Merge pull request #429 from xylar/global_ocean_mesh_reorg

Switch `global_ocean` and `hurricane` to framework base and culled mesh

compass/ocean/cached_files.json

@@ -103,5 +103,40 @@
     "ocean/global_convergence/qu/cosine_bell/QU60/init/namelist.ocean": "global_convergence/qu/cosine_bell/QU60/init/namelist.220528.ocean",
     "ocean/global_convergence/qu/cosine_bell/QU60/init/initial_state.nc": "global_convergence/qu/cosine_bell/QU60/init/initial_state.220528.nc",
     "ocean/global_convergence/qu/cosine_bell/QU90/init/namelist.ocean": "global_convergence/qu/cosine_bell/QU90/init/namelist.220528.ocean",
-    "ocean/global_convergence/qu/cosine_bell/QU90/init/initial_state.nc": "global_convergence/qu/cosine_bell/QU90/init/initial_state.220528.nc"
-}
+    "ocean/global_convergence/qu/cosine_bell/QU90/init/initial_state.nc": "global_convergence/qu/cosine_bell/QU90/init/initial_state.220528.nc",
+    "ocean/global_ocean/Icos240/mesh/base_mesh/mesh.msh": "global_ocean/Icos240/mesh/base_mesh/mesh.220814.msh",
+    "ocean/global_ocean/Icos240/mesh/base_mesh/base_mesh.nc": "global_ocean/Icos240/mesh/base_mesh/base_mesh.220814.nc",
+    "ocean/global_ocean/Icos240/mesh/base_mesh/cellWidthVsLatLon.nc": "global_ocean/Icos240/mesh/base_mesh/cellWidthVsLatLon.220814.nc",
+    "ocean/global_ocean/Icos240/mesh/base_mesh/graph.info": "global_ocean/Icos240/mesh/base_mesh/graph.220814.info",
+    "ocean/global_ocean/Icos240/mesh/cull_mesh/culled_mesh.nc": "global_ocean/Icos240/mesh/cull_mesh/culled_mesh.220814.nc",
+    "ocean/global_ocean/Icos240/mesh/cull_mesh/culled_graph.info": "global_ocean/Icos240/mesh/cull_mesh/culled_graph.220814.info",
+    "ocean/global_ocean/Icos240/mesh/cull_mesh/critical_passages_mask_final.nc": "global_ocean/Icos240/mesh/cull_mesh/critical_passages_mask_final.220814.nc",
+    "ocean/global_ocean/QU240/mesh/base_mesh/mesh.msh": "global_ocean/QU240/mesh/base_mesh/mesh.220814.msh",
+    "ocean/global_ocean/QU240/mesh/base_mesh/base_mesh.nc": "global_ocean/QU240/mesh/base_mesh/base_mesh.220814.nc",
+    "ocean/global_ocean/QU240/mesh/base_mesh/cellWidthVsLatLon.nc": "global_ocean/QU240/mesh/base_mesh/cellWidthVsLatLon.220814.nc",
+    "ocean/global_ocean/QU240/mesh/base_mesh/graph.info": "global_ocean/QU240/mesh/base_mesh/graph.220814.info",
+    "ocean/global_ocean/QU240/mesh/cull_mesh/culled_mesh.nc": "global_ocean/QU240/mesh/cull_mesh/culled_mesh.220814.nc",
+    "ocean/global_ocean/QU240/mesh/cull_mesh/culled_graph.info": "global_ocean/QU240/mesh/cull_mesh/culled_graph.220814.info",
+    "ocean/global_ocean/QU240/mesh/cull_mesh/critical_passages_mask_final.nc": "global_ocean/QU240/mesh/cull_mesh/critical_passages_mask_final.220814.nc",
+    "ocean/global_ocean/QUwISC240/mesh/base_mesh/mesh.msh": "global_ocean/QUwISC240/mesh/base_mesh/mesh.220814.msh",
