Merge pull request #501 from cbegeman/port-overflow-test-group

Port overflow test group

compass/ocean/__init__.py

@@ -11,6 +11,7 @@
 from compass.ocean.tests.isomip_plus import IsomipPlus
 from compass.ocean.tests.merry_go_round import MerryGoRound
 from compass.ocean.tests.nonhydro import Nonhydro
+from compass.ocean.tests.overflow import Overflow
 from compass.ocean.tests.planar_convergence import PlanarConvergence
 from compass.ocean.tests.soma import Soma
 from compass.ocean.tests.sphere_transport import SphereTransport
@@ -43,6 +44,7 @@ def __init__(self):
         self.add_test_group(IsomipPlus(mpas_core=self))
         self.add_test_group(MerryGoRound(mpas_core=self))
         self.add_test_group(Nonhydro(mpas_core=self))
+        self.add_test_group(Overflow(mpas_core=self))
         self.add_test_group(PlanarConvergence(mpas_core=self))
         self.add_test_group(Soma(mpas_core=self))
         self.add_test_group(SphereTransport(mpas_core=self))

compass/ocean/tests/overflow/__init__.py

@@ -0,0 +1,46 @@
+from compass.testgroup import TestGroup
+from compass.ocean.tests.overflow.default import Default
+from compass.ocean.tests.overflow.rpe_test import RpeTest
+
+
+class Overflow(TestGroup):
+    """
+    A test group for General Ocean Turbulence Model (GOTM) 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='overflow')
+
+        self.add_test_case(Default(test_group=self, resolution='10km'))
+        self.add_test_case(RpeTest(test_group=self, resolution='2km'))
+
+
+def configure(resolution, config):
+    """
+    Modify the configuration options for one of the overflow test cases
+
+    Parameters
+    ----------
+    resolution : str
+        The resolution of the test case
+
+    config : compass.config.CompassConfigParser
+        Configuration options for this test case
+    """
+    width = config.getint('overflow', 'width')
+    length = config.getint('overflow', 'length')
+
+    dc = float(resolution[:-2])
+    nx = int(width/dc)
+    ny = int(length/dc)
+
+    config.set('overflow', 'nx', str(nx),
+               comment='the number of mesh cells in the x direction')
+    config.set('overflow', 'ny', str(ny),
+               comment='the number of mesh cells in the y direction')
+    config.set('overflow', 'dc', str(dc*1e3),
+               comment='the distance between adjacent cell centers')

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

@@ -0,0 +1,45 @@
+from compass.testcase import TestCase
+from compass.ocean.tests.overflow.initial_state import InitialState
+from compass.ocean.tests.overflow.forward import Forward
+from compass.ocean.tests import overflow
+from compass.validate import compare_variables
+
+
+class Default(TestCase):
+    """
+    The default test case for the overflow test
+
+    Attributes
+    ----------
+    resolution : str
+        The resolution of the test case
+    """
+
+    def __init__(self, test_group, resolution):
+        """
+        Create the test case
+
+        Parameters
+        ----------
+        test_group : compass.ocean.tests.overflow.Overflow
+            The test group that this test case belongs to
+        """
+        super().__init__(test_group=test_group, name='default',
+                         subdir=f'{resolution}/default')
+        self.resolution = resolution
+        self.add_step(InitialState(test_case=self))
+        self.add_step(Forward(test_case=self, ntasks=4, openmp_threads=1))
+
+    def configure(self):
+        """
+        Modify the configuration options for this test case.
+        """
+        overflow.configure(self.resolution, self.config)
+
+    def validate(self):
+        """
+        Validate variables against a baseline
+        """
+        compare_variables(test_case=self,
+                          variables=['layerThickness', 'temperature'],
+                          filename1='forward/output.nc')

