Add sea-ice graph partitioning to files_for_e3sm test case

compass/ocean/tests/global_ocean/__init__.py

@@ -1,28 +1,31 @@
-from compass.testgroup import TestGroup
-
-from compass.ocean.tests.global_ocean.mesh import Mesh
-from compass.ocean.tests.global_ocean.mesh.qu240.dynamic_adjustment import \
-    QU240DynamicAdjustment
-from compass.ocean.tests.global_ocean.mesh.ec30to60.dynamic_adjustment import \
-    EC30to60DynamicAdjustment
-from compass.ocean.tests.global_ocean.mesh.arrm10to60.dynamic_adjustment \
-    import ARRM10to60DynamicAdjustment
-from compass.ocean.tests.global_ocean.mesh.so12to60.dynamic_adjustment import \
-    SO12to60DynamicAdjustment
-from compass.ocean.tests.global_ocean.mesh.wc14.dynamic_adjustment import \
-    WC14DynamicAdjustment
+from compass.ocean.tests.global_ocean.analysis_test import AnalysisTest
+from compass.ocean.tests.global_ocean.daily_output_test import DailyOutputTest
+from compass.ocean.tests.global_ocean.decomp_test import DecompTest
+from compass.ocean.tests.global_ocean.files_for_e3sm import FilesForE3SM
 from compass.ocean.tests.global_ocean.init import Init
+from compass.ocean.tests.global_ocean.mesh import Mesh
+from compass.ocean.tests.global_ocean.mesh.arrm10to60.dynamic_adjustment import (  # noqa: E501
+    ARRM10to60DynamicAdjustment,
+)
+from compass.ocean.tests.global_ocean.mesh.ec30to60.dynamic_adjustment import (
+    EC30to60DynamicAdjustment,
+)
+from compass.ocean.tests.global_ocean.mesh.qu240.dynamic_adjustment import (
+    QU240DynamicAdjustment,
+)
+from compass.ocean.tests.global_ocean.mesh.so12to60.dynamic_adjustment import (
+    SO12to60DynamicAdjustment,
+)
+from compass.ocean.tests.global_ocean.mesh.wc14.dynamic_adjustment import (
+    WC14DynamicAdjustment,
+)
+from compass.ocean.tests.global_ocean.monthly_output_test import (
+    MonthlyOutputTest,
+)
 from compass.ocean.tests.global_ocean.performance_test import PerformanceTest
 from compass.ocean.tests.global_ocean.restart_test import RestartTest
-from compass.ocean.tests.global_ocean.decomp_test import DecompTest
 from compass.ocean.tests.global_ocean.threads_test import ThreadsTest
-from compass.ocean.tests.global_ocean.analysis_test import AnalysisTest
-from compass.ocean.tests.global_ocean.daily_output_test import DailyOutputTest
-from compass.ocean.tests.global_ocean.monthly_output_test import \
-    MonthlyOutputTest
-from compass.ocean.tests.global_ocean.files_for_e3sm import FilesForE3SM
-from compass.ocean.tests.global_ocean.make_diagnostics_files import \
-    MakeDiagnosticsFiles
+from compass.testgroup import TestGroup
 
 
 class GlobalOcean(TestGroup):
@@ -226,5 +229,5 @@ def __init__(self, mpas_core):
                     test_group=self, mesh=mesh, init=init,
                     dynamic_adjustment=dynamic_adjustment))
 
-        # A test case for making diagnostics files from an existing mesh
-        self.add_test_case(MakeDiagnosticsFiles(test_group=self))
+        # A test case for making E3SM support files from an existing mesh
+        self.add_test_case(FilesForE3SM(test_group=self))

compass/ocean/tests/global_ocean/files_for_e3sm/README

@@ -4,13 +4,13 @@ only a subset of the files needed for E3SM support of a new
 ocean and sea-ice mesh.
 ***********************************************************
 
-After running run.py, the directory assembled_files is populated with links.
-The directory structure is identical to the E3SM inputdata and diagnostics
-directories found here:
+After running "compass run", the directory assembled_files is populated with
+links. The directory structure is identical to the E3SM inputdata and
+diagnostics directories found here:
 https://web.lcrc.anl.gov/public/e3sm/
 
 E3SM members should NOT attempt to upload these files.  The files produced here
 are only a subset of those needed to support a new mesh in E3SM and should not
 be uploaded on their own. E3SM experts who know how to produce the other
 coupling files may upload these files along with other required datasets to the
-LCRC server.
+LCRC server.

