Clean up "make all" for 5.2 branch

.git-blame-ignore-revs

@@ -22,6 +22,7 @@ e4d38681df23ccca0ae29581a45f8362574e0630
 a9d96219902cf609636886c7073a84407f450d9a
 d866510188d26d51bcd6d37239283db690af7e82
 0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
+e096358c832ab292ddfd22dd5878826c7c788968
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380

python/ctsm/test/test_sys_gen_mksurfdata_jobscript_multi.py

@@ -47,10 +47,12 @@ def tearDown(self):
         os.chdir(self._original_wd)
         shutil.rmtree(self._tempdir, ignore_errors=True)
 
-    def createJS(self, nodes, tasks_per_node, scenario, option_list=[]):
+    def createJS(self, nodes, tasks_per_node, scenario, option_list=None):
         """
         Create a JobScript by sending a list of options in
         """
+        if option_list is None:
+            option_list = []
         if len(option_list) > 1:
             sys.argv.extend(option_list)
         sys.argv.extend(

python/ctsm/test/test_sys_gen_mksurfdata_jobscript_single.py

@@ -50,10 +50,12 @@ def tearDown(self):
         os.chdir(self._original_wd)
         shutil.rmtree(self._tempdir, ignore_errors=True)
 
-    def createJS(self, nodes, tasks_per_node, option_list=[]):
+    def createJS(self, nodes, tasks_per_node, option_list=None):
         """
         Create a JobScript by sending a list of options in
         """
+        if option_list is None:
+            option_list = []
         if len(option_list) > 1:
             sys.argv.extend(option_list)
         sys.argv.extend(

python/ctsm/test/test_sys_mesh_modifier.py

@@ -44,10 +44,6 @@ def setUp(self):
             path_to_ctsm_root(), "tools/modify_input_files/modify_mesh_template.cfg"
         )
         self.testinputs_path = os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs")
-        fsurdat_in = os.path.join(
-            self.testinputs_path,
-            "surfdata_5x5_amazon_hist_16pfts_CMIP6_2000_c231031.nc",
-        )
         self._tempdir = tempfile.mkdtemp()
         self._cfg_file_path = os.path.join(self._tempdir, "modify_mesh_mask.cfg")
         self._mesh_mask_in = os.path.join(self._tempdir, "mesh_mask_in.nc")
@@ -72,7 +68,7 @@ def setUp(self):
         except subprocess.CalledProcessError as e:
             sys.exit(f"{e} ERROR using {configure_cmd}")
 
-    def createScripGridAndMask(self):
+    def createScripGridAndMask(self, fsurdat_in):
         """Create the SCRIP gird and mask file"""
         # Generate scrip file from fsurdat_in using nco
         # In the ctsm_py environment this requires running 'module load nco'
@@ -86,14 +82,14 @@ def createScripGridAndMask(self):
 
         # This could also alturnatively be done, by using the stored SCRIP grid file for the resolution under CESM inputdata
         ncks_cmd = (
-            f"ncks --rgr infer --rgr scrip={self.scrip_file} {self.fsurdat_in} {self.metadata_file}"
+            f"ncks --rgr infer --rgr scrip={self.scrip_file} {fsurdat_in} {self.metadata_file}"
         )
         try:
             subprocess.check_call(ncks_cmd, shell=True)
         except subprocess.CalledProcessError as e:
             err_msg = (
                 f"{e} ERROR using ncks to generate {self.scrip_file} from "
-                + f"{self.fsurdat_in}; MOST LIKELY SHOULD INVOKE module load nco"
+                + f"{fsurdat_in}; MOST LIKELY SHOULD INVOKE module load nco"
             )
             sys.exit(err_msg)
         # Run .env_mach_specific.sh to load esmf and generate mesh_mask_in
@@ -109,13 +105,13 @@ def createScripGridAndMask(self):
         # Generate landmask_file from fsurdat_in
         self._lat_varname = "LATIXY"  # same as in fsurdat_in
         self._lon_varname = "LONGXY"  # same as in fsurdat_in
-        fsurdat_in_data = xr.open_dataset(self.fsurdat_in)
+        fsurdat_in_data = xr.open_dataset(fsurdat_in)
         assert self._lat_varname in fsurdat_in_data.variables
         assert self._lon_varname in fsurdat_in_data.variables
         self._lat_dimname = fsurdat_in_data[self._lat_varname].dims[0]
         self._lon_dimname = fsurdat_in_data[self._lat_varname].dims[1]
 
