From f346de213c85eedd48f65877f8923ae0d9f92d9a Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Thu, 5 Dec 2024 07:57:41 -0600
Subject: [PATCH 01/11] Improve error message when refinement factor not found

---
 polaris/ocean/convergence/__init__.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/polaris/ocean/convergence/__init__.py b/polaris/ocean/convergence/__init__.py
index 0a04e50e7..b976200c7 100644
--- a/polaris/ocean/convergence/__init__.py
+++ b/polaris/ocean/convergence/__init__.py
@@ -1,6 +1,3 @@
-import numpy as np
-
-
 def get_resolution_for_task(config, refinement_factor,
                             refinement='both'):
     """
@@ -32,7 +29,8 @@ def get_resolution_for_task(config, refinement_factor,
 
     if refinement_factor not in refinement_factors:
         raise ValueError(
-            'refinement_factor not found in config option refinement_factors')
+            f'refinement_factor {refinement_factor} not found in config '
+            f'option {option}:\n {refinement_factors}')
 
     if refinement == 'time':
         resolution = base_resolution
@@ -74,7 +72,8 @@ def get_timestep_for_task(config, refinement_factor,
 
     if refinement_factor not in refinement_factors:
         raise ValueError(
-            'refinement_factor not found in config option refinement_factors')
+            f'refinement_factor {refinement_factor} not found in config '
+            f'option {option}:\n {refinement_factors}')
 
     resolution = get_resolution_for_task(
         config, refinement_factor, refinement=refinement)

From 037ec8c26290dbba8db1491fe181887344f7d2a6 Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Thu, 5 Dec 2024 06:51:48 -0600
Subject: [PATCH 02/11] A bit of cleanup in cosine bell forward

---
 polaris/ocean/tasks/cosine_bell/forward.py   | 4 ++--
 polaris/ocean/tasks/cosine_bell/forward.yaml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/polaris/ocean/tasks/cosine_bell/forward.py b/polaris/ocean/tasks/cosine_bell/forward.py
index 270f4048f..4bdf26479 100644
--- a/polaris/ocean/tasks/cosine_bell/forward.py
+++ b/polaris/ocean/tasks/cosine_bell/forward.py
@@ -8,7 +8,7 @@ class Forward(SphericalConvergenceForward):
     """
 
     def __init__(self, component, name, subdir, mesh, init,
-                 refinement_factor, refinement='both'):
+                 refinement_factor, refinement):
         """
         Create a new step
 
@@ -32,7 +32,7 @@ def __init__(self, component, name, subdir, mesh, init,
         refinement_factor : float
             The factor by which to scale space, time or both
 
-        refinement : str, optional
+        refinement : str
             Refinement type. One of 'space', 'time' or 'both' indicating both
             space and time
         """
diff --git a/polaris/ocean/tasks/cosine_bell/forward.yaml b/polaris/ocean/tasks/cosine_bell/forward.yaml
index 41bd59b6a..da8ef388a 100644
--- a/polaris/ocean/tasks/cosine_bell/forward.yaml
+++ b/polaris/ocean/tasks/cosine_bell/forward.yaml
@@ -90,7 +90,7 @@ Omega:
     History:
       Filename: output.nc
       Freq: {{ output_freq }}
-      FreqUnits: Seconds
+      FreqUnits: seconds
       Contents:
         - Tracers
         - LayerThickness

From 2f23adc7d23b46cc7486e4c0907052096cd535b7 Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Thu, 5 Dec 2024 08:24:47 -0600
Subject: [PATCH 03/11] Set refinement config options only once

---
 polaris/ocean/tasks/cosine_bell/__init__.py | 28 +++++++++++++--------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/polaris/ocean/tasks/cosine_bell/__init__.py b/polaris/ocean/tasks/cosine_bell/__init__.py
index 07b4e20bc..d0d012779 100644
--- a/polaris/ocean/tasks/cosine_bell/__init__.py
+++ b/polaris/ocean/tasks/cosine_bell/__init__.py
@@ -32,6 +32,7 @@ def add_cosine_bell_tasks(component):
                                 'spherical.cfg')
         config.add_from_package('polaris.ocean.tasks.cosine_bell',
                                 'cosine_bell.cfg')
+        _set_convergence_configs(config, prefix)
 
         for refinement in ['space', 'time', 'both']:
             for include_viz in [False, True]:
@@ -133,17 +134,8 @@ def _setup_steps(self, refinement):
             option = 'refinement_factors_time'
         else:
             option = 'refinement_factors_space'
-        refinement_factors = config.getlist('spherical_convergence',
-                                            f'{prefix}_{option}', dtype=str)
-        refinement_factors = ', '.join(refinement_factors)
-        config.set('convergence', option, value=refinement_factors)
-        refinement_factors = config.getlist('convergence',
-                                            option, dtype=float)
 
-        base_resolution = config.getfloat('spherical_convergence',
-                                          f'{prefix}_base_resolution')
-        config.set('convergence', 'base_resolution',
-                   value=f'{base_resolution:03g}')
+        refinement_factors = config.getlist('convergence', option, dtype=float)
 
         # start fresh with no steps
         for step in list(self.steps.values()):
@@ -233,3 +225,19 @@ def _setup_steps(self, refinement):
             self.add_step(step, symlink=symlink)
         else:
             self.add_step(step)
+
+
+def _set_convergence_configs(config, prefix):
+    for refinement in ['space', 'time']:
+        option = f'refinement_factors_{refinement}'
+        refinement_factors = config.getlist('spherical_convergence',
+                                            f'{prefix}_{option}', dtype=str)
+        refinement_factors = ', '.join(refinement_factors)
+        config.set('convergence', option, value=refinement_factors)
+        refinement_factors = config.getlist('convergence',
+                                            option, dtype=float)
+
+        base_resolution = config.getfloat('spherical_convergence',
+                                          f'{prefix}_base_resolution')
+        config.set('convergence', 'base_resolution',
+                   value=f'{base_resolution:03g}')

From 4107a9befbdd9d11de4dc09118c807f7ff12ab48 Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Thu, 5 Dec 2024 15:33:55 -0600
Subject: [PATCH 04/11] Update variable comparison to take datasets

This is needed if we are translating dimension and variable names
between native model names and common Polaris names.
---
 polaris/validate.py | 57 ++++++++++++++++++++++++++++++++-------------
 1 file changed, 41 insertions(+), 16 deletions(-)

diff --git a/polaris/validate.py b/polaris/validate.py
index 5a8ce7aaf..e650a4a36 100755
--- a/polaris/validate.py
+++ b/polaris/validate.py
@@ -5,7 +5,8 @@
 
 
 def compare_variables(variables, filename1, filename2, logger, l1_norm=0.0,
-                      l2_norm=0.0, linf_norm=0.0, quiet=True):
+                      l2_norm=0.0, linf_norm=0.0, quiet=True, ds1=None,
+                      ds2=None):
     """
     compare variables in the two files
 
@@ -49,6 +50,16 @@ def compare_variables(variables, filename1, filename2, logger, l1_norm=0.0,
         comparison is made.  This is generally desirable when using nonzero
         norm tolerance values.
 
