Merge pull request ESCOMP#2417 from ekluzek/addclm60

Addition of clm6_0 physics option

.git-blame-ignore-revs

@@ -42,3 +42,4 @@ cda0cf1412212e6f4363e6e8eb39f74c944b454d
 aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 6c6f57e948bfa31e60b383536cc21663fedb8b70
 9660667b1267dcd4150889f5f39db540158be74a
+665cf86102e09b4c4c5a140700676dca23bc55a9

.gitignore

@@ -105,13 +105,6 @@ unit_test_build
 # Tools executables
 /tools/mkprocdata_map/mkprocdata_map
 
-# mkmapdata output files
-/tools/mkmapdata/PET*.RegridWeightGen.Log
-/tools/mkmapdata/regrid.*.out
-/tools/mkmapdata/regrid.*.err
-/tools/mkmapdata/regrid.o*
-/tools/mkmapdata/map*.nc
-
 # run_neon output directories
 /tools/site_and_regional/listing.csv
 /tools/site_and_regional/????/

bld/CLMBuildNamelist.pm

@@ -4014,7 +4014,6 @@ sub setup_logic_megan {
 #-------------------------------------------------------------------------------
 
 sub setup_logic_soilm_streams {
-  # prescribed soil moisture streams require clm4_5/clm5_0/clm5_1
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_soil_moisture_streams');

bld/README

@@ -25,7 +25,6 @@ unit_testers --- Directory of scripts to test scipts in this directory
 
 ---------- XML Files describing namelists in namelist_files
 namelist_files/namelist_defaults_ctsm.xml --------- List of default values for the ctsm namelist
-namelist_files/namelist_defaults_ctsm_tools.xml --- List of default values for the ctsm tools
 namelist_files/namelist_defaults_overall.xml ------ List of default values for overall settings
 namelist_files/namelist_defaults_usr_files.xml ---- List of default values for the user-files
 namelist_files/namelist_definition_ctsm.xml -------- Definition of all namelist items for ctsm

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");
+my @version_strings = ("clm4_5", "clm5_0", "clm5_1", "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" );
+      my @vers_list = ( "clm4_5", "clm5_0", "clm5_1", "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");

bld/config_files/config_definition_ctsm.xml

@@ -5,10 +5,10 @@
 <config_definition>
 
 <entry id="phys" 
-       valid_values="clm4_5,clm5_0,clm5_1"
+       valid_values="clm4_5,clm5_0,clm5_1,clm6_0"
        value="clm4_5"
        category="physics">
-Specifies either clm4_5, clm5_0, or clm5_1 physics
+Specifies either clm4_5, clm5_0, clm5_1 (deprecated), or clm6_0 physics
 </entry>
 
 <entry id="clm_root" 

bld/namelist_files/namelist_defaults_drydep.xml

@@ -25,6 +25,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <megan_specifier>'ISOP = isoprene', 'C10H16 = pinene_a + carene_3 + thujene_a', 'CH3OH = methanol', 'C2H5OH = ethanol', 'CH2O = formaldehyde', 'CH3CHO = acetaldehyde', 'CH3COOH = acetic_acid', 'CH3COCH3 = acetone'</megan_specifier>
 
+<megan_factors_file phys="clm6_0" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
 <megan_factors_file phys="clm5_1" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
 <megan_factors_file phys="clm5_0" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
 <megan_factors_file phys="clm4_5" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>

bld/namelist_files/namelist_defaults_overall.xml

@@ -22,23 +22,12 @@ determine default values for namelists.
 