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

@@ -1,20 +1,31 @@
 import os
 
-from compass.io import symlink, package_path
-from compass.testcase import TestCase
-from compass.ocean.tests.global_ocean.files_for_e3sm.ocean_initial_condition \
-    import OceanInitialCondition
-from compass.ocean.tests.global_ocean.files_for_e3sm.seaice_initial_condition \
-    import SeaiceInitialCondition
-from compass.ocean.tests.global_ocean.files_for_e3sm.ocean_graph_partition \
-    import OceanGraphPartition
+from compass.io import package_path, symlink
+from compass.ocean.tests.global_ocean.configure import configure_global_ocean
+from compass.ocean.tests.global_ocean.files_for_e3sm.diagnostic_maps import (
+    DiagnosticMaps,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.diagnostic_masks import (
+    DiagnosticMasks,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.e3sm_to_cmip_maps import (
+    E3smToCmipMaps,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.ocean_graph_partition import (  # noqa: E501
+    OceanGraphPartition,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.ocean_initial_condition import (  # noqa: E501
+    OceanInitialCondition,
+)
 from compass.ocean.tests.global_ocean.files_for_e3sm.scrip import Scrip
-from compass.ocean.tests.global_ocean.files_for_e3sm.e3sm_to_cmip_maps import \
-    E3smToCmipMaps
-from compass.ocean.tests.global_ocean.files_for_e3sm.diagnostics_files \
-    import DiagnosticsFiles
+from compass.ocean.tests.global_ocean.files_for_e3sm.seaice_graph_partition import (  # noqa: E501
+    SeaiceGraphPartition,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.seaice_initial_condition import (  # noqa: E501
+    SeaiceInitialCondition,
+)
 from compass.ocean.tests.global_ocean.forward import get_forward_subdir
-from compass.ocean.tests.global_ocean.configure import configure_global_ocean
+from compass.testcase import TestCase
 
 
 class FilesForE3SM(TestCase):
@@ -34,12 +45,9 @@ class FilesForE3SM(TestCase):
     dynamic_adjustment : compass.ocean.tests.global_ocean.dynamic_adjustment.DynamicAdjustment
         The test case that performs dynamic adjustment to dissipate
         fast-moving waves from the initial condition
-
-    restart_filename : str
-        A restart file from the end of the dynamic adjustment test case to use
-        as the basis for an E3SM initial condition
-    """
-    def __init__(self, test_group, mesh, init, dynamic_adjustment):
+    """  # noqa: E501
+    def __init__(self, test_group, mesh=None, init=None,
+                 dynamic_adjustment=None):
         """
         Create test case for creating a global MPAS-Ocean mesh
 
@@ -48,62 +56,69 @@ def __init__(self, test_group, mesh, init, dynamic_adjustment):
         test_group : compass.ocean.tests.global_ocean.GlobalOcean
             The global ocean test group that this test case belongs to
 
-        mesh : compass.ocean.tests.global_ocean.mesh.Mesh
+        mesh : compass.ocean.tests.global_ocean.mesh.Mesh, optional
             The test case that produces the mesh for this run
 
-        init : compass.ocean.tests.global_ocean.init.Init
+        init : compass.ocean.tests.global_ocean.init.Init, optional
             The test case that produces the initial condition for this run
 
