Merge pull request #4 from rgknox/fates-drdt-decid-updates

updates for smp_sl

Externals.cfg

@@ -55,7 +55,7 @@ local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.12
+tag = cdeps1.0.13
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps

Externals_CLM.cfg

@@ -1,8 +1,8 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/NGEET/fates
-tag = sci.1.66.0_api.25.5.0
+repo_url = https://github.com/rgknox/fates
+branch = mpaiao-pr-drgt-decid
 required = True
 
 [externals_description]

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -493,7 +493,7 @@ 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.25.5.0_12pft_c230519.nc</fates_paramfile>
+<fates_paramfile>/glade/u/home/rgknox/ctsm/src/fates/parameter_files/fates_params_api.25.5.0_12pft_c230626.nc</fates_paramfile>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->

cime_config/testdefs/ExpectedTestFails.xml

@@ -44,13 +44,6 @@
     </phase>
   </test>
 
-  <test name="SMS_D_Ld1_PS.f09_g17.I1850Clm50BgcSpinup.cheyenne_intel.clm-cplhist">
-    <phase name="RUN">
-      <status>FAIL</status>
-      <issue>#1844</issue>
-    </phase>
-  </test>
-
   <!-- fates test suite failures -->
 
   <test name="ERS_Lm12.1x1_brazil.I2000Clm50FatesCruRsGs.cheyenne_intel.clm-FatesFireLightningPopDens">

cime_config/testdefs/testlist_clm.xml

@@ -1315,7 +1315,7 @@
       <option name="comment"  >Simple test to make sure the basic Fates-SP compset works"</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1_PS" grid="f09_g17" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
+  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="cheyenne" compiler="intel" category="prealpha"/>
@@ -1324,15 +1324,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_Vmct_D_Ld1_PS" grid="f09_g17" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >Spinup test with MCT driver</option>
-    </options>
-  </test>
   <test name="SMS_D_Ld1_PS" grid="f19_f19_mg17" compset="I2010Clm50Sp" testmods="clm/clm50cam6LndTuningMode">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>

cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm

@@ -2,6 +2,7 @@
 hist_mfilt        = 365
 hist_nhtfrq       = -24
 hist_empty_htapes = .true.
+hist_ndens = 1
 fates_spitfire_mode = 1
 hist_fincl1       = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
 'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_GDD',

cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm

@@ -3,6 +3,7 @@ hist_mfilt        = 365
 hist_nhtfrq       = -24
 hist_empty_htapes = .false.
 fates_spitfire_mode = 1
+hist_ndens = 1
 hist_fincl1       = 'FATES_CROWNAREA_PF', 'FATES_CANOPYCROWNAREA_PF',
 'FATES_NCL_AP', 'FATES_NPATCH_AP', 'FATES_VEGC_AP',
 'FATES_SECONDARY_FOREST_FRACTION', 'FATES_WOOD_PRODUCT',

cime_config/testdefs/testmods_dirs/clm/cplhist/shell_commands

@@ -1,12 +1,8 @@
-driver=`./xmlquery --value COMP_INTERFACE`
-if [ "$driver" = "nuopc" ]; then
-   ./xmlchange DATM_YR_ALIGN=1
-   ./xmlchange DATM_YR_END=84
-   ./xmlchange DATM_YR_START=82
-else
-   ./xmlchange DATM_CPLHIST_YR_ALIGN=1
-   ./xmlchange DATM_CPLHIST_YR_END=84
-   ./xmlchange DATM_CPLHIST_YR_START=82
-fi
-./xmlchange DATM_CPLHIST_CASE=b.e20.B1850.f09_g17.pi_control.all.221.cplhist
-./xmlchange DATM_CPLHIST_DIR=/glade/p/cesm/bgcwg_dev/forcing/b.e20.B1850.f09_g17.pi_control.all.221.cplhist/cpl/hist.mon
+./xmlchange DATM_CPLHIST_CASE=cam6ctsm51_cesm23a12c_ne30pg3g17_CPLHIST_1850
+./xmlchange DATM_CPLHIST_DIR=/glade/p/cgd/tss/CTSM_datm_forcing_data/atm_forcing.cdeps_datm.CPLHIST_cam6ctsm51_cesm23a12c_ne30pg3g17_1850
+./xmlchange DATM_YR_START=1
+./xmlchange DATM_YR_END=1
+./xmlchange DATM_YR_ALIGN=1
+
+# Needed until we have cplhist forcing with ndep - see https://github.com/escomp/ctsm/issues/1844
+./xmlchange DATM_PRESNDEP=none

cime_config/usermods_dirs/fates_sp/user_nl_clm

@@ -6,6 +6,7 @@ use_lch4 = .false.
 fates_spitfire_mode = 0
 use_fates_fixed_biogeog = .true.
 use_fates_nocomp = .true.
+hist_ndens = 1
 ! Turn off a list of fields that are not needed for FATES-SP mode
 hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS',
               'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', 'FATES_DAYSINCE_COLDLEAFON',

