noaa-ocs-modeling · Sep 21, 2021 · Sep 7, 2021 · Sep 7, 2021 · Sep 7, 2021 · Sep 7, 2021
diff --git a/coupledmodeldriver/generate/adcirc/base.py b/coupledmodeldriver/generate/adcirc/base.py
@@ -1,13 +1,13 @@
 from datetime import datetime, timedelta
-import os
 from os import PathLike
 from pathlib import Path
-import sys
 from typing import Any, Union
 
 from adcircpy import AdcircMesh, AdcircRun, Tides
 from adcircpy.forcing import BestTrackForcing
 from adcircpy.forcing.base import Forcing
+from adcircpy.mesh.fort13 import NodalAttributes
+from adcircpy.mesh.mesh import ModelForcings
 from adcircpy.server import SlurmConfig
 from nemspy.model import ADCIRCEntry
 
@@ -217,6 +217,7 @@ def __init__(
         :param attributes: attributes to set in `adcircpy.AdcircRun` object
         """
 
+        self.__mesh = None
         self.__base_mesh = None
 
         if tidal_spinup_timestep is None:
@@ -309,70 +310,72 @@ def adcircpy_forcings(self) -> [Forcing]:
 
     @property
     def adcircpy_mesh(self) -> AdcircMesh:
-        if self.__base_mesh is None:
-            self.__base_mesh = self['fort_14_path']
-
-        if not isinstance(self.__base_mesh, AdcircMesh):
-            LOGGER.info(f'opening mesh "{self.__base_mesh}"')
-            self.__base_mesh = AdcircMesh.open(self.__base_mesh, crs=4326)
-
-        mesh = self.__base_mesh.copy()
-
-        if self['fort_13_path'] is not None:
-            LOGGER.info(
-                f'reading attributes from "{os.path.relpath(self["fort_13_path"].resolve(), Path.cwd())}"'
-            )
-            if self['fort_13_path'].exists():
-                mesh.import_nodal_attributes(self['fort_13_path'])
-                for attribute_name in mesh.get_nodal_attribute_names():
-                    mesh.set_nodal_attribute_state(
-                        attribute_name, coldstart=True, hotstart=True
+        if self.__mesh is None:
+            mesh = self.base_mesh.copy()
+
+            # reconstruct mesh from base
+            mesh.forcings = ModelForcings(mesh)
+            mesh.nodal_attributes = NodalAttributes(mesh)
+
+            if self['fort_13_path'] is not None:
+                if self['fort_13_path'].exists():
+                    LOGGER.info(f'reading attributes from "{self["fort_13_path"]}"')
+                    mesh.import_nodal_attributes(self['fort_13_path'])
+                    for attribute_name in mesh.get_nodal_attribute_names():
+                        mesh.set_nodal_attribute_state(
+                            attribute_name, coldstart=True, hotstart=True
+                        )
+                else:
+                    LOGGER.warning(
+                        f'mesh values (nodal attributes) not found at "{self["fort_13_path"]}"'
                     )
-            else:
-                LOGGER.warning(
-                    f'mesh values (nodal attributes) not found at "{os.path.relpath(self["fort_13_path"].resolve(), Path.cwd())}"'
-                )
 
-        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']
+            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)
+                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)
+                mesh.add_forcing(adcircpy_forcing)
 
-        if not mesh.has_nodal_attribute('primitive_weighting_in_continuity_equation'):
-            LOGGER.debug(f'generating tau0 in mesh')
-            mesh.generate_tau0()
+            if not mesh.has_nodal_attribute('primitive_weighting_in_continuity_equation'):
+                LOGGER.debug(f'generating tau0 in mesh')
+                mesh.generate_tau0()
 
-        return mesh
+            self.__mesh = mesh
+
+        return self.__mesh
 
     @adcircpy_mesh.setter
     def adcircpy_mesh(self, adcircpy_mesh: Union[AdcircMesh, PathLike]):
-        if isinstance(adcircpy_mesh, AdcircMesh):
-            try:
-                adcircpy_mesh = adcircpy_mesh.copy()
-                LOGGER.debug(f'copying mesh object ({sys.getsizeof(adcircpy_mesh)} bytes)')
-            except Exception as error:
-                LOGGER.warning(f'unable to copy mesh object: {error}')
-
-        self.__base_mesh = adcircpy_mesh
+        self.__mesh = adcircpy_mesh
 
