Merge tag 'branch_tags/tmp-241219.n01.ctsm5.3.016' into merge-master-…

…20241230 Merge b4b-dev 20241220 This tag is in the temporary branch tmp-241219, while master remains "locked" in preparation for a cesm tag. The process was unorthodox, in that I (slevis) received a code review and made revisions and retested after having started the first merge steps.
slevis-lmwg · Dec 30, 2024 · f10b014 · f10b014
2 parents 2db5c6a + 6cf9dde
commit f10b014
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -52,3 +52,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
 753fda3ff0147837231a73c9c728dd9ce47b5997
 f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c
+bd535c710db78420b8e8b9d71d88d8339e899c59
diff --git a/.gitmodules b/.gitmodules
@@ -60,67 +60,67 @@ fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 [submodule "mizuRoute"]
 path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
-fxtag = cesm-coupling.n02_v2.1.2
+fxtag = cesm-coupling.n02_v2.1.3
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.0
+fxtag = ccs_config_cesm1.0.10
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.0.246
+fxtag = cime6.1.49
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps0.14.77
+fxtag = cmeps1.0.32
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.48
+fxtag = cdeps1.0.61
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.0.19
+fxtag = share1.1.6
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
-[submodule "mct"]
-path = libraries/mct
-url = https://github.com/MCSclimate/MCT
-fxtag = MCT_2.11.0
-fxrequired = ToplevelRequired
-# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
-fxDONOTUSEurl = https://github.com/MCSclimate/MCT
-
 [submodule "parallelio"]
 path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
-fxtag = pio2_6_2
+fxtag = pio2_6_3
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
+[submodule "mpi-serial"]
+path = libraries/mpi-serial
+url = https://github.com/ESMCI/mpi-serial
+fxtag = MPIserial_2.5.1
+fxrequired = ToplevelRequired
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial
+
 [submodule "doc-builder"]
 path = doc/doc-builder
 url = https://github.com/ESMCI/doc-builder

diff --git a/README b/README
@@ -126,9 +126,9 @@ cime_config/config_tests.xml ----- Define CTSM specific tests
 cime_config/config_pes.xml ------- Define Processor layouts for various CTSM grids and compsets
 cime_config/testdefs ------------- Directory for specification of CTSM testing
 cime_config/testdefs/ExpectedTestFails.xml -- List of tests that are expected to fail
-cime_config/usermods_dirs -------- Directories of sets of user-modification subdirs
+cime_config/usermods_dirs/clm ---- Directories of sets of user-modification subdirs
                                    (These are directories that add specific user modifications to
-                                    simulations created using "cime/scripts/create_newcase --user-mods-dir".)
+                                    simulations created using "cime/scripts/create_newcase --user-mods-dir clm/*)
 
 tools/mksurfdata_esmf --------- Directory to build program to create surface dataset 
                                 at any resolution.

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -71,7 +71,7 @@ REQUIRED OPTIONS
                               (if read they allow user_nl_clm and CLM_BLDNML_OPTS to expand
                                variables [for example to use \$DIN_LOC_ROOT])
                               (default current directory)
-     -lnd_frac "domainfile"   Land fraction file (the input domain file) (needed for LILAC)
+     -lnd_frac "domainfile"   Land fraction file (the input domain file) (only needed with --lilac option)
      -res "resolution"        Specify horizontal grid.  Use nlatxnlon for spectral grids;
                               dlatxdlon for fv grids (dlat and dlon are the grid cell size
                               in degrees for latitude and longitude respectively)
@@ -678,6 +678,18 @@ sub setup_cmdl_chk_res {
   }
 }
 
+#-------------------------------------------------------------------------------
+
+sub begins_with
+{
+    # Arguments: long-string, substring
+    # For an input long-string check if it starts with the substring
+    # For example, if a string like NEON_PRISM starts with NEON
+    return substr($_[0], 0, length($_[1])) eq $_[1];
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_cmdl_resolution {
   my ($opts, $nl_flags, $definition, $defaults, $envxml_ref) = @_;
 