+    ds1 : xarray.Dataset, optional
+        A dataset loaded from filename1.  This may save time if the dataset is
+        already loaded and allows for calculations to be performed or variables
+        to be renamed if necessary.
+
+    ds2 : xarray.Dataset, optional
+        A dataset loaded from filename2.  This may save time if the dataset is
+        already loaded and allows for calculations to be performed or variables
+        to be renamed if necessary.
+
     Returns
     -------
     all_pass : bool
@@ -61,18 +72,16 @@ def compare_variables(variables, filename1, filename2, logger, l1_norm=0.0,
             logger.error(f'File {filename} does not exist.')
             return False
 
-    ds1 = xr.open_dataset(filename1)
-    ds2 = xr.open_dataset(filename2)
+    if ds1 is None:
+        ds1 = xr.open_dataset(filename1)
+
+    if ds2 is None:
+        ds2 = xr.open_dataset(filename2)
 
     all_pass = True
 
     for variable in variables:
-        all_found = True
-        for ds, filename in [(ds1, filename1), (ds2, filename2)]:
-            if variable not in ds:
-                logger.error(f'Variable {variable} not in {filename}.')
-                all_found = False
-        if not all_found:
+        if not _all_found(ds1, filename1, ds2, filename2, variable, logger):
             all_pass = False
             continue
 
@@ -85,13 +94,8 @@ def compare_variables(variables, filename1, filename2, logger, l1_norm=0.0,
             all_pass = False
             continue
 
-        all_match = True
-        for dim in da1.sizes:
-            if da1.sizes[dim] != da2.sizes[dim]:
-                logger.error(f"Field sizes for variable {variable} don't "
-                             f"match files {filename1} and {filename2}.")
-                all_match = False
-        if not all_match:
+        if not _all_sizes_match(da1, filename1, da2, filename2, variable,
+                                logger):
             all_pass = False
             continue
 
@@ -139,6 +143,27 @@ def compare_variables(variables, filename1, filename2, logger, l1_norm=0.0,
     return all_pass
 
 
+def _all_found(ds1, filename1, ds2, filename2, variable, logger):
+    """ Is the variable found in both datasets? """
+    all_found = True
+    for ds, filename in [(ds1, filename1), (ds2, filename2)]:
+        if variable not in ds:
+            logger.error(f'Variable {variable} not in {filename}.')
+            all_found = False
+    return all_found
+
+
+def _all_sizes_match(da1, filename1, da2, filename2, variable, logger):
+    """ Do all dimension sizes match between the two variables? """
+    all_match = True
+    for dim in da1.sizes:
+        if da1.sizes[dim] != da2.sizes[dim]:
+            logger.error(f"Field sizes for variable {variable} don't "
+                         f"match files {filename1} and {filename2}.")
+            all_match = False
+    return all_match
+
+
 def _compute_norms(da1, da2, quiet, max_l1_norm, max_l2_norm, max_linf_norm,
                    time_index=None):
     """ Compute norms between variables in two DataArrays """

From 6e66aa19597b8e46779c9816b582d26dff54041a Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Thu, 5 Dec 2024 06:58:30 -0600
Subject: [PATCH 05/11] Add restart test to cosine bell

---
 polaris/ocean/tasks/cosine_bell/__init__.py   | 10 ++-
 .../tasks/cosine_bell/restart/__init__.py     | 86 +++++++++++++++++++
 .../tasks/cosine_bell/restart/forward.yaml    | 35 ++++++++
 .../tasks/cosine_bell/restart/restart_step.py | 85 ++++++++++++++++++
 .../tasks/cosine_bell/restart/validate.py     | 68 +++++++++++++++
 5 files changed, 283 insertions(+), 1 deletion(-)
 create mode 100644 polaris/ocean/tasks/cosine_bell/restart/__init__.py
 create mode 100644 polaris/ocean/tasks/cosine_bell/restart/forward.yaml
 create mode 100644 polaris/ocean/tasks/cosine_bell/restart/restart_step.py
 create mode 100644 polaris/ocean/tasks/cosine_bell/restart/validate.py

diff --git a/polaris/ocean/tasks/cosine_bell/__init__.py b/polaris/ocean/tasks/cosine_bell/__init__.py
index d0d012779..5cf365a79 100644
--- a/polaris/ocean/tasks/cosine_bell/__init__.py
+++ b/polaris/ocean/tasks/cosine_bell/__init__.py
@@ -11,6 +11,7 @@
 from polaris.ocean.tasks.cosine_bell.analysis import Analysis
 from polaris.ocean.tasks.cosine_bell.forward import Forward
 from polaris.ocean.tasks.cosine_bell.init import Init
+from polaris.ocean.tasks.cosine_bell.restart import Restart
 from polaris.ocean.tasks.cosine_bell.viz import Viz
 
 
@@ -22,7 +23,8 @@ def add_cosine_bell_tasks(component):
         the ocean component that the tasks will be added to
     """
 
-    for icosahedral, prefix in [(True, 'icos'), (False, 'qu')]:
+    for icosahedral, prefix, restart_refinement in [(True, 'icos', 8.0),
+                                                    (False, 'qu', 2.0)]:
 
         filepath = f'spherical/{prefix}/cosine_bell/cosine_bell.cfg'
         config = PolarisConfigParser(filepath=filepath)
@@ -42,6 +44,12 @@ def add_cosine_bell_tasks(component):
                                               include_viz=include_viz,
                                               refinement=refinement))
 
