Merge pull request #749 from hollyhan/hollyhan/landice/add-MALI-SLM-coupled-ISMIP6-runs

Add an option to setup coupled MALI-SLM runs in the ismip6 run testgroup

This PR adds to the `/landice/ismip6_run/ismip_ais_proj2300` testcase the option to setup coupled MALI-Sea Level Model simulations using the ismip6-Antarctica-2300 experimental protocol. 

With these changes, inclusion of the SLM can be activated through a test case cfg option.  This will set up required namelist and input settings, as well as the namelist.sealevel file used by SLM.  It will also set up an additional test case step that generates the required mapping files between MALI and SLM.  This must be run before any of the experiments are run.

This PR requires addition of Pyproj string `projections['ais-bedmap2-sphere'] = '+proj=stere +lat_ts=-71.0 +lat_0=-90 +lon_0=0.0 +k_0=1.0 +x_0=0.0 +y_0=0.0 +ellps=sphere'` in the MPAS-Tools script `set_lat_lon_fields_in_planar_grid.py` to set the latitude and longitude values as if MALI was projected on sphere rather than ellipse. The requirement has been merged here (https://github.com/MPAS-Dev/MPAS-Tools/pull/559/files).

Author: matthewhoffman

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

@@ -1,5 +1,8 @@
 import os
 
+from compass.landice.tests.ismip6_run.ismip6_ais_proj2300.create_slm_mapping_files import (  # noqa
+    CreateSlmMappingFiles,
+)
 from compass.landice.tests.ismip6_run.ismip6_ais_proj2300.set_up_experiment import (  # noqa
     SetUpExperiment,
 )
@@ -70,13 +73,32 @@ def configure(self):
         # each experiment (step) should be run manually
         self.steps_to_run = []
 
+        sea_level_model = self.config.getboolean('ismip6_run_ais_2300',
+                                                 'sea_level_model')
+        if sea_level_model:
+            subdir = 'mapping_files'
+            if os.path.exists(os.path.join(self.work_dir, subdir)):
+                print(f"WARNING: {subdir} path already exists; skipping.  "
+                      "Please remove the directory "
+                      f"{os.path.join(self.work_dir, subdir)} and execute "
+                      "'compass setup' again to set this experiment up.")
+            else:
+                self.add_step(
+                    CreateSlmMappingFiles(test_case=self,
+                                          name='mapping_files',
+                                          subdir=subdir))
+                self.steps_to_run.append('mapping_files')
+
     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.")
+                         "each experiment's subdirectory manually instead."
+                         "To create Sea-Level Model mapping files, submit"
+                         "job script or execute 'compass run' from the"
+                         "'mapping_files' subdirectory.")
 
     # no validate() method is needed

compass/landice/tests/ismip6_run/ismip6_ais_proj2300/albany_input.yaml

@@ -17,8 +17,7 @@ ANONYMOUS:
           # Zero Effective Pressure On Floating Ice At Nodes: true
           Zero Beta On Floating Ice: true
 
-    Cubature Degree: 4
-    Basal Cubature Degree: 8
+    Cubature Degree: 8
 
 # Discretization Description
   Discretization:
@@ -94,12 +93,6 @@ ANONYMOUS:
               Preconditioner Type: MueLu
               Preconditioner Types:
 
-                Ifpack:
-                  Overlap: 1
-                  Prec Type: ILU
-                  Ifpack Settings:
-                    'fact: level-of-fill': 0
-
                 Ifpack2:
                   Overlap: 1
                   Prec Type: ILUT
@@ -244,29 +237,3 @@ ANONYMOUS:
                       A: myRebalanceAFact
                       Coordinates: myRebalanceProlongatorFact
                       Importer: myRepartitionFact
-
-                ML:
-                  Base Method Defaults: none
-                  ML Settings:
-                    default values: SA
-                    ML output: 0
-                    'repartition: enable': 1
-                    'repartition: max min ratio': 1.327e+00
-                    'repartition: min per proc': 600
-                    'repartition: Zoltan dimensions': 2
-                    'repartition: start level': 4
-                    'semicoarsen: number of levels': 2
-                    'semicoarsen: coarsen rate': 14
-                    'smoother: sweeps': 4
-                    'smoother: type': Gauss-Seidel
-                    'smoother: Chebyshev eig boost': 1.2e+00
-                    'smoother: sweeps (level 0)': 1
-                    'smoother: type (level 0)': line Gauss-Seidel
-                    'smoother: line GS Type': standard
-                    'smoother: damping factor': 1.0e+00
-                    'smoother: pre or post': both
-                    'coarse: type': Gauss-Seidel
-                    'coarse: sweeps': 4
-                    'coarse: max size': 2000
-                    'coarse: pre or post': pre
-                    max levels: 7

