Merge tag 'ctsm5.1.dev035' into snow_occlusion_ctsm

Misc bfb enhancements and fixes (1) If CISM is running over Antarctica, use virtual glacier columns over Antarctica (2) Remove "mec" from some glacier/ice variable names (it is misleading to have "mec" in variable names when the ice landunit can actually have multiple columns *or* a single column) (ESCOMP#1294) (3) Add history file metadata on each variable's l2g_scale_type (adds a landunit_mask attribute) (ESCOMP#1343) (4) Use python3 in more shebang lines - needed to run python unit tests on cheyenne (5) New compset naming for IG compsets (ESCOMP#1289) (6) Remove calculation of fun_cost_fix that is overwritten (ESCOMP#1115) (7) Bypass grid-level water mass check when fates hydro is active (ESCOMP#1334) (8) Remove some dead code (ESCOMP#1333)
ckoven · Apr 20, 2021 · 51d3145 · 51d3145
2 parents f9a166d + 075b273
commit 51d3145
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diff --git a/Externals.cfg b/Externals.cfg
@@ -8,22 +8,22 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cism2_1_69
+tag = cism2_1_78
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_73
+tag = rtm1_0_76
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_38
+tag = mosart1_0_42
 required = True
 
 [mizuRoute]
@@ -37,21 +37,21 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = branch_tags/cime5.8.32_a02
+tag = branch_tags/cime5.8.42_a01
 required = True
 
 [cmeps]
 local_path = cime/src/drivers/nuopc/
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
-hash = 7654038
+tag = v0.9.0
 required = True
 
 [cdeps]
 local_path = components/cdeps
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
-hash = 45b7a85
+tag = v0.6.0
 required = True
 
 [doc-builder]
@@ -63,4 +63,3 @@ required = False
 
 [externals_description]
 schema_version = 1.0.0
-
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -167,6 +167,7 @@ OPTIONS
                               (Note: buildnml copies the file for use by the driver)
      -glc_nec <name>          Glacier number of elevation classes [0 | 3 | 5 | 10 | 36]
                               (default is 0) (standard option with land-ice model is 10)
+     -glc_use_antarctica      Set defaults appropriate for runs that include Antarctica
      -help [or -h]            Print usage to STDOUT.
      -light_res <value>       Resolution of lightning dataset to use for CN fire (360x720 or 94x192)
      -ignore_ic_date          Ignore the date on the initial condition files
@@ -253,6 +254,7 @@ sub process_commandline {
                clm_demand            => "null",
                help                  => 0,
                glc_nec               => "default",
+               glc_use_antarctica    => 0,
                light_res             => "default",
                lnd_tuning_mode       => "default",
                lnd_frac              => undef,
@@ -297,6 +299,7 @@ sub process_commandline {
              "note!"                     => \$opts{'note'},
              "megan!"                    => \$opts{'megan'},
              "glc_nec=i"                 => \$opts{'glc_nec'},
+             "glc_use_antarctica!"       => \$opts{'glc_use_antarctica'},
              "light_res=s"               => \$opts{'light_res'},
              "d:s"                       => \$opts{'dir'},
              "h|help"                    => \$opts{'help'},
@@ -1102,6 +1105,12 @@ sub setup_cmdl_spinup {
        $nl_flags->{'bgc_spinup'} = "off";
        $val = $defaults->get_value($var);
     }
+    # For AD spinup mode by default reseed dead plants
+    if ( $nl_flags->{$var} ne "off" ) {
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition,
+                    $defaults, $nl, "reseed_dead_plants", clm_accelerated_spinup=>$nl_flags->{$var},
+                    use_cn=>$nl_flags->{'use_cn'} );
+    }
   } else {
     if ( defined($nl->get_value("spinup_state")) ) {
        $log->fatal_error("spinup_state is accelerated (=1 or 2) which is for a BGC mode of CN or BGC," .
@@ -1616,6 +1625,11 @@ sub process_namelist_inline_logic {
   ##################################
   setup_logic_bgc_shared($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
 