+        component.add_task(Restart(component=component,
+                                   config=config,
+                                   icosahedral=icosahedral,
+                                   refinement_factor=restart_refinement,
+                                   refinement='both'))
+
 
 class CosineBell(Task):
     """
diff --git a/polaris/ocean/tasks/cosine_bell/restart/__init__.py b/polaris/ocean/tasks/cosine_bell/restart/__init__.py
new file mode 100644
index 000000000..0fb834e77
--- /dev/null
+++ b/polaris/ocean/tasks/cosine_bell/restart/__init__.py
@@ -0,0 +1,86 @@
+from polaris import Task
+from polaris.ocean.convergence import get_resolution_for_task
+from polaris.ocean.mesh.spherical import add_spherical_base_mesh_step
+from polaris.ocean.tasks.cosine_bell.init import Init
+from polaris.ocean.tasks.cosine_bell.restart.restart_step import RestartStep
+from polaris.ocean.tasks.cosine_bell.restart.validate import Validate
+
+
+class Restart(Task):
+    """
+    A cosine bell restart test case, which makes sure the model produces
+    identical results with one longer run and two shorter runs with a restart
+    in between.
+    """
+
+    def __init__(self, component, config, icosahedral, refinement_factor,
+                 refinement):
+        """
+        Create the convergence test
+
+        Parameters
+        ----------
+        component : polaris.ocean.Ocean
+            The ocean component that this task belongs to
+
+        config : polaris.config.PolarisConfigParser
+            A shared config parser
+
+        icosahedral : bool
+            Whether to use icosahedral, as opposed to less regular, JIGSAW
+            meshes
+
+        refinement_factor : float
+            The factor by which to scale space, time or both
+
+        refinement : str
+            Refinement type. One of 'space', 'time' or 'both' indicating both
+            space and time
+        """
+
+        if icosahedral:
+            prefix = 'icos'
+        else:
+            prefix = 'qu'
+
+        task_subdir = f'spherical/{prefix}/cosine_bell/restart'
+        name = f'{prefix}_cosine_bell_restart'
+        config_filename = 'cosine_bell.cfg'
+
+        super().__init__(component=component, name=name, subdir=task_subdir)
+
+        self.set_shared_config(config, link=config_filename)
+
+        resolution = get_resolution_for_task(
+            config, refinement_factor, refinement=refinement)
+
+        base_mesh_step, mesh_name = add_spherical_base_mesh_step(
+            component, resolution, icosahedral)
+
+        name = f'{prefix}_init_{mesh_name}'
+        init_subdir = f'spherical/{prefix}/cosine_bell/init/{mesh_name}'
+        if init_subdir in component.steps:
+            init_step = component.steps[init_subdir]
+        else:
+            init_step = Init(component=component, name=name,
+                             subdir=init_subdir, base_mesh=base_mesh_step)
+            init_step.set_shared_config(config, link=config_filename)
+
+        self.add_step(base_mesh_step, symlink=f'base_mesh/{mesh_name}')
+        self.add_step(init_step, symlink=f'init/{mesh_name}')
+
+        step_names = ['full_run', 'restart_run']
+        for name in step_names:
+            subdir = f'{task_subdir}/{name}'
+            step = RestartStep(
+                component=component, name=name, subdir=subdir,
+                mesh=base_mesh_step, init=init_step,
+                refinement_factor=refinement_factor,
+                refinement=refinement)
+            step.set_shared_config(
+                config, link=config_filename)
+            self.add_step(step)
+
+        self.add_step(Validate(component=component,
+                               step_subdirs=step_names,
+                               indir=task_subdir))
diff --git a/polaris/ocean/tasks/cosine_bell/restart/forward.yaml b/polaris/ocean/tasks/cosine_bell/restart/forward.yaml
new file mode 100644
index 000000000..986d4bb19
--- /dev/null
+++ b/polaris/ocean/tasks/cosine_bell/restart/forward.yaml
@@ -0,0 +1,35 @@
+ocean:
+  time_management:
+    config_start_time: {{ start_time }}
+    config_stop_time: none
+    config_run_duration: {{ run_duration }}
+
+mpas-ocean:
+  time_management:
+    config_do_restart: {{ do_restart }}
+  io:
+    config_write_output_on_startup: false
+  streams:
+    restart:
+      filename_template: ../restarts/rst.$Y-$M-$D_$h.$m.$s.nc
+      filename_interval: output_interval
+      output_interval: 0000-00-00_00:00:01
+    output:
+      output_interval: {{ output_interval }}
+
+Omega:
+  IOStreams:
+    InitialState:
+      FreqUnits: {{ init_freq_units }}
+    RestartRead:
+      UsePointerFile: false
+      Filename: ../restarts/rst.$Y-$M-$D_$h.$m.$s
+      StartTime: {{ restart_time }}
+    RestartWrite:
+      UsePointerFile: false
+      Filename: ../restarts/rst.$Y-$M-$D_$h.$m.$s
+      Freq: 1
+      FreqUnits: seconds
+    History:
+      Freq: {{ output_freq }}
+      FreqUnits: seconds
diff --git a/polaris/ocean/tasks/cosine_bell/restart/restart_step.py b/polaris/ocean/tasks/cosine_bell/restart/restart_step.py
new file mode 100644
index 000000000..4e6547a1c
--- /dev/null
+++ b/polaris/ocean/tasks/cosine_bell/restart/restart_step.py
@@ -0,0 +1,85 @@
+import os
+import time
+
+import numpy as np
+
+from polaris.ocean.convergence import get_timestep_for_task
+from polaris.ocean.model import get_time_interval_string
+from polaris.ocean.tasks.cosine_bell.forward import Forward
+
+
+class RestartStep(Forward):
+    """
+    A forward model step in the restart test case
+    """
+    def dynamic_model_config(self, at_setup):
+        """
+        Add model config options, namelist, streams and yaml files using config
+        options or template replacements that need to be set both during step
+        setup and at runtime
+
+        Parameters
+        ----------
+        at_setup : bool
+            Whether this method is being run during setup of the step, as
+            opposed to at runtime
+        """
+        super().dynamic_model_config(at_setup)
+
+        dt, _ = get_timestep_for_task(
+            self.config, self.refinement_factor, refinement=self.refinement)
+        dt = np.ceil(dt)
+
+        if self.name == 'full_run':
+            # 2 time steps without a restart
+            do_restart = False
+            start_time = 0.
+            run_duration = 2. * dt
+            output_interval = 2. * dt
+        elif self.name == 'restart_run':
+            # 1 time step from the restart at 1 time step
+            do_restart = True
+            start_time = dt
+            run_duration = dt
+            output_interval = dt
+        else:
+            raise ValueError(f'Unexpected step name {self.name}')
+
+        # to keep the time formatting from getting too complicated, we'll
+        # assume 2 time steps is never more than a day
+        start_time_str = time.strftime('0001-01-01_%H:%M:%S',
+                                       time.gmtime(start_time))
+
+        run_duration_str = get_time_interval_string(seconds=run_duration)
+
+        output_interval_str = get_time_interval_string(seconds=output_interval)
+
+        # For Omega, we want the output interval as a number of seconds
+        output_freq = int(output_interval)
+
+        if do_restart:
+            restart_time_str = start_time_str
+            init_freq_units = 'never'
+        else:
+            # Effectively never
+            restart_time_str = '99999-12-31_00:00:00'
+            init_freq_units = 'OnStartup'
+
+        package = 'polaris.ocean.tasks.cosine_bell.restart'
+        replacements = dict(
+            do_restart=do_restart,
+            start_time=start_time_str,
+            run_duration=run_duration_str,
+            output_interval=output_interval_str,
+            restart_time=restart_time_str,
+            init_freq_units=init_freq_units,
+            output_freq=f'{output_freq}'
+        )
+
+        self.add_yaml_file(package=package,
+                           yaml='forward.yaml',
+                           template_replacements=replacements)
+
+        restart_dir = os.path.abspath(os.path.join(
+            self.work_dir, '..', 'restarts'))
+        os.makedirs(restart_dir, exist_ok=True)
diff --git a/polaris/ocean/tasks/cosine_bell/restart/validate.py b/polaris/ocean/tasks/cosine_bell/restart/validate.py
new file mode 100644
index 000000000..c401d7d79
--- /dev/null
+++ b/polaris/ocean/tasks/cosine_bell/restart/validate.py
@@ -0,0 +1,68 @@
+import os
+
+from polaris.ocean.model import OceanIOStep
+from polaris.validate import compare_variables
+
+
+class Validate(OceanIOStep):
+    """
+    A step for comparing outputs between steps in a cosine bell run
+
+    Attributes
+    ----------
+    step_subdirs : list of str
+        The number of processors used in each run
+    """
+    def __init__(self, component, step_subdirs, indir):
+        """
+        Create the step
+
+        Parameters
+        ----------
+        component : polaris.Component
+            The component the step belongs to
+
+        step_subdirs : list of str
+            The number of processors used in each run
+
+        indir : str
+            the directory the step is in, to which ``name`` will be appended
+       """
+        super().__init__(component=component, name='validate', indir=indir)
+
+        self.step_subdirs = step_subdirs
+
+        for subdir in step_subdirs:
+            self.add_input_file(filename=f'output_{subdir}.nc',
+                                target=f'../{subdir}/output.nc')
+
+    def run(self):
+        """
+        Compare ``tracer1``, ``layerThickness`` and ``normalVelocity`` in the
+        outputs of two previous steps with each other
+        """
+        super().run()
+        step_subdirs = self.step_subdirs
+        logger = self.logger
+        variables = ['tracer1', 'layerThickness', 'normalVelocity']
+
+        filename1 = self.inputs[0]
+        filename2 = self.inputs[1]
+
+        all_pass = True
+        for filename in [filename1, filename2]:
+            if not os.path.exists(filename):
+                logger.error(f'File {filename} does not exist.')
+                all_pass = False
+
+        if all_pass:
+            ds1 = self.open_model_dataset(filename1)
+            ds2 = self.open_model_dataset(filename2)
+
+            all_pass = compare_variables(variables=variables,
+                                         filename1=filename1,
+                                         filename2=filename2, logger=logger,
+                                         ds1=ds1, ds2=ds2)
+        if not all_pass:
+            raise ValueError(f'Validation failed comparing outputs between '
+                             f'{step_subdirs[0]} and {step_subdirs[1]}.')