-    def createLandMaskFile(self):
+    def createLandMaskFile(self, fsurdat_in):
         """Create the LandMask file from the input fsurdat_in file"""
         if os.path.exists(self._landmask_file):
             os.remove(self._landmask_file)
@@ -124,14 +120,12 @@ def createLandMaskFile(self):
             + "-A -v -s 'landmask=LANDFRAC_MKSURFDATA.convert(NC_INT)' "
             + f"-A -v -s {self._lat_varname}={self._lat_varname} "
             + f"-A -v -s {self._lon_varname}={self._lon_varname} "
-            + f"{self.fsurdat_in} {self._landmask_file}"
+            + f"{fsurdat_in} {self._landmask_file}"
         )
         try:
             subprocess.check_call(ncap2_cmd, shell=True)
         except subprocess.CalledProcessError as e:
-            sys.exit(
-                f"{e} ERROR using ncap2 to generate {self._landmask_file} from {self.fsurdat_in}"
-            )
+            sys.exit(f"{e} ERROR using ncap2 to generate {self._landmask_file} from {fsurdat_in}")
 
     def tearDown(self):
         """
@@ -147,13 +141,13 @@ def test_allInfo(self):
         For a case where the mesh remains unchanged, it's just output as
         ocean so the mesh is output as all zero's rather than the all 1's that came in.
         """
-        self.fsurdat_in = os.path.join(
+        fsurdat_in = os.path.join(
             self.testinputs_path,
             "surfdata_5x5_amazon_hist_78pfts_CMIP6_2000_c230517.nc",
         )
 
-        self.createScripGridAndMask()
-        self.createLandMaskFile()
+        self.createScripGridAndMask(fsurdat_in)
+        self.createLandMaskFile(fsurdat_in)
         self._create_config_file()
 
         # run the mesh_mask_modifier tool
@@ -185,12 +179,12 @@ def test_modifyMesh(self):
         For a case where the mesh is changed.
         """
 
-        self.fsurdat_in = os.path.join(
+        fsurdat_in = os.path.join(
             self.testinputs_path,
             "surfdata_5x5_amazon_hist_78pfts_CMIP6_2000_c230517_modify_mask.nc",
         )
-        self.createScripGridAndMask()
-        self.createLandMaskFile()
+        self.createScripGridAndMask(fsurdat_in)
+        self.createLandMaskFile(fsurdat_in)
         self._create_config_file()
 
         if os.path.exists(self._mesh_mask_out):

python/ctsm/test/test_unit_modify_fsurdat.py

@@ -390,7 +390,8 @@ def test_check_varlist_lists_wrongsizes(self):
         settings = {"var_lev1": lev1list}
         with self.assertRaisesRegex(
             SystemExit,
-            " Variable var_lev1 is 8 is of the wrong size. It should be = 9 in input settings dictionary",
+            " Variable var_lev1 is 8 is of the wrong size."
+            + " It should be = 9 in input settings dictionary",
         ):
             self.modify_fsurdat.check_varlist(settings)
 

python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py

@@ -137,6 +137,74 @@ def get_parser():
     return parser
 
 
+def write_runscript(
+    scenario,
+    jobscript_file,
+    number_of_nodes,
+    tasks_per_node,
+    account,
+    walltime,
+    queue,
+    target_list,
+    resolution_dict,
+    dataset_dict,
+    env_specific_script,
+    mksurfdata,
+    runfile,
+):
+    """
+    Write run script
+    """
+    runfile.write("#!/bin/bash \n")
+    runfile.write(f"#PBS -A {account} \n")
+    runfile.write(f"#PBS -N mksrf_{scenario} \n")
+    runfile.write("#PBS -j oe \n")
+    runfile.write("#PBS -k eod \n")
+    runfile.write("#PBS -S /bin/bash \n")
+    runfile.write(f"#PBS -q {queue} \n")
+    runfile.write(f"#PBS -l walltime={walltime} \n")
+    runfile.write(
+        "#PBS -l select="
+        + f"{number_of_nodes}:ncpus={tasks_per_node}:mpiprocs={tasks_per_node}:mem=218GB \n"
+    )
+    runfile.write(
+        f"# This is a batch script to run a set of resolutions for mksurfdata_esmf {scenario}\n"
+    )
+    runfile.write(
+        "# NOTE: THIS SCRIPT IS AUTOMATICALLY GENERATED "
+        + "SO IN GENERAL YOU SHOULD NOT EDIT it!!\n\n"
+    )
+    runfile.write("\n")
+
+    # Run env_mach_specific.sh to control the machine dependent
+    # environment including the paths to compilers and libraries
+    # external to cime such as netcdf
+    runfile.write(". " + env_specific_script + "\n")
+    check = "if [ $? != 0 ]; then echo 'Error running env_specific_script'; exit -4; fi"
+    runfile.write(f"{check} \n")
+    for target in target_list:
+        res_set = dataset_dict[target][1]
+        if res_set not in resolution_dict:
+            abort(f"Resolution is not in the resolution_dict: {res_set}")
+        for res in resolution_dict[res_set]:
+            namelist = f"{scenario}_{res}.namelist"
+            command = os.path.join(os.getcwd(), "gen_mksurfdata_namelist")
+            command = command + " " + dataset_dict[target][0] + " " + res
+            command = command + " --silent"
+            command = command + f" --namelist {namelist}"
+            print(f"command is {command}")
+            sys.argv = [x for x in command.split(" ") if x]
+            main_nml()
+            print(f"generated namelist {namelist}")
+            output = f"time mpiexec {mksurfdata} < {namelist}"
+            runfile.write(f"{output} \n")
+            check = f"if [ $? != 0 ]; then echo 'Error running resolution {res}'; exit -4; fi"
+            runfile.write(f"{check} \n")
+            runfile.write(f"echo Successfully ran resolution {res}\n")
+
+    runfile.write(f"echo Successfully ran {jobscript_file}\n")
+
+
 def main():
     """
     See docstring at the top.
@@ -168,7 +236,13 @@ def main():
     # Determine resolution sets that are referenced in commands
     # TODO slevis: When new resolutions become supported in ccs_config, the
     # first entry will change to
-    # "standard_res_no_crop": ["0.9x1.25", "1.9x2.5", "mpasa60", "mpasa60-3conus", "mpasa60-3centralUS"],
+    # "standard_res_no_crop": [
+    # "0.9x1.25",
+    # "1.9x2.5",
+    # "mpasa60",
+    # "mpasa60-3conus",
+    # "mpasa60-3centralUS",
+    # ],
     # --------------------------
     resolution_dict = {
         "standard_res_no_crop": ["0.9x1.25", "1.9x2.5", "mpasa60"],
@@ -246,7 +320,8 @@ def main():
             "mpasa480",
         ),
         "crop-global-present-nldas": (
-            "--start-year 2000 --end-year 2000                                 --res",  # TODO slevis: --hirespft uses old data for now, so keep out
+            # TODO slevis: --hirespft uses old data for now, so keep out
+            "--start-year 2000 --end-year 2000                                 --res",
             "nldas_res",
         ),
         "crop-global-1850": (
@@ -370,7 +445,8 @@ def main():
     if not os.path.exists(args.bld_path):
         print(
             args.bld_path
-            + " directory does NOT exist -- build mksurdata_esmf before running this script -- using ./gen_mksurfdata_build.sh"
+            + " directory does NOT exist -- build mksurdata_esmf before running this script --"
+            + " using ./gen_mksurfdata_build.sh"
         )
         sys.exit(1)
 
