Merge pull request #3126 from jedwards4b/nuopc-cmeps

Nuopc cmeps removed.
Remove the nuopc driver and mediator to a separate repository https://github.com/ESCOMP/CMEPS.git

Test suite: scripts_regression_tests.py
Test baseline:
Test namelist changes:
Test status: bit for bit
Fixes

User interface changes?:

Update gh-pages html (Y/N)?:

Code review:

config/cesm/config_grids.xml

@@ -1412,6 +1412,7 @@
       <file grid="ocnice"  mask="tx0.1v2">$DIN_LOC_ROOT/share/domains/domain.ocn.tx0.1v2.161014.nc</file>
       <file grid="atm|lnd" mask="tx0.1v3">$DIN_LOC_ROOT/share/domains/domain.lnd.TL319_tx0.1v3.170730.nc</file>
       <file grid="ocnice"  mask="tx0.1v3">$DIN_LOC_ROOT/share/domains/domain.ocn.tx0.1v3.170730.nc</file>
+      <mesh driver="nuopc">$DIN_LOC_ROOT/share/meshes/TL319_151007_ESMFmesh.nc</mesh>
       <desc>TL319 grid for JRA55</desc>
     </domain>
 
@@ -1528,6 +1529,7 @@
 
     <domain name="JRA025">
       <nx>1440</nx> <ny>720</ny>
+      <mesh driver="nuopc">$DIN_LOC_ROOT/share/meshes/JRA025m.170209_ESMFmesh.nc</mesh>
       <!-- TODO (mvertens, 2018-12-02): create a domain file for this  -->
       <desc>JRA is 0.25 degree runoff grid for use with JRA-55 runoff data</desc>
     </domain>

config/cesm/machines/config_machines.xml

@@ -2276,13 +2276,13 @@ This allows using a different mpirun command to launch unit tests
       </modules>
       <modules mpilib="mvapich2">
         <command name="load">mvapich2/2.3b</command>
-        <command name="load">pnetcdf/1.8.1</command>
+        <command name="load">pnetcdf/1.11.0</command>
         <command name="load">parallel-netcdf/4.3.3.1</command>
       </modules>
       <modules mpilib="impi">
         <command name="rm">mvapich2</command>
         <command name="load">impi/18.0.2</command>
-        <command name="load">pnetcdf/1.8.1</command>
+        <command name="load">pnetcdf/1.11.0</command>
         <command name="load">parallel-netcdf/4.3.3.1</command>
       </modules>
       <modules mpilib="mpi-serial">
@@ -2350,13 +2350,13 @@ This allows using a different mpirun command to launch unit tests
       </modules>
       <modules mpilib="mvapich2">
         <command name="load">mvapich2/2.3b</command>
-        <command name="load">pnetcdf/1.8.1</command>
+        <command name="load">pnetcdf/1.11.0</command>
         <command name="load">parallel-netcdf/4.3.3.1</command>
       </modules>
       <modules mpilib="impi">
         <command name="rm">mvapich2</command>
         <command name="load">impi/17.0.3</command>
-        <command name="load">pnetcdf/1.8.1</command>
+        <command name="load">pnetcdf/1.11.0</command>
         <command name="load">parallel-netcdf/4.3.3.1</command>
       </modules>
       <modules mpilib="mpi-serial">

config/cesm/machines/config_pio.xml

@@ -25,12 +25,13 @@
     </values>
   </entry>
 
+  <!--
   <entry id="PIO_VERSION">
     <values>
       <value mach="stampede2-skx">1</value>
     </values>
   </entry>
-
+  -->
 
   <!--- uncomment and fill in relevant sections
   <entry id="PIO_ROOT">
@@ -57,7 +58,9 @@
 
   <entry id="PIO_REARRANGER">
     <values>
-      <value>$PIO_VERSION</value>
+      <!-- Note: problem not using box rearranger with nuopc caps -->
+      <!-- <value>$PIO_VERSION</value> -->
+      <value>1</value>
     </values>
   </entry>
 

scripts/create_test

@@ -157,6 +157,9 @@ def parse_command_line(args, description):
         parser.add_argument("--xml-testlist",
                             help="Use this testlist to lookup tests.The default is specified in config_files.xml")
 
+        parser.add_argument("--xml-driver", choices=('mct', 'nuopc', 'moab'),
+                            help="Override driver specified in tests and use this one.")
+
         parser.add_argument("testargs", nargs="*",
                             help="Tests to run. Testname form is TEST.GRID.COMPSET[.MACHINE_COMPILER]")
 
@@ -388,9 +391,9 @@ def parse_command_line(args, description):
                    "At least one of --xml-machine, --xml-testlist, "
                    "--xml-compiler, --xml-category or a valid test name must be provided.")
 