+  ##################################
+  # namelist group: cnphenology
+  ##################################
+  setup_logic_cnphenology($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
+
   #############################################
   # namelist group: soilwater_movement_inparm #
   #############################################
@@ -1902,7 +1916,7 @@ sub setup_logic_glacier {
      $log->fatal_error("glc_do_dynglacier can only be set via the env variable $clm_upvar: it can NOT be set in user_nl_clm");
   }
 
-  my $var = "maxpatch_glcmec";
+  my $var = "maxpatch_glc";
   add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'val'=>$nl_flags->{'glc_nec'} );
 
   my $val = $nl->get_value($var);
@@ -1917,7 +1931,8 @@ sub setup_logic_glacier {
   add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glc_snow_persistence_max_days');
 
   add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'albice');
-  add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_behavior');
+  add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_behavior',
+              'glc_use_antarctica'=>$opts->{'glc_use_antarctica'});
   add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_melt_behavior');
   add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_ice_runoff_behavior');
 }
@@ -2685,6 +2700,24 @@ sub setup_logic_bgc_shared {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_cnphenology {
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+  my @list  = (  "onset_thresh_depends_on_veg", "min_crtical_dayl_depends_on_lat" );
+  foreach my $var ( @list ) {
+    if (  &value_is_true($nl_flags->{'use_cn'}) ) {
+       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 
+                   'phys'=>$physv->as_string(), 'use_cn'=>$nl_flags->{'use_cn'} );
+    } else {
+       if ( defined($nl->get_value($var)) ) {
+          $log->fatal_error("$var should only be set if use_cn is on");
+       }
+    }
+  }
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_logic_supplemental_nitrogen {
   #
   # Supplemental Nitrogen for prognostic crop cases

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -57,6 +57,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <spinup_state clm_accelerated_spinup="on"  use_fates=".true." phys="clm4_5" >1</spinup_state>
 <spinup_state clm_accelerated_spinup="off"                               >0</spinup_state>
 
+<!-- Reseeding of dead plants normally only done for AD spinup -->
+<reseed_dead_plants clm_accelerated_spinup="on" use_cn=".true.">.true.</reseed_dead_plants>
+<reseed_dead_plants                                            >.false.</reseed_dead_plants>
+
 <for_testing_run_ncdiopio_tests>.false.</for_testing_run_ncdiopio_tests>
 
 <!-- Set to .true. in namelist to write hist fields master list file -->
@@ -442,8 +446,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
      Mountain glaciers: single_at_atm_topo
      Greenland - inside CISM grid but outside Greenland itself: virtual
      Greenland itself: virtual
-     Antarctica: multiple -->
-<glacier_region_behavior>'single_at_atm_topo','virtual','virtual','multiple'</glacier_region_behavior>
+     Antarctica: multiple
+
+     If CISM is running over Antarctica, then we change the Antarctica
+     behavior to virtual. Note that the Greenland behavior is always
+     virtual, even if Greenland isn't included in this run.
+-->
+<glacier_region_behavior glc_use_antarctica="0">'single_at_atm_topo','virtual','virtual','multiple'</glacier_region_behavior>
+<glacier_region_behavior glc_use_antarctica="1">'single_at_atm_topo','virtual','virtual','virtual' </glacier_region_behavior>
 
 <!-- Default glacier melt behavior is:
      Mountain glaciers: remains_in_place
@@ -473,9 +483,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c210112.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c210112.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c210112.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c210305.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c210217.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c210217.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -549,6 +559,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <initial_seed_at_planting use_crop=".true." phys="clm5_0" >3.d00</initial_seed_at_planting>
 <initial_seed_at_planting use_crop=".true." phys="clm4_5" >1.d00</initial_seed_at_planting>
 
