Add cached meshes and ICs to global_ocean

For most supported meshes (except SOwISC12to60) and for the PHC
initial condition, this merge adds "cached" versions of each mesh,
init and performance_test test case.  QU*240 meshes also have restart,
decomposition and thread tests.  The steps of each "cached" test case
use files from a new database, "compass_cache", that has the same
directory structure as the non-cached test cases, e.g.:
global_ocean/QU240/mesh/mesh
global_ocean/QU240/PHC/init/initial_state
The mesh and init test cases are just stubs that create the
expected symlinks and cause the cached files to be downloaded
during setup if needed.

Author: xylar

compass/ocean/cached_files.json

@@ -0,0 +1,29 @@
+{
+    "ocean/global_ocean/cached/QU240/mesh/mesh/culled_mesh.nc": "global_ocean/QU240/mesh/mesh/culled_mesh.210727.nc",
+    "ocean/global_ocean/cached/QU240/mesh/mesh/culled_graph.info": "global_ocean/QU240/mesh/mesh/culled_graph.210727.info",
+    "ocean/global_ocean/cached/QU240/mesh/mesh/critical_passages_mask_final.nc": "global_ocean/QU240/mesh/mesh/critical_passages_mask_final.210727.nc",
+    "ocean/global_ocean/cached/QU240/PHC/init/initial_state/initial_state.nc": "global_ocean/QU240/PHC/init/initial_state/initial_state.210727.nc",
+    "ocean/global_ocean/cached/QU240/PHC/init/initial_state/init_mode_forcing_data.nc": "global_ocean/QU240/PHC/init/initial_state/init_mode_forcing_data.210727.nc",
+    "ocean/global_ocean/cached/EC30to60/mesh/mesh/culled_mesh.nc": "global_ocean/EC30to60/mesh/mesh/culled_mesh.210727.nc",
+    "ocean/global_ocean/cached/EC30to60/mesh/mesh/culled_graph.info": "global_ocean/EC30to60/mesh/mesh/culled_graph.210727.info",
+    "ocean/global_ocean/cached/EC30to60/mesh/mesh/critical_passages_mask_final.nc": "global_ocean/EC30to60/mesh/mesh/critical_passages_mask_final.210727.nc",
+    "ocean/global_ocean/cached/EC30to60/PHC/init/initial_state/initial_state.nc": "global_ocean/EC30to60/PHC/init/initial_state/initial_state.210727.nc",
+    "ocean/global_ocean/cached/EC30to60/PHC/init/initial_state/init_mode_forcing_data.nc": "global_ocean/EC30to60/PHC/init/initial_state/init_mode_forcing_data.210727.nc",
+    "ocean/global_ocean/cached/WC14/mesh/mesh/culled_mesh.nc": "global_ocean/WC14/mesh/mesh/culled_mesh.210727.nc",
+    "ocean/global_ocean/cached/WC14/mesh/mesh/culled_graph.info": "global_ocean/WC14/mesh/mesh/culled_graph.210727.info",
+    "ocean/global_ocean/cached/WC14/mesh/mesh/critical_passages_mask_final.nc": "global_ocean/WC14/mesh/mesh/critical_passages_mask_final.210727.nc",
+    "ocean/global_ocean/cached/WC14/PHC/init/initial_state/initial_state.nc": "global_ocean/WC14/PHC/init/initial_state/initial_state.210727.nc",
+    "ocean/global_ocean/cached/WC14/PHC/init/initial_state/init_mode_forcing_data.nc": "global_ocean/WC14/PHC/init/initial_state/init_mode_forcing_data.210727.nc",
+    "ocean/global_ocean/cached/QUwISC240/mesh/mesh/culled_mesh.nc": "global_ocean/QUwISC240/mesh/mesh/culled_mesh.210727.nc",
+    "ocean/global_ocean/cached/QUwISC240/mesh/mesh/culled_graph.info": "global_ocean/QUwISC240/mesh/mesh/culled_graph.210727.info",
+    "ocean/global_ocean/cached/QUwISC240/mesh/mesh/critical_passages_mask_final.nc": "global_ocean/QUwISC240/mesh/mesh/critical_passages_mask_final.210727.nc",
+    "ocean/global_ocean/cached/QUwISC240/PHC/init/initial_state/initial_state.nc": "global_ocean/QUwISC240/PHC/init/initial_state/initial_state.210727.nc",
+    "ocean/global_ocean/cached/QUwISC240/PHC/init/initial_state/init_mode_forcing_data.nc": "global_ocean/QUwISC240/PHC/init/initial_state/init_mode_forcing_data.210727.nc",
+    "ocean/global_ocean/cached/QUwISC240/PHC/init/ssh_adjustment/adjusted_init.nc": "global_ocean/QUwISC240/PHC/init/ssh_adjustment/adjusted_init.210727.nc",
+    "ocean/global_ocean/cached/ECwISC30to60/mesh/mesh/culled_mesh.nc": "global_ocean/ECwISC30to60/mesh/mesh/culled_mesh.210727.nc",
+    "ocean/global_ocean/cached/ECwISC30to60/mesh/mesh/culled_graph.info": "global_ocean/ECwISC30to60/mesh/mesh/culled_graph.210727.info",
+    "ocean/global_ocean/cached/ECwISC30to60/mesh/mesh/critical_passages_mask_final.nc": "global_ocean/ECwISC30to60/mesh/mesh/critical_passages_mask_final.210727.nc",
+    "ocean/global_ocean/cached/ECwISC30to60/PHC/init/initial_state/initial_state.nc": "global_ocean/ECwISC30to60/PHC/init/initial_state/initial_state.210727.nc",
+    "ocean/global_ocean/cached/ECwISC30to60/PHC/init/initial_state/init_mode_forcing_data.nc": "global_ocean/ECwISC30to60/PHC/init/initial_state/init_mode_forcing_data.210727.nc",
+    "ocean/global_ocean/cached/ECwISC30to60/PHC/init/ssh_adjustment/adjusted_init.nc": "global_ocean/ECwISC30to60/PHC/init/ssh_adjustment/adjusted_init.210727.nc"
+}