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

@@ -0,0 +1,123 @@
+import shutil
+
+from mpas_tools.logging import check_call
+from mpas_tools.scrip.from_mpas import scrip_from_mpas
+
+from compass.step import Step
+
+
+class CreateSlmMappingFiles(Step):
+    """
+    A step for creating mapping files for the Sea Level Model
+
+    Attributes
+    ----------
+    """
+
+    def __init__(self, test_case, name, subdir):
+        """
+        Initialize step
+
+        Parameters
+        ----------
+
+        """
+
+        super().__init__(test_case=test_case, name=name, subdir=subdir)
+
+    def setup(self):
+        print("    Setting up mapping_file subdirectory")
+
+    def run(self):
+        """
+        Run this step of the test case
+        """
+
+        config = self.config
+        logger = self.logger
+        section = config['ismip6_run_ais_2300']
+        sea_level_model = section.getboolean('sea_level_model')
+        if sea_level_model:
+            self._build_mapping_files(config, logger)
+
+    def _build_mapping_files(self, config, logger):
+        """
+        Build mapping files between the MALI mesh and the SLM grid.
+
+        Parameters
+        ----------
+        config : compass.config.CompassConfigParser
+            Configuration options for a ismip6 forcing test case
+
+        logger : logging.Logger
+            A logger for output from the step
+        """
+
+        config = self.config
+        section = config['ismip6_run_ais_2300']
+        init_cond_path = section.get('init_cond_path')
+        nglv = section.getint('nglv')
+        section = config['parallel']
+        ntasks = section.getint('cores_per_node')
+
+        # create the mapping files
+        # first create scrip files
+        mali_scripfile = 'mali_scripfile.nc'
+        slm_scripfile = f'slm_nglv{nglv}scripfile.nc'
+        mali_meshfile = 'mali_meshfile_sphereLatLon.nc'
+
+        # slm scripfile
+        logger.info(f'creating scripfile for the SLM grid with '
+                    f'{nglv} Gauss-Legendre points in latitude')
+
+        args = ['ncremap',
+                '-g', slm_scripfile,
+                '-G',
+                f'latlon={nglv},{2*int(nglv)}#lat_typ=gss#lat_drc=n2s']
+
+        check_call(args, logger=logger)
+
+        # mali scripfile
+        # first have to adjust lat-lon values as if they are on sphere
+        shutil.copy(init_cond_path, mali_meshfile)
+        args = ['set_lat_lon_fields_in_planar_grid.py',
+                '--file', mali_meshfile,
+                '--proj', 'ais-bedmap2-sphere']
+
+        check_call(args, logger=logger)
+
+        logger.info('creating scrip file for the mali mesh')
+        scrip_from_mpas(mali_meshfile, mali_scripfile)
+
+        # create mapping file from MALI mesh to SLM grid
+        logger.info('creating MALI -> SLM grid mapfile with bilinear method')
+
+        parallel_executable = config.get("parallel", "parallel_executable")
+        # split the parallel executable into constituents
+        args = parallel_executable.split(' ')
+        args.extend(['-n', f'{ntasks}',
+                     'ESMF_RegridWeightGen',
+                     '-s', mali_scripfile,
+                     '-d', slm_scripfile,
+                     '-w', 'mapfile_mali_to_slm.nc',
+                     '-m', 'conserve',
+                     '-i', '-64bit_offset', '--netcdf4',
+                     '--src_regional'])
+
+        check_call(args, logger)
+
+        # create mapping file from SLM grid to MALI mesh
+        logger.info('SLM -> MALI mesh mapfile with bilinear method')
+        args = parallel_executable.split(' ')
+        args.extend(['-n', f'{ntasks}',
+                     'ESMF_RegridWeightGen',
+                     '-s', slm_scripfile,
+                     '-d', mali_scripfile,
+                     '-w', 'mapfile_slm_to_mali.nc',
+                     '-m', 'bilinear',
+                     '-i', '-64bit_offset', '--netcdf4',
+                     '--dst_regional'])
+
+        check_call(args, logger)
+
+        logger.info('mapping file creation complete')