From ed335a17e31979f729978ea04849a4574cbf8ab4 Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Tue, 10 Dec 2024 08:42:05 -0600
Subject: [PATCH 06/11] Remove unneeded RestartRead from Omega iostreams

Requires https://github.com/E3SM-Project/Omega/pull/184
---
 polaris/ocean/tasks/cosine_bell/forward.yaml           | 1 -
 polaris/ocean/tasks/manufactured_solution/forward.yaml | 1 -
 2 files changed, 2 deletions(-)

diff --git a/polaris/ocean/tasks/cosine_bell/forward.yaml b/polaris/ocean/tasks/cosine_bell/forward.yaml
index da8ef388a..a9513d5fa 100644
--- a/polaris/ocean/tasks/cosine_bell/forward.yaml
+++ b/polaris/ocean/tasks/cosine_bell/forward.yaml
@@ -95,4 +95,3 @@ Omega:
         - Tracers
         - LayerThickness
         - NormalVelocity
-    RestartRead: {}
diff --git a/polaris/ocean/tasks/manufactured_solution/forward.yaml b/polaris/ocean/tasks/manufactured_solution/forward.yaml
index 4f0073794..98e2ce8cb 100644
--- a/polaris/ocean/tasks/manufactured_solution/forward.yaml
+++ b/polaris/ocean/tasks/manufactured_solution/forward.yaml
@@ -55,4 +55,3 @@ Omega:
       - NormalVelocity
       - LayerThickness
       - SshCellDefault
-    RestartRead: {}

From cd9204fdf7cba07506b0f59fb2e7a00f7d9cf118 Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Tue, 10 Dec 2024 09:02:07 -0600
Subject: [PATCH 07/11] Fix UseStartEnd in restart run.