compass/ocean/tests/global_ocean/__init__.py

@@ -125,6 +125,34 @@ def __init__(self, mpas_core):
                     test_group=self, mesh=mesh, init=init,
                     time_integrator=time_integrator))
 
+            # tests with cached meshes and initial conditions
+            mesh = Mesh(test_group=self, mesh_name=mesh_name,
+                        cached=True)
+            self.add_test_case(mesh)
+
+            init = Init(test_group=self, mesh=mesh,
+                        initial_condition='PHC',
+                        with_bgc=False, cached=True)
+            self.add_test_case(init)
+
+            time_integrator = 'split_explicit'
+            self.add_test_case(
+                PerformanceTest(
+                    test_group=self, mesh=mesh, init=init,
+                    time_integrator=time_integrator))
+            self.add_test_case(
+                RestartTest(
+                    test_group=self, mesh=mesh, init=init,
+                    time_integrator=time_integrator))
+            self.add_test_case(
+                DecompTest(
+                    test_group=self, mesh=mesh, init=init,
+                    time_integrator=time_integrator))
+            self.add_test_case(
+                ThreadsTest(
+                    test_group=self, mesh=mesh, init=init,
+                    time_integrator=time_integrator))
+
         # for other meshes, we do fewer tests
         for mesh_name in ['EC30to60', 'ECwISC30to60']:
             mesh = Mesh(test_group=self, mesh_name=mesh_name)
@@ -149,6 +177,22 @@ def __init__(self, mpas_core):
                     test_group=self, mesh=mesh, init=init,
                     dynamic_adjustment=dynamic_adjustment))
 
