run `BestTrack` on 120m mesh v2.2 on Hera #77

ghost · 2021-04-13T14:32:49Z

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 · 2021-04-13T14:34:01Z

current BestTrack JSON:

CoupledModelDriver/coupledmodeldriver/configure/forcings/base.py

Lines 164 to 202 in 4ff84fa

    
           class BestTrackForcingJSON(WindForcingJSON): 
        
               name = 'BestTrack' 
        
               default_filename = f'configure_besttrack.json' 
        
               field_types = { 
        
                   'storm_id': str, 
        
                   'start_date': datetime, 
        
                   'end_date': datetime, 
        
               } 
        
               def __init__( 
        
                   self, storm_id: str, start_date: datetime, end_date: datetime, nws: int = 20, **kwargs 
        
               ): 
        
                   if 'fields' not in kwargs: 
        
                       kwargs['fields'] = {} 
        
                   kwargs['fields'].update(BestTrackForcingJSON.field_types) 
        
                   WindForcingJSON.__init__(self, nws=nws, **kwargs) 
        
                   self['storm_id'] = storm_id 
        
                   self['start_date'] = start_date 
        
                   self['end_date'] = end_date 
        
               @property 
        
               def adcircpy_forcing(self) -> BestTrackForcing: 
        
                   return BestTrackForcing( 
        
                       storm_id=self['storm_id'], 
        
                       nws=self['nws'], 
        
                       start_date=self['start_date'], 
        
                       end_date=self['end_date'], 
        
                   ) 
        
               @classmethod 
        
               def from_adcircpy(cls, forcing: BestTrackForcing) -> 'BestTrackForcingJSON': 
        
                   return cls( 
        
                       storm_id=forcing.storm_id, 
        
                       nws=forcing.NWS, 
        
                       start_date=forcing.start_date, 
        
                       end_date=forcing.end_date, 
        
                   )

ghost · 2021-04-13T14:49:07Z

this issue is related to #56

ghost · 2021-04-13T16:19:38Z

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 · 2021-04-14T14:39:35Z

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:

CoupledModelDriver/coupledmodeldriver/configure/forcings/base.py

Lines 186 to 193 in 4ff84fa

    
           @property 
        
           def adcircpy_forcing(self) -> BestTrackForcing: 
        
               return BestTrackForcing( 
        
                   storm_id=self['storm_id'], 
        
                   nws=self['nws'], 
        
                   start_date=self['start_date'], 
        
                   end_date=self['end_date'], 
        
               )

Then, add forcings to mesh:

CoupledModelDriver/coupledmodeldriver/configure/models.py

Lines 201 to 216 in a7bf10e

    
           LOGGER.debug(f'adding {len(self.forcings)} forcing(s) to mesh') 
        
           for adcircpy_forcing in self.adcircpy_forcings: 
        
               if isinstance(adcircpy_forcing, (Tides, BestTrackForcing)): 
        
                   adcircpy_forcing.start_date = self['modeled_start_time'] 
        
                   adcircpy_forcing.end_date = self['modeled_end_time'] 
        
               if ( 
        
                   isinstance(adcircpy_forcing, Tides) 
        
                   and self['tidal_spinup_duration'] is not None 
        
               ): 
        
                   adcircpy_forcing.spinup_time = self['tidal_spinup_duration'] 
        
                   adcircpy_forcing.start_date -= self['tidal_spinup_duration'] 
        
               elif isinstance(adcircpy_forcing, BestTrackForcing): 
        
                   adcircpy_forcing.clip_to_bbox(mesh.get_bbox(output_type='bbox'), mesh.crs) 
        
               mesh.add_forcing(adcircpy_forcing)

ghost · 2021-04-14T16:50:31Z

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 · 2021-04-14T16:57:56Z

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 · 2021-04-15T12:30:31Z

updated the code setting the output frequency:

