Merge b4b-dev (2024-10-10)

bld/unit_testers/build-namelist_test.pl

@@ -1287,6 +1287,13 @@ sub cat_and_create_namelistinfile {
                );
 foreach my $key ( keys(%failtest) ) {
    print( "$key\n" );
+   my $var;
+   foreach $var ( "phys" , "options", "namelst" ) {
+      if ( not exists $failtest{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for failtest $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    &make_config_cache($failtest{$key}{"phys"});
    my $options  = $failtest{$key}{"options"};
    my $namelist = $failtest{$key}{"namelst"};
@@ -1366,6 +1373,14 @@ sub cat_and_create_namelistinfile {
                );
 foreach my $key ( keys(%warntest) ) {
    print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "options", "namelst" ) {
+      if ( not exists $warntest{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for warntest $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    &make_config_cache($warntest{$key}{"phys"});
    my $options  = $warntest{$key}{"options"};
    my $namelist = $warntest{$key}{"namelst"};
@@ -1595,6 +1610,14 @@ sub cat_and_create_namelistinfile {
 
 foreach my $key ( keys(%finidat_files) ) {
    print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "atm_forc", "res", "bgc", "crop", "use_case", "start_ymd", "namelist" ) {
+      if ( not exists $finidat_files{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for finidat_file $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
    my $phys = $finidat_files{$key}{'phys'};
    print "physics = $phys\n";
    &make_config_cache($phys);

cime_config/config_component.xml

@@ -16,7 +16,7 @@
     <desc lnd="CLM45[%SP][%SP-VIC][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP]"                  >clm4.5:</desc>
     <desc lnd="CLM50[%SP][%SP-VIC][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm5.0:</desc>
     <desc lnd="CLM51[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%NWP-SP][%NWP-BGC-CROP]">clm5.1:</desc>
-    <desc lnd="CLM60[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
+    <desc lnd="CLM60[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
     <desc option="SP"              >Satellite phenology:</desc>
 
     <desc option="SP-VIC"          >Satellite phenology with VIC hydrology:</desc>
@@ -371,6 +371,10 @@
       <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
       <value                  compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
       <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
+      <value                  compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
+      <value                  compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
     </values>
     <group>run_component_ctsm</group>
     <file>env_case.xml</file>

cime_config/config_compsets.xml

@@ -200,13 +200,21 @@
     <alias>I1850Clm50BgcCropCmip6</alias>
     <lname>1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
   </compset>
+  <compset>
+    <alias>I1850Clm60BgcCropCmip6</alias>
+    <lname>1850_DATM%GSWP3v1_CLM60%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+  </compset>
 
   <!-- Primarily for testing the CMIP6WACCMDECK compset option -->
   <!-- Use the CMIP6 version (clm5_0) -->
   <compset>
     <alias>I1850Clm50BgcCropCmip6waccm</alias>
     <lname>1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
   </compset>
+  <compset>
+    <alias>I1850Clm60BgcCropCmip6waccm</alias>
+    <lname>1850_DATM%GSWP3v1_CLM60%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+  </compset>
 