---
 polaris/ocean/tasks/cosine_bell/restart/forward.yaml    | 1 +
 polaris/ocean/tasks/cosine_bell/restart/restart_step.py | 1 +
 2 files changed, 2 insertions(+)

diff --git a/polaris/ocean/tasks/cosine_bell/restart/forward.yaml b/polaris/ocean/tasks/cosine_bell/restart/forward.yaml
index 986d4bb19..2547ab6be 100644
--- a/polaris/ocean/tasks/cosine_bell/restart/forward.yaml
+++ b/polaris/ocean/tasks/cosine_bell/restart/forward.yaml
@@ -23,6 +23,7 @@ Omega:
       FreqUnits: {{ init_freq_units }}
     RestartRead:
       UsePointerFile: false
+      UseStartEnd: {{ not_restart }}
       Filename: ../restarts/rst.$Y-$M-$D_$h.$m.$s
       StartTime: {{ restart_time }}
     RestartWrite:
diff --git a/polaris/ocean/tasks/cosine_bell/restart/restart_step.py b/polaris/ocean/tasks/cosine_bell/restart/restart_step.py
index 4e6547a1c..28934c0ac 100644
--- a/polaris/ocean/tasks/cosine_bell/restart/restart_step.py
+++ b/polaris/ocean/tasks/cosine_bell/restart/restart_step.py
@@ -68,6 +68,7 @@ def dynamic_model_config(self, at_setup):
         package = 'polaris.ocean.tasks.cosine_bell.restart'
         replacements = dict(
             do_restart=do_restart,
+            not_restart=not do_restart,
             start_time=start_time_str,
             run_duration=run_duration_str,
             output_interval=output_interval_str,

From ee6d56d49fbdded9c4876fa4dc7ad43a877d6e32 Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Mon, 16 Dec 2024 06:40:05 -0600
Subject: [PATCH 08/11] Move validate step and fix docstring

---
 polaris/ocean/tasks/cosine_bell/restart/__init__.py       | 2 +-
 polaris/ocean/tasks/cosine_bell/{restart => }/validate.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)
 rename polaris/ocean/tasks/cosine_bell/{restart => }/validate.py (97%)

diff --git a/polaris/ocean/tasks/cosine_bell/restart/__init__.py b/polaris/ocean/tasks/cosine_bell/restart/__init__.py
index 0fb834e77..e33f1f8ca 100644
--- a/polaris/ocean/tasks/cosine_bell/restart/__init__.py
+++ b/polaris/ocean/tasks/cosine_bell/restart/__init__.py
@@ -3,7 +3,7 @@
 from polaris.ocean.mesh.spherical import add_spherical_base_mesh_step
 from polaris.ocean.tasks.cosine_bell.init import Init
 from polaris.ocean.tasks.cosine_bell.restart.restart_step import RestartStep
-from polaris.ocean.tasks.cosine_bell.restart.validate import Validate
+from polaris.ocean.tasks.cosine_bell.validate import Validate
 
 
 class Restart(Task):
diff --git a/polaris/ocean/tasks/cosine_bell/restart/validate.py b/polaris/ocean/tasks/cosine_bell/validate.py
similarity index 97%
rename from polaris/ocean/tasks/cosine_bell/restart/validate.py
rename to polaris/ocean/tasks/cosine_bell/validate.py
index c401d7d79..056218bfe 100644
--- a/polaris/ocean/tasks/cosine_bell/restart/validate.py
+++ b/polaris/ocean/tasks/cosine_bell/validate.py
@@ -23,7 +23,7 @@ def __init__(self, component, step_subdirs, indir):
             The component the step belongs to
 
         step_subdirs : list of str
-            The number of processors used in each run
+            Subdirectories for the steps with outputs to compare
 
         indir : str
             the directory the step is in, to which ``name`` will be appended

From b6dcacb13539142b6bbc86e4d339c3b6c199cc10 Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Mon, 23 Dec 2024 07:48:58 -0600
Subject: [PATCH 09/11] Address reviewer comments

Add a `do_restart` attribute to keep track of which runs are
restart runs, rather than using the step name.
---
 polaris/ocean/tasks/cosine_bell/forward.py            | 11 ++++++++++-
 polaris/ocean/tasks/cosine_bell/restart/__init__.py   |  3 ++-
 .../ocean/tasks/cosine_bell/restart/restart_step.py   | 10 ++++------
 3 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/polaris/ocean/tasks/cosine_bell/forward.py b/polaris/ocean/tasks/cosine_bell/forward.py
index 4bdf26479..5e4da4b84 100644
--- a/polaris/ocean/tasks/cosine_bell/forward.py
+++ b/polaris/ocean/tasks/cosine_bell/forward.py
@@ -5,10 +5,15 @@ class Forward(SphericalConvergenceForward):
     """
     A step for performing forward ocean component runs as part of the cosine
     bell test case
+
+    Attributes
+    ----------
+    do_restart : bool
+        Whether this is a restart run
     """
 
     def __init__(self, component, name, subdir, mesh, init,
-                 refinement_factor, refinement):
+                 refinement_factor, refinement, do_restart=False):
         """
         Create a new step
 
@@ -35,6 +40,9 @@ def __init__(self, component, name, subdir, mesh, init,
         refinement : str
             Refinement type. One of 'space', 'time' or 'both' indicating both
             space and time
+
+        do_restart : bool, optional
+            Whether this is a restart run
         """
         package = 'polaris.ocean.tasks.cosine_bell'
         validate_vars = ['normalVelocity', 'tracer1']
@@ -46,6 +54,7 @@ def __init__(self, component, name, subdir, mesh, init,
                          graph_target=f'{mesh.path}/graph.info',
                          refinement_factor=refinement_factor,
                          refinement=refinement)
+        self.do_restart = do_restart
 
     def setup(self):
         """
diff --git a/polaris/ocean/tasks/cosine_bell/restart/__init__.py b/polaris/ocean/tasks/cosine_bell/restart/__init__.py
index e33f1f8ca..c35a1252e 100644
--- a/polaris/ocean/tasks/cosine_bell/restart/__init__.py
+++ b/polaris/ocean/tasks/cosine_bell/restart/__init__.py
@@ -72,11 +72,12 @@ def __init__(self, component, config, icosahedral, refinement_factor,
         step_names = ['full_run', 'restart_run']
         for name in step_names:
             subdir = f'{task_subdir}/{name}'
+            do_restart = (name == 'restart_run')
             step = RestartStep(
                 component=component, name=name, subdir=subdir,
                 mesh=base_mesh_step, init=init_step,
                 refinement_factor=refinement_factor,
-                refinement=refinement)
+                refinement=refinement, do_restart=do_restart)
             step.set_shared_config(
                 config, link=config_filename)
             self.add_step(step)
diff --git a/polaris/ocean/tasks/cosine_bell/restart/restart_step.py b/polaris/ocean/tasks/cosine_bell/restart/restart_step.py
index 28934c0ac..7f8771e35 100644
--- a/polaris/ocean/tasks/cosine_bell/restart/restart_step.py
+++ b/polaris/ocean/tasks/cosine_bell/restart/restart_step.py
@@ -26,24 +26,22 @@ def dynamic_model_config(self, at_setup):
         """
         super().dynamic_model_config(at_setup)
 