-        dynamic_adjustment : compass.ocean.tests.global_ocean.dynamic_adjustment.DynamicAdjustment
+        dynamic_adjustment : compass.ocean.tests.global_ocean.dynamic_adjustment.DynamicAdjustment, optional
             The test case that performs dynamic adjustment to dissipate
             fast-moving waves from the initial condition
-        """
+        """  # noqa: E501
         name = 'files_for_e3sm'
-        time_integrator = dynamic_adjustment.time_integrator
-        subdir = get_forward_subdir(init.init_subdir, time_integrator, name)
+        if dynamic_adjustment is not None:
+            time_integrator = dynamic_adjustment.time_integrator
+            subdir = get_forward_subdir(
+                init.init_subdir, time_integrator, name)
+        else:
+            subdir = name
 
         super().__init__(test_group=test_group, name=name, subdir=subdir)
         self.mesh = mesh
         self.init = init
         self.dynamic_adjustment = dynamic_adjustment
 
-        restart_filename = os.path.join(
-            '..', 'dynamic_adjustment',
-            dynamic_adjustment.restart_filenames[-1])
-        self.restart_filename = restart_filename
-
-        self.add_step(
-            OceanInitialCondition(test_case=self,
-                                  restart_filename=restart_filename))
-
-        self.add_step(
-            OceanGraphPartition(test_case=self, mesh=mesh,
-                                restart_filename=restart_filename))
-
-        self.add_step(
-            SeaiceInitialCondition(
-                test_case=self, restart_filename=restart_filename,
-                with_ice_shelf_cavities=mesh.with_ice_shelf_cavities))
-
-        self.add_step(
-            Scrip(
-                test_case=self, restart_filename=restart_filename,
-                with_ice_shelf_cavities=mesh.with_ice_shelf_cavities))
-
-        self.add_step(
-            E3smToCmipMaps(
-                test_case=self, restart_filename=restart_filename))
-
-        self.add_step(
-            DiagnosticsFiles(
-                test_case=self, restart_filename=restart_filename,
-                with_ice_shelf_cavities=mesh.with_ice_shelf_cavities))
+        self.add_step(OceanInitialCondition(test_case=self))
+        self.add_step(OceanGraphPartition(test_case=self))
+        self.add_step(SeaiceInitialCondition(test_case=self))
+        self.add_step(SeaiceGraphPartition(test_case=self))
+        self.add_step(Scrip(test_case=self))
+        self.add_step(E3smToCmipMaps(test_case=self))
+        self.add_step(DiagnosticMaps(test_case=self))
+        self.add_step(DiagnosticMasks(test_case=self))
 
     def configure(self):
         """
         Modify the configuration options for this test case
         """
-        configure_global_ocean(test_case=self, mesh=self.mesh, init=self.init)
+        mesh = self.mesh
+        init = self.init
+        dynamic_adjustment = self.dynamic_adjustment
+        config = self.config
+        work_dir = self.work_dir
+
+        if mesh is not None:
+            configure_global_ocean(test_case=self, mesh=mesh,
+                                   init=init)
         package = 'compass.ocean.tests.global_ocean.files_for_e3sm'
         with package_path(package, 'README') as target:
-            symlink(str(target), '{}/README'.format(self.work_dir))
+            symlink(str(target), f'{work_dir}/README')
+
+        if mesh is not None:
+            config.set('files_for_e3sm', 'with_ice_shelf_cavities',
+                       f'{mesh.with_ice_shelf_cavities}')
+
+            mesh_path = mesh.get_cull_mesh_path()
+            graph_filename = os.path.join(
+                self.base_work_dir, mesh_path, 'culled_graph.info')
+            graph_filename = os.path.abspath(graph_filename)
+            config.set('files_for_e3sm', 'graph_filename', graph_filename)
+
+        if dynamic_adjustment is not None:
+            restart_filename = os.path.join(
+                work_dir, '..', 'dynamic_adjustment',
+                dynamic_adjustment.restart_filenames[-1])
+            restart_filename = os.path.abspath(restart_filename)
+            config.set('files_for_e3sm', 'ocean_restart_filename',
+                       restart_filename)