Merge pull request #785 from sbrus89/subgrid_pr

Add test cases for subgrid scale wetting and drying corrections

compass/ocean/__init__.py

@@ -1,5 +1,6 @@
 from compass.mpas_core import MpasCore
 from compass.ocean.tests.baroclinic_channel import BaroclinicChannel
+from compass.ocean.tests.buttermilk_bay import ButtermilkBay
 from compass.ocean.tests.dam_break import DamBreak
 from compass.ocean.tests.drying_slope import DryingSlope
 from compass.ocean.tests.global_convergence import GlobalConvergence
@@ -37,6 +38,7 @@ def __init__(self):
         super().__init__(name='ocean')
 
         self.add_test_group(BaroclinicChannel(mpas_core=self))
+        self.add_test_group(ButtermilkBay(mpas_core=self))
         self.add_test_group(DamBreak(mpas_core=self))
         self.add_test_group(DryingSlope(mpas_core=self))
         self.add_test_group(GlobalConvergence(mpas_core=self))

compass/ocean/tests/buttermilk_bay/__init__.py

@@ -0,0 +1,18 @@
+from compass.ocean.tests.buttermilk_bay.default import Default
+from compass.testgroup import TestGroup
+
+
+class ButtermilkBay(TestGroup):
+    """
+    A test group for Buttermilk Bay (subgrid wetting-and-drying) test cases
+    """
+
+    def __init__(self, mpas_core):
+        """
+        mpas_core : compass.MpasCore
+            the MPAS core that this test group belongs to
+        """
+        super().__init__(mpas_core=mpas_core, name='buttermilk_bay')
+        for wetdry in ['standard', 'subgrid']:
+            self.add_test_case(
+                Default(test_group=self, wetdry=wetdry))

compass/ocean/tests/buttermilk_bay/buttermilk_bay.cfg

@@ -0,0 +1,33 @@
+[job]
+
+wall_time = 2:00:00
+
+
+# config options for buttermilk bay
+[buttermilk_bay]
+
+# dimensions of domain in x and y directions (m)
+Lx = 4608
+Ly = 4608
+
+# a list of resolutions (m) to test
+resolutions = 256, 128, 64
+
+# time step per resolution (s/m), since dt is proportional to resolution
+dt_per_m = 0.02
+
+# the number of cells per core to aim for
+goal_cells_per_core = 300
+
+# the approximate maximum number of cells per core (the test will fail if too
+# few cores are available)
+max_cells_per_core = 3000
+
+# config options for visualizing drying slope ouptut
+[buttermilk_bay_viz]
+
+# coordinates (in km) for timeseries plot
+points = [2.8, 0.53], [1.9, 1.66], [2.4, 3.029], [2.51, 3.027], [1.26, 1.56]
+
+# generate contour plots at a specified interval between output timesnaps
+plot_interval = 1

compass/ocean/tests/buttermilk_bay/default/__init__.py

@@ -0,0 +1,141 @@
+import numpy as np
+
+from compass.config import CompassConfigParser
+from compass.ocean.tests.buttermilk_bay.forward import Forward
+from compass.ocean.tests.buttermilk_bay.initial_state import InitialState
+from compass.ocean.tests.buttermilk_bay.viz import Viz
+from compass.testcase import TestCase
+from compass.validate import compare_variables
+
+
+class Default(TestCase):
+    """
+    The default buttermilk_bay test case
+
+    Attributes
+    ----------
+    wetdry : str
+        The type of wetting and drying (``standard``, ``subgrid``)
+    """
+
+    def __init__(self, test_group, wetdry):
+        """
+        Create the test case
+
+        Parameters
+        ----------
+        test_group : compass.ocean.tests.buttermilk_bay.ButtermilkBay
+            The test group that this test case belongs to
+
+        wetdry : str
+            The type of wetting and drying used (``standard``, ``subgrid``)
+        """
+        name = wetdry
+        subdir = wetdry
+        super().__init__(test_group=test_group, name=name,
+                         subdir=subdir)
+
+        self.resolutions = None
+        self.wetdry = wetdry
+        # add the steps with default resolutions so they can be listed
+        config = CompassConfigParser()
+        config.add_from_package('compass.ocean.tests.buttermilk_bay',
+                                'buttermilk_bay.cfg')
+        self._setup_steps(config)
+
+    def configure(self):
+        """
+        Set config options for the test case
+        """
+        config = self.config
+        # set up the steps again in case a user has provided new resolutions
+        self._setup_steps(config)
+
+        self.update_cores()
+
+    def update_cores(self):
+        """ Update the number of cores and min_tasks for each forward step """
+
+        config = self.config
+
+        goal_cells_per_core = config.getfloat('buttermilk_bay',
+                                              'goal_cells_per_core')
+        max_cells_per_core = config.getfloat('buttermilk_bay',
+                                             'max_cells_per_core')
+        lx = config.getfloat('buttermilk_bay', 'Lx')
+        ly = config.getfloat('buttermilk_bay', 'Ly')
+
+        for resolution in self.resolutions:
+
+            nx = 2 * int(0.5 * lx / resolution + 0.5)
+            ny = 2 * int(0.5 * ly * (2. / np.sqrt(3)) / resolution + 0.5)
+
+            approx_cells = nx * ny
+            # ideally, about 300 cells per core
+            # (make it a multiple of 4 because...it looks better?)
+            ntasks = max(1,
+                         4 * round(approx_cells / (4 * goal_cells_per_core)))
+            # In a pinch, about 3000 cells per core
+            min_tasks = max(1,
+                            round(approx_cells / max_cells_per_core))
+
+            res_name = f'{resolution}m'
+            step = self.steps[f'forward_{res_name}']
+            step.ntasks = ntasks
+            step.min_tasks = min_tasks
+
+            config.set('buttermilk_bay', f'{res_name}_ntasks', str(ntasks),
+                       comment=f'Target core count for {res_name} mesh')
+            config.set('buttermilk_bay', f'{res_name}_min_tasks',
+                       str(min_tasks),
+                       comment=f'Minimum core count for {res_name} mesh')
+
+    def _setup_steps(self, config):
+        """ setup steps given resolutions """
+
+        default_resolutions = '256, 128, 64'
+
+        # set the default values that a user may change before setup
+        config.set('buttermilk_bay', 'resolutions', default_resolutions,
+                   comment='a list of resolutions (m) to test')
+
+        # get the resolutions back, perhaps with values set in the user's
+        # config file
+        resolutions = config.getlist('buttermilk_bay',
+                                     'resolutions', dtype=int)
+
+        if self.resolutions is not None and self.resolutions == resolutions:
+            return
+
+        # start fresh with no steps
+        self.steps = dict()
+        self.steps_to_run = list()
+
+        self.resolutions = resolutions
+
+        for resolution in self.resolutions:
+
+            res_name = f'{resolution}m'
+
+            init_step = InitialState(test_case=self,
+                                     name=f'initial_state_{res_name}',
+                                     resolution=resolution,
+                                     wetdry=self.wetdry)
+            self.add_step(init_step)
+            self.add_step(Forward(test_case=self,
+                                  name=f'forward_{res_name}',
+                                  resolution=resolution,
+                                  wetdry=self.wetdry))
+        self.add_step(Viz(test_case=self,
+                          wetdry=self.wetdry,
+                          resolutions=resolutions))
+
+    def validate(self):
+        """
+        Validate variables against a baseline
+        """
+        super().validate()
+        variables = ['layerThickness', 'normalVelocity']
+        for res in self.resolutions:
+            compare_variables(test_case=self, variables=variables,
+                              filename1=f'forward_{res}m/output.nc')