compass/ocean/tests/overflow/forward.py

@@ -0,0 +1,74 @@
+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 overflow
+    test cases.
+    """
+    def __init__(self, test_case, name='forward', subdir=None,
+                 ntasks=1, min_tasks=None, openmp_threads=1, nu=None):
+        """
+        Create a new test case
+
+        Parameters
+        ----------
+        test_case : compass.TestCase
+            The test case this step belongs to
+
+        name : str
+            the name of the test case
+
+        subdir : str, optional
+            the subdirectory for the step.  The default is ``name``
+
+        ntasks : int, optional
+            the number of tasks the step would ideally use.  If fewer tasks
+            are available on the system, the step will run on all available
+            tasks as long as this is not below ``min_tasks``
+
+        min_tasks : int, optional
+            the number of tasks the step requires.  If the system has fewer
+            than this number of tasks, the step will fail
+
+        openmp_threads : int, optional
+            the number of OpenMP threads the step will use
+
+        """
+        if min_tasks is None:
+            min_tasks = ntasks
+        super().__init__(test_case=test_case, name=name, subdir=subdir,
+                         ntasks=ntasks, min_tasks=min_tasks,
+                         openmp_threads=openmp_threads)
+        self.add_namelist_file('compass.ocean.tests.overflow',
+                               'namelist.forward')
+        if nu is not None:
+            # update the viscosity to the requested value
+            options = {'config_mom_del2': f'{nu}'}
+            self.add_namelist_options(options)
+
+        # make sure output is double precision
+        self.add_streams_file('compass.ocean.streams', 'streams.output')
+
+        self.add_streams_file('compass.ocean.tests.overflow',
+                              'streams.forward')
+
+        self.add_input_file(filename='init.nc',
+                            target='../initial_state/ocean.nc')
+        self.add_input_file(filename='mesh.nc',
+                            target='../initial_state/culled_mesh.nc')
+        self.add_input_file(filename='graph.info',
+                            target='../initial_state/culled_graph.info')
+
+        self.add_model_as_input()
+
+        self.add_output_file(filename='output.nc')
+
+    # no setup() is needed
+
+    def run(self):
+        """
+        Run this step of the test case
+        """
+        run_model(self)

compass/ocean/tests/overflow/initial_state.py

@@ -0,0 +1,82 @@
+import xarray
+
+from mpas_tools.planar_hex import make_planar_hex_mesh
+from mpas_tools.io import write_netcdf
+from mpas_tools.mesh.conversion import convert, cull
+
+from compass.step import Step
+from compass.model import run_model
+
+
+class InitialState(Step):
+    """
+    A step for creating a mesh and initial condition for overflow test
+    cases
+    """
+    def __init__(self, test_case):
+        """
+        Create the step
+
+        Parameters
+        ----------
+        test_case : compass.testcase.Testcase
+            The test case this step belongs to
+        """
+        super().__init__(test_case=test_case, name='initial_state', ntasks=1,
+                         min_tasks=1, openmp_threads=1)
+
+        self.add_namelist_file('compass.ocean.tests.overflow',
+                               'namelist.init', mode='init')
+
+        self.add_streams_file('compass.ocean.tests.overflow',
+                              'streams.init', mode='init')
+
+        for file in ['base_mesh.nc', 'culled_mesh.nc', 'culled_graph.info',
+                     'ocean.nc']:
+            self.add_output_file(file)
+
+        self.add_model_as_input()
+
+    def run(self):
+        """
+        Run this step of the test case
+        """
+        config = self.config
+        logger = self.logger
+
+        section = config['overflow']
+        nx = section.getint('nx')
+        ny = section.getint('ny')
+        dc = section.getfloat('dc')
+
+        self.update_namelist_at_runtime(
+           {'config_overflow_dc': f'{dc}'})
+
+        logger.info(' * Make planar hex mesh')
+        ds_mesh = make_planar_hex_mesh(nx=nx, ny=ny, dc=dc, nonperiodic_x=True,
+                                       nonperiodic_y=False)
+        logger.info(' * Completed Make planar hex mesh')
+        write_netcdf(ds_mesh, 'base_mesh.nc')
+
+        logger.info(' * Cull mesh boundaries')
+        ds_mesh = cull(ds_mesh, logger=logger)
+        logger.info(' * Convert mesh')
+        ds_mesh = convert(ds_mesh, graphInfoFileName='culled_graph.info',
+                          logger=logger)
+        logger.info(' * Completed Convert mesh')
+        write_netcdf(ds_mesh, 'culled_mesh.nc')
+
+        run_model(self, namelist='namelist.ocean',
+                  streams='streams.ocean')
+
+        postrun_data = xarray.open_dataset('ocean.nc')
+        logger.info(' * Cull mesh dam boundaries')
+        postrun_data_cull = cull(postrun_data, logger=logger)
+        logger.info(' * Convert mesh')
+        postrun_data_cull = convert(postrun_data_cull,
+                                    graphInfoFileName='culled_graph.info',
+                                    logger=logger)
+        write_netcdf(postrun_data_cull, 'culled_mesh.nc')
+
+        run_model(self, namelist='namelist.ocean',
+                  streams='streams.ocean')