@@ -713,7 +725,7 @@ sub setup_cmdl_resolution {
   $nl_flags->{'neon'} = ".false.";
   $nl_flags->{'neonsite'} = "";
   if ( $nl_flags->{'res'} eq "CLM_USRDAT" ) {
-    if ( $opts->{'clm_usr_name'} eq "NEON" ) {
+    if ( begins_with($opts->{'clm_usr_name'}, "NEON") ) {
        $nl_flags->{'neon'} = ".true.";
        $nl_flags->{'neonsite'} = $envxml_ref->{'NEONSITE'};
        $log->verbose_message( "This is a NEON site with NEONSITE = " . $nl_flags->{'neonsite'} );
@@ -1989,7 +2001,7 @@ sub setup_logic_lnd_frac {
                      "env variables) AND fatmlndfrac on namelist");
        }
        if ( $opts->{$var} =~ /UNSET/ ) {
-          $log->fatal_error("-lnd_frac was set as UNSET in the CTSM build-namelist set it with the env variables: LND_DOMAIN_PATH/LND_DOMAIN_FILE.");
+          $log->fatal_error("-lnd_frac was set as UNSET in the CTSM build-namelist, it's required with the --lilac option");
        }
        my $lnd_frac = SetupTools::expand_xml_var( $opts->{$var}, $envxml_ref);
        add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fatmlndfrc','val'=>$lnd_frac );
@@ -1999,20 +2011,22 @@ sub setup_logic_lnd_frac {
      if (defined $nl->get_value('fatmlndfrc')) {
        # do nothing - use value provided by config_grid.xml and clm.cpl7.template
      } else {
-       $log->fatal_error("fatmlndfrc was NOT sent into CLM build-namelist.");
+       $log->fatal_error("fatmlndfrc was NOT sent into CLM build-namelist, it is required for the --lilac option.");
      }
   #
   # For the NUOPC driver neither lnd_frac nor fatmlndfrc need to be set
   #
-  } else {
+  } elsif ($opts->{'driver'} eq "nuopc" ) {
      if ( defined($opts->{$var}) ) {
        if ( $opts->{$var} !~ /UNSET/ ) {
-          $log->fatal_error("$var should NOT be set for the NUOPC driver as it is unused" );
+          $log->fatal_error("$var should NOT be set for the NUOPC driver as it is unused (only used by the --lilac option)" );
        }
      }
      if ( defined($nl->get_value('fatmlndfrc')) ) {
        $log->fatal_error("fatmlndfrac should NOT be set in the namelist for the NUOPC driver as it is unused" );
      }
+  } else {
+       $log->fatal_error("Input --driver type of $opts->{'driver'} is an invalid option. Correct this in xml variable COMP_iINTERFACE in your case" );
   }
 }
 
@@ -2113,7 +2127,7 @@ sub setup_logic_roughness_methods {
   my $phys = $physv->as_string();
   if ( $phys eq "clm4_5" || $phys eq "clm5_0" ) {
     if ( $var eq "Meier2022" ) {
-      $log->fatal_error("z0param_method = $var and phys = $phys, but this method has been tested only with clm5_1 and later versions; to use with earlier versions, disable this error, and add Meier2022 parameters to the corresponding params file");
+      $log->fatal_error("z0param_method = $var and phys = $phys, but this method has been tested only with clm6_0 and later versions; to use with earlier versions, disable this error, and add Meier2022 parameters to the corresponding params file");
     }
   }
 }
@@ -2757,7 +2771,7 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
   # this check has to be here and not earlier since use_init_interp is set here and hillslope is already set above in setup_logic_hillslope
   if ( &value_is_true($nl->get_value($useinitvar)) && value_is_true($nl->get_value("use_hillslope")) ) {
      $log->warning("WARNING: You have set use_hillslope while $useinitvar is TRUE.\n This means all hillslope columns in a gridcell will read identical values from initial conditions, even if the initial conditions (finidat) file has hillslope information. If you are sure you want this behaviour, add -ignore_warnings to CLM_BLDNML_OPTS.")
-  }
+}
 