     @property
     def base_mesh(self) -> AdcircMesh:
+        if self.__base_mesh is None:
+            if self.__mesh is not None:
+                self.__base_mesh = self.__mesh
+            else:
+                self.__base_mesh = self['fort_14_path']
+        if not isinstance(self.__base_mesh, AdcircMesh):
+            LOGGER.info(f'opening mesh "{self.__base_mesh}"')
+            self.__base_mesh = AdcircMesh.open(self.__base_mesh, crs=4326)
+        # deconstruct mesh into a base mesh that can be pickled
+        self.__base_mesh.forcings = None
+        self.__base_mesh.nodal_attributes = None
         return self.__base_mesh
 
     @base_mesh.setter
-    def base_mesh(self, base_mesh: AdcircMesh):
+    def base_mesh(self, base_mesh: Union[AdcircMesh, PathLike]):
         self.__base_mesh = base_mesh
 
     @property
@@ -389,9 +392,7 @@ def adcircpy_driver(self) -> AdcircRun:
         )
 
         if self['stations_file_path'] is not None:
-            LOGGER.info(
-                f'importing stations from "{os.path.relpath(self["stations_file_path"].resolve(), Path.cwd())}"'
-            )
+            LOGGER.info(f'importing stations from "{self["stations_file_path"]}"')
             driver.import_stations(self['stations_file_path'])
 
         if self['modeled_timestep'] is not None:
@@ -501,7 +502,12 @@ def adcircpy_driver(self) -> AdcircRun:
     def nemspy_entry(self) -> ADCIRCEntry:
         return ADCIRCEntry(processors=self['processors'], **self['nems_parameters'])
 
+    def __setitem__(self, key: str, value: Any):
+        super().__setitem__(key, value)
+        self.__mesh = None
+
     def __copy__(self) -> 'ADCIRCJSON':
         instance = super().__copy__()
         instance.base_mesh = self.base_mesh
+        instance.forcings = self.forcings
         return instance
diff --git a/coupledmodeldriver/generate/adcirc/configure.py b/coupledmodeldriver/generate/adcirc/configure.py
@@ -152,10 +152,18 @@ def forcings(self) -> [ForcingJSON]:
     def adcircpy_mesh(self) -> AdcircMesh:
         return self['adcirc'].adcircpy_mesh
 
+    @adcircpy_mesh.setter
+    def adcircpy_mesh(self, adcircpy_mesh: AdcircMesh):
+        self['adcirc'].adcircpy_mesh = adcircpy_mesh
+
     @property
     def adcircpy_driver(self) -> AdcircRun:
         return self['adcirc'].adcircpy_driver
 
+    @adcircpy_driver.setter
+    def adcircpy_driver(self, adcircpy_driver: AdcircRun):
+        self['adcirc'].adcircpy_driver = adcircpy_driver
+
     def __copy__(self) -> 'ADCIRCRunConfiguration':
         return self.__class__.from_configurations(
             [copy(configuration) for configuration in self.configurations]
@@ -305,11 +313,6 @@ def add_forcing(self, forcing: ForcingJSON):
             forcing = self[self.add(forcing)]
             self['adcirc'].add_forcing(forcing)
 
-    def __copy__(self) -> 'NEMSADCIRCRunConfiguration':
-        return self.__class__.from_configurations(
-            [copy(configuration) for configuration in self.configurations]
-        )
-
     @classmethod
     def from_configurations(
         cls, configurations: [ConfigurationJSON]

diff --git a/coupledmodeldriver/generate/adcirc/generate.py b/coupledmodeldriver/generate/adcirc/generate.py
@@ -173,15 +173,17 @@ def generate_adcirc_configuration(
     if do_spinup:
         spinup_directory = output_directory / 'spinup'
 