 -->
 
-<clm_start_type phys="clm5_1"  use_cndv=".true." >arb_ic</clm_start_type>
-<clm_start_type phys="clm5_0"  use_cndv=".true." >arb_ic</clm_start_type>
-<clm_start_type phys="clm4_5"  use_cndv=".true." >arb_ic</clm_start_type>
-<clm_start_type phys="clm4_5"  use_fates=".true.">arb_ic</clm_start_type>
-<clm_start_type phys="clm5_1"  use_fates=".true.">arb_ic</clm_start_type>
-<clm_start_type phys="clm5_0"  use_fates=".true.">arb_ic</clm_start_type>
-<clm_start_type phys="clm4_5"  sim_year="1850"   >startup</clm_start_type>
-<clm_start_type phys="clm5_1"  sim_year="1850"   >startup</clm_start_type>
-<clm_start_type phys="clm5_0"  sim_year="1850"   >startup</clm_start_type>
-<clm_start_type phys="clm4_5"  sim_year="2000"   >startup</clm_start_type>
-<clm_start_type phys="clm5_1"  sim_year="2000"   >startup</clm_start_type>
-<clm_start_type phys="clm5_0"  sim_year="2000"   >startup</clm_start_type>
-<clm_start_type phys="clm4_5"                    >arb_ic</clm_start_type>
-<clm_start_type phys="clm5_0"                    >arb_ic</clm_start_type>
-<clm_start_type phys="clm5_1"                    >arb_ic</clm_start_type>
-<clm_start_type phys="clm4_5"  use_fates=".true.">arb_ic</clm_start_type>
+<clm_start_type                                  >arb_ic</clm_start_type>
 <clm_start_type bgc_spinup="on"                  >cold</clm_start_type>
+<clm_start_type                use_cndv=".true." >cold</clm_start_type>
+<clm_start_type                use_fates=".true.">cold</clm_start_type>
+<clm_start_type                sim_year="1850"   >startup</clm_start_type>
+<clm_start_type                sim_year="2000"   >startup</clm_start_type>
 
 <clm_start_type sim_year_range="1850-2100">arb_ic</clm_start_type>
 

bld/namelist_files/namelist_definition_ctsm.xml

@@ -1374,35 +1374,6 @@ Toggle to turn on the dynamic root model
 Toggle to turn on on diagnostic Snow Radiative Effect
 </entry>
 
-
-<!--                                                   -->
-<!-- mkmapdata  namelist                               -->
-<!--                                                   -->
-<entry id="scripgriddata" type="char*256" category="mkmapdata"
-       input_pathname="abs" group="clmexp" valid_values="" >
-SCRIP format grid data file
-</entry>
-
-<entry id="scripgriddata_lrgfile_needed" type="char*256" category="mkmapdata"
-       group="clmexp" valid_values="none,64bit_offset,netcdf4" >
-Flag to pass to the ESMF mapping utility, telling it what kind of large
-file support is needed for an output file generated with this grid as
-either the source or destination ('none', '64bit_offset' or 'netcdf4'). 
-</entry>
-
-<entry id="scripgriddata_type" type="char*256" category="mkmapdata"
-       group="clmexp" valid_values="SCRIP,UGRID" >
-Flag to pass to the ESMF mapping utility, telling it what kind of grid
-file this is (SCRIP or UGRID).
-</entry>
-
-<entry id="scripgriddata_meshname" type="char*256" category="mkmapdata"
-       group="clmexp" valid_values="" >
-For UGRID files, flag to pass to the ESMF mapping utility, telling it the
-name of the dummy variable that has all of the topology information stored
-in its attributes. (Only used if scripgriddata_src_type = UGRID.)
-</entry>
-
 <!--                                                   -->
 <!-- mksurfdata namelist                               -->
 <!--                                                   -->
@@ -2222,7 +2193,7 @@ Land mask description
 <!-- lnd_tuning_mode, there needs to be a setting for: CRUv7, GSWP3v1, and cam6.0 for each valid physics option -->
 <entry id="lnd_tuning_mode" type="char*20" category="default_settings"
        group="default_settings"
-       valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm5_0_cam6.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_cam6.0">
+       valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm5_0_cam6.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_cam6.0,clm6_0_GSWP3v1,clm6_0_cam6.0">
 General configuration of model version and atmospheric forcing to tune the model to run under.
 This sets the model to run with constants and initial conditions that were set to run well under 
 the configuration of model version and atmospheric forcing. To run well constants would need to be changed

bld/unit_testers/build-namelist_test.pl

@@ -78,7 +78,7 @@ sub make_config_cache {
 <?xml version="1.0"?>
 <config_definition>
 <commandline></commandline>
-<entry id="phys" value="$phys" list="" valid_values="clm4_5,clm5_0,clm5_1">Specifies clm physics</entry>
+<entry id="phys" value="$phys" list="" valid_values="clm4_5,clm5_0,clm5_1,clm6_0">Specifies clm physics</entry>
 </config_definition>
 EOF
    $fh->close();
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1990;
+my $ntests = 2455;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1201;
+   $ntests += 1511;
 }
 plan( tests=>$ntests );
 
