Merge branch 'main' into feature/schism

# Conflicts:
#	coupledmodeldriver/generate/adcirc/base.py
#	coupledmodeldriver/generate/adcirc/generate.py
#	coupledmodeldriver/generate/adcirc/script.py
#	tests/data/reference/adcirc/hera_shinnecock_ike/configure_adcirc.json
#	tests/data/reference/adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15
#	tests/data/reference/adcirc/hera_shinnecock_ike/spinup/fort.15
#	tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/configure_adcirc.json
#	tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/adcprep.job
#	tests/data/reference/adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15
#	tests/data/reference/adcirc/local_shinnecock_ike/configure_adcirc.json
#	tests/data/reference/adcirc/local_shinnecock_ike/runs/unperturbed/fort.15
#	tests/data/reference/adcirc/local_shinnecock_ike/spinup/fort.15
#	tests/data/reference/adcirc/stampede2_shinnecock_ike/configure_adcirc.json
#	tests/data/reference/adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15
#	tests/data/reference/adcirc/stampede2_shinnecock_ike/spinup/fort.15
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.coldstart
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/config.rc.hotstart
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/configure_adcirc.json
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/job_adcprep_hera.job
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.coldstart
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/model_configure.hotstart
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.coldstart
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/nems.configure.hotstart
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/adcprep.job
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/config.rc
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/fort.15
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/model_configure
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/runs/unperturbed/nems.configure
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/adcprep.job
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/config.rc
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/fort.15
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/model_configure
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike/spinup/nems.configure
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/config.rc.coldstart
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/configure_adcirc.json
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/job_adcprep_hera.job
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/model_configure.coldstart
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/nems.configure.coldstart
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/adcprep.job
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/config.rc
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/fort.15
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/model_configure
#	tests/data/reference/nems_adcirc/hera_shinnecock_ike_nospinup/runs/unperturbed/nems.configure
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.coldstart
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/config.rc.hotstart
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/configure_adcirc.json
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.coldstart
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/model_configure.hotstart
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.coldstart
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/nems.configure.hotstart
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/config.rc
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/fort.15
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/model_configure
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/runs/unperturbed/nems.configure
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/config.rc
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/fort.15
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/model_configure
#	tests/data/reference/nems_adcirc/local_shinnecock_ike/spinup/nems.configure
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.coldstart
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/config.rc.hotstart
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/configure_adcirc.json
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.coldstart
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/model_configure.hotstart
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.coldstart
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/nems.configure.hotstart
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/adcprep.job
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/config.rc
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/fort.15
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/model_configure
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/runs/unperturbed/nems.configure
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/adcprep.job
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/config.rc
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/fort.15
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/model_configure
#	tests/data/reference/nems_adcirc/stampede2_shinnecock_ike/spinup/nems.configure

coupledmodeldriver/generate/adcirc/base.py

@@ -128,6 +128,7 @@ class ADCIRCJSON(CirculationModelJSON, NEMSCapJSON, AttributeJSON):
 
     field_types = {
         'adcprep_executable': Path,
+        'aswip_executable_path': Path,
         'modeled_start_time': datetime,
         'modeled_duration': timedelta,
         'modeled_timestep': timedelta,
@@ -158,6 +159,7 @@ def __init__(
         tidal_spinup_duration: timedelta = None,
         tidal_spinup_timestep: timedelta = None,
         forcings: [ForcingJSON] = None,
+        aswip_executable_path: PathLike = None,
         source_filename: PathLike = None,
         slurm_configuration: SlurmJSON = None,
         use_original_mesh: bool = False,
@@ -182,6 +184,7 @@ def __init__(
         :param mesh_files: file paths to `fort.13`, `fort.14`
         :param executable: file path to `adcirc` or `NEMS.x`
         :param adcprep_executable: file path to `adcprep`
+        :param aswip_executable_path: file path to `aswip`
         :param modeled_start_time: start time in model run
         :param modeled_duration: duration of model run
         :param modeled_timestep: time interval between model steps
@@ -228,6 +231,7 @@ def __init__(
         AttributeJSON.__init__(self, attributes=attributes, **kwargs)
 
         self['adcprep_executable'] = adcprep_executable
+        self['aswip_executable_path'] = aswip_executable_path
         self['tidal_spinup_duration'] = tidal_spinup_duration
         self['tidal_spinup_timestep'] = tidal_spinup_timestep
         self['source_filename'] = source_filename

