Merge pull request #397 from hollyhan/add_ismip6_run_testgroup

Add ismip6 run testgroup

This PR adds a test group on running Antarctic simulations for the ISMIP6 2300 experimental protocol https://www.climate-cryosphere.org/wiki/index.php?title=ISMIP6-Projections2300-Antarctica.

Each experiment is a step that is meant to be run manually. A user must specify input files and experiments to set up in the config file.

compass/job/__init__.py

@@ -1,11 +1,12 @@
-from jinja2 import Template
-from importlib import resources
 import os
+from importlib import resources
+
 import numpy as np
+from jinja2 import Template
 
 
 def write_job_script(config, machine, target_cores, min_cores, work_dir,
-                     suite=''):
+                     suite='', pre_run_commands='', post_run_commands=''):
     """
 
     Parameters
@@ -28,6 +29,14 @@ def write_job_script(config, machine, target_cores, min_cores, work_dir,
 
     suite : str, optional
         The name of the suite
+
+    pre_run_commands : str, optional
+        Optional commands to be inserted into job script prior to calling
+        compass run
+
+    post_run_commands : str, optional
+        Optional commands to be inserted into job script after calling of
+        compass run
     """
 
     if config.has_option('parallel', 'account'):
@@ -38,8 +47,8 @@ def write_job_script(config, machine, target_cores, min_cores, work_dir,
     cores_per_node = config.getint('parallel', 'cores_per_node')
 
     # as a rule of thumb, let's do the geometric mean between min and target
-    cores = np.sqrt(target_cores*min_cores)
-    nodes = int(np.ceil(cores/cores_per_node))
+    cores = np.sqrt(target_cores * min_cores)
+    nodes = int(np.ceil(cores / cores_per_node))
 
     partition = config.get('job', 'partition')
     if partition == '<<<default>>>':
@@ -87,7 +96,8 @@ def write_job_script(config, machine, target_cores, min_cores, work_dir,
     text = template.render(job_name=job_name, account=account,
                            nodes=f'{nodes}', wall_time=wall_time, qos=qos,
                            partition=partition, constraint=constraint,
-                           suite=suite)
+                           suite=suite, pre_run_commands=pre_run_commands,
+                           post_run_commands=post_run_commands)
     text = _clean_up_whitespace(text)
     if suite == '':
         script_filename = 'job_script.sh'

compass/job/job_script.template

@@ -18,5 +18,6 @@
 {%- endif %}
 
 source load_compass_env.sh
+{{ pre_run_commands }}
 compass run {{suite}}
-
+{{ post_run_commands }}

compass/landice/__init__.py

@@ -9,6 +9,7 @@
 from compass.landice.tests.humboldt import Humboldt
 from compass.landice.tests.hydro_radial import HydroRadial
 from compass.landice.tests.ismip6_forcing import Ismip6Forcing
+from compass.landice.tests.ismip6_run import Ismip6Run
 from compass.landice.tests.kangerlussuaq import Kangerlussuaq
 from compass.landice.tests.koge_bugt_s import KogeBugtS
 from compass.landice.tests.mismipplus import MISMIPplus
@@ -38,6 +39,7 @@ def __init__(self):
         self.add_test_group(Humboldt(mpas_core=self))
         self.add_test_group(HydroRadial(mpas_core=self))
         self.add_test_group(Ismip6Forcing(mpas_core=self))
+        self.add_test_group(Ismip6Run(mpas_core=self))
         self.add_test_group(Kangerlussuaq(mpas_core=self))
         self.add_test_group(KogeBugtS(mpas_core=self))
         self.add_test_group(MISMIPplus(mpas_core=self))

compass/landice/tests/ismip6_run/__init__.py

@@ -0,0 +1,22 @@
+from compass.landice.tests.ismip6_run.ismip6_ais_proj2300 import (
+    Ismip6AisProj2300,
+)
+from compass.testgroup import TestGroup
+
+
+class Ismip6Run(TestGroup):
+    """
+    A test group for automated setup of a suite of standardized
+    ISMIP6 simulations
+
+    Attributes
+    ----------
+    """
+    def __init__(self, mpas_core):
+        """
+        mpas_core : compass.landice.Landice
+            the MPAS core that this test group belongs to
+        """
+        super().__init__(mpas_core=mpas_core, name='ismip6_run')
+
+        self.add_test_case(Ismip6AisProj2300(test_group=self))

compass/landice/tests/ismip6_run/ismip6_ais_proj2300/__init__.py

@@ -0,0 +1,82 @@
+import os
+
+from compass.landice.tests.ismip6_run.ismip6_ais_proj2300.set_up_experiment import (  # noqa
+    SetUpExperiment,
+)
+from compass.testcase import TestCase
+
+
+class Ismip6AisProj2300(TestCase):
+    """
+    A test case for automated setup of a suite of standardized
+    simulations for ISMIP6-Projections2300-Antarctica
+    See: https://www.climate-cryosphere.org/wiki/index.php?title=ISMIP6-Projections2300-Antarctica)  # noqa
+    """
+
+    def __init__(self, test_group):
+        """
+        Create the test case
+
+        Parameters
+        ----------
+        test_group : compass.landice.tests.ismip6_run.Ismip6Run
+            The test group that this test case belongs to
+
+        """
+        name = 'ismip6_ais_proj2300'
+
+        super().__init__(test_group=test_group, name=name,
+                         subdir=name)
+
+    def configure(self):
+        """
+        Set up the desired ISMIP6 AIS 2300 experiments.
+
+        Read the list from the config of which experiments the
+        user wants to set up.  Call thee add_step method and add the
+        experiment to steps_to_run.  Those operations are typically done
+        in the constructor, but they are done here so that the list to set up
+        can be adjusted in the config, and the config is not available until
+        this point.
+        """
+
+        # user can specify any of: 'all', 'tier1', 'tier2', or a
+        # comma-delimited list (or a single experiment)
+        exp_list = self.config.get('ismip6_run_ais_2300', 'exp_list')
+        if exp_list == "tier1":
+            exp_list = ['hist', 'ctrlAE'] + \
+                       [f'expAE{i:02}' for i in range(1, 7)]
+        elif exp_list == "tier2":
+            exp_list = [f'expAE{i:02}' for i in range(7, 15)]
+        elif exp_list == "all":
+            exp_list = ['hist', 'ctrlAE'] + \
+                       [f'expAE{i:02}' for i in range(1, 15)]
+        else:
+            exp_list = exp_list.split(",")
+        mesh_res = self.config.getint('ismip6_run_ais_2300', 'mesh_res')
+
+        for exp in exp_list:
+            if os.path.exists(os.path.join(self.work_dir, exp)):
+                print(f"WARNING: {exp} path already exists; skipping.  "
+                      "Please remove the directory "
+                      f"{os.path.join(self.work_dir, exp)} and execute "
+                      "'compass setup' again to set this experiment up.")
+            else:
+                exp_name = f'{exp}_{mesh_res:02}'
+                self.add_step(
+                    SetUpExperiment(test_case=self, name=exp_name,
+                                    subdir=exp_name, exp=exp))
+        # Do not add experiments to step to steps_to_run;
+        # each experiment (step) should be run manually
+        self.steps_to_run = []
+
+    def run(self):
+        """
+        A dummy run method
+        """
+        raise ValueError("ERROR: 'compass run' has no functionality at the "
+                         "test case level for this test.  "
+                         "Please submit the job script in "
+                         "each experiment's subdirectory manually instead.")
+
+    # no validate() method is needed