compass/landice/tests/ismip6_run/ismip6_ais_proj2300/ismip6_ais_proj2300.cfg

@@ -44,3 +44,28 @@ von_mises_parameter_path = UNKNOWN
 
 # Whether facemelting should be included in the runs
 use_face_melting = False
+
+# True if running coupled MALI-sea level model simulation
+sea_level_model = False
+
+# NOTE: for the directories related to the sea-level model input/outputs, the slash '/' at the end of the directory name is necessary.
+# Path to the directory containing globally defined ice thickness field for the sea-level model
+slm_input_ice = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/icemodel/
+
+# Path to the directory containing earth model for the sea-level model
+slm_input_earth = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/earthmodel/
+
+# Earth structure profile
+# possible values: any file name string of earth model file.
+# Note that there is no single representative earth model for the globe or
+# any region of the globe (e.g., West Antarctica, East Antarctica, Greenland)
+# But for this test, we use 'prem_512.l60K2C.sum18p6.dum19p2.tz19p4.lm22' for West Antarctica
+# and 'prem_coll_512.l120C.ump5.lm10' for East Antarctica. Other earthmodels that can be used
+# should exist in the path defined in the config option 'slm_input_earth'.
+slm_earth_structure = prem_512.l60K2C.sum18p6.dum19p2.tz19p4.lm22
+
+# Path to the diectory containing other input files (present-day global topography and sea-level model grid files)
+slm_input_others = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/others/
+
+# number of gauss-legendre nodes in latitude (typically an integer multiple of 512)
+nglv = 2048

compass/landice/tests/ismip6_run/ismip6_ais_proj2300/ismip6_ais_proj2300_4km_chicoma.cfg

@@ -3,7 +3,7 @@
 # Can be "tier1", "tier2", "all", or a comma-delimited list of runs
 # "tier1" is expAE01-expAE06 plus hist and ctrlAE
 # "tier2" is expAE07-expAE14
-exp_list = hist,ctrlAE,expAE05
+exp_list = hist,ctrlAE,expAE01,expAE02,expAE05
 
 # Resolution that will be set up, in km.  Should be one of 4, 8, as those are
 # the two resolutions currently supported.
@@ -43,3 +43,28 @@ von_mises_parameter_path = UNKNOWN
 
 # Whether facemelting should be included in the runs
 use_face_melting = True
+
+# True if running coupled MALI-sea level model simulation
+sea_level_model = False
+
+# NOTE: for the directories related to the sea-level model input/outputs, the slash '/' at the end of the directory name is necessary.
+# Path to the base directory containing globally defined ice thickness field for the sea-level model
+slm_input_ice = /usr/projects/climate/hollyhan/SeaLevelModel_Inputs/icemodel/
+
+# Path to the directory containing earth model for the sea-level model
+slm_input_earth = /usr/projects/climate/hollyhan/SeaLevelModel_Inputs/earthmodel/
+
+# Earth structure profile
+# possible values: any file name string of earth model file.
+# Note that there is no single representative earth model for the globe or
+# any region of the globe (e.g., West Antarctica, East Antarctica, Greenland)
+# But for this test, we use 'prem_512.l60K2C.sum18p6.dum19p2.tz19p4.lm22' for West Antarctica
+# and 'prem_coll_512.l120C.ump5.lm10' for East Antarctica. Other earthmodels that can be used
+# should exist in the path defined in the config option 'slm_input_earth'.
+slm_earth_structure = prem_512.l60K2C.sum18p6.dum19p2.tz19p4.lm22
+
+# Path to the diectory containing other input files (present-day global topography and sea-level model grid files)
+slm_input_others = /usr/projects/climate/hollyhan/SeaLevelModel_Inputs/others/
+
+# number of gauss-legendre nodes in latitude (typically an integer multiple of 512)
+nglv = 2048

compass/landice/tests/ismip6_run/ismip6_ais_proj2300/ismip6_ais_proj2300_4km_nersc.cfg

