merge in master

adrifoster · Sep 17, 2024 · 228cbda · 228cbda
2 parents 10241e7 + b4199d8
commit 228cbda
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diff --git a/.gitmodules b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.77.2_api.36.0.0
+fxtag = sci.1.78.2_api.36.0.0
 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

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -1998,6 +1998,7 @@
   <test name="SMS" grid="f45_f45_mg37" compset="I2000Clm60FatesSpRsGs" testmods="clm/FatesColdSatPhen">
     <machines>
       <machine name="derecho" compiler="nvhpc" category="aux_clm"/>
+      <machine name="derecho" compiler="nvhpc" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -3169,7 +3170,7 @@
   <test name="SMS_D" grid="1x1_brazil" compset="I2000Clm60FatesSpCruRsGs" testmods="clm/FatesColdSatPhen">
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="gnu" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>

diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
@@ -26,7 +26,4 @@ hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_NEP', 'FATES_HET_RESP', 'FATES_FIRE_CLOSS', 'FATES_FIRE_FLUX_EL',
 'FATES_CBALANCE_ERROR', 'FATES_ERROR_EL', 'FATES_LEAF_ALLOC',
 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
-'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC',
-'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU'
-
-! fates_paramfile = '/glade/work/afoster/CTSM/src/fates/parameter_files/fates_param_fuel.nc'
+'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm
@@ -26,7 +26,7 @@ hist_fincl1       = 'FATES_TLONGTERM',
 'FATES_MORTALITY_CROWNSCORCH_SZPF','FATES_MORTALITY_CAMBIALBURN_SZPF','FATES_MORTALITY_TERMINATION_SZPF',
 'FATES_MORTALITY_LOGGING_SZPF','FATES_MORTALITY_FREEZING_SZPF','FATES_MORTALITY_SENESCENCE_SZPF',
 'FATES_MORTALITY_AGESCEN_SZPF','FATES_MORTALITY_AGESCEN_ACPF','FATES_MORTALITY_CANOPY_SZPF',
-'FATES_M3_MORTALITY_CANOPY_SZPF','FATES_M3_MORTALITY_USTORY_SZPF','FATES_C13DISC_SZPF',
+'FATES_M3_MORTALITY_CANOPY_SZPF','FATES_M3_MORTALITY_USTORY_SZPF',
 'FATES_STOREC_CANOPY_SZPF','FATES_LEAFC_CANOPY_SZPF','FATES_LAI_CANOPY_SZPF','FATES_CROWNAREA_CANOPY_SZPF',
 'FATES_CROWNAREA_USTORY_SZPF','FATES_NPLANT_CANOPY_SZPF','FATES_MORTALITY_USTORY_SZPF','FATES_STOREC_USTORY_SZPF',
 'FATES_LEAFC_USTORY_SZPF','FATES_LAI_USTORY_SZPF','FATES_NPLANT_USTORY_SZPF','FATES_CWD_ABOVEGROUND_DC',

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm
@@ -7,3 +7,5 @@ use_fates_nocomp = .true.
 use_fates_fixed_biogeog = .true.
 use_fates_sp = .false.
 use_fates_potentialveg = .false.
+hist_fincl1 = 'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU',
+'FATES_TRANSITION_MATRIX_LULU'
diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,83 @@
 ===============================================================
+Tag name: ctsm5.2.028
+Originator(s): rgknox (Ryan Knox, LBNL, [email protected])
+               glemieux (Gregory Lemieux, LBNL, [email protected])
+Date: Thu 05 Sep 2024 02:47:14 PM MDT
+One-line Summary: FATES history flushing update
+
+Purpose and description of changes
+----------------------------------
+
+This updates the way in which FATES history output is flushed during model initialization
+utilizing a new FATES-side subroutine, flush_all_hvars.  This update also makes corrections
+to a subset of FATES testmods as well as expands the FATES test list by duplicating two
+existing tests to run on different compilers for better coverage.  The FATES submodule tag
+has been updated to the latest scientific tag as well.
+
+
+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 #2657 Add FATES_TRANSITIONS_MATRIX_LULU to FatesColdLUH2 testmods
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+
+Adds nvhpc and gnu FatesSatColdPhen smoke tests to the fates list to expand compiler
+coverage.
+
+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: Yes, for FATES tests only
+
+Changes are consistent with differences in FATES_EFFECT_WSPEED due to NGEET/fates#1215
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+
+   FATES: sci.1.77.2_api.36.0.0 -> sci.1.78.2_api.36.0.0
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2594
+
+===============================================================
+===============================================================
 Tag name: ctsm5.2.027
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Wed 28 Aug 2024 09:13:22 PM MDT