+            # tests with cached meshes and initial conditions
+            mesh = Mesh(test_group=self, mesh_name=mesh_name,
+                        cached=True)
+            self.add_test_case(mesh)
+
+            init = Init(test_group=self, mesh=mesh,
+                        initial_condition='PHC',
+                        with_bgc=False, cached=True)
+            self.add_test_case(init)
+
+            time_integrator = 'split_explicit'
+            self.add_test_case(
+                PerformanceTest(
+                    test_group=self, mesh=mesh, init=init,
+                    time_integrator=time_integrator))
+
         # SOwISC12to60: just the version with cavities for now
         for mesh_name in ['SOwISC12to60']:
             mesh = Mesh(test_group=self, mesh_name=mesh_name)
@@ -172,6 +216,23 @@ def __init__(self, mpas_core):
                     test_group=self, mesh=mesh, init=init,
                     dynamic_adjustment=dynamic_adjustment))
 
+            # tests with cached meshes and initial conditions,
+            # not yet supported as we work out some output issues
+            # mesh = Mesh(test_group=self, mesh_name=mesh_name,
+            #             cached=True)
+            # self.add_test_case(mesh)
+
+            # init = Init(test_group=self, mesh=mesh,
+            #             initial_condition='PHC',
+            #             with_bgc=False, cached=True)
+            # self.add_test_case(init)
+
+            # time_integrator = 'split_explicit'
+            # self.add_test_case(
+            #     PerformanceTest(
+            #         test_group=self, mesh=mesh, init=init,
+            #        time_integrator=time_integrator))
+
         # WC14: just the version without cavities
         for mesh_name in ['WC14']:
             mesh = Mesh(test_group=self, mesh_name=mesh_name)
@@ -195,5 +256,21 @@ def __init__(self, mpas_core):
                     test_group=self, mesh=mesh, init=init,
                     dynamic_adjustment=dynamic_adjustment))
 
+            # tests with cached meshes and initial conditions
+            mesh = Mesh(test_group=self, mesh_name=mesh_name,
+                        cached=True)
+            self.add_test_case(mesh)
+
+            init = Init(test_group=self, mesh=mesh,
+                        initial_condition='PHC',
+                        with_bgc=False, cached=True)
+            self.add_test_case(init)
+
+            time_integrator = 'split_explicit'
+            self.add_test_case(
+                PerformanceTest(
+                    test_group=self, mesh=mesh, init=init,
+                    time_integrator=time_integrator))
+
         # A test case for making diagnostics files from an existing mesh
         self.add_test_case(MakeDiagnosticsFiles(test_group=self))

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

@@ -26,7 +26,8 @@ class Init(TestCase):
         The subdirectory within the test group for all test cases with this
         initial condition
     """
-    def __init__(self, test_group, mesh, initial_condition, with_bgc):
+    def __init__(self, test_group, mesh, initial_condition, with_bgc,
+                 cached=False):
         """
         Create the test case
 
@@ -43,14 +44,16 @@ def __init__(self, test_group, mesh, initial_condition, with_bgc):
 
         with_bgc : bool
             Whether to include biogeochemistry (BGC) in the initial condition
+
+        cached : bool, optional
+            Whether to use a cached initial state instead of computing one
         """
         name = 'init'
-        mesh_name = mesh.mesh_name
         if with_bgc:
             ic_dir = '{}_BGC'.format(initial_condition)
         else:
             ic_dir = initial_condition
-        self.init_subdir = os.path.join(mesh_name, ic_dir)
+        self.init_subdir = os.path.join(mesh.mesh_subdir, ic_dir)
         subdir = os.path.join(self.init_subdir, name)
         super().__init__(test_group=test_group, name=name, subdir=subdir)
 