-            test_data = get_tests_from_xml(args.xml_machine, args.xml_category,
-                                           args.xml_compiler, args.xml_testlist,
-                                           machine_name, args.compiler)
+            test_data = get_tests_from_xml(xml_machine=args.xml_machine, xml_category=args.xml_category,
+                                           xml_compiler=args.xml_compiler, xml_testlist=args.xml_testlist,
+                                           machine=machine_name, compiler=args.compiler, driver=args.xml_driver)
             test_names = [item["name"] for item in test_data]
             for test_datum in test_data:
                 test_extra_data[test_datum["name"]] = test_datum

scripts/lib/CIME/code_checker.py

@@ -26,10 +26,11 @@ def _run_pylint(on_file, interactive):
         cmd_options +=",relative-import"
 
     # add init-hook option
-    cmd_options += " --init-hook='sys.path.extend((\"%s\",\"%s\",\"%s\"))'"%\
+    cmd_options += " --init-hook='sys.path.extend((\"%s\",\"%s\",\"%s\",\"%s\"))'"%\
         (os.path.join(cimeroot,"scripts","lib"),
          os.path.join(cimeroot,"scripts","Tools"),
-         os.path.join(cimeroot,"scripts","fortran_unit_testing","python"))
+         os.path.join(cimeroot,"scripts","fortran_unit_testing","python"),
+         os.path.join(cimeroot,"src","drivers","nuopc","cime_config","runseq"))
 
     cmd = "%s %s %s" % (pylint, cmd_options, on_file)
     logger.debug("pylint command is %s"%cmd)

scripts/lib/CIME/namelist.py

@@ -1178,32 +1178,34 @@ def _write(self, out_file, groups, format_, sorted_groups):
         for group_name in group_names:
             if format_ == 'nml':
                 out_file.write("&{}\n".format(group_name))
-            group = self._groups[group_name]
-            for name in sorted(group.keys()):
-                values = group[name]
-
-                # @ is used in a namelist to put the same namelist variable in multiple groups
-                # in the write phase, all characters in the namelist variable name after
-                # the @ and including the @ should be removed
-                if "@" in name:
-                    name = re.sub('@.+$', "", name)
-
-                # To prettify things for long lists of values, build strings
-                # line-by-line.
-                if values[0] == "True" or values[0] == "False":
-                    values[0] = values[0].replace("True",".true.").replace("False",".false.")
-                lines = ["  {}{} {}".format(name, equals, values[0])]
-                for value in values[1:]:
-                    if value == "True" or value == "False":
-                        value = value.replace("True",".true.").replace("False",".false.")
-                    if len(lines[-1]) + len(value) <= 77:
-                        lines[-1] += ", " + value
-                    else:
-                        lines[-1] += ",\n"
-                        lines.append("      " + value)
-                lines[-1] += "\n"
-                for line in lines:
-                    out_file.write(line)
+            # allow empty group
+            if group_name in self._groups:
+                group = self._groups[group_name]
+                for name in sorted(group.keys()):
+                    values = group[name]
+
+                    # @ is used in a namelist to put the same namelist variable in multiple groups
+                    # in the write phase, all characters in the namelist variable name after
+                    # the @ and including the @ should be removed
+                    if "@" in name:
+                        name = re.sub('@.+$', "", name)
+
+                    # To prettify things for long lists of values, build strings
+                    # line-by-line.
+                    if values[0] == "True" or values[0] == "False":
+                        values[0] = values[0].replace("True",".true.").replace("False",".false.")
+                    lines = ["  {}{} {}".format(name, equals, values[0])]
+                    for value in values[1:]:
+                        if value == "True" or value == "False":
+                            value = value.replace("True",".true.").replace("False",".false.")
+                        if len(lines[-1]) + len(value) <= 77:
+                            lines[-1] += ", " + value
+                        else:
+                            lines[-1] += ",\n"
+                            lines.append("      " + value)
+                    lines[-1] += "\n"
+                    for line in lines:
+                        out_file.write(line)
             if format_ == 'nml':
                 out_file.write("/\n")
             if format_ == 'nmlcontents':
@@ -1220,7 +1222,7 @@ def _write_nuopc(self, out_file, groups, sorted_groups, skip_comps):
             group_names = groups
 
         for group_name in group_names:
-            if "_attributes" not in group_name and "nuopc_" not in group_name:
+            if "_attributes" not in group_name and "nuopc_" not in group_name and "_no_group" not in group_name:
                 continue
             if "_attributes" in group_name:
                 out_file.write("{}::\n".format(group_name))