+    "ocean/global_ocean/QUwISC240/mesh/base_mesh/base_mesh.nc": "global_ocean/QUwISC240/mesh/base_mesh/base_mesh.220814.nc",
+    "ocean/global_ocean/QUwISC240/mesh/base_mesh/cellWidthVsLatLon.nc": "global_ocean/QUwISC240/mesh/base_mesh/cellWidthVsLatLon.220814.nc",
+    "ocean/global_ocean/QUwISC240/mesh/base_mesh/graph.info": "global_ocean/QUwISC240/mesh/base_mesh/graph.220814.info",
+    "ocean/global_ocean/QUwISC240/mesh/cull_mesh/culled_mesh.nc": "global_ocean/QUwISC240/mesh/cull_mesh/culled_mesh.220814.nc",
+    "ocean/global_ocean/QUwISC240/mesh/cull_mesh/culled_graph.info": "global_ocean/QUwISC240/mesh/cull_mesh/culled_graph.220814.info",
+    "ocean/global_ocean/QUwISC240/mesh/cull_mesh/critical_passages_mask_final.nc": "global_ocean/QUwISC240/mesh/cull_mesh/critical_passages_mask_final.220814.nc",
+    "ocean/global_ocean/EC30to60/mesh/base_mesh/mesh.msh": "global_ocean/EC30to60/mesh/base_mesh/mesh.220814.msh",
+    "ocean/global_ocean/EC30to60/mesh/base_mesh/base_mesh.nc": "global_ocean/EC30to60/mesh/base_mesh/base_mesh.220814.nc",
+    "ocean/global_ocean/EC30to60/mesh/base_mesh/cellWidthVsLatLon.nc": "global_ocean/EC30to60/mesh/base_mesh/cellWidthVsLatLon.220814.nc",
+    "ocean/global_ocean/EC30to60/mesh/base_mesh/graph.info": "global_ocean/EC30to60/mesh/base_mesh/graph.220814.info",
+    "ocean/global_ocean/EC30to60/mesh/cull_mesh/culled_mesh.nc": "global_ocean/EC30to60/mesh/cull_mesh/culled_mesh.220814.nc",
+    "ocean/global_ocean/EC30to60/mesh/cull_mesh/culled_graph.info": "global_ocean/EC30to60/mesh/cull_mesh/culled_graph.220814.info",
+    "ocean/global_ocean/EC30to60/mesh/cull_mesh/critical_passages_mask_final.nc": "global_ocean/EC30to60/mesh/cull_mesh/critical_passages_mask_final.220814.nc",
+    "ocean/global_ocean/ECwISC30to60/mesh/base_mesh/mesh.msh": "global_ocean/ECwISC30to60/mesh/base_mesh/mesh.220814.msh",
+    "ocean/global_ocean/ECwISC30to60/mesh/base_mesh/base_mesh.nc": "global_ocean/ECwISC30to60/mesh/base_mesh/base_mesh.220814.nc",
+    "ocean/global_ocean/ECwISC30to60/mesh/base_mesh/cellWidthVsLatLon.nc": "global_ocean/ECwISC30to60/mesh/base_mesh/cellWidthVsLatLon.220814.nc",
+    "ocean/global_ocean/ECwISC30to60/mesh/base_mesh/graph.info": "global_ocean/ECwISC30to60/mesh/base_mesh/graph.220814.info",
+    "ocean/global_ocean/ECwISC30to60/mesh/cull_mesh/culled_mesh.nc": "global_ocean/ECwISC30to60/mesh/cull_mesh/culled_mesh.220814.nc",
+    "ocean/global_ocean/ECwISC30to60/mesh/cull_mesh/culled_graph.info": "global_ocean/ECwISC30to60/mesh/cull_mesh/culled_graph.220814.info",
+    "ocean/global_ocean/ECwISC30to60/mesh/cull_mesh/critical_passages_mask_final.nc": "global_ocean/ECwISC30to60/mesh/cull_mesh/critical_passages_mask_final.220814.nc"
+}