@@ -61,11 +64,12 @@ def __init__(self, test_group, mesh, initial_condition, with_bgc):
         self.add_step(
             InitialState(
                 test_case=self, mesh=mesh,
-                initial_condition=initial_condition, with_bgc=with_bgc))
+                initial_condition=initial_condition, with_bgc=with_bgc,
+                cached=cached))
 
         if mesh.with_ice_shelf_cavities:
             self.add_step(
-                SshAdjustment(test_case=self, cores=4))
+                SshAdjustment(test_case=self, cores=4, cached=cached))
 
     def configure(self):
         """

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

@@ -22,7 +22,7 @@ class InitialState(Step):
     with_bgc : bool
         Whether to include biogeochemistry (BGC) in the initial condition
     """
-    def __init__(self, test_case, mesh, initial_condition, with_bgc):
+    def __init__(self, test_case, mesh, initial_condition, with_bgc, cached):
         """
         Create the step
 
@@ -36,16 +36,28 @@ def __init__(self, test_case, mesh, initial_condition, with_bgc):
 
         with_bgc : bool
             Whether to include biogeochemistry (BGC) in the initial condition
+
+        cached : bool
+            Whether to use a cached initial state instead of computing one
         """
         if initial_condition not in ['PHC', 'EN4_1900']:
             raise ValueError('Unknown initial_condition {}'.format(
                 initial_condition))
 
-        super().__init__(test_case=test_case, name='initial_state')
+        super().__init__(test_case=test_case, name='initial_state',
+                         cached=cached)
         self.mesh = mesh
         self.initial_condition = initial_condition
         self.with_bgc = with_bgc
 
+        outputs = ['initial_state.nc', 'init_mode_forcing_data.nc']
+
+        for filename in outputs:
+            self.add_output_file(filename)
+
+        if self.cached:
+            return
+
         package = 'compass.ocean.tests.global_ocean.init'
 
         # generate the namelist, replacing a few default options
@@ -133,9 +145,6 @@ def __init__(self, test_case, mesh, initial_condition, with_bgc):
 
         self.add_model_as_input()
 
-        for file in ['initial_state.nc', 'init_mode_forcing_data.nc']:
-            self.add_output_file(filename=file)
-
     def setup(self):
         """
         Set up the test case in the work directory, including downloading any

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

@@ -7,7 +7,8 @@ class SshAdjustment(Step):
     A step for iteratively adjusting the pressure from the weight of the ice
     shelf to match the sea-surface height as part of ice-shelf 2D test cases
     """
-    def __init__(self, test_case, cores=None, min_cores=None, threads=None):
+    def __init__(self, test_case, cached, cores=None, min_cores=None,
+                 threads=None):
         """
         Create the step
 
@@ -16,6 +17,9 @@ def __init__(self, test_case, cores=None, min_cores=None, threads=None):
         test_case : compass.ocean.tests.global_ocean.init.Init
             The test case this step belongs to
 
+        cached : bool
+            Whether to use a cached initial state instead of computing one
+
         cores : int, optional
             the number of cores the step would ideally use.  If fewer cores
             are available on the system, the step will run on all available
@@ -32,7 +36,15 @@ def __init__(self, test_case, cores=None, min_cores=None, threads=None):
         if min_cores is None:
             min_cores = cores
         super().__init__(test_case=test_case, name='ssh_adjustment',
-                         cores=cores, min_cores=min_cores, threads=threads)
+                         cores=cores, min_cores=min_cores, threads=threads,
+                         cached=cached)
+
+        output = 'adjusted_init.nc'
+
+        self.add_output_file(output)
+
+        if self.cached:
+            return
 
         self.add_namelist_file(
             'compass.ocean.tests.global_ocean', 'namelist.forward')
@@ -59,8 +71,6 @@ def __init__(self, test_case, cores=None, min_cores=None, threads=None):
 
         self.add_model_as_input()
 
-        self.add_output_file(filename='adjusted_init.nc')
-
     def setup(self):
         """
         Set up the test case in the work directory, including downloading any

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

@@ -16,10 +16,14 @@ class Mesh(TestCase):
     mesh_step : compass.ocean.tests.global_ocean.mesh.mesh.MeshStep
         The step for creating the mesh
 
+    mesh_subdir : str
+        The subdirectory within the test group for all test cases with this
+        mesh
+
     with_ice_shelf_cavities : bool
         Whether the mesh includes ice-shelf cavities
     """
-    def __init__(self, test_group, mesh_name):
+    def __init__(self, test_group, mesh_name, cached=False):
         """
         Create test case for creating a global MPAS-Ocean mesh
 
@@ -30,34 +34,48 @@ def __init__(self, test_group, mesh_name):
 
         mesh_name : str
             The name of the mesh
+
+        cached : bool, optional
+            Whether to use a cached initial state instead of computing one
         """
         name = 'mesh'
-        subdir = '{}/{}'.format(mesh_name, name)
+        if cached:
+            mesh_subdir = f'cached/{mesh_name}'
+        else:
+            mesh_subdir = mesh_name
+        subdir = f'{mesh_subdir}/{name}'
         super().__init__(test_group=test_group, name=name, subdir=subdir)
         if mesh_name in 'QU240':
             self.mesh_step = QU240Mesh(self, mesh_name,
-                                       with_ice_shelf_cavities=False)
+                                       with_ice_shelf_cavities=False,
+                                       cached=cached)
         elif mesh_name in 'QUwISC240':
             self.mesh_step = QU240Mesh(self, mesh_name,
-                                       with_ice_shelf_cavities=True)
+                                       with_ice_shelf_cavities=True,
+                                       cached=cached)
         elif mesh_name in 'EC30to60':
             self.mesh_step = EC30to60Mesh(self, mesh_name,
-                                          with_ice_shelf_cavities=False)
+                                          with_ice_shelf_cavities=False,
+                                          cached=cached)
         elif mesh_name in 'ECwISC30to60':
             self.mesh_step = EC30to60Mesh(self, mesh_name,
-                                          with_ice_shelf_cavities=True)
+                                          with_ice_shelf_cavities=True,
+                                          cached=cached)
         elif mesh_name in 'SOwISC12to60':
             self.mesh_step = SO12to60Mesh(self, mesh_name,
-                                          with_ice_shelf_cavities=True)
+                                          with_ice_shelf_cavities=True,
+                                          cached=cached)
         elif mesh_name in 'WC14':
             self.mesh_step = WC14Mesh(self, mesh_name,
-                                      with_ice_shelf_cavities=False)
+                                      with_ice_shelf_cavities=False,
+                                      cached=cached)
         else:
             raise ValueError('Unknown mesh name {}'.format(mesh_name))
 
         self.add_step(self.mesh_step)
 
         self.mesh_name = mesh_name
+        self.mesh_subdir = mesh_subdir
         self.with_ice_shelf_cavities = self.mesh_step.with_ice_shelf_cavities
 
     def configure(self):

compass/ocean/tests/global_ocean/mesh/ec30to60/__init__.py

@@ -8,25 +8,28 @@ class EC30to60Mesh(MeshStep):
     """
     A step for creating EC30to60 and ECwISC30to60 meshes
     """
-    def __init__(self, test_case, mesh_name, with_ice_shelf_cavities):
+    def __init__(self, test_case, mesh_name, with_ice_shelf_cavities, cached):
         """
         Create a new step
 
         Parameters
         ----------
-        test_case : compass.TestCase
+        test_case : compass.ocean.tests.global_ocean.Mesh
             The test case this step belongs to
 
         mesh_name : str
             The name of the mesh
 
         with_ice_shelf_cavities : bool
             Whether the mesh includes ice-shelf cavities
+
+        cached : bool
+            Whether to use a cached initial state instead of computing one
         """
 
         super().__init__(test_case, mesh_name, with_ice_shelf_cavities,
                          package=self.__module__,
-                         mesh_config_filename='ec30to60.cfg')
+                         mesh_config_filename='ec30to60.cfg', cached=cached)
 
     def build_cell_width_lat_lon(self):
         """