+<!-- CN Phenology -->
+<onset_thresh_depends_on_veg     use_cn=".true." phys="clm5_1" >.true.</onset_thresh_depends_on_veg>
+<min_crtical_dayl_depends_on_lat use_cn=".true." phys="clm5_1" >.true.</min_crtical_dayl_depends_on_lat>
+<onset_thresh_depends_on_veg                                   >.false.</onset_thresh_depends_on_veg>
+<min_crtical_dayl_depends_on_lat                               >.false.</min_crtical_dayl_depends_on_lat>
 
 <!-- turnover time modifications    -->
 <decomp_depth_efolding phys="clm4_5" >0.5</decomp_depth_efolding>

diff --git a/bld/namelist_files/namelist_defaults_ctsm_tools.xml b/bld/namelist_files/namelist_defaults_ctsm_tools.xml
@@ -269,7 +269,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- urban -->
 <mksrf_furban   hgrid="3x3min"   lmask="LandScan2004"
->lnd/clm2/rawdata/mksrf_urban_0.05x0.05_simyr2000.c170724.nc</mksrf_furban>
+>lnd/clm2/rawdata/mksrf_urban_0.05x0.05_simyr2000.c120621.nc</mksrf_furban>
 
 <mksrf_furban   hgrid="3x3min"   lmask="LandScan2004" sim_year="PtVg"
 >lnd/clm2/rawdata/mksrf_urban_0.05x0.05_zerourbanpct.c181014.nc</mksrf_furban>

diff --git a/bld/namelist_files/namelist_defaults_overall.xml b/bld/namelist_files/namelist_defaults_overall.xml
@@ -82,18 +82,18 @@ determine default values for namelists.
 <!-- Default land/ocean mask type -->
 <mask hgrid="0.23x0.31"           >gx1v6</mask>
 <mask hgrid="0.47x0.63"           >gx1v6</mask>
-<mask hgrid="0.9x1.25"            >gx1v6</mask>
-<mask hgrid="1.9x2.5"             >gx1v6</mask>
+<mask hgrid="0.9x1.25"            >gx1v7</mask>
+<mask hgrid="1.9x2.5"             >gx1v7</mask>
 <mask hgrid="2.5x3.33"            >gx3v7</mask>
 <mask hgrid="4x5"                 >gx3v7</mask>
-<mask hgrid="10x15"               >USGS</mask>
+<mask hgrid="10x15"               >gx3v7</mask>
 
 <mask hgrid="360x720cru"          >cruncep</mask>
-<mask hgrid="128x256"             >USGS</mask>
-<mask hgrid="64x128"              >USGS</mask>
+<mask hgrid="128x256"             >gx1v7</mask>
+<mask hgrid="64x128"              >gx1v7</mask>
 <mask hgrid="48x96"               >gx3v7</mask>
-<mask hgrid="32x64"               >USGS</mask>
-<mask hgrid="8x16"                >USGS</mask>
+<mask hgrid="32x64"               >gx3v7</mask>
+<mask hgrid="8x16"                >gx3v7</mask>
 
 <mask hgrid="94x192"              >T62</mask>
 
@@ -111,7 +111,7 @@ determine default values for namelists.
 <mask hgrid="1x1_urbanc_alpha"    >test</mask>
 <mask hgrid="1x1_numaIA"          >navy</mask>
 <mask hgrid="1x1_smallvilleIA"    >test</mask>
-<mask                             >gx1v6</mask>
+<mask                             >gx1v7</mask>
 
 <!-- Default glacier model options -->
 

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -501,7 +501,7 @@ If TRUE, irrigation will be active.
 If TRUE, fsat will be set to zero for crop columns.
 </entry> 
 
-<entry id="maxpatch_glcmec" type="integer"  category="clm_physics"
+<entry id="maxpatch_glc" type="integer"  category="clm_physics"
        group="clm_inparm" valid_values="1,3,5,10,36" >
 Number of  multiple elevation classes over glacier points.
 </entry>
@@ -1096,6 +1096,18 @@ Initial seed Carbon to use at planting
 (only used when CN is on as well as crop)
 </entry>
 
+<entry id="onset_thresh_depends_on_veg" type="logical" category="physics"
+       group="cnphenology">
+Phenology onset depends on the vegetation type
+(only used when CN is on)
+</entry>
+
+<entry id="min_crtical_dayl_depends_on_lat" type="logical" category="physics"
+       group="cnphenology">
+The minimum critical day length for onset depends on latitude
+(only used when CN is on)
+</entry>
+
 <entry id="use_ozone" type="logical" category="physics"
        group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on ozone stress
@@ -1537,7 +1549,7 @@ If TRUE, repartition rain/snow from atmosphere based on temperature.
 