   <!-- clm5_0 (CMIP6) version with BGC-Crop and CRU forcing -->
   <compset>

cime_config/testdefs/testlist_clm.xml

@@ -1732,7 +1732,7 @@
       <option name="comment"       >Repeat ERS_Ly20_Mmpi-serial...cropMonthlyNoinitial test with matrixcnOn</option>
     </options>
   </test>
-  <test name="ERS_Ly3" grid="f10_f10_mg37" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic">
+  <test name="ERS_Ly3" grid="f10_f10_mg37" compset="I1850Clm60BgcCropCmip6" testmods="clm/basic">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1987,7 +1987,7 @@
       <option name="comment"  >Simple test to make sure the basic Fates-SP compset works"</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
+  <test name="SMS_D_Ld1" grid="ne30pg3_t232" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
@@ -1996,7 +1996,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1" grid="ne30pg3_t061" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
+  <test name="SMS_D_Ld1" grid="ne30pg3_t232" compset="I1850Clm50BgcSpinup" testmods="clm/cplhist--clm/matrixcnOn">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
@@ -2431,7 +2431,7 @@
       <option name="comment"  >include a production intel test of Clm45</option>
     </options>
   </test>
-  <test name="SMS_Ld2_D_PS" grid="f09_g17" compset="I1850Clm50BgcCropCmip6" testmods="clm/basic_interp">
+  <test name="SMS_Ld2_D_PS" grid="f09_g17" compset="I1850Clm60BgcCropCmip6" testmods="clm/basic_interp">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -3262,7 +3262,7 @@
       <option name="comment">12 month exact restart FATES single site debug test covering anthropogenic fire ignition mode.</option>
     </options>
   </test>
-  <test name="SMS_Lm1" grid="f10_f10_mg37" compset="I1850Clm50BgcCropCmip6waccm" testmods="clm/basic">
+  <test name="SMS_Lm1" grid="f10_f10_mg37" compset="I1850Clm60BgcCropCmip6waccm" testmods="clm/basic">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
       <machine name="derecho" compiler="gnu" category="prealpha"/>

doc/ChangeLog

@@ -1,4 +1,72 @@
 ===============================================================
+Tag name: ctsm5.3.006
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, [email protected])
+Date: Fri Oct 11 07:01:09 MDT 2024
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+- Fix clm-basic tests (resolves ESCOMP/CTSM#2787)
+- Change testlist_clm ne30pg3_t061 tests to ne30pg3_t232 (resolves ESCOMP/CTSM#2702)
+- Remove unused variable elevclass_o in mkglcmecMod.F90 (resolves ESCOMP/CTSM#2802)
+- Add a check in failtest, warntest, finidat_files, so when a new test or finidat file are added and one of the subkeys is misspelled you will get an error and tester will die (resolves ESCOMP/CTSM#2673)
+- Move from deprecated shr_file to shr_log
+- Set eflx_building_lun to spval properly (resolves ESCOMP/CTSM#2793)
+
+
+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:
+- ESCOMP/CTSM#2787 (aux_clm "clm-basic" tests fail as of ctsm5.3.0 because they need c13 in finidat; https://github.com/ESCOMP/CTSM/issues/2787)
+- ESCOMP/CTSM#2702 (Tests failing in ctsm5.2.019 for CESM alpha testing; https://github.com/ESCOMP/CTSM/issues/2702)
+- ESCOMP/CTSM#2802 (Array elevclass_o in mksurfdata_esmf/src/mkglcmecMod.F90 is not allocated before use; https://github.com/ESCOMP/CTSM/issues/2802)
+- ESCOMP/CTSM#2673 (Catch use of namelist attribute in failure testing in perl build-namelist tester; https://github.com/ESCOMP/CTSM/issues/2673)
+- ESCOMP/CTSM#2793 (Potential typo/bug in EnergyFluxType.F90; https://github.com/ESCOMP/CTSM/issues/2793)
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Other details
+-------------
+
+Pull Requests that document the changes:
+- ESCOMP/CTSM#2798: Fix clm-basic tests (https://github.com/ESCOMP/CTSM/pull/2798)
+- ESCOMP/CTSM#2799: Change testlist_clm ne30pg3_t061 tests to ne30pg3_t232 (https://github.com/ESCOMP/CTSM/pull/2799)
+- ESCOMP/CTSM#2804: Remove unused variable elevclass_o in mkglcmecMod.F90 (https://github.com/ESCOMP/CTSM/pull/2804)
+- ESCOMP/CTSM#2678: Add check in build-namelist_test.pl (https://github.com/ESCOMP/CTSM/pull/2678)
+- ESCOMP/CTSM#2627: move from depricated shr_file to shr_log (https://github.com/ESCOMP/CTSM/pull/2627)
+- ESCOMP/CTSM#2806: Set eflx_building_lun to spval properly (https://github.com/ESCOMP/CTSM/pull/2806)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.005
 Originator(s): dmleung (Danny Leung)
 Date: Thu 10 Oct 2024 03:15:52 AM MDT
@@ -91,7 +159,7 @@ Pull Requests that document the changes (include PR ids):
 ===============================================================
 ===============================================================
 Tag name: ctsm5.3.004
-Originator(s): samrabin (Sam Rabin)
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, [email protected])
 Date: Mon Oct  7 21:25:20 MDT 2024
 One-line Summary: Move hillslope data off surface datasets
 

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.006 samrabin 10/11/2024 Merge b4b-dev
        ctsm5.3.005     erik 10/10/2024 Hardcoded tuning adjustments for Leung_2024 dust emissions
        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

src/biogeophys/EnergyFluxType.F90

@@ -579,7 +579,7 @@ subroutine InitHistory(this, bounds, is_simple_buildtemp, is_prog_buildtemp)
             avgflag='A', long_name='urban heating flux', &
             ptr_col=this%eflx_urban_heat_col, set_nourb=0._r8, c2l_scale_type='urbanf')
     else
-       this%eflx_urban_ac_lun(begl:endl) = spval
+       this%eflx_building_lun(begl:endl) = spval
        call hist_addfld1d (fname='EFLXBUILD', units='W/m^2',  &
             avgflag='A', long_name='building heat flux from change in interior building air temperature', &
             ptr_lunit=this%eflx_building_lun, set_nourb=0._r8, l2g_scale_type='unity')

src/cpl/nuopc/lnd_comp_nuopc.F90

@@ -29,7 +29,7 @@ module lnd_comp_nuopc
   use NUOPC_Model            , only : NUOPC_ModelGet
   use shr_kind_mod           , only : r8 => shr_kind_r8, cl=>shr_kind_cl
   use shr_sys_mod            , only : shr_sys_abort
-  use shr_file_mod           , only : shr_file_getlogunit, shr_file_setlogunit
+  use shr_log_mod            , only : shr_log_setLogUnit, shr_log_getLogUnit
   use shr_orb_mod            , only : shr_orb_decl, shr_orb_params, SHR_ORB_UNDEF_REAL, SHR_ORB_UNDEF_INT
   use shr_cal_mod            , only : shr_cal_noleap, shr_cal_gregorian, shr_cal_ymd2date
   use spmdMod                , only : masterproc, mpicom, spmd_init
@@ -66,7 +66,7 @@ module lnd_comp_nuopc
   private :: clm_orbital_init    ! Initialize the orbital information
   private :: clm_orbital_update  ! Update the orbital information
   private :: CheckImport
-  
+
   !--------------------------------------------------------------------------
   ! Private module data
   !--------------------------------------------------------------------------
@@ -333,8 +333,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
     !----------------------------------------------------------------------------
     ! reset shr logging to original values
     !----------------------------------------------------------------------------
-
-    call shr_file_setLogUnit (shrlogunit)
+    call shr_log_setLogUnit(shrlogunit)
     call ESMF_LogWrite(subname//' done', ESMF_LOGMSG_INFO)
 
   end subroutine InitializeAdvertise
@@ -497,8 +496,8 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
     ! Reset shr logging to my log file
     !----------------------------------------------------------------------------
 
-    call shr_file_getLogUnit (shrlogunit)
-    call shr_file_setLogUnit (iulog)
+    call shr_log_getLogUnit (shrlogunit)
+    call shr_log_setLogUnit (iulog)
 #if (defined _MEMTRACE)
     if (masterproc) then
        lbnum=1
@@ -683,7 +682,7 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
     endif
 
-    call shr_file_setLogUnit (shrlogunit)
+    call shr_log_setLogUnit (shrlogunit)
 
 #if (defined _MEMTRACE)
     if(masterproc) then
@@ -774,8 +773,8 @@ subroutine ModelAdvance(gcomp, rc)
     ! Reset share log units
     !--------------------------------
 