compass/ocean/tests/global_ocean/mesh/cull.py → compass/ocean/mesh/cull.py

@@ -1,16 +1,133 @@
 import xarray
+import os
 
 from geometric_features import GeometricFeatures, FeatureCollection, \
     read_feature_collection
 from mpas_tools.mesh.conversion import cull
 from mpas_tools.mesh.mask import compute_mpas_flood_fill_mask
 import mpas_tools.io
 from mpas_tools.io import write_netcdf
+from mpas_tools.ocean import inject_bathymetry
 from mpas_tools.ocean.coastline_alteration import widen_transect_edge_masks, \
     add_critical_land_blockages, add_land_locked_cells_to_mask
 from mpas_tools.viz.paraview_extractor import extract_vtk
 from mpas_tools.logging import LoggingContext, check_call
 
+from compass.step import Step
+
+
+class CullMeshStep(Step):
+    """
+    A step for culling a global MPAS-Ocean mesh
+
+    Attributes
+    ----------
+    base_mesh_step : compass.mesh.spherical.SphericalBaseStep
+        The base mesh step containing input files to this step
+
+    with_ice_shelf_cavities : bool
+        Whether the mesh includes ice-shelf cavities
+
+    do_inject_bathymetry : bool
+        Whether to interpolate bathymetry from a data file so it
+        can be used as a culling criteria
+
+    preserve_floodplain : bool
+        Whether to leave land cells in the mesh based on bathymetry
+        specified by do_inject_bathymetry
+    """
+
+    def __init__(self, test_case, base_mesh_step, with_ice_shelf_cavities,
+                 name='cull_mesh', subdir=None, do_inject_bathymetry=False,
+                 preserve_floodplain=False):
+        """
+        Create a new step
+
+        Parameters
+        ----------
+        test_case : compass.ocean.tests.global_ocean.mesh.Mesh
+            The test case this step belongs to
+
+        base_mesh_step : compass.mesh.spherical.SphericalBaseStep
+            The base mesh step containing input files to this step
+
+        with_ice_shelf_cavities : bool
+            Whether the mesh includes ice-shelf cavities
+
+        name : str, optional
+            the name of the step
+
+        subdir : str, optional
+            the subdirectory for the step.  The default is ``name``
+
+        do_inject_bathymetry : bool, optional
+            Whether to interpolate bathymetry from a data file so it
+            can be used as a culling criteria
+
+        preserve_floodplain : bool, optional
+            Whether to leave land cells in the mesh based on bathymetry
+            specified by do_inject_bathymetry
+        """
+        super().__init__(test_case, name=name, subdir=subdir,
+                         cpus_per_task=None, min_cpus_per_task=None)
+        self.base_mesh_step = base_mesh_step
+
+        for file in ['culled_mesh.nc', 'culled_graph.info',
+                     'critical_passages_mask_final.nc']:
+            self.add_output_file(filename=file)
+
+        self.with_ice_shelf_cavities = with_ice_shelf_cavities
+        self.do_inject_bathymetry = do_inject_bathymetry
+        self.preserve_floodplain = preserve_floodplain
+
+    def setup(self):
+        """
+        Set up the test case in the work directory, including downloading any
+        dependencies.
+        """
+        super().setup()
+        if self.do_inject_bathymetry:
+            self.add_input_file(
+                filename='earth_relief_15s.nc',
+                target='SRTM15_plus_earth_relief_15s.nc',
+                database='bathymetry_database')
+
+        # get the these properties from the config options
+        config = self.config
+        # todo: move to constrain_resources()
+        self.cpus_per_task = config.getint('spherical_mesh',
+                                           'cull_mesh_cpus_per_task')
+        self.min_cpus_per_task = config.getint('spherical_mesh',
+                                               'cull_mesh_min_cpus_per_task')
+
+        base_path = self.base_mesh_step.path
+        base_filename = self.base_mesh_step.config.get(
+            'spherical_mesh', 'mpas_mesh_filename')
+        target = os.path.join(base_path, base_filename)
+        self.add_input_file(filename='base_mesh.nc', work_dir_target=target)
+
+    def run(self):
+        """
+        Run this step of the test case
+        """
+        with_ice_shelf_cavities = self.with_ice_shelf_cavities
+        logger = self.logger
+
+        # only use progress bars if we're not writing to a log file
+        use_progress_bar = self.log_filename is None
+
+        do_inject_bathymetry = self.do_inject_bathymetry
+        preserve_floodplain = self.preserve_floodplain
+
+        cull_mesh(with_critical_passages=True, logger=logger,
+                  use_progress_bar=use_progress_bar,
+                  preserve_floodplain=preserve_floodplain,
+                  with_cavities=with_ice_shelf_cavities,
+                  process_count=self.cpus_per_task)
+
+        if do_inject_bathymetry:
+            inject_bathymetry(mesh_file='culled_mesh.nc')
+
 