 <entry id="glcmec_downscale_longwave" type="logical" category="clm_physics"
        group="atm2lnd_inparm" valid_values="" >
-If TRUE, downscale longwave radiation over glc_mec landunits.
+If TRUE, downscale longwave radiation over glacier landunits.
 This downscaling is conservative.
 <default>Default: .true.</default>
 </entry>
@@ -2003,7 +2015,7 @@ CLM datasets exist for years: 1000 (for testing), 1850, and 2000
 
 <entry id="sim_year_range" type="char*9" category="default_settings"
        group="default_settings" valid_values=
-"constant,1000-1002,1000-1004,850-1850,1850-1855,1850-2000,1850-2005,1850-2100,1980-2015,2000-2100">
+"constant,1000-1002,1000-1004,850-1850,1850-1855,1850-2000,1850-2005,1850-2100,1980-2015,2000-2025,2000-2100">
 Range of years to simulate transitory datasets for (such as dynamic: land-use datasets, aerosol-deposition, Nitrogen deposition rates etc.)
 Constant means simulation will be held at a constant year given in sim_year.
 A sim_year_range of 1000-1002 or 1000-1004 corresponds to data used for testing only, NOT corresponding to any real datasets.

diff --git a/bld/namelist_files/use_cases/stdurbpt_pd.xml b/bld/namelist_files/use_cases/stdurbpt_pd.xml
@@ -10,7 +10,7 @@
 
 <hist_fincl1>'TBUILD','BUILDHEAT','TRAFFICFLUX','WASTEHEAT','SWup','LWup','Rnet','Qh','Qle','Qstor','Qtau','Qanth','Wind','Qair','Tair','PSurf','Rainf','SWdown','LWdown','COSZEN'</hist_fincl1>
 
-<hist_fincl2>'TG','TBOT','FIRE','FIRA','FLDS','FSDS','FSR','FSA','FGEV','FSH','FGR','TSOI','ERRSOI','BUILDHEAT','SABV','SABG','FSDSVD','FSDSND','FSDSVI','FSDSNI','FSRVD','FSRND','FSRVI','FSRNI','TSA','FCTR','FCEV','QBOT','Q2M','H2OSOI','H2OSNO','SOILLIQ','SOILICE','SWup','LWup','Rnet','Qh','Qle','Qstor','Qtau','Qanth','Wind','Qair','Tair','PSurf','Rainf','SWdown','LWdown','SoilAlpha_U','ZWT','WA'
+<hist_fincl2>'TG','TBOT','FIRE','FIRA','FLDS','FSDS','FSR','FSA','FGEV','FSH','FGR','TSOI','ERRSOI','BUILDHEAT','SABV','SABG','FSDSVD','FSDSND','FSDSVI','FSDSNI','FSRVD','FSRND','FSRVI','FSRNI','TSA','FCTR','FCEV','QBOT','Q2M','H2OSOI','H2OSNO','SOILLIQ','SOILICE','SWup','LWup','Rnet','Qh','Qle','Qstor','Qtau','Qanth','Wind','Qair','Tair','PSurf','Rainf','SWdown','LWdown','SoilAlpha_U','ZWT'
 </hist_fincl2>
 
 <hist_fincl3>'SWup','LWup','Rnet','Qh','Qle','Qstor','Qtau','Qanth','Wind','Qair','Tair','PSurf','Rainf','SWdown','LWdown','FSA','FIRA','TG','COSZEN','SoilAlpha_U','TBUILD','BUILDHEAT'

