Merge tag 'ctsm5.1.dev123' into add_mizuRoute

Updates needed for pFUnit 4 and other externals updates (1) Lots of small changes needed for the update to pFUnit4. Note that this is a backwards-incompatible update, so we will require pFUnit 4 moving forward. (2) Externals updates: some of these are needed for the update to pFUnit 4; others are included to update externals to those in a recent CESM alpha tag. Conflicts: Externals.cfg bld/unit_testers/build-namelist_test.pl
ekluzek · Jan 8, 2024 · e056fdd · e056fdd
2 parents 3bf9178 + 8df94cb
commit e056fdd
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diff --git a/.config_files.xml b/.config_files.xml
@@ -5,31 +5,31 @@
 <entry_id>
 
   <!-- This is the same as the default entry in
-       cime/config/cesm/config_files.xml except for the value for CTSM:
-       In a standalone CTSM checkout, COMP_ROOT_DIR_LND is $SRCROOT
+       cime/config/cesm/config_files.xml except for the value for CLM:
+       In a standalone CLM checkout, COMP_ROOT_DIR_LND is $SRCROOT
        rather than $SRCROOT/components/clm.
 
        However, because of the way overrides are handled, we need to
        re-specify the full information here rather than just overriding
-       the value for CTSM.
+       the value for CLM.
   -->
   <entry id="COMP_ROOT_DIR_LND">
     <type>char</type>
     <default_value>unset</default_value>
     <values>
-      <value component="clm"       >$SRCROOT</value>
-      <value component="ctsm"      >$SRCROOT</value>
-      <value component="dlnd" comp_interface="mct">$SRCROOT/components/cpl7/components/data_comps_mct/dlnd</value>
-      <value component="dlnd" comp_interface="nuopc">$SRCROOT/components/cdeps/dlnd</value>
-      <value component="slnd"  comp_interface="mct"     >$SRCROOT/components/cpl7/components/stub_comps_mct/slnd</value>
-      <value component="xlnd" comp_interface="mct"      >$SRCROOT/components/cpl7/components/xcpl_comps_mct/xlnd</value>
-      <value component="slnd"  comp_interface="nuopc"    >$CIMEROOT/src/components/stub_comps_nuopc/slnd</value>
-      <value component="xlnd"  comp_interface="nuopc"    >$CIMEROOT/src/components/xcpl_comps_nuopc/xlnd</value>
+      <value component="clm"                         >$SRCROOT</value>
+      <value component="slim"                        >$SRCROOT/components/slim/</value>
+      <value component="dlnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/data_comps_$COMP_INTERFACE/dlnd</value>
+      <value component="dlnd" comp_interface="nuopc" >$SRCROOT/components/cdeps/dlnd</value>
+      <value component="slnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/stub_comps_$COMP_INTERFACE/slnd</value>
+      <value component="slnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/stub_comps_$COMP_INTERFACE/slnd</value>
+      <value component="xlnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
+      <value component="xlnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
     </values>
     <group>case_comps</group>
     <file>env_case.xml</file>
     <desc>Root directory of the case land model component  </desc>
-    <schema>$CIMEROOT/config/xml_schemas/config_compsets.xsd</schema>
+    <schema>$CIMEROOT/CIME/data/config/xml_schemas/config_compsets.xsd</schema>
   </entry>
 
 </entry_id>
diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -17,5 +17,5 @@ jobs:
              # Using pyproject.toml makes sure this testing is consistent with our python directory testing
              options: "--check --config python/pyproject.toml"
              src:     "./python"
-             # Version should be coordinated with the ctsm_py conda environment under the python directory
+             # Version should be coordinated with the ctsm_pylib conda environment under the python directory
              version: "22.3.0"
diff --git a/Externals.cfg b/Externals.cfg
@@ -23,7 +23,7 @@ required = True
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_47
+tag = mosart1_0_48
 required = True
 
 [mizuRoute]
@@ -34,15 +34,14 @@ repo_url = https://github.com/nmizukami/mizuRoute
 # Branch that is being used
 #branch = cesm-coupling
 # specitic hash or tag along the above branch
-hash = 48e65434280b9dc62400cd902fb0c154e410ed1b
-#tag =  cesm-coupling.n02_v2.1.1
+#hash = 48e65434280b9dc62400cd902fb0c154e410ed1b
+tag =  cesm-coupling.n02_v2.1.2
 required = True
 
 [ccs_config]
-#hash = 4dcfe92902dc436271e2cec0bba6fc58e8ad4af6 # Naoki
-hash = f0cc1b87208fc4279916cc4509719067ba22afa2
+hash = 9f2b4e7f5bb8ff09ccfe2dee1de5b61ef0af64f8
 #branch = mizuroutelakegrids
-#tag = ccs_config_cesm0.0.38
+#tag = ccs_config_cesm0.0.64
 protocol = git
 #repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 repo_url = https://github.com/ekluzek/ccs_config_cesm.git
@@ -53,36 +52,36 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.75
+tag = cime6.0.108
 required = True
 
 [cmeps]
-#tag = cmeps0.13.71
+#tag = cmeps0.14.21
 #branch = lndrofmapfilefix
-hash = 0602beb046a5053620f7dcfaf9e792c8d7fd738e
+hash = 8f378f7e9a7bcaa265639556f2e60078860d1761
 protocol = git
 #repo_url = https://github.com/ESCOMP/CMEPS.git
 repo_url = https://github.com/ekluzek/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps0.12.65
+tag = cdeps1.0.9
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
 externals =  Externals_CDEPS.cfg
 required = True
 
 [cpl7]
-tag = cpl7.0.14
+tag = cpl77.0.5
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
 local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.13
+tag = share1.0.17
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
@@ -96,7 +95,7 @@ local_path = libraries/mct
 required = True
 
 [parallelio]
-tag = pio2_5_7
+tag = pio2_5_10
 protocol = git
 repo_url = https://github.com/NCAR/ParallelIO
 local_path = libraries/parallelio

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.59.7_api.24.1.0
+tag = sci.1.65.3_api.25.4.0
 required = True
 
 [externals_description]

diff --git a/README.md b/README.md
@@ -43,15 +43,19 @@ CTSM code management is provided primarily by:
 Software engineering team:
 - [Erik Kluzek](https://github.com/ekluzek)
 - [Bill Sacks](https://github.com/billsacks)
-- [Mariana Vertenstein](https://github.com/mvertens)
-- [Negin Sobhani](https://github.com/negin513)
 - [Sam Levis](https://github.com/slevisconsulting)
+- [Adrianna Foster](https://github.com/adrifoster)
+- [Sam Rabin](https://github.com/samsrabin)
+- [Greg Lemieux](https://github.com/glemieux)
+- [Ryan Knox](https://github.com/rgknox)
 
 Science team:
 - [Dave Lawrence](https://github.com/dlawrenncar)
 - [Will Wieder](https://github.com/wwieder)
 - [Danica Lombardozzi](https://github.com/danicalombardozzi)
 - [Keith Oleson](https://github.com/olyson)
 - [Sean Swenson](https://github.com/swensosc)
-- [Mike Barlage](https://github.com/barlage)
+- [Jackie Shuman](https://github.com/jkshuman)
+- [Peter Lawrence](https://github.com/lawrencepj1)
 - [Rosie Fisher](https://github.com/rosiealice)
+- Gordon Bonan
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -1687,11 +1687,6 @@ sub process_namelist_inline_logic {
   #############################################
   setup_logic_rooting_profile($opts,  $nl_flags, $definition, $defaults, $nl);
 
-  #############################################
-  # namelist group: friction_velocity         #
-  #############################################
-  setup_logic_friction_vel($opts,  $nl_flags, $definition, $defaults, $nl);
-
   #############################
   # namelist group: cngeneral #
   #############################
@@ -1711,6 +1706,11 @@ sub process_namelist_inline_logic {
   #############################################
   setup_logic_canopyfluxes($opts,  $nl_flags, $definition, $defaults, $nl);
 
