Merge Pull Request #2868 from E3SM-Project/scream/bartgol/eamxx/check…

…-nlev-consistency-with-IC-file-at-buildnml-time

Automatically Merged using E3SM Pull Request AutoTester
PR Title: EAMxx: add buildnml-time check for IC file and cmake option compatibility
PR Author: bartgol
PR LABELS: AT: AUTOMERGE, scripts, CIME, AT: Skip weaver, AT: Skip Stand-Alone Testing, code usability

components/eamxx/cime_config/eamxx_buildnml.py

@@ -11,12 +11,14 @@
 import xml.dom.minidom as md
 
 # Add path to scream libs
-sys.path.append(os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "scripts"))
+EAMXXROOT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+sys.path.append(os.path.join(EAMXXROOT, "scripts"))
 
 # SCREAM imports
 from eamxx_buildnml_impl import get_valid_selectors, get_child, refine_type, \
         resolve_all_inheritances, gen_atm_proc_group, check_all_values, find_node
 from atm_manip import apply_atm_procs_list_changes_from_buffer, apply_non_atm_procs_list_changes_from_buffer
+from utils import run_cmd_no_fail
 
 from utils import ensure_yaml # pylint: disable=no-name-in-module
 ensure_yaml()
@@ -163,6 +165,22 @@ def perform_consistency_checks(case, xml):
     CIME.utils.CIMEError: ERROR: rrtmgp::rad_frequency incompatible with restart frequency.
      Please, ensure restart happens on a step when rad is ON
      For daily (or less frequent) restart, rad_frequency must divide ATM_NCPL
+    >>> case = MockCase({'SCREAM_CMAKE_OPTIONS':'SCREAM_NUM_VERTICAL_LEV 15'})
+    >>> xml_str = '''
+    ... <params>
+    ...   <initial_conditions>
+    ...     <Filename>{}/eamxx_buildnml_unittest.nc</Filename>
+    ...   </initial_conditions>
+    ... </params>
+    ... '''.format(os.path.join(EAMXXROOT,'cime_config/tests'))
+    >>> xml = ET.fromstring(xml_str)
+    >>> perform_consistency_checks(case,xml)
+    >>> case = MockCase({'SCREAM_CMAKE_OPTIONS':'SCREAM_NUM_VERTICAL_LEV 20'})
+    >>> perform_consistency_checks(case,xml)
+    Traceback (most recent call last):
+    CIME.utils.CIMEError: ERROR: Error! IC file contains a number of levels different from the cmake option SCREAM_NUM_VERTICAL_LEV
+      ic file, lev: 15
+      SCREAM_NUM_VERTICAL_LEV: 20
     """
 
     # RRTMGP can be supercycled. Restarts cannot fall in the middle
@@ -205,6 +223,27 @@ def perform_consistency_checks(case, xml):
                     " Please, ensure restart happens on a step when rad is ON\n"
                     " For daily (or less frequent) restart, rad_frequency must divide ATM_NCPL")
 
+    # Check that SCREAM_NUM_VERTICAL_LEV matches nlev in the IC file
+    scream_opts = case.get_value("SCREAM_CMAKE_OPTIONS")
+    tokens = scream_opts.split()
+    expect (len(tokens) % 2 == 0, "Error! SCREAM_CMAKE_OPTIONS should contain a string of the form 'option1 value1 option2 value2 ...'\n")
+    it = iter(tokens)
+    cmake_args_dict = {}
+    for item in it:
+        cmake_args_dict[item] = next(it)
+
+    nlevs_cmake = int(cmake_args_dict['SCREAM_NUM_VERTICAL_LEV'])
+    ic_xml = find_node(xml,"initial_conditions")
+    if ic_xml is not None:
+        ic_fname = get_child(ic_xml,"Filename")
+        cmd = f"ncdump -h {ic_fname.text}" + r" | sed '/variables:/q' | awk '/\<lev/{ print $3 }'"
+        nlevs_ic = int(run_cmd_no_fail(cmd))
+        expect (nlevs_cmake == nlevs_ic,
+                "Error! IC file contains a number of levels different from the cmake option SCREAM_NUM_VERTICAL_LEV\n"
+                f"  ic file, lev: {nlevs_ic}\n"
+                f"  SCREAM_NUM_VERTICAL_LEV: {nlevs_cmake}")
+
+
 ###############################################################################
 def ordered_dump(data, item, Dumper=yaml.SafeDumper, **kwds):
 ###############################################################################

components/eamxx/cime_config/eamxx_buildnml_impl.py

@@ -17,6 +17,8 @@ class MockCase(object):
 