@@ -43,4 +43,29 @@ calving_method = restore
 von_mises_parameter_path = UNKNOWN
 
 # Whether facemelting should be included in the runs
-use_face_melting = False
+use_face_melting = True
+
+# True if running coupled MALI-sea level model simulation
+sea_level_model = False
+
+# NOTE: for the directories related to the sea-level model input/outputs, the slash '/' at the end of the directory name is necessary.
+# Path to the base directory containing globally defined ice thickness field for the sea-level model
+slm_input_ice = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/icemodel/
+
+# Path to the directory containing earth model for the sea-level model
+slm_input_earth = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/earthmodel/
+
+# Earth structure profile
+# possible values: any file name string of earth model file.
+# Note that there is no single representative earth model for the globe or
+# any region of the globe (e.g., West Antarctica, East Antarctica, Greenland)
+# But for this test, we use 'prem_512.l60K2C.sum18p6.dum19p2.tz19p4.lm22' for West Antarctica
+# and 'prem_coll_512.l120C.ump5.lm10' for East Antarctica. Other earthmodels that can be used
+# should exist in the path defined in the config option 'slm_input_earth'.
+slm_earth_structure = prem_512.l60K2C.sum18p6.dum19p2.tz19p4.lm22
+
+# Path to the diectory containing other input files (present-day global topography and sea-level model grid files)
+slm_input_others = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/others/
+
+# number of gauss-legendre nodes in latitude (typically an integer multiple of 512)
+nglv = 2048

compass/landice/tests/ismip6_run/ismip6_ais_proj2300/ismip6_ais_proj2300_8km_nersc.cfg

@@ -44,3 +44,28 @@ von_mises_parameter_path = UNKNOWN
 
 # Whether facemelting should be included in the runs
 use_face_melting = False
+
+# True if running coupled MALI-sea level model simulation
+sea_level_model = False
+
+# NOTE: for the directories related to the sea-level model input/outputs, the slash '/' at the end of the directory name is necessary.
+# Path to the directory containing globally defined ice thickness field for the sea-level model
+slm_input_ice = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/icemodel/
+
+# Path to the directory containing earth model for the sea-level model
+slm_input_earth = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/earthmodel/
+
+# Earth structure profile
+# possible values: any file name string of earth model file.
+# Note that there is no single representative earth model for the globe or
+# any region of the globe (e.g., West Antarctica, East Antarctica, Greenland)
+# But for this test, we use 'prem_512.l60K2C.sum18p6.dum19p2.tz19p4.lm22' for West Antarctica
+# and 'prem_coll_512.l120C.ump5.lm10' for East Antarctica. Other earthmodels that can be used
+# should exist in the path defined in the config option 'slm_input_earth'.
+slm_earth_structure = prem_512.l60K2C.sum18p6.dum19p2.tz19p4.lm22
+
+# Path to the diectory containing other input files (present-day global topography and sea-level model grid files)
+slm_input_others = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/others/
+
+# number of gauss-legendre nodes in latitude (typically an integer multiple of 512)
+nglv = 2048

compass/landice/tests/ismip6_run/ismip6_ais_proj2300/namelist.landice

@@ -6,6 +6,11 @@
     config_thickness_advection = 'fo'
     config_tracer_advection = 'fo'
 
+    config_uplift_method = 'none'
+    config_slm_coupling_interval = 5
+    config_MALI_to_SLM_weights_file = 'mapfile_mali_to_slm.nc'
+    config_SLM_to_MALI_weights_file = 'mapfile_slm_to_mali.nc'
+
     config_calving = 'none'
     config_apply_calving_mask = .false.
     config_restore_calving_front_prevent_retreat = .false.
@@ -50,7 +55,7 @@
     config_do_restart = .true.
     config_restart_timestamp_name = 'restart_timestamp'
     config_start_time ='file'
-    config_stop_time = '2300-01-01_00:00:00'
+    config_stop_time = '2301-01-01_00:00:00'
     config_calendar_type = 'noleap'
 
     config_stats_interval = 0