+        spinup_configuration = copy(base_configuration)
+
         spinup_kwargs = {
             'directory': spinup_directory,
-            'configuration': copy(base_configuration),
+            'configuration': spinup_configuration,
             'duration': spinup_duration,
-            'relative_paths': relative_paths,
-            'overwrite': overwrite,
-            'use_original_mesh': use_original_mesh,
             'local_fort13_filename': local_fort13_filename,
             'local_fort14_filename': local_fort14_filename,
+            'link_mesh': True,
+            'relative_paths': relative_paths,
+            'overwrite': overwrite,
             'platform': platform,
             'adcirc_processors': adcirc_processors,
             'slurm_account': slurm_account,
@@ -202,16 +204,21 @@ def generate_adcirc_configuration(
     for run_name, run_configuration in perturbations.items():
         run_directory = runs_directory / run_name
 
+        link_mesh = (
+            use_original_mesh
+            or run_configuration.adcircpy_mesh == base_configuration.adcircpy_mesh
+        )
+
         run_kwargs = {
             'directory': run_directory,
             'name': run_name,
             'phase': run_phase,
             'configuration': run_configuration,
-            'relative_paths': relative_paths,
-            'overwrite': overwrite,
-            'use_original_mesh': use_original_mesh,
             'local_fort13_filename': local_fort13_filename,
             'local_fort14_filename': local_fort14_filename,
+            'link_mesh': link_mesh,
+            'relative_paths': relative_paths,
+            'overwrite': overwrite,
             'platform': platform,
             'adcirc_processors': adcirc_processors,
             'slurm_account': slurm_account,
@@ -224,6 +231,8 @@ def generate_adcirc_configuration(
         }
 
         if parallel:
+            # destroy stored copy of adcircpy mesh, because it cannot be pickled across processes
+            run_configuration.adcircpy_mesh = None
             futures.append(process_pool.submit(write_run_directory, **run_kwargs))
         else:
             write_run_directory(**run_kwargs)
@@ -264,9 +273,9 @@ def write_spinup_directory(
     duration: timedelta,
     local_fort14_filename: PathLike,
     local_fort13_filename: PathLike = None,
+    link_mesh: bool = False,
     relative_paths: bool = False,
     overwrite: bool = False,
-    use_original_mesh: bool = False,
     platform: Platform = None,
     adcirc_processors: int = None,
     slurm_account: str = None,
@@ -277,7 +286,7 @@ def write_spinup_directory(
 ) -> Path:
     if not isinstance(directory, Path):
         directory = Path(directory)
-    if not isinstance(local_fort13_filename, Path):
+    if local_fort13_filename is not None and not isinstance(local_fort13_filename, Path):
         local_fort13_filename = Path(local_fort13_filename)
 
     if not directory.exists():
@@ -404,17 +413,17 @@ def write_spinup_directory(
     adcircpy_driver.write(
         directory,
         overwrite=overwrite,
-        fort13=None if use_original_mesh else 'fort.13',
-        fort14=None,
+        fort13=None if link_mesh else 'fort.13',
+        fort14=None if link_mesh else 'fort.14',
         fort22='fort.22' if 'besttrack' in configuration else None,
         coldstart='fort.15',
         hotstart=None,
         driver=None,
     )
-    if use_original_mesh:
-        if local_fort13_filename.exists():
+    if link_mesh:
+        if local_fort13_filename is not None and local_fort13_filename.exists():
             create_symlink(local_fort13_filename, directory / 'fort.13', relative=True)
-    create_symlink(local_fort14_filename, directory / 'fort.14', relative=True)
+        create_symlink(local_fort14_filename, directory / 'fort.14', relative=True)
 
     return directory
 
@@ -426,9 +435,9 @@ def write_run_directory(
     configuration: Union[ADCIRCRunConfiguration, NEMSADCIRCRunConfiguration],
     local_fort14_filename: PathLike,
     local_fort13_filename: PathLike = None,
+    link_mesh: bool = False,
     relative_paths: bool = False,
     overwrite: bool = False,
-    use_original_mesh: bool = False,
     platform: Platform = None,
     adcirc_processors: int = None,
     slurm_account: str = None,
@@ -443,7 +452,7 @@ def write_run_directory(
         directory = Path(directory)
     if spinup_directory is not None and not isinstance(spinup_directory, Path):
         spinup_directory = Path(spinup_directory)
-    if not isinstance(local_fort13_filename, Path):
+    if local_fort13_filename is not None and not isinstance(local_fort13_filename, Path):
         local_fort13_filename = Path(local_fort13_filename)
 