coupledmodeldriver/generate/adcirc/generate.py

@@ -11,9 +11,12 @@
     ADCIRCRunConfiguration,
     NEMSADCIRCRunConfiguration,
 )
-from coupledmodeldriver.generate.adcirc.script import AdcircMeshPartitionJob, AdcircRunJob
-from coupledmodeldriver.script import EnsembleCleanupScript, EnsembleRunScript
-from coupledmodeldriver.utilities import LOGGER, create_symlink, get_logger
+from coupledmodeldriver.generate.adcirc.script import AdcircRunJob, \
+    AdcircSetupJob
+from coupledmodeldriver.script import EnsembleCleanupScript, \
+    EnsembleRunScript
+from coupledmodeldriver.utilities import LOGGER, create_symlink, \
+    get_logger
 
 
 class RunPhase(Enum):
@@ -81,73 +84,63 @@ def generate_adcirc_configuration(
     email_type = ensemble_configuration['slurm']['email_type']
     email_address = ensemble_configuration['slurm']['email_address']
 
-    original_fort13_filename = ensemble_configuration['adcirc'].fort13_path
-    original_fort14_filename = ensemble_configuration['adcirc'].fort14_path
-    adcirc_executable = ensemble_configuration['adcirc']['executable']
-    adcprep_executable = ensemble_configuration['adcirc']['adcprep_executable']
+    original_fort13_filename = ensemble_configuration['adcirc']['fort_13_path']
+    original_fort14_filename = ensemble_configuration['adcirc']['fort_14_path']
+    adcirc_path = ensemble_configuration['adcirc']['executable']
+    adcprep_path = ensemble_configuration['adcirc']['adcprep_executable']
+    aswip_path = ensemble_configuration['adcirc']['aswip_executable_path']
     adcirc_processors = ensemble_configuration['adcirc']['processors']
     tidal_spinup_duration = ensemble_configuration['adcirc']['tidal_spinup_duration']
     source_filename = ensemble_configuration['adcirc']['source_filename']
     use_original_mesh = ensemble_configuration['adcirc']['use_original_mesh']
 
-    # if original_fort13_filename is not None and not original_fort13_filename.is_absolute():
-    #     original_fort13_filename = starting_directory / original_fort13_filename
-    # if original_fort14_filename is not None and not original_fort14_filename.is_absolute():
-    #     original_fort14_filename = starting_directory / original_fort14_filename
-    # if adcirc_executable is not None and not adcirc_executable.is_absolute():
-    #     adcirc_executable = starting_directory / adcirc_executable
-    # if adcprep_executable is not None and not adcprep_executable.is_absolute():
-    #     adcprep_executable = starting_directory / adcprep_executable
-    # if source_filename is not None and not source_filename.is_absolute():
-    #     source_filename = starting_directory / source_filename
-
     if use_nems:
         nems_configuration = ensemble_configuration['nems'].nemspy_modeling_system
         run_processors = nems_configuration.processors
         run_executable = ensemble_configuration['nems']['executable']
     else:
         nems_configuration = None
         run_processors = adcirc_processors
-        run_executable = adcirc_executable
+        run_executable = adcirc_path
 
     if source_filename is not None:
         LOGGER.debug(f'sourcing modules from "{source_filename}"')
 
     if original_fort14_filename is None or not original_fort14_filename.exists():
         raise FileNotFoundError(f'mesh XY not found at "{original_fort14_filename}"')
 
-    adcprep_run_name = 'ADCIRC_MESH_PREP'
-    adcprep_job_script_filename = output_directory / f'job_adcprep_{platform.name.lower()}.job'
+    setup_job_name = 'ADCIRC_SETUP'
+    setup_script_filename = output_directory / f'job_setup_{platform.name.lower()}.job'
 
     local_fort13_filename = output_directory / 'fort.13'
     local_fort14_filename = output_directory / 'fort.14'
     local_fort15_filename = output_directory / 'fort.15'
 
-    spinup_tides = tidal_spinup_duration is not None
+    run_tidal_spinup = tidal_spinup_duration is not None
 
