Merge tag 'ctsm5.3.004' into dustemis_tune4cesm3

Move hillslope data off surface datasets

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.78.2_api.36.0.0
+fxtag = sci.1.78.3_api.36.1.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release

bld/CLMBuildNamelist.pm

@@ -2759,8 +2759,7 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
 
   # this check has to be here and not earlier since use_init_interp is set here and hillslope is already set above in setup_logic_hillslope
   if ( &value_is_true($nl->get_value($useinitvar)) && value_is_true($nl->get_value("use_hillslope")) ) {
-     $log->warning("WARNING: You have set use_hillslope while $useinitvar is TRUE.\n This means all hillslope columns in a gridcell will read identical values" .
-                   " from initial conditions. If you are sure you want this behaviour:")
+     $log->warning("WARNING: You have set use_hillslope while $useinitvar is TRUE.\n This means all hillslope columns in a gridcell will read identical values from initial conditions, even if the initial conditions (finidat) file has hillslope information. If you are sure you want this behaviour, add -ignore_warnings to CLM_BLDNML_OPTS.")
   }
 
 } # end initial conditions
@@ -3637,6 +3636,10 @@ sub setup_logic_hillslope {
   if ( (! &value_is_true($use_hillslope)) && &value_is_true($use_hillslope_routing) ) {
       $log->fatal_error("Cannot turn on use_hillslope_routing when use_hillslope is off\n" );
   }
+  my $hillslope_file = $nl->get_value('hillslope_file');
+  if ( &value_is_true($use_hillslope) && ( ! defined($hillslope_file) ) ) {
+    $log->fatal_error("You must provide hillslope_file if use_hillslope is .true.\n" );
+  }
 }
 
 #-------------------------------------------------------------------------------

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -560,7 +560,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.0.0_12pft_c240517.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.1.0_14pft_c241003.nc</fates_paramfile>
+
 
 <!-- ================================================================== -->
 <!-- Default surface roughness parameterization                         -->

bld/namelist_files/namelist_definition_ctsm.xml

@@ -962,6 +962,11 @@ Full pathname datafile with fates parameters
 Full pathname of surface data file.
 </entry>
 
+<entry id="hillslope_file" type="char*256"     category="datasets"
+       input_pathname="abs" group="clm_inparm" valid_values="" >
+Full pathname of hillslope data file.
+</entry>
+
 <entry id="fsnowoptics" type="char*256" category="datasets" 
        input_pathname="abs" group="clm_inparm" valid_values="" >
 SNICAR (SNow, ICe, and Aerosol Radiative model) optical data file name

cime_config/testdefs/ExpectedTestFails.xml

@@ -245,13 +245,6 @@
     </phase>
   </test>
 
-  <test name="SMS_D_Ld5.5x5_amazon.I1850Clm51Bgc.derecho_gnu.clm-HillslopeC">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#2423</issue>
-    </phase>
-  </test>
-
   <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdTwoStream">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
@@ -280,6 +273,13 @@
     </phase>
   </test>
 
+  <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdLandUse">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2810</issue>
+    </phase>
+  </test>
+
   <!-- Other submodule test list failures (MOSART, RTM, etc. -->
 
   <test name="SMS_Lh3.f10_f10_mg37.I2000Clm51Sp.derecho_intel.mosart-clmAccelSpinupIgnoreWarn">

cime_config/testdefs/testlist_clm.xml

@@ -1773,7 +1773,7 @@
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">01:40:00</option>
+      <option name="wallclock">02:30:00</option>
       <option name="comment"  >Repeat ERS_Ly5_P128x1...cropMonthOutput test with matrixcnOn</option>
     </options>
   </test>
@@ -3511,23 +3511,24 @@
     </options>
   </test>
 
-  <test name="SMS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I1850Clm60Bgc" testmods="clm/HillslopeC">
+  <test name="SMS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I2000Clm60Bgc" testmods="clm/HillslopeC">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="hillslope"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
+      <option name="comment">Serial test of 5x5_amazon hillslopes</option>
     </options>
   </test>
 
-  <test name="SMS_D_Ld5" grid="5x5_amazon" compset="I1850Clm60Bgc" testmods="clm/HillslopeC">
+  <test name="SMS_D_Ld5" grid="5x5_amazon" compset="I2000Clm60Bgc" testmods="clm/HillslopeC">
     <machines>
-      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="hillslope"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment">Add a non-FATES test to aux_clm for 5x5_amazon that fails because of the ccs_config issue, can remove once this passes</option>
+      <option name="comment">Parallel test of 5x5_amazon hillslopes</option>
     </options>
   </test>
 

cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands

@@ -0,0 +1,8 @@
+SRCDIR=`./xmlquery SRCROOT --value`
+CASEDIR=`./xmlquery CASEROOT --value`
+FATESDIR=$SRCDIR/src/fates
+FATESPARAMFILE=$CASEDIR/fates_params_hydrograsstempfix.nc
+
+ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
+
+$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_allom_smode --val 1 --allpfts

cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm

@@ -2,6 +2,7 @@ hist_mfilt        = 365
 hist_nhtfrq       = -24
 hist_empty_htapes = .true.
 use_fates_planthydro= .true.
+fates_paramfile = '$CASEROOT/fates_params_hydrograsstempfix.nc'
 hist_fincl1       = 'FATES_ERRH2O_SZPF', 'FATES_TRAN_SZPF',
 'FATES_SAPFLOW_SZPF', 'FATES_ITERH1_SZPF','FATES_ABSROOT_H2O_SZPF',
 'FATES_TRANSROOT_H2O_SZPF','FATES_STEM_H2O_SZPF','FATES_LEAF_H2O_SZPF',

cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/shell_commands

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-./xmlchange CLM_BLDNML_OPTS="-i-clm_demand -flanduse_timeseries" --append
+./xmlchange CLM_BLDNML_OPTS="-clm_demand flanduse_timeseries" --append

cime_config/testdefs/testmods_dirs/clm/Hillslope/shell_commands

@@ -1,7 +1,19 @@
 ./xmlchange CLM_BLDNML_OPTS="-bgc sp"
 DIN_LOC_ROOT=$(./xmlquery --value DIN_LOC_ROOT)
-meshfile=$DIN_LOC_ROOT/lnd/clm2/testdata/ESMFmesh_10x15_synthetic_cosphill_1.0.nc
-./xmlchange ATM_DOMAIN_MESH=${meshfile},LND_DOMAIN_MESH=${meshfile}
+
+# Set hillslope_file. Needed for any grids without default hillslope_file already set by CTSM.
+lnd_grid=$(./xmlquery --value LND_GRID)
+if [[ ${lnd_grid} == "10x15" ]]; then
+    # Synthetic data
+    hillslope_file='$DIN_LOC_ROOT/lnd/clm2/testdata/surfdata_10x15_hist_1850_78pfts_c240216.synth_hillslopes_241001.nc'
+elif [[ ${lnd_grid} == "5x5_amazon" ]]; then
+    # Real data
+    hillslope_file='/glade/derecho/scratch/samrabin/hillslopes_5x5_amazon/hand_analysis_global/combined/hilldata_5x5_amazon_hist_2000_78pfts_c240216.nc'
+else
+    echo "ERROR: Hillslope file not found for LND_GRID=${lnd_grid}" >&2
+    exit 1
+fi
+echo -e "hillslope_file = '${hillslope_file}'\n" >> user_nl_clm
 
 # -ignore_warnings is needed as long as we don't allow use_hillslope and use_init_interp together
 ./xmlchange --append CLM_BLDNML_OPTS=-ignore_warnings

cime_config/testdefs/testmods_dirs/clm/Hillslope/user_nl_clm

@@ -6,6 +6,4 @@ hillslope_transmissivity_method = 'LayerSum'
 hillslope_pft_distribution_method = 'PftLowlandUpland'
 hillslope_soil_profile_method = 'Uniform'
 
-fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_10x15_hist_2000_78pfts_c240905.synthetic_hillslopes3.nc'
-
 use_ssre = .false.

doc/ChangeLog

@@ -1,4 +1,144 @@
 ===============================================================
+Tag name: ctsm5.3.004
+Originator(s): samrabin (Sam Rabin)
+Date: Mon Oct  7 21:25:20 MDT 2024
+One-line Summary: Move hillslope data off surface datasets
+
+Purpose and description of changes
+----------------------------------
+
+Moves hillslope data off surface datasets onto its own separate hillslope_file. This makes it so we don't need to generate new surface datasets specifically for hillslope testing whenever the surface datasets are updated.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Not in real runs, only our testing.
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2434 (https://github.com/ESCOMP/CTSM/pull/2434)
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.003
+Originator(s): rgknox (Ryan Knox, LBNL, [email protected])
+               glemieux (Gregory Lemieux, LBNL, [email protected])
+Date: Mon Oct 07 10:33:14 AM MDT 2024
+One-line Summary: FATES default parameter file update
+
+Purpose and description of changes
+----------------------------------
+
+This tag updates the default parameter file for FATES bringing in a number of updates:
+   - adds two new arctic shrub pfts
+   - updates the default sapwood allometry mode for grass pfts
+   - updates understory leaf turnover specifications for longer turnover rates
+   - changes the default behavior of nutrient uptake
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+   Fixes #2783 -- Error in FatescoldLandUse testmod
+   Fixes FATES#1211 -- Switching the default fates_cnp_prescribed_* parameters from 1 to 0
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+   FatesColdLandUse build has been added to the list of expected failures due to #2810
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline:
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: FATES mode
+    - what platforms/compilers: ALL
+    - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+   fates: sci.1.78.2_api.36.0.0 -> sci.1.78.3_api.36.1.0
+
+Pull Requests that document the changes (include PR ids):
+   https://github.com/ESCOMP/CTSM/pull/2700
+   https://github.com/NGEET/fates/pull/1255
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.002
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Thu 26 Sep 2024 03:10:40 PM MDT
+One-line Summary: Duplicate tag of ctsm5.3.001
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.001
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Thu 26 Sep 2024 03:10:40 PM MDT

doc/ChangeSum

@@ -1,5 +1,8 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.004 samrabin 10/07/2024 Move hillslope data off surface datasets
+       ctsm5.3.003 multiple 10/07/2024 FATES default parameter file update
+       ctsm5.3.002 multiple 09/26/2024 Duplicate tag (same as 5.3.001)
        ctsm5.3.001 multiple 09/26/2024 Merge b4b-dev
          ctsm5.3.0 multiple 09/24/2024 Update surface datasets, CN Matrix, CLM60: excess ice on, explicit A/C on, crop calendars, Sturm snow, Leung dust emissions, prigent roughness data
        ctsm5.2.029 multiple 09/24/2024 New surface datasets: double tag of ctsm5.3.0