Update performance test

Move cropping of inactive top cells to ForwardStep so it is
explicitly included as an output of that step.

Give `init.nc` as the mesh file for cropping.

For validation, point to the output file from the version of the
performance test without inactive top cells for `filename2`.

compass/ocean/tests/global_ocean/forward.py

@@ -7,6 +7,7 @@
 from compass.model import run_model
 from compass.testcase import TestCase
 from compass.step import Step
+from compass.ocean.inactive_top_cells import remove_inactive_top_cells_output
 
 
 class ForwardStep(Step):
@@ -121,6 +122,9 @@ def __init__(self, test_case, mesh, init, time_integrator, name='forward',
 
         self.add_output_file(filename='output.nc')
 
+        if self.init.with_inactive_top_cells:
+            self.add_output_file(filename='output_crop.nc')
+
     def setup(self):
         """
         Set up the test case in the work directory, including downloading any
@@ -141,10 +145,15 @@ def run(self):
         Run this step of the testcase
         """
         run_model(self)
+
+        if self.init.with_inactive_top_cells:
+            remove_inactive_top_cells_output(in_filename='output.nc',
+                                             out_filename='output_crop.nc',
+                                             mesh_filename='init.nc')
+
         add_mesh_and_init_metadata(self.outputs, self.config,
                                    init_filename='init.nc')
 
-
 class ForwardTestCase(TestCase):
     """
     A parent class for test cases for forward runs with global MPAS-Ocean mesh

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

@@ -1,7 +1,8 @@
+import os
+
 from compass.validate import compare_variables, compare_timers
 from compass.ocean.tests.global_ocean.forward import ForwardTestCase, \
-    ForwardStep
-from compass.ocean.inactive_top_cells import remove_inactive_top_cells_output
+    ForwardStep, get_forward_subdir
 
 
 class PerformanceTest(ForwardTestCase):
@@ -62,17 +63,21 @@ def validate(self):
         compare_variables(test_case=self, variables=variables,
                           filename1='forward/output.nc')
 
-        if self.config.has_option('vertical_grid', 'inactive_top_cells'):
-            offset = self.config.getint('vertical_grid', 'inactive_top_cells')
-            if offset > 0:
-                remove_inactive_top_cells_output('forward/output.nc',
-                                                 inactive_top_cells=offset)
-                variables = ['temperature', 'salinity', 'layerThickness', 
-                             'normalVelocity']
-                compare_variables(test_case=self, variables=variables,
-                                  filename1='forward/output_crop.nc',
-                                  filename2='forward/output_comp.nc',
-                                  quiet=False, check_outputs=False)
+        if self.init.with_inactive_top_cells:
+            # construct the work directory for the other test
+            subdir = get_forward_subdir(self.init.inactive_top_comp_subdir,
+                                        self.time_integrator, self.name)
+            filename2 = os.path.join(self.base_work_dir, self.mpas_core.name,
+                                     self.test_group.name, subdir,
+                                     'forward/output.nc')
+
+            variables = ['temperature', 'salinity', 'layerThickness',
+                         'normalVelocity']
+            compare_variables(test_case=self, variables=variables,
+                              filename1='forward/output_crop.nc',
+                              filename2=filename2,
+                              quiet=False, check_outputs=False,
+                              skip_if_step_not_run=False)
 
         if self.mesh.with_ice_shelf_cavities:
             variables = [