+        do_restart = self.do_restart
+
         dt, _ = get_timestep_for_task(
             self.config, self.refinement_factor, refinement=self.refinement)
         dt = np.ceil(dt)
 
-        if self.name == 'full_run':
+        if not do_restart:
             # 2 time steps without a restart
-            do_restart = False
             start_time = 0.
             run_duration = 2. * dt
             output_interval = 2. * dt
-        elif self.name == 'restart_run':
+        else:
             # 1 time step from the restart at 1 time step
-            do_restart = True
             start_time = dt
             run_duration = dt
             output_interval = dt
-        else:
-            raise ValueError(f'Unexpected step name {self.name}')
 
         # to keep the time formatting from getting too complicated, we'll
         # assume 2 time steps is never more than a day

From 8085c6d3b893fa3939cf52ee0f84b36ce02e687f Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Mon, 23 Dec 2024 09:26:33 -0600
Subject: [PATCH 10/11] Update the docs

---
 docs/developers_guide/framework/validation.md | 30 ++++++----
 docs/developers_guide/ocean/api.md            | 11 +++-
 .../ocean/tasks/cosine_bell.md                | 30 ++++++++--
 docs/users_guide/ocean/tasks/cosine_bell.md   | 57 +++++++++++--------
 4 files changed, 88 insertions(+), 40 deletions(-)

diff --git a/docs/developers_guide/framework/validation.md b/docs/developers_guide/framework/validation.md
index f237bfeef..c4047152a 100644
--- a/docs/developers_guide/framework/validation.md
+++ b/docs/developers_guide/framework/validation.md
@@ -35,9 +35,9 @@ be compared against a baseline, if one is provided, after the step as run.
 
 In addition to baseline validation, it is often useful to compare files between
 steps of a run.  This is done by adding later step to perform the validation.
-This validation step will use the function 
-{py:func}`polaris.validate.compare_variables()` to compare variables in a file 
-with a given relative path (`filename1`) with the same variables in another 
+This validation step will use the function
+{py:func}`polaris.validate.compare_variables()` to compare variables in a file
+with a given relative path (`filename1`) with the same variables in another
 file (`filename2`).
 
 As a compact example of creating a validate step for a restart run:
@@ -58,7 +58,7 @@ class Validate(Step):
         super().run()
         variables = ['temperature', 'salinity', 'layerThickness',
                      'normalVelocity']
-        all_pass = compare_variables(variables, 
+        all_pass = compare_variables(variables,
                                      filename1='output_full_run.nc',
                                      filename2='output_restart_run.nc',
                                      logger=self.logger)
@@ -68,12 +68,12 @@ class Validate(Step):
 
 ```
 
-The 2 files `../full_run/output.nc` and `../restart_run/output.nc` are 
-symlinked locally and compared to make sure the variables `temperature`, 
+The 2 files `../full_run/output.nc` and `../restart_run/output.nc` are
+symlinked locally and compared to make sure the variables `temperature`,
 `salinity`, `layerThickness`, and `normalVelocity` are identical between the
 two.
 
-By default, the output is "quiet".  If you set `quiet=False`, typical output 
+By default, the output is "quiet".  If you set `quiet=False`, typical output
 will look like this:
 
 ```none
@@ -186,7 +186,7 @@ normalVelocity       Time index: 0, 1, 2
 
 ## Norms
 
-In circumstance where you would like to allow comparison to pass with non-zero 
+In circumstance where you would like to allow comparison to pass with non-zero
 differences between variables, you can supply keyword arguments
 `l1_norm`, `l2_norm` and/or `linf_norm` to give the desired maximum
 values for these norms, above which the comparison will fail, raising a
@@ -196,8 +196,18 @@ values for these norms, above which the comparison will fail, raising a
 If you want different nonzero norm values for different variables,
 the easiest solution is to call {py:func}`polaris.validate.compare_variables()`
 separately for each variable and with different norm values specified.
-You will need to "and" together the results from calling 
-{py:func}`polaris.validate.compare_variables()`.  When you specify a nonzero 
+You will need to "and" together the results from calling
+{py:func}`polaris.validate.compare_variables()`.  When you specify a nonzero
 norm, you may want polaris to print the norm values it is using for comparison
 when the results are printed.  To do so, use the optional `quiet=False`
 argument.
+
+## Datasets
+
+In some cases, a comparison cannot be made directly between the datasets loaded
+from the two files to be compared. Instead, the datasets require manipulation
+for some reason. Currently, this is the case for datasets from the Omega model,
+which need to have their variables renamed to the MPAS-Ocean names for use in
+Polaris.  The `ds1` and `ds2` keyword arguments are used to supply datasets
+corresponding to `filename1` and `filename2`, respectively, in such
+circumstances.
diff --git a/docs/developers_guide/ocean/api.md b/docs/developers_guide/ocean/api.md
index c1f2fa9fa..e35e5b04d 100644
--- a/docs/developers_guide/ocean/api.md
+++ b/docs/developers_guide/ocean/api.md
@@ -99,14 +99,21 @@
    init.cosine_bell
 
    forward.Forward
-   forward.Forward.compute_cell_count
-   forward.Forward.dynamic_model_config
 
    analysis.Analysis
    analysis.Analysis.exact_solution
 
+   validate.Validate
+   validate.Validate.run
+
    viz.Viz
    viz.Viz.run
+
+   restart.Restart
+
+   restart.RestartStep
+   restart.RestartStep.dynamic_model_config
+
 ```
 
 ### geostrophic
diff --git a/docs/developers_guide/ocean/tasks/cosine_bell.md b/docs/developers_guide/ocean/tasks/cosine_bell.md
index 50a08c3ad..10e4e653c 100644
--- a/docs/developers_guide/ocean/tasks/cosine_bell.md
+++ b/docs/developers_guide/ocean/tasks/cosine_bell.md
@@ -2,15 +2,18 @@
 
 # cosine_bell
 
-The {py:class}`polaris.ocean.tasks.cosine_bell.CosineBell`
+In most cases, the {py:class}`polaris.ocean.tasks.cosine_bell.CosineBell`
 test performs a series of 24-day runs that advect a bell-shaped tracer blob
 around the sphere.  The resolution of the sphere varies (by default, between
 60 and 240 km).  Advected results are compared with a known exact solution to
 determine the rate of convergence.
 
+There is also a restart test, described below, that performs only two time
+steps of the test to verify the exact restart capability.
+
 ## framework
 
-The config options for the `cosine_bell` tests are described in 
+The config options for the `cosine_bell` tests are described in
 {ref}`ocean-cosine-bell` in the User's Guide.
 
 Additionally, the test uses a `forward.yaml` file with a few common
@@ -38,18 +41,24 @@ descends from {py:class}`polaris.ocean.convergence.spherical.SphericalConvergenc
 and defines a step for running MPAS-Ocean from an initial condition produced in
 an `init` step. See {ref}`dev-ocean-convergence` for some relevant
 discussion of the parent class. The time step is determined from the resolution
-based on the `dt_per_km` config option in the `[convergence_forward]` 
+based on the `dt_per_km` config option in the `[convergence_forward]`
 section.  Other model config options are taken from `forward.yaml`.
 
 ### analysis
 
 The class {py:class}`polaris.ocean.tasks.cosine_bell.analysis.Analysis`
 descends from
-{py:class}`polaris.ocean.convergence.ConvergenceAnalysis`,
+{py:class}`polaris.ocean.convergence.analysis.ConvergenceAnalysis`,
 and defines a step for computing the error norm (L2) for the results
 at each resolution, saving them in `convergence_tracer1.csv` and plotting them
 in `convergence_tracer1.png`.
 
+### validate
+
+The class {py:class}`polaris.ocean.tasks.cosine_bell.validate.Validate` is a
+step for validating the results between two cosine-bell runs.  It is currently
+used to verify bit-for-bit restart in the `restart` test described below.
+
 ### viz
 
 The visualization step is available only in the `cosine_bell/with_viz`
@@ -76,3 +85,16 @@ colorbar_limits = 0.0, 1.0
 ```
 
 See {ref}`dev-visualization-global` for more details.
+
+## restart
+
+The {py:class}`polaris.ocean.tasks.cosine_bell.restart.Restart` class defines
+a restart check that performs two time steps of the Cosine Bell test at coarse
+resolution, then performs reruns the second time step, as a restart run to
+verify the bit-for-bit restart capability for tracer advection.
+
+### restart_step
+
+The {py:class}`polaris.ocean.tasks.cosine_bell.restart.RestartStep` class
+defines both steps of the restart run, the "full" run (2 time steps) and the
+"restart" run (repeating the last time step after a restart).
diff --git a/docs/users_guide/ocean/tasks/cosine_bell.md b/docs/users_guide/ocean/tasks/cosine_bell.md
index 5230fa36b..df9db26b5 100644
--- a/docs/users_guide/ocean/tasks/cosine_bell.md
+++ b/docs/users_guide/ocean/tasks/cosine_bell.md
@@ -4,52 +4,61 @@
 
 ## description
 
-The `cosine_bell` and `cosine_bell/with_viz` tasks implement the Cosine
-Bell test case as first described in
+The `cosine_bell/convergence_*` and `cosine_bell/convergence_*/with_viz` tasks
+implement the Cosine Bell test case as first described in
 [Williamson et al. 1992](<https://doi.org/10.1016/S0021-9991(05)80016-6>)
 but using the variant from Sec. 3a of
 [Skamarock and Gassmann](https://doi.org/10.1175/MWR-D-10-05056.1).  A flow
 field representing solid-body rotation transports a bell-shaped perturbation
 in a tracer $\psi$ once around the sphere, returning to its initial location.
 
-The task is a convergence test with time step varying proportionately to grid
-size. The result of the `analysis` step of the task is a plot like the
-following showing convergence as a function of the number of cells:
+The `convergence_both` task is a convergence test with time step varying
+proportionately to cell size, while `convergence_time` and `convergence_space`
+vary only the time step and the cell size, respectively. The result of the
+`analysis` step of each task is a plot like the following showing convergence
+as a function of the cell size and/or the time step:
 
 ```{image} images/cosine_bell_convergence.png
 :align: center
 :width: 500 px
 ```
 
-The `cosine_bell/with_viz` variant also includes visualization of the initial
+The `with_viz` variant also includes visualization of the initial
 and final state on a lat-lon grid for each resolution.  The visualization is
-not included in the `cosine_bell` version of the task in order to not slow down
+not included in the other versions of the task in order to not slow down
 regression testing.
 
+Another task, `cosine_bell/restart`, performs two time steps of the Cosine Bell
+test at coarse resolution, then performs reruns the second time step,
+as a restart run to verify the bit-for-bit restart capability for tracer
+advection.
+
 ## suppported models
 
-These tasks support only MPAS-Ocean.
+These tasks support both MPAS-Ocean and Omega.
 
