Merge remote-tracking branch 'slevis-lmwg/new_rawpftlai' into changel…

…og_readme_update
ekluzek · Sep 12, 2024 · 3c0bda1 · 3c0bda1
2 parents 2f5bd73 + a4d105d
commit 3c0bda1
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Showing 9 changed files with 183 additions and 108 deletions.
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -2506,8 +2506,9 @@ sub setup_logic_surface_dataset {
   # consistent with it
   # MUST BE AFTER: setup_logic_demand which is where flanduse_timeseries is set
   #
-  my ($opts, $nl_flags, $definition, $defaults, $nl, $xmlvar_ref) = @_;
+  my ($opts_in, $nl_flags, $definition, $defaults, $nl, $xmlvar_ref) = @_;
 
+  my $opts = $opts_in;
   $nl_flags->{'flanduse_timeseries'} = "null";
   my $flanduse_timeseries = $nl->get_value('flanduse_timeseries');
   if (defined($flanduse_timeseries)) {
@@ -2523,6 +2524,11 @@ sub setup_logic_surface_dataset {
   if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_cndv'}) ) {
      $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with dynamic vegetation (use_cndv=.true)." );
   }
+  # Turn test option off for NEON until after XML is interpreted
+  my $test_files = $opts->{'test'};
+  if ( &value_is_true($nl_flags->{'neon'})) {
+     $opts->{'test'} = 0;
+  }
   #
   # Always get the crop version of the datasets now and let the code turn it into the form desired
   # Provided this isn't with FATES on
@@ -2548,7 +2554,7 @@ sub setup_logic_surface_dataset {
                  'use_crop'=>$nl_flags->{'use_crop'} );
   }
   #
-  # Expand the XML variables for NEON cases so that NEONSITE will be used
+  # Expand the XML variables for NEON cases so that NEONSITE will be used and test for existence
   #
   if ( &value_is_true($nl_flags->{'neon'}) ) {
      my $fsurdat = $nl->get_value($var);
@@ -2557,6 +2563,9 @@ sub setup_logic_surface_dataset {
         my $group = $definition->get_group_name($var);
         $nl->set_variable_value($group, $var, $newval);
         $log->verbose_message( "This is a NEON site and the fsurdat file selected is: $newval" );
+        if ( $test_files and ($newval !~ /null|none/) and (! -f remove_leading_and_trailing_quotes($newval) ) ) {
+          $log->fatal_error("file not found: $var = $newval");
+        }
      }
   }
 }

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -42,7 +42,7 @@ sub make_env_run {
     my %settings = @_;
 
     # Set default settings
-    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE",  LND_SETS_DUST_EMIS_DRV_FLDS=>"TRUE", NEONSITE=>"" );
+    my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE",  LND_SETS_DUST_EMIS_DRV_FLDS=>"TRUE", NEONSITE=>"", PLUMBER2SITE=>"" );
     # Set any settings that came in from function call
     foreach my $item ( keys(%settings) ) {
        $env_vars{$item} = $settings{$item};
@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3349;
+my $ntests = 3994;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 2007;
+   $ntests += 2437;
 }
 plan( tests=>$ntests );
 