@@ -387,53 +463,20 @@ def main():
     # --------------------------
     with open(jobscript_file, "w", encoding="utf-8") as runfile:
 
-        runfile.write("#!/bin/bash \n")
-        runfile.write(f"#PBS -A {account} \n")
-        runfile.write(f"#PBS -N mksrf_{scenario} \n")
-        runfile.write("#PBS -j oe \n")
-        runfile.write("#PBS -k eod \n")
-        runfile.write("#PBS -S /bin/bash \n")
-        runfile.write(f"#PBS -q {queue} \n")
-        runfile.write(f"#PBS -l walltime={walltime} \n")
-        runfile.write(
-            f"#PBS -l select={number_of_nodes}:ncpus={tasks_per_node}:mpiprocs={tasks_per_node}:mem=218GB \n"
-        )
-        runfile.write(
-            f"# This is a batch script to run a set of resolutions for mksurfdata_esmf {scenario} \n"
-        )
-        runfile.write(
-            "# NOTE: THIS SCRIPT IS AUTOMATICALLY GENERATED SO IN GENERAL YOU SHOULD NOT EDIT it!!\n\n"
+        write_runscript(
+            scenario,
+            jobscript_file,
+            number_of_nodes,
+            tasks_per_node,
+            account,
+            walltime,
+            queue,
+            target_list,
+            resolution_dict,
+            dataset_dict,
+            env_specific_script,
+            mksurfdata,
+            runfile,
         )
-        runfile.write("\n")
-
-        n_p = int(tasks_per_node) * int(number_of_nodes)
-
-        # Run env_mach_specific.sh to control the machine dependent
-        # environment including the paths to compilers and libraries
-        # external to cime such as netcdf
-        runfile.write(". " + env_specific_script + "\n")
-        check = "if [ $? != 0 ]; then echo 'Error running env_specific_script'; exit -4; fi"
-        runfile.write(f"{check} \n")
-        for target in target_list:
-            res_set = dataset_dict[target][1]
-            if res_set not in resolution_dict:
-                abort(f"Resolution is not in the resolution_dict: {res_set}")
-            for res in resolution_dict[res_set]:
-                namelist = f"{scenario}_{res}.namelist"
-                command = os.path.join(os.getcwd(), "gen_mksurfdata_namelist")
-                command = command + " " + dataset_dict[target][0] + " " + res
-                command = command + " --silent"
-                command = command + f" --namelist {namelist}"
-                print(f"command is {command}")
-                sys.argv = [x for x in command.split(" ") if x]
-                main_nml()
-                print(f"generated namelist {namelist}")
-                output = f"time mpiexec {mksurfdata} < {namelist}"
-                runfile.write(f"{output} \n")
-                check = f"if [ $? != 0 ]; then echo 'Error running resolution {res}'; exit -4; fi"
-                runfile.write(f"{check} \n")
-                runfile.write(f"echo Successfully ran resolution {res}\n")
-
-        runfile.write(f"echo Successfully ran {jobscript_file}\n")
 
     print(f"echo Successfully created jobscript {jobscript_file}\n")