doc/ChangeLog

@@ -1,4 +1,198 @@
 ===============================================================
+Tag name: ctsm5.1.dev128
+Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049)
+Date: Thu Jun  1 15:31:52 MDT 2023
+One-line Summary: Update FATES tests to double precision
+
+Purpose and description of changes
+----------------------------------
+
+This pull request updates the fates tests to set the output
+precision to double precision.  The usermod fates_sp is similarly
+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.)
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+
+CTSM issues fixed (include CTSM Issue #):
+- Resolves https://github.com/ESCOMP/CTSM/issues/1986
+
+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):
+
+    cheyenne ---- OK
+    izumi ------- OK
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    cheyenne ---- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+  FATES tests run against fates-sci.1.65.6_api.25.4.0-ctsm5.1.dev127 baseline
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes, but only for fates tests and compsets
+
+  Summarize any changes to answers, i.e.,
+    - Differences are due to changing hist_ndens to 1 (double precision)
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+https://github.com/ESCOMP/CTSM/pull/2010
+
+===============================================================
+===============================================================
+Tag name: ctsm5.1.dev127
+Originator(s): sacks (Bill Sacks)
+Date: Fri May 19 04:48:30 MDT 2023
+One-line Summary: Fix nuopc cplhist test
+
+Purpose and description of changes
+----------------------------------
+
+Make some changes to the cplhist testmod that fix the cplhist test,
+based on testing done by Keith Oleson:
+- Point to new cplhist forcing data generated and used by Adam
+  Herrington and Keith Oleson
+- Use DATM_PRESNDEP=none until
+  https://github.com/escomp/ctsm/issues/1844 is resolved
+
+Also, remove mct cplhist test.
+
+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.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+CTSM issues fixed (include CTSM Issue #):
+- Takes steps towards addressing ESCOMP/CTSM#1844 (Create new auxiliary
+  history file for cplhist test with ndep data)
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+- Changes cplhist test; new test is
+  SMS_D_Ld1.ne30pg3_t061.I1850Clm50BgcSpinup.cheyenne_intel.clm-cplhist
+- Removes mct cplhist test
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- PASS
+    izumi ------- PASS
+
+    Note that there were no baselines for the new test
+    (SMS_D_Ld1.ne30pg3_t061.I1850Clm50BgcSpinup.cheyenne_intel.clm-cplhist)
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+Other details
+-------------
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+- cdeps: cdeps1.0.12 -> cdeps1.0.13
+
+Pull Requests that document the changes (include PR ids):
+https://github.com/ESCOMP/CTSM/pull/1999
+
+===============================================================
+===============================================================
+Tag name: ctsm5.1.dev126
+Originator(s): jpalex (John Alex)
+Date: Thu May 18 17:21:59 MDT 2023
+One-line Summary: Clean up some loops in UrbanTimeVarType
+
+Purpose and description of changes
+----------------------------------
+
+Refactor some inefficient and confusing looping structures in
+UrbanTimeVarType.F90
+
+
+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.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+CTSM issues fixed (include CTSM Issue #):
+- Resolves ESCOMP/CTSM#1514 (Inefficient and confusing looping structures in UrbanTimeVarType.F90)
+
+Testing summary:
+----------------
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- PASS
+    izumi ------- PASS
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+https://github.com/ESCOMP/CTSM/pull/2005
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev125
 Originator(s): jpalex (John Alex)
 Date: Wed May 17 08:56:41 MDT 2023

doc/ChangeSum

@@ -1,5 +1,8 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev128 glemieux 06/01/2023 Update FATES tests to double precision
+    ctsm5.1.dev127    sacks 05/19/2023 Fix nuopc cplhist test
+    ctsm5.1.dev126   jpalex 05/18/2023 Clean up some loops in UrbanTimeVarType
     ctsm5.1.dev125   jpalex 05/17/2023 Added cache for clock step_size in clm_time_manager.F90
     ctsm5.1.dev124     erik 05/09/2023 Initialization memory update, new surface datasets for new grids, add option for running NEON with PRISM data
     ctsm5.1.dev123    sacks 05/01/2023 Updates needed for pFUnit 4 and other externals updates

src/cpl/share_esmf/UrbanTimeVarType.F90

@@ -252,16 +252,13 @@ subroutine urbantv_interp(this, bounds)
     ! Determine this%tbuilding_max for all landunits
     do l = bounds%begl,bounds%endl
        if (lun%urbpoi(l)) then
-          ig = 0
-          do g = bounds%begg,bounds%endg
-             ig = ig+1
-             if (g == lun%gridcell(l)) exit
-          end do
-          do n = isturb_MIN,isturb_MAX
-             if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then
-                this%t_building_max(l) = dataptr2d(ig,n)
-             end if
-          end do
+          ! Note that since l is within [begl, endl] bounds, we can assume
+          ! lun%gricell(l) is within [begg, endg]
+          ig = lun%gridcell(l) - bounds%begg + 1
+
+          ! Since we are within an urban land unit, we know that
+          ! lun%itype is within [pisturb_MIN, isturb_MAX]
+          this%t_building_max(l) = dataptr2d(ig, lun%itype(l))
        else
           this%t_building_max(l) = spval
        end if
@@ -272,9 +269,7 @@ subroutine urbantv_interp(this, bounds)
     found = .false.
     do l = bounds%begl,bounds%endl
        if (lun%urbpoi(l)) then
-          ig = 0
           do g = bounds%begg,bounds%endg
-             ig = ig+1
              if (g == lun%gridcell(l)) exit
           end do
           if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then

src/main/clm_driver.F90

@@ -1151,7 +1151,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
                   atm2lnd_inst, soilstate_inst, temperature_inst, active_layer_inst, &
                   water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, &
                   water_inst%wateratm2lndbulk_inst, canopystate_inst, soilbiogeochem_carbonflux_inst, &
-                  frictionvel_inst)
+                  frictionvel_inst, soil_water_retention_curve)
 
              ! TODO(wjs, 2016-04-01) I think this setFilters call should be replaced by a
              ! call to reweight_wrapup, if it's needed at all.