 def cull_mesh(with_cavities=False, with_critical_passages=False,
               custom_critical_passages=None, custom_land_blockages=None,

compass/ocean/mesh/floodplain.py

@@ -0,0 +1,63 @@
+from mpas_tools.ocean import inject_bathymetry, inject_preserve_floodplain
+
+from compass.mesh.spherical import QuasiUniformSphericalMeshStep
+
+
+class FloodplainMeshStep(QuasiUniformSphericalMeshStep):
+    """
+    A step for creating a global MPAS-Ocean mesh that includes variables
+    needed for preserving a floodplain
+
+    preserve_floodplain : bool
+        Whether the mesh includes land cells
+    """
+
+    def __init__(self, test_case, name='base_mesh', subdir=None,
+                 cell_width=None, preserve_floodplain=True):
+        """
+        Create a new step
+
+        Parameters
+        ----------
+        test_case : compass.testcase.TestCase
+            The test case this step belongs to
+
+        name : str
+            the name of the step
+
+        subdir : {str, None}
+            the subdirectory for the step.  The default is ``name``
+
+        cell_width : float, optional
+            The approximate cell width in km of the mesh if constant resolution
+
+        preserve_floodplain : bool, optional
+            Whether the mesh includes land cells
+        """
+
+        super().__init__(test_case=test_case, name=name, subdir=subdir,
+                         cell_width=cell_width)
+
+        self.preserve_floodplain = preserve_floodplain
+
+        self.add_input_file(filename='earth_relief_15s.nc',
+                            target='SRTM15_plus_earth_relief_15s.nc',
+                            database='bathymetry_database')
+
+    def run(self):
+        """
+        Run this step of the test case
+        """
+        super().run()
+
+        config = self.config
+
+        mesh_filename = config.get('spherical_mesh', 'mpas_mesh_filename')
+
+        inject_bathymetry(mesh_file=mesh_filename)
+        if self.preserve_floodplain:
+            floodplain_elevation = config.getfloat('spherical_mesh',
+                                                   'floodplain_elevation')
+            inject_preserve_floodplain(
+                mesh_file=mesh_filename,
+                floodplain_elevation=floodplain_elevation)

compass/ocean/tests/global_ocean/__init__.py

@@ -36,7 +36,7 @@ def __init__(self, mpas_core):
         super().__init__(mpas_core=mpas_core, name='global_ocean')
 