-    call shr_file_getLogUnit (shrlogunit)
-    call shr_file_setLogUnit (iulog)
+    call shr_log_getLogUnit (shrlogunit)
+    call shr_log_setLogUnit (iulog)
 
 #if (defined _MEMTRACE)
     if(masterproc) then
@@ -864,7 +863,7 @@ subroutine ModelAdvance(gcomp, rc)
        rstwr = .false.
        if (nlend .and. write_restart_at_endofrun) then
           rstwr = .true.
-       else 
+       else
           call ESMF_ClockGetAlarm(clock, alarmname='alarm_restart', alarm=alarm, rc=rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
           if (ESMF_AlarmIsCreated(alarm, rc=rc)) then
@@ -964,7 +963,7 @@ subroutine ModelAdvance(gcomp, rc)
     ! Reset shr logging to my original values
     !--------------------------------
 
-    call shr_file_setLogUnit (shrlogunit)
+    call shr_log_setLogUnit (shrlogunit)
 
     call ESMF_LogWrite(subname//' done', ESMF_LOGMSG_INFO)
 
@@ -1289,14 +1288,14 @@ subroutine CheckImport(gcomp, rc)
     type(ESMF_GridComp) :: gcomp
     integer, intent(out) :: rc
     character(len=*) , parameter :: subname = "("//__FILE__//":CheckImport)"
-    
+
     ! This is the routine that enforces the explicit time dependence on the
     ! import fields. This simply means that the timestamps on the Fields in the
-    ! importState are checked against the currentTime on the Component's 
+    ! importState are checked against the currentTime on the Component's
     ! internalClock. Consequenty, this model starts out with forcing fields
-    ! at the current time as it does its forward step from currentTime to 
+    ! at the current time as it does its forward step from currentTime to
     ! currentTime + timeStep.
-    
+
     ! local variables
     type(ESMF_Clock)              :: clock
     type(ESMF_Time)               :: time
@@ -1320,19 +1319,19 @@ subroutine CheckImport(gcomp, rc)
     ! query the component for info
     call NUOPC_CompGet(gcomp, name=name, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
-    
+
     ! query the Component for its clock and importState
     call ESMF_GridCompGet(gcomp, clock=clock, importState=importState, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
 
     ! get the current time out of the clock
     call ESMF_ClockGet(clock, currTime=time, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
-    
+
     ! check that Fields in the importState show correct timestamp
     allCurrent = NUOPC_IsAtTime(importState, time, fieldList=fieldList, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
-      
+
     if (.not.allCurrent) then
       !TODO: introduce and use INCOMPATIBILITY return codes!!!!
       do i=1, size(fieldList)
@@ -1354,6 +1353,6 @@ subroutine CheckImport(gcomp, rc)
         rcToReturn=rc)
       return  ! bail out
     endif
-    
+
   end subroutine CheckImport
 end module lnd_comp_nuopc

tools/mksurfdata_esmf/src/mkglcmecMod.F90

@@ -49,7 +49,6 @@ subroutine mkglcmecInit( pioid_o )
     ! local variables:
     type(var_desc_t)      :: pio_varid
     type(io_desc_t)       :: pio_iodesc
-    real(r8), allocatable :: elevclass_o(:)          ! elevation classes
     integer               :: rcode
     character(len=*), parameter :: subname = 'mkglcmecInit'
     !-----------------------------------------------------------------------
@@ -100,8 +99,6 @@ subroutine mkglcmecInit( pioid_o )
        call shr_sys_abort()
     end if
 
-    elevclass_o(:) = elevclass(:)
-
     if (root_task)  write(ndiag, '(a)') trim(subname)//" writing out GLC_MEC"
     rcode = pio_inq_varid(pioid_o, 'GLC_MEC', pio_varid)
     rcode = pio_put_var(pioid_o, pio_varid, elevclass)