@@ -366,7 +366,7 @@ sub cat_and_create_namelistinfile {
 print "\n===============================================================================\n";
 print "Test the NEON sites\n";
 print "=================================================================================\n";
-my $phys = "clm5_1";
+my $phys = "clm6_0";
 $mode = "-phys $phys";
 &make_config_cache($phys);
 my $neondir      = "../../cime_config/usermods_dirs/NEON";
@@ -575,7 +575,7 @@ sub cat_and_create_namelistinfile {
      "onset_threh w SP"          =>{ options=>" -envxml_dir . -bgc sp",
                                      namelst=>"onset_thresh_depends_on_veg=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "dribble_crphrv w/o CN"     =>{ options=>" -envxml_dir . -bgc sp",
                                      namelst=>"dribble_crophrv_xsmrpool_2atm=.true.",
@@ -715,7 +715,7 @@ sub cat_and_create_namelistinfile {
      "NEONlightresButGlobal"     =>{ options=>"--res 4x5 --bgc bgc --envxml_dir . --light_res 106x740",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "spno-fire"                 =>{ options=>"-bgc sp -envxml_dir . -use_case 2000_control",
                                      namelst=>"fire_method='nofire'",
@@ -905,27 +905,27 @@ sub cat_and_create_namelistinfile {
      "lnd_frac set to UNSET"     =>{ options=>"-driver mct -lnd_frac UNSET -envxml_dir .",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "lnd_frac set but nuopc"    =>{ options=>"-driver nuopc -lnd_frac $DOMFILE -envxml_dir .",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "lnd_frac not set but lilac"=>{ options=>"-driver nuopc -lilac -envxml_dir . -lnd_frac UNSET",
                                      namelst=>"fsurdat='surfdata.nc'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "fatmlndfrc set but nuopc"  =>{ options=>"-driver nuopc -envxml_dir .",
                                      namelst=>"fatmlndfrc='frac.nc'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     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=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "branch but NO nrevsn"      =>{ options=>"-clm_start_type branch -envxml_dir .",
                                      namelst=>"",
@@ -965,7 +965,7 @@ sub cat_and_create_namelistinfile {
      "useFATESWcrop"             =>{ options=>"-bgc fates -envxml_dir . -no-megan -crop",
                                      namelst=>"",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "useFATESWcreatecrop"       =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"create_crop_landunit=.true.",
@@ -980,37 +980,37 @@ sub cat_and_create_namelistinfile {
      "useFATESWbMH"              =>{ options=>"-bgc fates -envxml_dir . -no-megan",
                                      namelst=>"use_biomass_heat_storage=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "FireNoneButFATESfireon"    =>{ options=>"-bgc fates -envxml_dir . -no-megan -light_res none",
                                      namelst=>"fates_spitfire_mode=4",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "FATESwspitfireOffLigtOn"    =>{ options=>"-bgc fates -envxml_dir . -no-megan -light_res 360x720",
                                      namelst=>"fates_spitfire_mode=0",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "useFATESWluna"             =>{ options=>"--bgc fates --envxml_dir . --no-megan",
                                      namelst=>"use_luna=TRUE",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "useFATESWfun"              =>{ options=>"--bgc fates --envxml_dir . --no-megan",
                                      namelst=>"use_fun=TRUE",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "useFATESWOsuplnitro"       =>{ options=>"--bgc fates --envxml_dir . --no-megan",
                                      namelst=>"suplnitro='NONE'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "FireNoneButBGCfireon"    =>{ options=>"-bgc bgc -envxml_dir . -light_res none",
                                      namelst=>"fire_method='li2021gswpfrc'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "createcropFalse"           =>{ options=>"-bgc bgc -envxml_dir . -no-megan",
                                      namelst=>"create_crop_landunit=.false.",
@@ -1271,7 +1271,7 @@ sub cat_and_create_namelistinfile {
      "methane off W nitrif_denit"=>{ options=>"-bgc bgc -envxml_dir .",
                                      namelst=>"use_nitrif_denitrif=.true.,use_lch4=.false.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "soilm_stream w transient"  =>{ options=>"-res 0.9x1.25 -envxml_dir . -use_case 20thC_transient",
                                      namelst=>"use_soil_moisture_streams=T,soilm_tintalgo='linear'",
@@ -1291,12 +1291,12 @@ sub cat_and_create_namelistinfile {
      "FUN_wo_flexCN"             =>{ options=>"-envxml_dir . -bgc bgc",
                                      namelst=>"use_fun=.true.,use_flexiblecn=.false.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
      "NotNEONbutNEONlightres"    =>{ options=>"--res CLM_USRDAT --clm_usr_name regional --envxml_dir . --bgc bgc --light_res 106x174",
                                      namelst=>"fsurdat='build-namelist_test.pl'",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
-                                     phys=>"clm5_1",
+                                     phys=>"clm6_0",
                                    },
                );
 foreach my $key ( keys(%warntest) ) {
@@ -1319,7 +1319,7 @@ sub cat_and_create_namelistinfile {
 #
 # Loop over all physics versions
 #
-foreach my $phys ( "clm4_5", "clm5_0", "clm5_1" ) {
+foreach my $phys ( "clm4_5", "clm5_0", "clm5_1", "clm6_0" ) {
 $mode = "-phys $phys";
 &make_config_cache($phys);
 