 } # end initial conditions
 
@@ -3395,13 +3409,6 @@ sub setup_logic_mineral_nitrogen_dynamics {
     }
   }
 
-  if (  &value_is_true($nl_flags->{'use_cn'}) && &value_is_true($nl->get_value('use_fun')) ) {
-    my $var = $nl->get_value('nfix_method');
-    if ( $var ne "'Houlton'" && $var ne "'Bytnerowicz'" ) {
-      $log->fatal_error("$var is incorrect entry for the namelist variable nfix_method; expected Houlton or Bytnerowicz");
-    }
-  }
-
 }
 
 
@@ -4759,8 +4766,6 @@ sub setup_logic_fates {
               my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
               if ( ! defined($nl->get_value($var))  ) {
                  $log->fatal_error("$var is required when use_fates_inventory_init is set" );
-              } elsif ( ! -f "$fname" ) {
-                 $log->fatal_error("$fname does NOT point to a valid filename" );
               }
            }
         }
@@ -4791,8 +4796,6 @@ sub setup_logic_fates {
                     my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
                     if ( ! defined($nl->get_value($var))  ) {
                        $log->fatal_error("$var is required when use_fates_luh is set and use_fates_potentialveg is false" );
-                    } elsif ( ! -f "$fname" ) {
-                       $log->fatal_error("$var does NOT point to a valid filename" );
                     }
                  }
               }
@@ -4805,8 +4808,6 @@ sub setup_logic_fates {
                     my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
                     if ( ! defined($nl->get_value($var))  ) {
                       $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" );
-                    } elsif ( ! -f "$fname" ) {
-                      $log->fatal_error("$var does NOT point to a valid filename" );
                     }
                  }
               }
@@ -4848,8 +4849,6 @@ sub setup_logic_fates {
               my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
               if ( ! defined($nl->get_value($var))  ) {
                 $log->fatal_error("$var is required when fates_harvest_mode is landuse_timeseries" );
-              } elsif ( ! -f "$fname" ) {
-                $log->fatal_error("$var does NOT point to a valid filename" );
               }
            }
         }
@@ -5210,6 +5209,7 @@ sub write_output_files {
   }
   push @groups, "clm_humanindex_inparm";
   push @groups, "cnmresp_inparm";
+  push @groups, "cnfun_inparm";
   push @groups, "photosyns_inparm";
   push @groups, "cnfire_inparm";
   push @groups, "cn_general";

diff --git a/bld/config_files/clm_phys_vers.pm b/bld/config_files/clm_phys_vers.pm
@@ -28,7 +28,7 @@ use bigint;
 #use warnings;
 #use diagnostics;
 
-my @version_strings = ("clm4_5", "clm5_0", "clm5_1", "clm6_0");
+my @version_strings = ("clm4_5", "clm5_0", "clm6_0");
 
 #-------------------------------------------------------------------------------
 
@@ -88,7 +88,7 @@ if ( ! defined(caller) && $#ARGV == -1 ) {
    sub testit {
       print "unit tester\n";
       my %lastv;
-      my @vers_list = ( "clm4_5", "clm5_0", "clm5_1", "clm6_0" );
+      my @vers_list = ( "clm4_5", "clm5_0", "clm6_0" );
       foreach my $vers ( @vers_list ) {
          my $phys = config_files::clm_phys_vers->new($vers);
          isa_ok($phys, "config_files::clm_phys_vers", "created clm_phys_vers object");

diff --git a/bld/config_files/config_definition_ctsm.xml b/bld/config_files/config_definition_ctsm.xml
@@ -5,10 +5,10 @@
 <config_definition>
 
 <entry id="phys" 
-       valid_values="clm4_5,clm5_0,clm5_1,clm6_0"
+       valid_values="clm4_5,clm5_0,clm6_0"
        value="clm4_5"
        category="physics">
-Specifies either clm4_5, clm5_0, clm5_1 (deprecated), or clm6_0 physics
+Specifies either clm4_5, clm5_0, or clm6_0 physics
 </entry>
 
 <entry id="clm_root"