scripts/lib/CIME/test_utils.py

@@ -11,7 +11,7 @@
 logger = logging.getLogger(__name__)
 
 def get_tests_from_xml(xml_machine=None,xml_category=None,xml_compiler=None, xml_testlist=None,
-                       machine=None, compiler=None):
+                       machine=None, compiler=None, driver=None):
     """
     Parse testlists for a list of tests
     """
@@ -46,6 +46,19 @@ def get_tests_from_xml(xml_machine=None,xml_category=None,xml_compiler=None, xml
             test["name"] = CIME.utils.get_full_test_name(test["testname"], grid=test["grid"], compset=test["compset"],
                                                          machine=thismach, compiler=thiscompiler,
                                                          testmod=None if "testmods" not in test else test["testmods"])
+            if driver:
+                # override default or specified driver
+                founddriver = False
+                for specdriver in ("Vnuopc","Vmct","Vmoab"):
+                    if specdriver in test["name"]:
+                        test["name"] = test["name"].replace(specdriver,"V{}".format(driver))
+                        founddriver = True
+                if not founddriver:
+                    name = test["name"]
+                    index = name.find('.')
+                    test["name"] = name[:index] + "_V{}".format(driver) + name[index:]
+
+
             logger.debug("Adding test {} with compiler {}".format(test["name"], test["compiler"]))
         listoftests += newtests
         logger.debug("Found {:d} tests".format(len(listoftests)))

scripts/tests/scripts_regression_tests.py

@@ -729,6 +729,8 @@ def test_m_createnewcase_alternate_drivers(self):
         cls = self.__class__
         model = CIME.utils.get_model()
         for driver in ("nuopc", "moab"):
+            if not os.path.exists(os.path.join(get_cime_root(),"src","drivers",driver)):
+                self.skipTest("Skipping driver test for {}, driver not found".format(driver))
             if ((model == 'cesm' and driver == 'moab') or
                 (model == 'e3sm' and driver == 'nuopc')):
                 continue

src/components/data_comps/dice/nuopc/dice_comp_mod.F90

@@ -118,14 +118,16 @@ module dice_comp_mod
 !===============================================================================
 
   subroutine dice_comp_advertise(importState, exportState, flds_scalar_name, &
-       ice_present, ice_prognostic, fldsFrIce_num, fldsFrIce, fldsToIce_num, fldsToIce, rc)
+       ice_present, ice_prognostic, flds_i2o_per_cat, &
+       fldsFrIce_num, fldsFrIce, fldsToIce_num, fldsToIce, rc)
 
     ! input/output arguments
     type(ESMF_State)     , intent(inout) :: importState
     type(ESMF_State)     , intent(inout) :: exportState
     character(len=*)     , intent(in)    :: flds_scalar_name
     logical              , intent(in)    :: ice_present
     logical              , intent(in)    :: ice_prognostic
+    logical              , intent(in)    :: flds_i2o_per_cat
     integer              , intent(out)   :: fldsToIce_num
     integer              , intent(out)   :: fldsFrIce_num
     type (fld_list_type) , intent(out)   :: fldsToIce(:)
@@ -154,6 +156,15 @@ subroutine dice_comp_advertise(importState, exportState, flds_scalar_name, &
     call dshr_fld_add(data_fld='ifrac', data_fld_array=avifld, model_fld='Si_ifrac', model_fld_array=avofld, &
          model_fld_concat=flds_i2x, model_fld_index=kiFrac, fldlist_num=fldsFrIce_num, fldlist=fldsFrIce)
 
+    if (flds_i2o_per_cat) then
+       call dshr_fld_add(model_fld='Si_ifrac_01'        , model_fld_concat=flds_i2x, model_fld_index=kiFrac_01)
+       call dshr_fld_add(model_fld='Fioi_swpen_ifrac_01', model_fld_concat=flds_i2x, model_fld_index=kswpen_iFrac_01)
+       call dshr_fld_add(med_fld='Si_ifrac_n', fldlist_num=fldsFrIce_num, fldlist=fldsFrIce, &
+            ungridded_lbound=1, ungridded_ubound=1)
+       call dshr_fld_add(med_fld='Fioi_swpen_ifrac_n', fldlist_num=fldsFrIce_num, fldlist=fldsFrIce, &
+            ungridded_lbound=1, ungridded_ubound=1)
+    end if
+
     ! export fields that have no corresponding stream field (computed internally)
 
     call dshr_fld_add(model_fld='Si_imask', model_fld_concat=flds_i2x, model_fld_index=km, &
@@ -500,7 +511,7 @@ subroutine dice_comp_init(flds_i2o_per_cat, mpicom, compid, my_task, master_task
     ! optional per thickness category fields
     if (flds_i2o_per_cat) then
        kiFrac_01       = mct_aVect_indexRA(i2x,'Si_ifrac_01')
-       kswpen_iFrac_01 = mct_aVect_indexRA(i2x,'PFioi_swpen_ifrac_01')
+       kswpen_iFrac_01 = mct_aVect_indexRA(i2x,'Fioi_swpen_ifrac_01')
     end if
 
     call mct_aVect_init(x2i, rList=flds_x2i, lsize=lsize)
@@ -966,10 +977,11 @@ end subroutine dice_comp_import
 