     if not directory.exists():
@@ -564,17 +573,17 @@ def write_run_directory(
     adcircpy_driver.write(
         directory,
         overwrite=overwrite,
-        fort13=None if use_original_mesh else 'fort.13',
-        fort14=None,
+        fort13=None if link_mesh else 'fort.13',
+        fort14=None if link_mesh else 'fort.14',
         fort22='fort.22' if 'besttrack' in configuration else None,
         coldstart=None,
         hotstart='fort.15',
         driver=None,
     )
-    if use_original_mesh:
-        if local_fort13_filename.exists():
+    if link_mesh:
+        if local_fort13_filename is not None and local_fort13_filename.exists():
             create_symlink(local_fort13_filename, directory / 'fort.13', relative=True)
-    create_symlink(local_fort14_filename, directory / 'fort.14', relative=True)
+        create_symlink(local_fort14_filename, directory / 'fort.14', relative=True)
 
     if do_spinup:
         for hotstart_filename in ['fort.67.nc', 'fort.68.nc']:

diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@
 from setuptools import config, find_packages, setup
 
 DEPENDENCIES = {
-    'adcircpy>=1.0.39': ['gdal', 'fiona'],
+    'adcircpy>=1.0.41': ['gdal', 'fiona'],
     'filelock': [],
     'file-read-backwards': [],
     'nemspy>=1.0.3': [],

diff --git a/tests/data/reference/test_hera_adcirc/runs/unperturbed/fort.15 b/tests/data/reference/test_hera_adcirc/runs/unperturbed/fort.15
@@ -1,4 +1,4 @@
-created on 2021-09-07 10:26                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2021-09-07 14:16                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER

diff --git a/tests/data/reference/test_hera_adcirc_nems_atmesh_ww3data/runs/unperturbed/fort.15 b/tests/data/reference/test_hera_adcirc_nems_atmesh_ww3data/runs/unperturbed/fort.15
@@ -1,4 +1,4 @@
-created on 2021-09-07 10:26                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2021-09-07 14:16                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER

diff --git a/tests/data/reference/test_hera_adcirc_tidal/runs/unperturbed/fort.15 b/tests/data/reference/test_hera_adcirc_tidal/runs/unperturbed/fort.15
@@ -1,4 +1,4 @@
-created on 2021-09-07 10:26                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2021-09-07 14:16                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER

diff --git a/tests/data/reference/test_hera_adcirc_tidal/spinup/fort.15 b/tests/data/reference/test_hera_adcirc_tidal/spinup/fort.15
@@ -1,4 +1,4 @@
-created on 2021-09-07 10:26                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2021-09-07 14:16                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER

diff --git a/tests/data/reference/test_hera_adcirc_tidal_besttrack_nems_ww3data/runs/unperturbed/fort.15 b/tests/data/reference/test_hera_adcirc_tidal_besttrack_nems_ww3data/runs/unperturbed/fort.15
@@ -1,4 +1,4 @@
-created on 2021-09-07 10:26                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2021-09-07 14:17                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER

diff --git a/tests/data/reference/test_hera_adcirc_tidal_besttrack_nems_ww3data/spinup/fort.15 b/tests/data/reference/test_hera_adcirc_tidal_besttrack_nems_ww3data/spinup/fort.15
@@ -1,4 +1,4 @@
-created on 2021-09-07 10:26                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2021-09-07 14:17                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER

diff --git a/...ta/reference/test_hera_adcirc_tidal_besttrack_nems_ww3data_aswip/runs/unperturbed/fort.15 b/...ta/reference/test_hera_adcirc_tidal_besttrack_nems_ww3data_aswip/runs/unperturbed/fort.15
@@ -1,4 +1,4 @@
-created on 2021-09-07 10:27                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2021-09-07 14:17                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER