Merge pull request #5 from glemieux/fates-landuse-v2-deconflict_006

Merge up to ctsm5.2.006 and deconflict
mvdebolskiy · May 31, 2024 · 071d076 · 071d076
2 parents 10728d9 + 1dc3d3c
commit 071d076
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diff --git a/.config_files.xml b/.config_files.xml
@@ -19,11 +19,8 @@
     <values>
       <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>

diff --git a/.gitignore b/.gitignore
@@ -75,7 +75,6 @@ buildnmlc
 td.*.status
 td.*.log
 td.*.status.xFail
-test_driver_*.sh
 
 # mksurfdata output
 surfdata_*.log

diff --git a/Externals.cfg b/Externals.cfg
@@ -8,7 +8,7 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_99
+tag = cismwrap_2_1_100
 externals = Externals_CISM.cfg
 required = True
 
@@ -27,14 +27,14 @@ tag = mosart1_0_49
 required = True
 
 [mizuRoute]
-local_path = components/mizuRoute
+tag = cesm-coupling.n02_v2.1.2
 protocol = git
-repo_url = https://github.com/nmizukami/mizuRoute
-hash = 34723c2
+local_path = components/mizuroute
+repo_url = https://github.com/ESCOMP/mizuRoute
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.92
+tag = ccs_config_cesm0.0.106
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,33 +44,26 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.217_httpsbranch03
+tag = cime6.0.238_httpsbranch01
 required = True
 
 [cmeps]
-tag = cmeps0.14.50
+tag = cmeps0.14.63
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.28
+tag = cdeps1.0.33
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
 externals =  Externals_CDEPS.cfg
 required = True
 
-[cpl7]
-tag = cpl77.0.7
-protocol = git
-repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
-local_path = components/cpl7
-required = True
-
 [share]
-tag = share1.0.18
+tag = share1.0.19
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share

diff --git a/README b/README
@@ -47,7 +47,6 @@ doc --------------- Documentation of CTSM.
 bld --------------- build-namelist scripts for CTSM.
 src --------------- CTSM Source code.
 lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model)
-test -------------- CTSM Testing scripts for CTSM offline tools (deprecated)
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
 manage_externals -- Script to manage the external source directories (deprecated)
@@ -57,7 +56,7 @@ python ------------ Python modules used in tools and testing and automated check
 Directory structure only for a CTSM checkout:
 
 components -------- Other active sub-components needed for CTSM to run (river routing and land-ice models)
-libraries --------- CESM libraries: MCT (Model Coupling Toolkit) and PIO (deprecated)
+libraries --------- CESM libraries: PIO (deprecated)
 share ------------- CESM shared code
 ccs_config -------- CIME configure files (for grids, compsets, and machines) for CESM
 
@@ -68,7 +67,6 @@ components/cdeps -------------------- CESM top level data model shared code (for
 components/cism --------------------- CESM Community land Ice Sheet Model.
 components/mosart ------------------- Model for Scale Adaptive River Transport
 components/rtm ---------------------- CESM River Transport Model.
-components/cpl7 --------------------- CESM top level driver for MCT driver (deprecated will be removed)
 
 Top level documentation ($CTSMROOT):
 
@@ -154,7 +152,7 @@ Source code directory structure:
 
 src/biogeochem ---- Biogeochemisty
 src/main ---------- Main control and high level code
-src/cpl ----------- Land model high level caps for NUOPC driver (and MCT and LILAC)
+src/cpl ----------- Land model high level caps for NUOPC driver (and LILAC)
 src/biogeophys ---- Biogeophysics (Hydrology)
 src/dyn_subgrid --- Dynamic land unit change
 src/init_interp --- Online interpolation

diff --git a/README.NUOPC_driver.md b/README.NUOPC_driver.md
@@ -40,12 +40,3 @@ ESMF_PROFILING_LEVEL --- Verbosity level for ESMF profiling
 nuopc.runseq is a text file that determines how the driver operates. You can change the operation
 by having an updated copy in your case directory.
 
-
-## What if I want to use the MCT driver?
-
-The MCT driver is now deprecated, and will be removed. So at this point we don't
-suggest using it anymore.
-
-For more notes see:
-
-https://docs.google.com/presentation/d/1yjiKSEV53JDAJbYxhpY2T9GTxlWFzQAn
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 MCT driver and LILAC)
+     -lnd_frac "domainfile"   Land fraction file (the input domain file) (needed for LILAC)
      -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)
@@ -83,7 +83,7 @@ REQUIRED OPTIONS
                               (default 2000)
      -structure "structure"   The overall structure being used [ standard | fast ]
 OPTIONS
-     -driver "value"          CESM driver type you will run with [ mct | nuopc ]
+     -driver "value"          CESM driver type you will run with [ nuopc ]
      -bgc "value"             Build CLM with BGC package [ sp | bgc | fates ]
                               (default is sp).
                                 CLM Biogeochemistry mode
@@ -1894,10 +1894,10 @@ sub setup_logic_lnd_frac {
   my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_;
 
   #
-  # fatmlndfrc is required for the MCT driver (or LILAC), but uneeded for NUOPC
+  # fatmlndfrc is required for LILAC but uneeded for NUOPC
   #
   my $var = "lnd_frac";
-  if ( ($opts->{'driver'} eq "mct") || $opts->{'lilac'} ) {
+  if ( $opts->{'lilac'} ) {
      if ( defined($opts->{$var}) ) {
        if ( defined($nl->get_value('fatmlndfrc')) ) {
          $log->fatal_error("Can NOT set both -lnd_frac option (set via LND_DOMAIN_PATH/LND_DOMAIN_FILE " .
@@ -3839,9 +3839,7 @@ sub setup_logic_popd_streams {
      }
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_popdens', 'phys'=>$nl_flags->{'phys'},
                  'cnfireson'=>$nl_flags->{'cnfireson'}, 'hgrid'=>"0.5x0.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
-     #
-     # TODO (mvertens, 2021-06-22) the following is needed for MCT since a use case enforces this  - so for now stream_meshfile_popdens will be added to the mct
-     # stream namelist but simply not used
+
     if ($opts->{'driver'} eq "nuopc" ) {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_popdens', 'hgrid'=>"0.5x0.5");
         my $inputdata_rootdir = $nl_flags->{'inputdata_rootdir'};
@@ -3855,12 +3853,6 @@ sub setup_logic_popd_streams {
             $val = &quote_string( $val );
             $nl->set_variable_value($group, $var, $val);
         }
-    } else {
-        my $var = 'stream_meshfile_popdens';
-        my $group = $definition->get_group_name($var);
-        my $val = "none";
-        $val = &quote_string( $val );
-        $nl->set_variable_value($group, $var, $val);
     }
   } else {
      # If bgc is NOT CN/CNDV or fire_method==nofire then make sure none of the popdens settings are set

diff --git a/bld/config_files/config_definition_ctsm.xml b/bld/config_files/config_definition_ctsm.xml
@@ -18,11 +18,11 @@ Root directory of CLM source distribution (directory above CLM configure).
 </entry>
 
 <entry id="comp_intf" 
-       valid_values="ESMF,MCT,cpl_\$COMP" 
-       value="MCT"
+       valid_values="ESMF,cpl_\$COMP"
+       value="ESMF"
        category="directories">
 Component framework interface to use 
-(Model Coupling Toolkit, or Earth System Modeling Framework)
+(Earth System Modeling Framework)
 </entry>
 
 <entry id="usr_src" 

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -163,8 +163,8 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-# CHANGELOG: SRABIN ADDED 8 NTESTS 1999->2007, MASTER WAS AT 3313, 3313+8 = 3321
-my $ntests = 3321;
+# CHANGELOG: SRABIN ADDED 8 NTESTS 1999->2007, CTSM5.2.006 WAS AT 3254
+my $ntests = 3262;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2008;
@@ -315,7 +315,7 @@ sub cat_and_create_namelistinfile {
 print "=================================================================================\n";
 
 my $startfile = "clmrun.clm2.r.1964-05-27-00000.nc";
-foreach my $driver ( "mct", "nuopc" ) {
+foreach my $driver ( "nuopc" ) {
    print "   For $driver driver\n\n";
    # configuration, structure, irrigate, verbose, clm_demand, ssp_rcp, test, sim_year, use_case
    foreach my $options ( "-res 0.9x1.25 -configuration nwp",
@@ -336,13 +336,7 @@ sub cat_and_create_namelistinfile {
       my $file = $startfile;
       &make_env_run();
       my $base_options = "-envxml_dir . -driver $driver";
-      if ( $driver eq "mct" ) {
-         $base_options = "$base_options -lnd_frac $DOMFILE";
-         # Skip the MCT test for excess ice streams
-         if ( $options =~ /use_excess_ice_streams=.true./ ) {
-           next;
-         }
-      } else {
+      if ( $driver eq "nuopc" ) {
          $base_options = "$base_options -namelist '&a force_send_to_atm = .false./'";
       }
       eval{ system( "$bldnml $base_options $options > $tempfile 2>&1 " ); };
@@ -549,11 +543,6 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
-     "exice stream on, but mct"    =>{ options=>"--res 0.9x1.25 --envxml_dir . --driver mct --lnd_frac $DOMFILE ",
-                                     namelst=>"use_excess_ice=.true., use_excess_ice_streams=.true.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_0",
-                                   },
      "clm50CNDVwtransient"       =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15 -ignore_warnings",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -899,16 +888,6 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
-     "both lnd_frac and on nml"  =>{ options=>"-driver mct -lnd_frac $DOMFILE -envxml_dir .",
-                                     namelst=>"fatmlndfrc='frac.nc'",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_0",
-                                   },
-     "lnd_frac set to UNSET"     =>{ options=>"-driver mct -lnd_frac UNSET -envxml_dir .",
-                                     namelst=>"",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm6_0",
-                                   },
      "lnd_frac set but nuopc"    =>{ options=>"-driver nuopc -lnd_frac $DOMFILE -envxml_dir .",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -924,11 +903,6 @@ sub cat_and_create_namelistinfile {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm6_0",
                                    },
-     "force_send but not nuopc"  =>{ options=>"-driver mct -lnd_frac $DOMFILE -envxml_dir .",
-                                     namelst=>"force_send_to_atm = .false.",
-                                     GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm6_0",
-                                   },
      "branch but NO nrevsn"      =>{ options=>"-clm_start_type branch -envxml_dir .",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

diff --git a/bld/unit_testers/xFail/expectedClmTestFails.xml b/bld/unit_testers/xFail/expectedClmTestFails.xml
@@ -20,20 +20,6 @@
       </goldbach>
    </namelistTest>
 
-   <tools_test_driver>
-         <yellowstone>
-            <INTEL>
-            </INTEL>
-         </yellowstone>
-         <goldbach>
-            <INTEL>
-               <entry testId="sm684" failType="FAIL">goldbach not recognized</entry>
-               <entry testId="smf84" failType="FAIL">goldbach not recognized</entry>
-               <entry testId="smfc4" failType="FAIL">goldbach not recognized</entry>
-            </INTEL>
-         </goldbach>
-   </tools_test_driver>
-
    <unit_tests>
          <yellowstone>
             <INTEL>