CoupledModelDriver/coupledmodeldriver/configure/models.py

Lines 284 to 346 in 4eea406

    
           if self['output_elevations']: 
        
               if self['output_surface']: 
        
                   driver.set_elevation_surface_output( 
        
                       sampling_rate=self['modeled_output_interval'], 
        
                       start=self['modeled_start_time'], 
        
                       spinup=self['tidal_spinup_timestep'], 
        
                       spinup_start=spinup_start, 
        
                   ) 
        
               if self['output_stations']: 
        
                   driver.set_elevation_stations_output( 
        
                       sampling_rate=self['modeled_output_interval'], 
        
                       start=self['modeled_start_time'], 
        
                       spinup=self['tidal_spinup_timestep'], 
        
                       spinup_start=spinup_start, 
        
                   ) 
        
           if self['output_velocities']: 
        
               if self['output_surface']: 
        
                   driver.set_velocity_surface_output( 
        
                       sampling_rate=self['modeled_output_interval'], 
        
                       start=self['modeled_start_time'], 
        
                       spinup=self['tidal_spinup_timestep'], 
        
                       spinup_start=spinup_start, 
        
                   ) 
        
               if self['output_stations']: 
        
                   driver.set_velocity_stations_output( 
        
                       sampling_rate=self['modeled_output_interval'], 
        
                       start=self['modeled_start_time'], 
        
                       spinup=self['tidal_spinup_timestep'], 
        
                       spinup_start=spinup_start, 
        
                   ) 
        
           if self['output_concentrations']: 
        
               if self['output_surface']: 
        
                   driver.set_concentration_surface_output( 
        
                       sampling_rate=self['modeled_output_interval'], 
        
                       start=self['modeled_start_time'], 
        
                       spinup=self['tidal_spinup_timestep'], 
        
                       spinup_start=spinup_start, 
        
                   ) 
        
               if self['output_stations']: 
        
                   driver.set_concentration_stations_output( 
        
                       sampling_rate=self['modeled_output_interval'], 
        
                       start=self['modeled_start_time'], 
        
                       spinup=self['tidal_spinup_timestep'], 
        
                       spinup_start=spinup_start, 
        
                   ) 
        
           if self['output_meteorological_factors']: 
        
               if self['output_surface']: 
        
                   driver.set_meteorological_surface_output( 
        
                       sampling_rate=self['modeled_output_interval'], 
        
                       start=self['modeled_start_time'], 
        
                       spinup=self['tidal_spinup_timestep'], 
        
                       spinup_start=spinup_start, 
        
                   ) 
        
               if self['output_stations']: 
        
                   driver.set_meteorological_stations_output( 
        
                       sampling_rate=self['modeled_output_interval'], 
        
                       start=self['modeled_start_time'], 
        
                       spinup=self['tidal_spinup_timestep'], 
        
                       spinup_start=spinup_start, 
        
                   )

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 · 2021-04-15T12:40:23Z

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 · 2021-04-15T12:43:00Z

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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#77 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQ3T4UMRAWNIHQT2QYNKYYLTI3NERANCNFSM423O6MLA> .

-- 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 · 2021-04-15T15:11:20Z

blocked by oceanmodeling/adcircpy#76 when passing end and spinup_end to driver.set_elevation_surface_output():

CoupledModelDriver/coupledmodeldriver/configure/models.py

Lines 293 to 309 in 7e8dfb9

    
           if self['tidal_spinup_duration'] is not None: 
        
               spinup_start = self['modeled_start_time'] - self['tidal_spinup_duration'] 
        
               spinup_end = self['modeled_start_time'] 
        
           else: 
        
               spinup_start = None 
        
               spinup_end = None 
        
           if self['output_elevations']: 
        
               if self['output_surface']: 
        
                   driver.set_elevation_surface_output( 
        
                       sampling_rate=self['surface_output_interval'], 
        
                       start=self['modeled_start_time'], 
        
                       end=self['modeled_end_time'], 
        
                       spinup=self['tidal_spinup_timestep'], 
        
                       spinup_start=spinup_start, 
        
                       spinup_end=spinup_end, 
        
                   )

ghost · 2021-04-16T17:28:01Z

issue solved by oceanmodeling/adcircpy#77

ghost · 2021-04-16T17:31:40Z

added fort.22 reading with oceanmodeling/adcircpy#78

ghost · 2021-04-19T18:27:37Z

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

ghost self-assigned this Apr 13, 2021

ghost added the adcirc-v55-hsofs label Apr 13, 2021

ghost changed the title ~~run BestTrack on 120m mesh v2.2~~ run BestTrack on 120m mesh v2.2 on Hera Apr 13, 2021

ghost closed this as completed Apr 19, 2021

This issue was closed.

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run `BestTrack` on 120m mesh v2.2 on Hera #77

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run BestTrack on 120m mesh v2.2 on Hera #77

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

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run `BestTrack` on 120m mesh v2.2 on Hera #77

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