compass/ocean/tests/overflow/namelist.forward

@@ -0,0 +1,7 @@
+config_dt='0000_00:01:00'
+config_btr_dt='0000_00:00:09'
+config_run_duration='0000_00:12:00'
+config_use_cvmix_convection=.true.
+config_implicit_bottom_drag_coeff=1.0e-2
+config_use_mom_del2=.true.
+config_mom_del2=1.0e3

compass/ocean/tests/overflow/namelist.init

@@ -0,0 +1,4 @@
+config_init_configuration='overflow'
+config_overflow_use_distances=.true.
+config_overflow_layer_type='sigma'
+config_overflow_vert_levels=50

compass/ocean/tests/overflow/overflow.cfg

@@ -0,0 +1,11 @@
+# Options related to the overflow case
+[overflow]
+
+# The width of the domain in the across-slope dimension (km)
+width = 40
+
+# The length of the domain in the along-slope dimension (km)
+length = 200
+
+# Viscosity values to test for rpe test case
+viscosities = 1, 5, 10, 100, 1000

compass/ocean/tests/overflow/rpe_test/__init__.py

@@ -0,0 +1,71 @@
+from compass.testcase import TestCase
+from compass.ocean.tests.overflow.initial_state import InitialState
+from compass.ocean.tests.overflow.forward import Forward
+from compass.ocean.tests.overflow.rpe_test.analysis import Analysis
+from compass.ocean.tests import overflow
+
+
+class RpeTest(TestCase):
+    """
+    The reference potential energy (RPE) test case for the overflow
+    test group performs a 40h integration of the model forward in time at
+    5 different values of the viscosity at the given resolution.
+
+    Attributes
+    ----------
+    resolution : str
+        The resolution of the test case
+    """
+
+    def __init__(self, test_group, resolution='1km'):
+        """
+        Create the test case
+
+        Parameters
+        ----------
+        test_group : compass.ocean.tests.overflow.Overflow
+            The test group that this test case belongs to
+
+        """
+        name = 'rpe_test'
+        subdir = f'{resolution}/{name}'
+        super().__init__(test_group=test_group, name=name,
+                         subdir=subdir)
+
+        self.resolution = resolution
+        self.nus = None
+
+
+    def configure(self):
+        """
+        Modify the configuration options for this test case.
+        """
+        config = self.config
+        resolution = self.resolution
+
+        overflow.configure(resolution, config)
+
+        nus = config.getlist('overflow', 'viscosities', dtype=float)
+        self.nus = nus
+
+        self.add_step(
+            InitialState(test_case=self))
+
+        for index, nu in enumerate(nus):
+            name = f'rpe_test_{index + 1}_nu_{int(nu)}'
+            step = Forward(
+                test_case=self, name=name, subdir=name,
+                ntasks=64, min_tasks=16, openmp_threads=1,
+                nu=float(nu))
+
+            step.add_namelist_file(
+                'compass.ocean.tests.overflow.rpe_test',
+                'namelist.forward')
+            step.add_streams_file(
+                'compass.ocean.tests.overflow.rpe_test',
+                'streams.forward')
+            self.add_step(step)
+
+        self.add_step(
+            Analysis(test_case=self, resolution=resolution, nus=nus))
+    # no run() is needed because we're doing the default: running all steps