@@ -393,9 +393,67 @@ sub cat_and_create_namelistinfile {
    my $namelistfile = "temp.namelistinfile_$site";
    &cat_and_create_namelistinfile( $neondefaultfile, $neonsitefile, $namelistfile );
    #
+   # Now run  the site for both bgc and non-FATES
+   #
+   foreach my $bgc ( "bgc", "fates") {
+      if ( ($bgc eq "bgc") or ($site ne "STER" and $site ne "KONA")) {
+         my $options = "--res CLM_USRDAT --clm_usr_name NEON --no-megan --bgc $bgc --use_case 2018_control --infile $namelistfile";
+         eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };
+         is( $@, '', "options: $options" );
+         $cfiles->checkfilesexist( "$options", $mode );
+         $cfiles->shownmldiff( "default", $mode );
+         if ( defined($opts{'compare'}) ) {
+            $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode );
+            $cfiles->dodiffonfile(      "lnd_in",    "$options", $mode );
+            $cfiles->comparefiles( "$options", $mode, $opts{'compare'} );
+         }
+         if ( defined($opts{'generate'}) ) {
+            $cfiles->copyfiles( "$options", $mode );
+         }
+      }
+   }
+   system( "/bin/rm $namelistfile" );
+   &cleanup();
+}
+print "\n===============================================================================\n";
+print "Test the PLUMBER2 sites\n";
+print "=================================================================================\n";
+my $phys = "clm6_0";
+$mode = "-phys $phys";
+&make_config_cache($phys);
+my $plumdir      = "../../cime_config/usermods_dirs/PLUMBER2";
+foreach my $site ( 
+    "AR-SLu",  "AU-Emr",  "AU-TTE",  "CA-NS1",  "CA-SF3",  "CN-HaM",  "DE-Obe",  "ES-ES1",  "FR-Gri",  "IE-Dri",  "IT-LMa",  "IT-SRo",  "RU-Fyo",  "US-Aud",  "US-Ho1",  "US-Ne2",  "US-Syv",  "ZM-Mon",
+    "AT-Neu",  "AU-Gin",  "AU-Tum",  "CA-NS2",  "CH-Cha",  "CN-Qia",  "DE-Seh",  "ES-ES2",  "FR-Hes",  "IT-Amp",  "IT-Mal",  "JP-SMF",  "RU-Zot",  "US-Bar",  "US-KS2",  "US-Ne3",  "US-Ton",
+    "AU-ASM",  "AU-GWW",  "AU-Whr",  "CA-NS4",  "CH-Dav",  "CZ-wet",  "DE-SfN",  "ES-LgS",  "FR-LBr",  "IT-BCi",  "IT-MBo",  "NL-Ca1",  "SD-Dem",  "US-Bkg",  "US-Los",  "US-NR1",  "US-Tw4",
+    "AU-Cow",  "AU-How",  "AU-Wrr",  "CA-NS5",  "CH-Fru",  "DE-Bay",  "DE-Tha",  "ES-LMa",  "FR-Lq1",  "IT-CA1",  "IT-Noe",  "NL-Hor",  "SE-Deg",  "US-Blo",  "US-Me2",  "US-PFa",  "US-Twt",
+    "AU-Cpr",  "AU-Lit",  "AU-Ync",  "CA-NS6",  "CH-Oe1",             "DE-Wet",  "ES-VDA",  "FR-Lq2",  "IT-CA2",  "IT-Non",  "NL-Loo",  "UK-Gri",  "US-Bo1",  "US-Me4",  "US-Prr",  "US-UMB",
+    "AU-Ctr",  "AU-Otw",  "BE-Bra",  "CA-NS7",  "CN-Cha",  "DE-Geb",  "DK-Fou",  "FI-Hyy",  "FR-Pue",  "IT-CA3",  "IT-PT1",  "PL-wet",  "UK-Ham",  "US-Cop",  "US-Me6",  "US-SP1",  "US-Var",
+    "AU-Cum",  "AU-Rig",  "BE-Lon",  "CA-Qcu",  "CN-Cng",  "DE-Gri",  "DK-Lva",  "FI-Kaa",  "GF-Guy",  "IT-Col",  "IT-Ren",  "PT-Esp",  "UK-PL3",  "US-FPe",  "US-MMS",  "US-SP2",  "US-WCr",
+    "AU-DaP",  "AU-Rob",  "BE-Vie",  "CA-Qfo",  "CN-Dan",  "DE-Hai",  "DK-Ris",  "FI-Lom",  "HU-Bug",  "IT-Cpz",  "IT-Ro1",  "PT-Mi1",  "US-AR1",  "US-GLE",  "US-MOz",  "US-SP3",  "US-Whs",
+    "AU-DaS",  "AU-Sam",  "BR-Sa3",  "CA-SF1",  "CN-Din",  "DE-Kli",  "DK-Sor",  "FI-Sod",  "ID-Pag",  "IT-Isp",  "IT-Ro2",  "PT-Mi2",  "US-AR2",  "US-Goo",  "US-Myb",  "US-SRG",  "US-Wkg",
+    "AU-Dry",  "AU-Stp",  "BW-Ma1",  "CA-SF2",  "CN-Du2",  "DE-Meh",  "DK-ZaH",  "FR-Fon",  "IE-Ca1",  "IT-Lav",  "IT-SR2",  "RU-Che",  "US-ARM",  "US-Ha1",  "US-Ne1",  "US-SRM",  "ZA-Kru"
+ ) {
+   &make_env_run( PLUMBER2SITE=>"$site" );
+   #
+   # Concatonate  default usermods and specific sitetogether expanding env variables while doing that
+   #
+   if ( ! -d "$plumdir/$site" ) {
+      print "PLUMBER2 directory is not there: $plumdir/$site\n";
+      die "ERROR:: PLUMBER2 site does not exist: $site\n";
+   }
+   my $plumdefaultfile = "$plumdir/defaults/user_nl_clm";
+   my $plumsitefile = "$plumdir/$site/user_nl_clm";
+   if ( ! -f $plumsitefile )  {
+      $plumsitefile = undef;
+   }
+   $ENV{'PLUMBER2'} = $site;
+   my $namelistfile = "temp.namelistinfile_$site";
+   &cat_and_create_namelistinfile( $plumdefaultfile, $plumsitefile, $namelistfile );
+   #
    # Now run  the site
    #
-   my $options = "--res CLM_USRDAT --clm_usr_name NEON --no-megan --bgc bgc --use_case 2018_control --infile $namelistfile";
+   my $options = "--res CLM_USRDAT --clm_usr_name PLUMBER2 --no-megan --bgc sp --infile $namelistfile";
    eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };
    is( $@, '', "options: $options" );
    $cfiles->checkfilesexist( "$options", $mode );

diff --git a/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm
@@ -6,6 +6,6 @@ hillslope_transmissivity_method = 'LayerSum'
 hillslope_pft_distribution_method = 'PftLowlandUpland'
 hillslope_soil_profile_method = 'Uniform'
 