 (ocean-cosine-bell-mesh)=
 ## mesh
 
 Two global mesh variants are tested, quasi-uniform (QU) and icosohydral. There
-are also variants to test convergence in space, time, or both space and time.
-In addition, the tests can be set up with or without the viz step. Thus, there
-are 12 variants of the task:
+are also variants to test convergence in space, time, or both space and time
+as well as the restart test. In addition, the tests can be set up with or
+without the viz step. Thus, there are 14 variants of the task:
 ```
-ocean/spherical/icos/cosine_bell/convergence_both/
-ocean/spherical/icos/cosine_bell/convergence_both/with_viz
-ocean/spherical/qu/cosine_bell/convergence_both/
-ocean/spherical/qu/cosine_bell/convergence_both/with_viz
-ocean/spherical/icos/cosine_bell/convergence_space/
+ocean/spherical/icos/cosine_bell/convergence_space
 ocean/spherical/icos/cosine_bell/convergence_space/with_viz
-ocean/spherical/qu/cosine_bell/convergence_space/
-ocean/spherical/qu/cosine_bell/convergence_space/with_viz
-ocean/spherical/icos/cosine_bell/convergence_time/
+ocean/spherical/icos/cosine_bell/convergence_time
 ocean/spherical/icos/cosine_bell/convergence_time/with_viz
-ocean/spherical/qu/cosine_bell/convergence_time/
+ocean/spherical/icos/cosine_bell/convergence_both
+ocean/spherical/icos/cosine_bell/convergence_both/with_viz
+ocean/spherical/icos/cosine_bell/restart
+ocean/spherical/qu/cosine_bell/convergence_space
+ocean/spherical/qu/cosine_bell/convergence_space/with_viz
+ocean/spherical/qu/cosine_bell/convergence_time
 ocean/spherical/qu/cosine_bell/convergence_time/with_viz
+ocean/spherical/qu/cosine_bell/convergence_both
+ocean/spherical/qu/cosine_bell/convergence_both/with_viz
+ocean/spherical/qu/cosine_bell/restart
 ```
 The default resolutions used in the task depends on the mesh type.
 
@@ -85,10 +94,10 @@ qu_base_resolution = 120.
 qu_refinement_factors = 0.5, 0.75, 1., 1.25, 1.5, 1.75, 2.
 ```
 
-To alter the resolutions used in this task, you will need to create your own
-config file (or add a `spherical_convergence` section to a config file if
-you're already using one).  The resolutions are a comma-separated list of the
-resolution of the mesh in km.  If you specify a different list
+To alter the resolutions used in the convergence tasks, you will need to create
+your own config file (or add a `spherical_convergence` section to a config file
+if you're already using one).  The resolutions are a comma-separated list of
+the resolution of the mesh in km.  If you specify a different list
 before setting up `cosine_bell`, steps will be generated with the requested
 resolutions.  (If you alter `icos_resolutions` or `qu_resolutions`) in the
 task's config file in the work directory, nothing will happen.)  For `icos`

From 2b6571ddcb8a513382a92e95c7c7397be8728a64 Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Mon, 23 Dec 2024 09:49:29 -0600
Subject: [PATCH 11/11] Add cosine bell restart to pr and nightly suites

Update cosine_bell suite to include all tests.

Remove cosine_bell_cached_init suite, which has not been well
maintained.
---
 polaris/ocean/suites/cosine_bell.txt             | 16 ++++++++++++++--
 polaris/ocean/suites/cosine_bell_cached_init.txt |  8 --------
 polaris/ocean/suites/nightly.txt                 |  1 +
 polaris/ocean/suites/pr.txt                      |  1 +
 4 files changed, 16 insertions(+), 10 deletions(-)
 delete mode 100644 polaris/ocean/suites/cosine_bell_cached_init.txt

diff --git a/polaris/ocean/suites/cosine_bell.txt b/polaris/ocean/suites/cosine_bell.txt
index 7ef38e541..81ea683d1 100644
--- a/polaris/ocean/suites/cosine_bell.txt
+++ b/polaris/ocean/suites/cosine_bell.txt
@@ -1,2 +1,14 @@
-ocean/spherical/icos/cosine_bell
-ocean/spherical/qu/cosine_bell
+ocean/spherical/icos/cosine_bell/convergence_space
+ocean/spherical/icos/cosine_bell/convergence_space/with_viz
+ocean/spherical/icos/cosine_bell/convergence_time
+ocean/spherical/icos/cosine_bell/convergence_time/with_viz
+ocean/spherical/icos/cosine_bell/convergence_both
+ocean/spherical/icos/cosine_bell/convergence_both/with_viz
+ocean/spherical/icos/cosine_bell/restart
+ocean/spherical/qu/cosine_bell/convergence_space
+ocean/spherical/qu/cosine_bell/convergence_space/with_viz
+ocean/spherical/qu/cosine_bell/convergence_time
+ocean/spherical/qu/cosine_bell/convergence_time/with_viz
+ocean/spherical/qu/cosine_bell/convergence_both
+ocean/spherical/qu/cosine_bell/convergence_both/with_viz
+ocean/spherical/qu/cosine_bell/restart
diff --git a/polaris/ocean/suites/cosine_bell_cached_init.txt b/polaris/ocean/suites/cosine_bell_cached_init.txt
deleted file mode 100644
index 021e294c1..000000000
--- a/polaris/ocean/suites/cosine_bell_cached_init.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-ocean/spherical/icos/cosine_bell
-  cached: icos_base_mesh_60km icos_init_60km icos_base_mesh_120km icos_init_120km
-  cached: icos_base_mesh_240km icos_init_240km icos_base_mesh_480km icos_init_480km
-ocean/spherical/qu/cosine_bell
-  cached: qu_base_mesh_60km qu_init_60km qu_base_mesh_90km qu_init_90km
-  cached: qu_base_mesh_120km qu_init_120km qu_base_mesh_150km qu_init_150km
-  cached: qu_base_mesh_180km qu_init_180km qu_base_mesh_210km qu_init_210km
-  cached: qu_base_mesh_240km qu_init_240km
diff --git a/polaris/ocean/suites/nightly.txt b/polaris/ocean/suites/nightly.txt
index e2b2ef4aa..e1760b595 100644
--- a/polaris/ocean/suites/nightly.txt
+++ b/polaris/ocean/suites/nightly.txt
@@ -5,3 +5,4 @@ ocean/planar/ice_shelf_2d/5km/z-star/default/with_restart
 ocean/planar/ice_shelf_2d/5km/z-level/default/with_restart
 ocean/planar/inertial_gravity_wave/convergence_both
 # ocean/planar/manufactured_solution
+ocean/spherical/icos/cosine_bell/restart
diff --git a/polaris/ocean/suites/pr.txt b/polaris/ocean/suites/pr.txt
index 4bb3cf52a..c7fc1b175 100644
--- a/polaris/ocean/suites/pr.txt
+++ b/polaris/ocean/suites/pr.txt
@@ -9,3 +9,4 @@ ocean/planar/internal_wave/vlr/default
 # ocean/planar/manufactured_solution
 ocean/single_column/cvmix
 ocean/single_column/ideal_age
+ocean/spherical/icos/cosine_bell/restart