compass/ocean/tests/buttermilk_bay/forward.py

@@ -0,0 +1,122 @@
+import time
+
+from compass.model import run_model
+from compass.step import Step
+
+
+class Forward(Step):
+    """
+    A step for performing forward MPAS-Ocean runs as part of buttermilk bay
+    test cases.
+    """
+    def __init__(self, test_case, resolution,
+                 name,
+                 coord_type='single_layer',
+                 wetdry='standard'):
+        """
+        Create a new test case
+
+        Parameters
+        ----------
+        test_case : compass.TestCase
+            The test case this step belongs to
+
+        resolution : float
+            The resolution of the test case
+
+        name : str
+            The name of the test case
+
+        subdir : str, optional
+            The subdirectory for the step.  The default is ``name``
+
+        coord_type : str, optional
+            Vertical coordinate configuration
+        """
+
+        self.resolution = resolution
+
+        super().__init__(test_case=test_case, name=name)
+
+        self.add_namelist_file('compass.ocean.tests.buttermilk_bay',
+                               'namelist.forward')
+
+        res_name = f'{resolution}m'
+        self.add_namelist_file('compass.ocean.tests.buttermilk_bay',
+                               f'namelist.{coord_type}.forward')
+
+        if wetdry == 'subgrid':
+            self.add_namelist_file('compass.ocean.tests.buttermilk_bay',
+                                   'namelist.subgrid.forward')
+            self.add_streams_file('compass.ocean.tests.buttermilk_bay',
+                                  'streams.subgrid.forward')
+        else:
+            self.add_streams_file('compass.ocean.tests.buttermilk_bay',
+                                  'streams.forward')
+        input_path = f'../initial_state_{res_name}'
+        self.add_input_file(filename='mesh.nc',
+                            target=f'{input_path}/culled_mesh.nc')
+        self.add_input_file(filename='init.nc',
+                            target=f'{input_path}/ocean.nc')
+        self.add_input_file(filename='graph.info',
+                            target=f'{input_path}/culled_graph.info')
+        self.add_input_file(filename='forcing.nc',
+                            target=f'{input_path}/init_mode_forcing_data.nc')
+
+        self.add_model_as_input()
+
+        self.add_output_file(filename='output.nc')
+
+    def setup(self):
+        """
+        Set namelist options based on config options
+        """
+        dt = self.get_dt()
+        self.add_namelist_options({'config_dt': dt})
+        self._get_resources()
+
+    def constrain_resources(self, available_cores):
+        """
+        Update resources at runtime from config options
+        """
+        self._get_resources()
+        super().constrain_resources(available_cores)
+
+    def run(self):
+        """
+        Run this step of the testcase
+        """
+        # update dt in case the user has changed dt_per_m
+        dt = self.get_dt()
+        self.update_namelist_at_runtime(options={'config_dt': dt},
+                                        out_name='namelist.ocean')
+
+        run_model(self)
+
+    def get_dt(self):
+        """
+        Get the time step
+
+        Returns
+        -------
+        dt : str
+            the time step in HH:MM:SS
+        """
+        config = self.config
+        # dt is proportional to resolution
+        dt_per_m = config.getfloat('buttermilk_bay', 'dt_per_m')
+
+        dt = dt_per_m * self.resolution
+        # https://stackoverflow.com/a/1384565/7728169
+        dt = time.strftime('%H:%M:%S', time.gmtime(dt))
+
+        return dt
+
+    def _get_resources(self):
+        """ get the these properties from the config options """
+        config = self.config
+        self.ntasks = config.getint('buttermilk_bay',
+                                    f'{self.resolution}m_ntasks')
+        self.min_tasks = config.getint('buttermilk_bay',
+                                       f'{self.resolution}m_min_tasks')
+        self.openmp_threads = 1