-fsurdat = '$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_2000_78pfts_c240216.synthetic_hillslopes.nc'
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_10x15_hist_2000_78pfts_c240905.synthetic_hillslopes3.nc'
 
 use_ssre = .false.
diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm
@@ -18,9 +18,6 @@
 ! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
 !----------------------------------------------------------------------------------
 
-flanduse_timeseries = ' '   ! This isn't needed for a non transient case, but will be once we start using transient compsets
-fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/NEON/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_2000_16pfts_c240206.nc"
-
 ! h1 output stream 
 hist_fincl2 = 'FATES_AUTORESP','FCEV','FCTR','FGEV','FIRA','FSA','FSH','FATES_GPP','FATES_GPP_PF','H2OSOI',
              'SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FATES_NPP','FATES_NPP_PF','FATES_VEGC','FATES_VEGC_PF'

diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm
@@ -18,9 +18,6 @@
 ! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
 !----------------------------------------------------------------------------------
 
-flanduse_timeseries = ' '   ! This isn't needed for a non transient case, but will be once we start using transient compsets
-fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_2000_78pfts_c240206.nc"
-
 ! h1 output stream 
 hist_fincl2 = 'AR','ELAI','FCEV','FCTR','FGEV','FIRA','FSA','FSH','GPP','H2OSOI',
              'HR','SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FV','NET_NMIN_vr'

diff --git a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm b/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm
@@ -19,6 +19,6 @@
 !----------------------------------------------------------------------------------
 
 flanduse_timeseries = ' '   ! This isn't needed for a non transient case, but will be once we start using transient compsets
-fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/surfdata_1x1_PLUMBER2_${PLUMBER2SITE}_hist_2000_16pfts_c240326.nc"
+fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/PLUMBER2/ctsm5.3.0/surfdata_1x1_PLUMBER2_${PLUMBER2SITE}_hist_2000_16pfts_c240908.nc"
 
 ! custom namelist changes for each site / case
diff --git a/tools/mksurfdata_esmf/README.md b/tools/mksurfdata_esmf/README.md
@@ -179,6 +179,10 @@ for example try --res 1.9x2.5 --start-year 1850 --end-year 1850:
  make all-subset
 ```
 
+ As of 2024/9/12 one needs to generate NEON and PLUMBER2 fsurdat files by
+ running ./neon_surf_wrapper and ./plumber2_surf_wrapper manually in the
+ /tools/site_and_regional directory.
+
 <!-- = -->
 ## NOTES
 <!-- = -->

diff --git a/tools/mksurfdata_esmf/src/mksoiltexMod.F90 b/tools/mksurfdata_esmf/src/mksoiltexMod.F90
@@ -13,13 +13,15 @@ module mksoiltexMod
   use mkutilsMod       , only : chkerr
   use mkdiagnosticsMod , only : output_diagnostics_index
   use mkfileMod        , only : mkfile_output  
-  use mkvarctl         , only : root_task, ndiag, spval
+  use mkvarctl         , only : root_task, ndiag, spval, mpicom
   use mkvarctl         , only : unsetsoil
   use mkvarpar         , only : nlevsoi
 
   implicit none
   private ! By default make data private
 
+#include <mpif.h>
+
   public :: mksoiltex      ! Set soil texture
 
   integer                :: mapunit_value_max
@@ -61,6 +63,7 @@ subroutine mksoiltex(file_mesh_i, file_mapunit_i, file_lookup_i, mesh_o, pioid_o
     integer                :: k,l,m,n
     integer                :: nlay          ! number of soil layers
     integer                :: n_scid
+    integer                :: mapunit_value_max_local
     integer , allocatable  :: mask_i(:)
     real(r4), pointer      :: dataptr(:)
     integer                :: mapunit       ! temporary igbp soil mapunit
@@ -165,6 +168,8 @@ subroutine mksoiltex(file_mesh_i, file_mapunit_i, file_lookup_i, mesh_o, pioid_o
     do ni = 1,ns_i
        if (mapunit_i(ni) == 0.) then
           mask_i(ni) = 0
+       else
+          mask_i(ni) = 1
        end if
     end do
     call ESMF_MeshSet(mesh_i, elementMask=mask_i, rc=rc)
@@ -200,7 +205,12 @@ subroutine mksoiltex(file_mesh_i, file_mapunit_i, file_lookup_i, mesh_o, pioid_o
 
     ! Determine mapunit_value_max (set it as a module variable so that it can be
     ! accessible to gen_dominant_mapunit) - this is needed in the dynamic mask routine
-    mapunit_value_max = maxval(dataptr)
+    !
+    ! Note that dataptr (obtained from the input field) contains just a subset of the
+    ! source data, based on the source data decomposition. So we need an mpi_allreduce to
+    ! determine the global maximum value of mapunit.
+    mapunit_value_max_local = maxval(dataptr)
+    call mpi_allreduce(mapunit_value_max_local, mapunit_value_max, 1, MPI_INTEGER, MPI_MAX, mpicom, rcode)
 
     ! Determine values in field_o
     call ESMF_FieldGet(field_o, farrayptr=dataptr, rc=rc)