     def __init__(self, kv_dict):
         self._kv_dict = dict(kv_dict)
+        if 'SCREAM_CMAKE_OPTIONS' not in self._kv_dict.keys():
+            self._kv_dict['SCREAM_CMAKE_OPTIONS'] = "SCREAM_NUM_VERTICAL_LEV 10"
 
     def get_value(self, key):
         if key in self._kv_dict:

components/eamxx/cime_config/namelist_defaults_scream.xml

@@ -37,6 +37,8 @@ be lost if SCREAM_HACK_XML is not enabled.
     <selector name="hgrid" case_env="ATM_GRID"/>
     <selector name="dyn" case_env="CAM_TARGET"/>
     <selector name="nlev" case_env="SCREAM_CMAKE_OPTIONS" regex=".*SCREAM_NUM_VERTICAL_LEV ([0-9]+).*"/>
+    <!-- For intenal testing only -->
+    <selector name="test_sel" case_env="SCREAM_CMAKE_OPTIONS" regex=".*SCREAM_NUM_TRACERS ([0-9]+).*"/>
   </selectors>
 
   <!-- List of scream grids for a given compset. I/O can only happen on these grids -->
@@ -301,10 +303,10 @@ be lost if SCREAM_HACK_XML is not enabled.
     <!-- For internal testing only -->
     <testOnly inherit="atm_proc_base">
       <my_param type="array(integer)">1,2</my_param>
-      <my_param nlev="1" append="base">3,4</my_param>
-      <my_param nlev="1" append="last">5,6</my_param>
-      <my_param nlev="2" append="last">3,4</my_param>
-      <my_param nlev="2" append="base">5,6</my_param>
+      <my_param test_sel="1" append="base">3,4</my_param>
+      <my_param test_sel="1" append="last">5,6</my_param>
+      <my_param test_sel="2" append="last">3,4</my_param>
+      <my_param test_sel="2" append="base">5,6</my_param>
     </testOnly>
 
     <!-- Simple Prescribed Aerosols (SPA) -->

components/eamxx/scripts/cime-nml-tests

@@ -10,7 +10,7 @@ from utils import check_minimum_python_version, expect, ensure_pylint, get_times
 
 check_minimum_python_version(3, 6)
 
-from machines_specs import is_machine_supported
+from machines_specs import is_machine_supported, setup_mach_env
 
 import unittest, argparse, sys, os, shutil
 from pathlib import Path
@@ -202,12 +202,12 @@ class TestBuildnml(unittest.TestCase):
         self._chg_atmconfig([("mac_aero_mic::atm_procs_list", "shoc,cldFraction,spa,p3,testOnly")], case)
 
         # Test case 1: append to base, then to last. Should give all 3 entries stacked
-        run_cmd_no_fail(f"./xmlchange --append SCREAM_CMAKE_OPTIONS='SCREAM_NUM_VERTICAL_LEV 1'", from_dir=case)
+        run_cmd_no_fail(f"./xmlchange --append SCREAM_CMAKE_OPTIONS='SCREAM_NUM_TRACERS 1'", from_dir=case)
         run_cmd_no_fail("./case.setup", from_dir=case)
         self._get_values(case,"my_param","1,2,3,4,5,6")
 
         # Test case 2: append to last, then to base. Should give 1st and 3rd entry
-        run_cmd_no_fail(f"./xmlchange --append SCREAM_CMAKE_OPTIONS='SCREAM_NUM_VERTICAL_LEV 2'", from_dir=case)
+        run_cmd_no_fail(f"./xmlchange --append SCREAM_CMAKE_OPTIONS='SCREAM_NUM_TRACERS 2'", from_dir=case)
         run_cmd_no_fail("./case.setup", from_dir=case)
         self._get_values(case,"my_param","1,2,5,6")
 
@@ -429,6 +429,7 @@ def scripts_tests(machine=None):
     if machine:
         expect(is_machine_supported(machine), "Machine {} is not supported".format(machine))
         CONFIG["machine"] = machine
+        setup_mach_env(machine)
 
     unittest.main(verbosity=2)
 

components/eamxx/scripts/jenkins/jenkins_common_impl.sh

@@ -151,7 +151,7 @@ if [ $skip_testing -eq 0 ]; then
         scripts_fail=1
       fi
 
-      ./scripts/cime-nml-tests
+      ./scripts/cime-nml-tests -m mappy
       if [[ $? != 0 ]]; then
         fails=$fails+1;
         scripts_fail=1