-    if spinup_tides:
+    if run_tidal_spinup:
         run_phase = RunPhase.HOTSTART
         coldstart_run_name = 'ADCIRC_SPINUP'
         hotstart_run_name = 'ADCIRC_HOTSTART'
-        coldstart_run_script_filename = (
+        coldstart_script_filename = (
             output_directory / f'job_adcirc_{platform.name.lower()}.job.spinup'
         )
-        hotstart_run_script_filename = (
+        hotstart_script_filename = (
             output_directory / f'job_adcirc_{platform.name.lower()}.job.hotstart'
         )
-        run_script_filename = hotstart_run_script_filename
+        run_script_filename = hotstart_script_filename
     else:
         run_phase = RunPhase.COLDSTART
         coldstart_run_name = 'ADCIRC_COLDSTART'
         hotstart_run_name = None
-        coldstart_run_script_filename = (
+        coldstart_script_filename = (
             output_directory / f'job_adcirc_{platform.name.lower()}.job.coldstart'
         )
-        hotstart_run_script_filename = None
-        run_script_filename = coldstart_run_script_filename
+        hotstart_script_filename = None
+        run_script_filename = coldstart_script_filename
 
     if use_nems:
-        if spinup_tides:
+        if run_tidal_spinup:
             LOGGER.debug(f'setting spinup to {tidal_spinup_duration}')
             tidal_spinup_nems_configuration = ModelingSystem(
                 nems_configuration.start_time - tidal_spinup_duration,
@@ -185,7 +178,7 @@ def generate_adcirc_configuration(
             else:
                 filename.rename(coldstart_filename)
 
-        if spinup_tides:
+        if run_tidal_spinup:
             hotstart_filenames = nems_configuration.write(
                 output_directory,
                 overwrite=overwrite,
@@ -213,27 +206,34 @@ def generate_adcirc_configuration(
     ensemble_run_script_filename = output_directory / f'run_{platform.name.lower()}.sh'
     ensemble_cleanup_script_filename = output_directory / f'cleanup.sh'
 
-    LOGGER.debug(f'setting mesh partitioner "{adcprep_executable}"')
-    adcprep_script = AdcircMeshPartitionJob(
+    if 'besttrack' in ensemble_configuration:
+        use_aswip = ensemble_configuration['besttrack']['nws'] == 20
+    else:
+        use_aswip = False
+
+    LOGGER.debug(f'setting mesh partitioner "{adcprep_path}"')
+    setup_script = AdcircSetupJob(
         platform=platform,
         adcirc_mesh_partitions=adcirc_processors,
         slurm_account=slurm_account,
         slurm_duration=job_duration,
         slurm_partition=partition,
-        slurm_run_name=adcprep_run_name,
-        adcprep_path=adcprep_executable,
+        slurm_run_name=setup_job_name,
+        adcprep_path=adcprep_path,
+        aswip_path=aswip_path,
+        use_aswip=use_aswip,
         slurm_email_type=email_type,
         slurm_email_address=email_address,
-        slurm_error_filename=f'{adcprep_run_name}.err.log',
-        slurm_log_filename=f'{adcprep_run_name}.out.log',
+        slurm_error_filename=f'{setup_job_name}.err.log',
+        slurm_log_filename=f'{setup_job_name}.out.log',
         source_filename=source_filename,
     )
 
-    LOGGER.debug(f'writing mesh partitioning job script "{adcprep_job_script_filename.name}"')
-    adcprep_script.write(adcprep_job_script_filename, overwrite=overwrite)
+    LOGGER.debug(f'writing setup job script "{setup_script_filename.name}"')
+    setup_script.write(setup_script_filename, overwrite=overwrite)
 
     LOGGER.debug(f'setting run executable "{run_executable}"')
-    coldstart_run_script = AdcircRunJob(
+    coldstart_script = AdcircRunJob(
         platform=platform,
         slurm_tasks=run_processors,
         slurm_account=slurm_account,
@@ -248,11 +248,11 @@ def generate_adcirc_configuration(
         source_filename=source_filename,
     )
 
-    LOGGER.debug(f'writing coldstart run script "{coldstart_run_script_filename.name}"')
-    coldstart_run_script.write(coldstart_run_script_filename, overwrite=overwrite)
+    LOGGER.debug(f'writing coldstart run script "{coldstart_script_filename.name}"')
+    coldstart_script.write(coldstart_script_filename, overwrite=overwrite)
 
-    if spinup_tides:
-        hotstart_run_script = AdcircRunJob(
+    if run_tidal_spinup:
+        hotstart_script = AdcircRunJob(
             platform=platform,
             slurm_tasks=run_processors,
             slurm_account=slurm_account,
@@ -267,8 +267,8 @@ def generate_adcirc_configuration(
             source_filename=source_filename,
         )
 
-        LOGGER.debug(f'writing hotstart run script "{hotstart_run_script_filename.name}"')
-        hotstart_run_script.write(hotstart_run_script_filename, overwrite=overwrite)
+        LOGGER.debug(f'writing hotstart run script "{hotstart_script_filename.name}"')
+        hotstart_script.write(hotstart_script_filename, overwrite=overwrite)
 
     try:
         # instantiate AdcircRun object.
@@ -300,7 +300,7 @@ def generate_adcirc_configuration(
     if local_fort15_filename.exists():
         os.remove(local_fort15_filename)
 