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -138,7 +138,7 @@ sub make_config_cache {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1551;
+my $ntests = 1552;
 if ( defined($opts{'compare'}) ) {
    $ntests += 1044;
 }
@@ -446,6 +446,11 @@ sub make_config_cache {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
+     "onset_threh w SP"          =>{ options=>" -envxml_dir . -bgc sp",
+                                     namelst=>"onset_thresh_depends_on_veg=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                   },
      "dribble_crphrv w/o CN"     =>{ options=>" -envxml_dir . -bgc sp",
                                      namelst=>"dribble_crophrv_xsmrpool_2atm=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -803,7 +808,7 @@ sub make_config_cache {
                                      phys=>"clm5_0",
                                    },
      "glc_nec inconsistent"      =>{ options=>"-envxml_dir .",
-                                     namelst=>"maxpatch_glcmec=5",
+                                     namelst=>"maxpatch_glc=5",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },

diff --git a/cime_config/buildlib b/cime_config/buildlib
@@ -133,6 +133,9 @@ def _main_func():
                 # to use its directories in place of stub_rof
                 paths.append(os.path.join(lnd_root,"lilac","stub_rof"))
 
+            if (driver == 'lilac' or driver == 'nuopc'):
+                paths.append(os.path.join(lnd_root,"src","cpl","share_esmf"))
+
             with open(filepath_file, "w") as filepath:
                 filepath.write("\n".join(paths))
                 filepath.write("\n")

diff --git a/cime_config/buildnml b/cime_config/buildnml
@@ -60,6 +60,7 @@ def buildnml(case, caseroot, compname):
     run_refdate = case.get_value("RUN_REFDATE")
     run_reftod = case.get_value("RUN_REFTOD")
     glc_nec = case.get_value("GLC_NEC")
+    cism_use_antarctica = case.get_value("CISM_USE_ANTARCTICA")
     mask = case.get_value("MASK_GRID")
 
     # -----------------------------------------------------
@@ -127,6 +128,18 @@ def buildnml(case, caseroot, compname):
     else:
         nomeg = ""
 
+    if cism_use_antarctica is None:
+        # This is the case for compsets without CISM, where the CISM_USE_ANTARCTICA xml
+        # variable isn't defined
+        glc_use_antarctica_flag = ""
+    elif isinstance(cism_use_antarctica, bool):
+        if cism_use_antarctica:
+            glc_use_antarctica_flag = "-glc_use_antarctica"
+        else:
+            glc_use_antarctica_flag = ""
+    else:
+        expect(False, "Unexpected value for CISM_USE_ANTARCTICA: {}".format(cism_use_antarctica))
+
     if clm_nml_use_case != "UNSET":
         usecase = "-use_case %s" %clm_nml_use_case
     else:
@@ -218,12 +231,12 @@ def buildnml(case, caseroot, compname):
         command = ("%s -cimeroot %s -infile %s -csmdata %s -inputdata %s %s -namelist \"&clm_inparm  start_ymd=%s %s/ \" "
                    "%s %s -res %s %s -clm_start_type %s -envxml_dir %s "
                    "-configuration %s -structure %s "
-                   "-lnd_frac %s -glc_nec %s -co2_ppmv %s -co2_type %s -config %s "
+                   "-lnd_frac %s -glc_nec %s %s -co2_ppmv %s -co2_type %s -config %s "
                    "%s %s %s %s"
                    %(cmd, _CIMEROOT, infile, din_loc_root, inputdata_file, ignore, start_ymd, clm_namelist_opts, 
                      nomeg, usecase, lnd_grid, clmusr, start_type, caseroot,
                      configuration, structure,
-                     lndfrac_file, glc_nec, ccsm_co2_ppmv, clm_co2_type, config_cache_file,
+                     lndfrac_file, glc_nec, glc_use_antarctica_flag, ccsm_co2_ppmv, clm_co2_type, config_cache_file,
                      clm_bldnml_opts, spinup, tuning, gridmask))
 
         rc, out, err = run_cmd(command, from_dir=ctsmconf)