+  ##########################################################
+  # namelist group: friction_velocity (after canopyfluxes) #
+  ##########################################################
+  setup_logic_friction_vel($opts,  $nl_flags, $definition, $defaults, $nl);
+
   #############################################
   # namelist group: canopyhydrology_inparm #
   #############################################
@@ -2491,6 +2491,7 @@ sub setup_logic_dynamic_subgrid {
    setup_logic_do_transient_lakes($opts, $nl_flags, $definition, $defaults, $nl);
    setup_logic_do_transient_urban($opts, $nl_flags, $definition, $defaults, $nl);
    setup_logic_do_harvest($opts, $nl_flags, $definition, $defaults, $nl);
+   setup_logic_do_grossunrep($opts, $nl_flags, $definition, $defaults, $nl);
 
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_dynbal_baselines');
    if ( &value_is_true($nl->get_value('reset_dynbal_baselines')) &&
@@ -2836,6 +2837,63 @@ sub setup_logic_do_harvest {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_do_grossunrep {
+   #
+   # Set do_grossunrep default value, and perform error checking on do_grossunrep
+   #
+   # Assumes the following are already set in the namelist (although it's okay
+   # for them to be unset if that will be their final state):
+   # - flanduse_timeseries
+   # - use_cn
+   # - use_fates
+   #
+   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+
+   my $var = 'do_grossunrep';
+
+   # Start by assuming a default value of '.true.'. Then check a number of
+   # conditions under which do_grossunrep cannot be true. Under these
+   # conditions: (1) set default value to '.false.'; (2) make sure that the
+   # value is indeed false (e.g., that the user didn't try to set it to true).
+
+   my $default_val = ".false.";
+
+   # cannot_be_true will be set to a non-empty string in any case where
+   # do_grossunrep should not be true; if it turns out that do_grossunrep IS true
+   # in any of these cases, a fatal error will be generated
+   my $cannot_be_true = "";
+
+   if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) {
+      $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)";
+   }
+   elsif (&value_is_true($nl->get_value('use_fates'))) {
+      $cannot_be_true = "$var currently doesn't work with FATES";
+   }
+   elsif (!&value_is_true($nl->get_value('use_cn'))) {
+      $cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)";
+   }
+
+   if ($cannot_be_true) {
+      $default_val = ".false.";
+   }
+
+   if (!$cannot_be_true) {
+      # Note that, if the variable cannot be true, we don't call add_default
+      # - so that we don't clutter up the namelist with variables that don't
+      # matter for this case
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, val=>$default_val);
+   }
+
+   # Make sure the value is false when it needs to be false - i.e., that the
+   # user hasn't tried to set a true value at an inappropriate time.
+
+   if (&value_is_true($nl->get_value($var)) && $cannot_be_true) {
+      $log->fatal_error($cannot_be_true);
+   }
+
+}
+
+#-------------------------------------------------------------------------------
 sub setup_logic_spinup {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
@@ -3683,6 +3741,10 @@ sub setup_logic_fire_emis {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
   if ($opts->{'fire_emis'} ) {
+     if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
+       $log->warning("Fire emission can NOT be on when FATES is also on.\n" .
+                   "  DON'T use the '-fire_emis' option when '-bgc fates' is activated");
+    }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_factors_file');
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_specifier');
   } else {
@@ -3898,10 +3960,11 @@ sub setup_logic_rooting_profile {
 #-------------------------------------------------------------------------------
 
 sub setup_logic_friction_vel {
-  #
+  # Must be after canopyfluxes so that use_biomass_heat_storage will be set
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable' );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable',
+     'use_biomass_heat_storage'=>$nl_flags->{'use_biomass_heat_storage'}, 'phys'=>$nl_flags->{'phys'} );
 }
 
 #-------------------------------------------------------------------------------
@@ -3926,6 +3989,11 @@ sub setup_logic_canopyfluxes {
   if ( &value_is_true($nl->get_value('use_biomass_heat_storage') ) && &value_is_true( $nl_flags->{'use_fates'}) ) {
      $log->fatal_error('use_biomass_heat_storage can NOT be set to true when fates is on');
   }
+  if ( &value_is_true($nl->get_value('use_biomass_heat_storage')) ) {
+     $nl_flags->{'use_biomass_heat_storage'} = ".true.";
+  } else {
+     $nl_flags->{'use_biomass_heat_storage'} = ".false.";
+  }
 }
 
 #-------------------------------------------------------------------------------