github.com/JaimeCalzadaNOAA/adcircpy/issues/76 when passing end and spinup_end to driver.set_elevation_surface_output(): https://github.com/noaa-ocs-modeling/CoupledModelDriver/blob/7e8dfb9035593cb58add4443b3aef214c9bdcd6a/coupledmodeldriver/configure/models.py#L293-L309

ghost commented 3 years ago

issue solved by https://github.com/JaimeCalzadaNOAA/adcircpy/pull/77

ghost commented 3 years ago

added fort.22 reading with https://github.com/JaimeCalzadaNOAA/adcircpy/pull/78

ghost commented 3 years ago

run completed successfully at /scratch2/COASTAL/coastal/save/shared/working/zach/adcirc/run_20210416_hsofs_120m_v2.2_besttrack