   !===============================================================================
 
-  subroutine dice_comp_export(exportState, rc)
+  subroutine dice_comp_export(exportState, flds_i2o_per_cat, rc)
 
     ! input/output variables
     type(ESMF_State)     :: exportState
+    logical, intent(in)  :: flds_i2o_per_cat
     integer, intent(out) :: rc
 
     ! local variables
@@ -981,6 +993,13 @@ subroutine dice_comp_export(exportState, rc)
     call dshr_export(i2x%rattr(kiFrac,:) , exportState, 'Si_ifrac', rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
+    if (flds_i2o_per_cat) then
+       call dshr_export(i2x%rattr(kiFrac_01,:), exportState, 'Si_ifrac_n', ungridded_index=1, rc=rc)
+       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+       call dshr_export(i2x%rattr(kswpen_iFrac_01,:), exportState, 'Fioi_swpen_ifrac_n', ungridded_index=1, rc=rc)
+       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    end if
+
     call dshr_export(i2x%rattr(km,:) , exportState, 'Si_imask', rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 

src/components/data_comps/dice/nuopc/ice_comp_nuopc.F90

@@ -230,9 +230,13 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
     endif
 
+    call NUOPC_CompAttributeGet(gcomp, name='flds_i2o_per_cat', value=cvalue, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    read(cvalue,*) flds_i2o_per_cat 
+
     call dice_comp_advertise(importstate, exportState, flds_scalar_name, &
-       ice_present, ice_prognostic, &
-       fldsFrIce_num, fldsFrIce, fldsToIce_num, fldsToIce, rc)
+         ice_present, ice_prognostic, flds_i2o_per_cat, &
+         fldsFrIce_num, fldsFrIce, fldsToIce_num, fldsToIce, rc)
 
     !----------------------------------------------------------------------------
     ! Reset shr logging to original values
@@ -347,6 +351,10 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
     Emesh = ESMF_MeshCreate(filename=trim(cvalue), fileformat=ESMF_FILEFORMAT_ESMFMESH, rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
+    if (my_task == master_task) then
+       write(logunit,*) " obtaining dice mesh from " // trim(cvalue)
+    end if
+
     !--------------------------------
     ! Initialize model
     !--------------------------------
@@ -406,7 +414,7 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
          calendar, modeldt, current_ymd, current_tod, cosArg)
 
     ! Pack export state
-    call dice_comp_export(exportState, rc=rc)
+    call dice_comp_export(exportState, flds_i2o_per_cat, rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
     call State_SetScalar(dble(nxg),flds_scalar_index_nx, exportState, &
@@ -539,7 +547,7 @@ subroutine ModelAdvance(gcomp, rc)
     ! Pack export state
     !--------------------------------
 
-    call dice_comp_export(exportState, rc=rc)
+    call dice_comp_export(exportState, flds_i2o_per_cat, rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
     !--------------------------------

src/components/xcpl_comps/xglc/nuopc/glc_comp_nuopc.F90

@@ -494,7 +494,7 @@ subroutine field_setexport(exportState, fldname, lon, lat, nf, ungridded_index,
     else
        call ESMF_FieldGet(lfield, farrayPtr=data1d, rc=rc)
        if (chkerr(rc,__LINE__,u_FILE_u)) return
-       if (fldname == 'Sg_icemask' .or. 'fldname == Sg_icemask_coupled_fluxes' .or. fldname == 'Sg_ice_covered') then
+       if (fldname == 'Sg_icemask' .or.  fldname == 'Sg_icemask_coupled_fluxes' .or. fldname == 'Sg_ice_covered') then
           data1d(:) = 1._r8
        else
           do i = 1,size(data1d)

src/drivers/mct/cime_config/config_component_cesm.xml

@@ -55,7 +55,7 @@
     <default_value>0</default_value>
     <group>run_flags</group>
     <file>env_run.xml</file>
-    <desc>Sets level of task-to-node mapping output for the whole model 
+    <desc>Sets level of task-to-node mapping output for the whole model
     (0: no output; 1: compact; 2: verbose).</desc>
   </entry>