@@ -1558,7 +1558,7 @@ sub cat_and_create_namelistinfile {
 #
 # Test ALL SSP's for f09...
 #
-$phys = "clm5_1";
+$phys = "clm6_0";
 $mode = "-phys $phys";
 &make_config_cache($phys);
 my $res = "0.9x1.25";
@@ -1594,10 +1594,10 @@ sub cat_and_create_namelistinfile {
 }
 
 print "\n==================================================\n";
-print "Test clm4.5/clm5.0/clm5_1 resolutions \n";
+print "Test clm4.5/clm5.0/clm5_1/clm6_0 resolutions \n";
 print "==================================================\n";
 
-foreach my $phys ( "clm4_5", 'clm5_0', 'clm5_1' ) {
+foreach my $phys ( "clm4_5", 'clm5_0', 'clm5_1', "clm6_0" ) {
   my $mode = "-phys $phys";
   &make_config_cache($phys);
   my @clmoptions = ( "-bgc bgc -envxml_dir .", "-bgc bgc -envxml_dir . -clm_accelerated_spinup=on", "-bgc bgc -envxml_dir . -light_res 360x720",
@@ -1697,7 +1697,7 @@ sub cat_and_create_namelistinfile {
 my $res = "0.9x1.25";
 my $mask = "gx1v7";
 my $simyr = "1850";
-foreach my $phys ( "clm4_5", 'clm5_0', 'clm5_1' ) {
+foreach my $phys ( "clm4_5", 'clm5_0', 'clm5_1', 'clm6_0' ) {
   my $mode = "-phys $phys";
   &make_config_cache($phys);
   my @forclist = ();
@@ -1708,6 +1708,9 @@ sub cat_and_create_namelistinfile {
         if ( $lndtuningmode eq "clm5_1_CRUv7" ) {
            next;
         }
+        if ( $lndtuningmode eq "clm6_0_CRUv7" ) {
+           next;
+        }
         my $clmoptions = "-res $res -mask $mask -sim_year $simyr -envxml_dir . -lnd_tuning_mod $lndtuningmode -bgc $bgc";
         &make_env_run( );
         eval{ system( "$bldnml $clmoptions > $tempfile 2>&1 " ); };

cime_config/SystemTests/mksurfdataesmf.py

@@ -64,7 +64,7 @@ def build_phase(self, sharedlib_only=False, model_only=False):
             nml_script_path = os.path.join(self._tool_path, "gen_mksurfdata_namelist")
             gen_jobscript_path = os.path.join(self._tool_path, "gen_mksurfdata_jobscript_single")
             gen_mksurfdata_namelist = f"{nml_script_path} --res {self._res} --start-year {self._model_yr} --end-year {self._model_yr}"
-            gen_mksurfdata_jobscript = f"{gen_jobscript_path} --number-of-nodes 1 --tasks-per-node 64 --namelist-file {self._fsurdat_namelist}"
+            gen_mksurfdata_jobscript = f"{gen_jobscript_path} --number-of-nodes 1 --tasks-per-node 64 --namelist-file {self._fsurdat_namelist} --bld-path {self._tool_bld}"
 
             # Rm tool_bld and build executable that will generate fsurdat
             try:
@@ -76,6 +76,7 @@ def build_phase(self, sharedlib_only=False, model_only=False):
             try:
                 subprocess.check_call(f"{build_script_path} --blddir {self._tool_bld}", shell=True)
             except subprocess.CalledProcessError as e:
+                print(f"build directory = {self._tool_bld}\n")
                 sys.exit(
                     f"{e} ERROR RUNNING {build_script_path}. DETAILS IN {self._TestStatus_log_path}"
                 )