-    if spinup_tides:
+    if run_tidal_spinup:
         tidal_spinup_directory = output_directory / 'spinup'
         if not tidal_spinup_directory.exists():
             tidal_spinup_directory.mkdir(parents=True, exist_ok=True)
@@ -324,12 +324,10 @@ def generate_adcirc_configuration(
             local_fort14_filename, tidal_spinup_directory / 'fort.14', relative=True
         )
         create_symlink(
-            adcprep_job_script_filename, tidal_spinup_directory / 'adcprep.job', relative=True,
+            setup_script_filename, tidal_spinup_directory / 'setup.job', relative=True,
         )
         create_symlink(
-            coldstart_run_script_filename,
-            tidal_spinup_directory / 'adcirc.job',
-            relative=True,
+            coldstart_script_filename, tidal_spinup_directory / 'adcirc.job', relative=True,
         )
         if use_nems:
             create_symlink(
@@ -377,7 +375,7 @@ def generate_adcirc_configuration(
                 create_symlink(local_fort13_filename, run_directory / 'fort.13', relative=True)
         create_symlink(local_fort14_filename, run_directory / 'fort.14', relative=True)
         create_symlink(
-            adcprep_job_script_filename, run_directory / 'adcprep.job', relative=True,
+            setup_script_filename, run_directory / 'setup.job', relative=True,
         )
         create_symlink(
             run_script_filename, run_directory / 'adcirc.job', relative=True,
@@ -398,7 +396,7 @@ def generate_adcirc_configuration(
                 run_directory / 'config.rc',
                 relative=True,
             )
-        if spinup_tides:
+        if run_tidal_spinup:
             for hotstart_filename in ['fort.67.nc', 'fort.68.nc']:
                 try:
                     create_symlink(
@@ -423,7 +421,7 @@ def generate_adcirc_configuration(
             'echo deleting previous ADCIRC output',
             f'sh {ensemble_cleanup_script_filename.name}',
         ],
-        spinup=spinup_tides,
+        run_spinup=run_tidal_spinup,
     )
     run_script.write(ensemble_run_script_filename, overwrite=overwrite)
 

coupledmodeldriver/generate/adcirc/script.py

@@ -73,7 +73,7 @@ def __init__(
         )
 
 
-class AdcircMeshPartitionJob(AdcircJob):
+class AdcircSetupJob(AdcircJob):
     """ script for performing domain decomposition with `adcprep` """
 
     def __init__(
@@ -84,6 +84,8 @@ def __init__(
         slurm_duration: timedelta,
         slurm_run_name: str,
         adcprep_path: PathLike = None,
+        aswip_path: PathLike = None,
+        use_aswip: bool = False,
         slurm_tasks: int = 1,
         commands: [str] = None,
         **kwargs,
@@ -106,18 +108,35 @@ def __init__(
             if isinstance(adcprep_path, Path):
                 adcprep_path = adcprep_path.as_posix()
 
+        if aswip_path is None:
+            aswip_path = 'aswip'
+        else:
+            if isinstance(aswip_path, Path):
+                aswip_path = aswip_path.as_posix()
+
         self.adcprep_path = adcprep_path
+        self.aswip_path = aswip_path
+        self.use_aswip = use_aswip
+
+        setup_commands = []
+
+        adcprep_commands = [
+            f'{self.adcprep_path} --np {self.adcirc_partitions} --partmesh',
+            f'{self.adcprep_path} --np {self.adcirc_partitions} --prepall',
+        ]
         if self.launcher is not None:
-            self.commands.extend(
-                [
-                    f'{self.launcher} {self.adcprep_path} --np {self.adcirc_partitions} --partmesh',
-                    f'{self.launcher} {self.adcprep_path} --np {self.adcirc_partitions} --prepall',
-                ]
-            )
-        else:
-            self.commands.extend(
+            adcprep_commands = [f'{self.launcher} {line}' for line in adcprep_commands]
+        setup_commands.extend(adcprep_commands)
+
+        if self.use_aswip:
+            setup_commands.append('')
+
+            setup_commands.extend(
                 [
-                    f'{self.adcprep_path} --np {self.adcirc_partitions} --partmesh',
-                    f'{self.adcprep_path} --np {self.adcirc_partitions} --prepall',
+                    f'{self.aswip_path}',
+                    'mv fort.22 fort.22.original',
+                    'mv NWS_20_fort.22 fort.22',
                 ]
             )
+
+        self.commands.extend(setup_commands)