         # we do a lot of tests for QU240/QUwISC240
-        for mesh_name in ['QU240', 'QUwISC240']:
+        for mesh_name in ['QU240', 'Icos240', 'QUwISC240']:
             mesh = Mesh(test_group=self, mesh_name=mesh_name)
             self.add_test_case(mesh)
 

compass/ocean/tests/global_ocean/configure.py

@@ -18,8 +18,8 @@ def configure_global_ocean(test_case, mesh, init=None):
         The test case that produces the initial condition for this run
     """
     config = test_case.config
-    mesh_step = mesh.mesh_step
-    config.add_from_package(mesh_step.package, mesh_step.mesh_config_filename,
+    config.add_from_package('compass.mesh', 'mesh.cfg')
+    config.add_from_package(mesh.package, mesh.mesh_config_filename,
                             exception=True)
 
     if mesh.with_ice_shelf_cavities:

compass/ocean/tests/global_ocean/files_for_e3sm/ocean_graph_partition.py

@@ -38,7 +38,7 @@ def __init__(self, test_case, mesh, restart_filename):
         self.add_input_file(filename='restart.nc',
                             target='../{}'.format(restart_filename))
 
-        mesh_path = mesh.mesh_step.path
+        mesh_path = mesh.get_cull_mesh_path()
         self.add_input_file(
             filename='graph.info',
             work_dir_target='{}/culled_graph.info'.format(mesh_path))

compass/ocean/tests/global_ocean/forward.py

@@ -103,7 +103,7 @@ def __init__(self, test_case, mesh, init, time_integrator, name='forward',
             self.add_streams_file(
                 'compass.ocean.tests.global_ocean', 'streams.bgc')
 
-        mesh_package = mesh.mesh_step.package
+        mesh_package = mesh.package
         mesh_package_contents = list(contents(mesh_package))
         mesh_namelists = ['namelist.forward',
                           f'namelist.{time_integrator.lower()}']

compass/ocean/tests/global_ocean/global_ocean.cfg

@@ -1,15 +1,19 @@
-# options for global ocean testcases
-[global_ocean]
+# options for spherical meshes
+[spherical_mesh]
 
-## each mesh should replace these with appropriate values in its config file
-
-## config options related to the mesh step
+## config options related to the step for culling land from the mesh
 # number of cores to use
-mesh_cpus_per_task = 18
+cull_mesh_cpus_per_task = 18
 # minimum of cores, below which the step fails
-mesh_min_cpus_per_task = 1
+cull_mesh_min_cpus_per_task = 1
 # maximum memory usage allowed (in MB)
-mesh_max_memory = 1000
+cull_mesh_max_memory = 1000
+
+
+# options for global ocean testcases
+[global_ocean]
+
+## each mesh should replace these with appropriate values in its config file
 
 ## config options related to the initial_state step
 # number of cores to use

compass/ocean/tests/global_ocean/init/initial_state.py

@@ -113,7 +113,7 @@ def __init__(self, test_case, mesh, initial_condition, with_bgc):
                        '1timeLevel.nc',
                 database='initial_condition_database')
 
-        mesh_path = mesh.mesh_step.path
+        mesh_path = self.mesh.get_cull_mesh_path()
 
         self.add_input_file(
             filename='mesh.nc',
@@ -123,7 +123,7 @@ def __init__(self, test_case, mesh, initial_condition, with_bgc):
             filename='graph.info',
             work_dir_target=f'{mesh_path}/culled_graph.info')
 
-        if mesh.with_ice_shelf_cavities:
+        if self.mesh.with_ice_shelf_cavities:
             self.add_input_file(
                 filename='land_ice_mask.nc',
                 work_dir_target=f'{mesh_path}/land_ice_mask.nc')

compass/ocean/tests/global_ocean/init/ssh_adjustment.py

@@ -49,7 +49,7 @@ def __init__(self, test_case, ntasks=None, min_tasks=None,
         self.add_streams_file('compass.ocean.tests.global_ocean.init',
                               'streams.ssh_adjust')
 
-        mesh_path = test_case.mesh.mesh_step.path
+        mesh_path = test_case.mesh.get_cull_mesh_path()
         init_path = test_case.steps['initial_state'].path
 
         self.add_input_file(