Merge pull request #97 from mvertens/feature/update_to_ctsm5.3.011

update to ctsm5.3.011

.git-blame-ignore-revs

@@ -51,3 +51,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 1a49e547ba3c48fa483f9ae81a8f05adcd6b888c
 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
 753fda3ff0147837231a73c9c728dd9ce47b5997
+f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.78.2_api.36.0.0
+fxtag = sci.1.78.3_api.36.1.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
@@ -60,47 +60,47 @@ 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/NorESMhub/ccs_config_noresm.git
-fxtag = ccs_config_noresm0.0.33
+fxtag = ccs_config_noresm0.0.38
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NorESMhub/ccs_config_noresm
 
 [submodule "cime"]
 path = cime
-url = https://github.com/ESMCI/cime
-fxtag = cime6.0.246
+url = https://github.com/NorESMhub/cime
+fxtag = cime6.1.28_noresm_v0
 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
+url = https://github.com/NorESMhub/CMEPS.git
+fxtag = cmeps1.0.20_noresm_v0
 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 = cdeps1.0.53
 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
+url = https://github.com/NorESMhub/NorESM_share
+fxtag = share1.1.2_noresm_v0
 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
@@ -116,7 +116,7 @@ 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

bld/CLMBuildNamelist.pm

@@ -2588,12 +2588,9 @@ sub setup_logic_initial_conditions {
   my $finidat = $nl->get_value($var);
   $nl_flags->{'excess_ice_on_finidat'} = "unknown";
   if ( $nl_flags->{'clm_start_type'} =~ /cold/ ) {
-    if (defined $finidat ) {
-      $log->warning("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incomptable with using a cold start" .
+    if (defined $finidat && !&value_is_true(($nl->get_value('use_fates')))) {
+      $log->fatal_error("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incompatible with using a cold start" .
               " (by setting CLM_FORCE_COLDSTART=on)." );
-      $log->warning("Overridding input $var file with one specifying that this is a cold start from arbitrary initial conditions." );
-      my $group = $definition->get_group_name($var);
-      $nl->set_variable_value($group, $var, "' '" );
     }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
                 $var, 'val'=>"' '", 'no_abspath'=>1);
@@ -2756,6 +2753,12 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
         $log->fatal_error("$useinitvar is being set for you but a $var was not found, so $useinitvar, init_interp_attributes, and finidat must not be set correctly for this configuration in the namelist_default file" );
      }
   }
+
+  # this check has to be here and not earlier since use_init_interp is set here and hillslope is already set above in setup_logic_hillslope
+  if ( &value_is_true($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
 
 #-------------------------------------------------------------------------------
@@ -3596,17 +3599,6 @@ sub setup_logic_luna {
   if ( &value_is_true($nl->get_value('lnc_opt') ) && not &value_is_true( $nl_flags->{'use_cn'}) ) {
      $log->fatal_error("Cannot turn lnc_opt to true when bgc=sp" );
   }
-  my $var = "jmaxb1";
-  if ( &value_is_true( $nl_flags->{'use_luna'} ) ) {
-     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-                 'use_luna'=>$nl_flags->{'use_luna'} );
-  }
-  my $val = $nl->get_value($var);
-  if ( ! &value_is_true( $nl_flags->{'use_luna'} ) ) {
-     if ( defined($val) ) {
-        $log->fatal_error("Cannot set $var when use_luna is NOT on" );
-     }
-  }
 }
 
 #-------------------------------------------------------------------------------
@@ -3630,6 +3622,10 @@ sub setup_logic_hillslope {
   if ( (! &value_is_true($use_hillslope)) && &value_is_true($use_hillslope_routing) ) {
       $log->fatal_error("Cannot turn on use_hillslope_routing when use_hillslope is off\n" );
   }
+  my $hillslope_file = $nl->get_value('hillslope_file');
+  if ( &value_is_true($use_hillslope) && ( ! defined($hillslope_file) ) ) {
+    $log->fatal_error("You must provide hillslope_file if use_hillslope is .true.\n" );
+  }
 }
 
 #-------------------------------------------------------------------------------
@@ -4516,8 +4512,6 @@ sub setup_logic_canopyhydrology {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'interception_fraction' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'maximum_leaf_wetted_fraction' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_clm5_fpi' );
 }
 
@@ -4536,7 +4530,6 @@ sub setup_logic_snowpack {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'wind_dependent_snow_density');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_overburden_compaction_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lotmp_snowdensity_method');
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upplim_destruct_metamorph');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc_ela');