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.2.028   rgknox 09/05/2024 FATES history flushing update
        ctsm5.2.027     erik 08/28/2024 Merge b4b-dev
        ctsm5.2.026   slevis 08/23/2024 Turn on excess ice, explicit AC, Leung_2023 for clm6
        ctsm5.2.025 samrabin 08/23/2024 Minor fixes to li2024 fire methods

diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
@@ -137,7 +137,6 @@ module CLMFatesInterfaceMod
    use FatesParametersInterface, only : fates_parameters_type
 
    use FatesInterfaceMod     , only : DetermineGridCellNeighbors
-   use FatesIOVariableKindMod, only : group_dyna_simple, group_dyna_complx
    use FatesHistoryInterfaceMod, only : fates_hist
    use FatesRestartInterfaceMod, only : fates_restart_interface_type
 
@@ -1241,14 +1240,6 @@ subroutine dynamics_driv(this, nc, bounds_clump,      &
          call this%WrapUpdateFatesSeedInOut(bounds_clump)
       end if
 
-      ! ---------------------------------------------------------------------------------
-      ! Flush arrays to values defined by %flushval (see registry entry in
-      ! subroutine define_history_vars()
-      ! ---------------------------------------------------------------------------------
-      call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_simple)
-
-      call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_complx)
-
       ! ---------------------------------------------------------------------------------
       ! Part II: Call the FATES model now that input boundary conditions have been
       ! provided.
@@ -2019,23 +2010,16 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, &
                                                                 this%fates(nc)%sites, &
                                                                 this%fates(nc)%bc_out)
 
+
                ! ------------------------------------------------------------------------
-               ! Update history IO fields that depend on ecosystem dynamics
+               ! Flush FATES history variables.
+               ! The flushing process sets all columns outside of FATES perview to
+               ! the ignore value. This only needs to be done once, because FATES will
+               ! not overwright values outside the columns that it is in charge of.
                ! ------------------------------------------------------------------------
-               if(fates_history_dimlevel(2)>0) then
-                  call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_simple)
-                  do s = 1,this%fates(nc)%nsites
-                     call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), &
-                          upfreq_in=group_dyna_simple)
-                  end do
-                  if(fates_history_dimlevel(2)>1) then
-                     call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_complx)
-                     do s = 1,this%fates(nc)%nsites
-                        call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), &
-                             upfreq_in=group_dyna_complx)
-                     end do
-                  end if
-               end if
+
+               call fates_hist%flush_all_hvars(nc)    
+
                call fates_hist%update_history_dyn( nc,                     &
                                                    this%fates(nc)%nsites,  &
                                                    this%fates(nc)%sites,   &
@@ -2220,22 +2204,15 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, &
                 soilbiogeochem_carbonflux_inst, .false.)
 
            ! ------------------------------------------------------------------------
-           ! Update history IO fields that depend on ecosystem dynamics
+           ! Flush and zero FATES history variables.
+           ! The flushing process sets all columns outside of FATES perview to
+           ! the ignore value. This only needs to be done once, because FATES will
+           ! not overwright values outside the columns that it is in charge of.
+           ! We also start off by setting all values on FATES columns to zero.
            ! ------------------------------------------------------------------------
-           if(fates_history_dimlevel(2)>0) then
-              call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_simple)
-              do s = 1,this%fates(nc)%nsites
-                 call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), &
-                      upfreq_in=group_dyna_simple)
-              end do
-              if(fates_history_dimlevel(2)>1) then
-                 call fates_hist%flush_hvars(nc,upfreq_in=group_dyna_complx)
-                 do s = 1,this%fates(nc)%nsites
-                    call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), &
-                         upfreq_in=group_dyna_complx)
-                 end do
-              end if
-           end if
+
+           call fates_hist%flush_all_hvars(nc)
+
            call fates_hist%update_history_dyn( nc,                     &
                 this%fates(nc)%nsites,                                  &
                 this%fates(nc)%sites,                                   &
@@ -3626,9 +3603,6 @@ subroutine wrap_hydraulics_drive(this, bounds_clump, nc, &
             this%fates(nc)%bc_out(s)%plant_stored_h2o_si
    end do
 
-
-   ! Update History Buffers that need to be updated after hydraulics calls
-
    call fates_hist%update_history_hydraulics(nc, &
          this%fates(nc)%nsites, &
          this%fates(nc)%sites, &