Merge pull request #937 from brian-eaton/misc01

cam6_3_142: Miscellaneous tag

bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml

@@ -95,7 +95,7 @@
 	 'OMEGA_24_COS', 'OMEGA_24_SIN', 'OMEGA_12_COS', 'OMEGA_12_SIN', 'OMEGA_08_COS', 'OMEGA_08_SIN'
 </fincl5>
 <!-- Average every day -->
-<fincl7>
+<fincl7 dyn="fv">
          'MSKtem', 'PS', 'PSL', 'VTHzm', 'UVzm', 'UWzm', 'Uzm', 'Vzm', 'THzm','Wzm', 'PHIS'
 </fincl7>
 

cime_config/buildnml

@@ -61,12 +61,14 @@ def buildnml(case, caseroot, compname):
     # call buildcpp to set both cppdefs and config_cache.xml file for generating namelist
     #--------------------------------------------------------------------
     call_buildcpp = False
-    if not os.path.exists(os.path.join(caseroot,"LockedFiles","env_build.xml")):
+    camconf = os.path.join(caseroot, "Buildconf", "camconf")
+    filename = os.path.join(camconf, "config_cache.xml")
+    if not os.path.isfile(filename):
         call_buildcpp = True
     else:
         file1 = os.path.join(caseroot,"env_build.xml")
         file2 = os.path.join(caseroot,"LockedFiles","env_build.xml")
-        if not filecmp.cmp(file1, file2):
+        if os.path.isfile(file2) and not filecmp.cmp(file1, file2):
             call_buildcpp = True
     if call_buildcpp:
         cmd = os.path.join(os.path.join(srcroot,"cime_config","buildcpp"))
@@ -78,8 +80,6 @@ def buildnml(case, caseroot, compname):
             raise
 
     # Verify that we have a config_cache file (generated by the call to buildcpp)
-    camconf = os.path.join(caseroot, "Buildconf", "camconf")
-    filename = os.path.join(camconf, "config_cache.xml")
     expect(os.path.isfile(filename),
            " Missing config_cache.xml - cannot run build-namelist")
 

cime_config/config_tests.xml

@@ -23,6 +23,7 @@ TMC   CAM mass conservation test
     <STOP_N>9</STOP_N>
     <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
     <HIST_N>$STOP_N</HIST_N>
+    <ALLOW_SINGLE_EXE>TRUE</ALLOW_SINGLE_EXE>
   </test>
 
   <test NAME="SUB">

cime_config/testdefs/testmods_dirs/cam/outfrq1d_physgrid_tem_mpasa120_wcmsc/shell_commands

@@ -1,2 +1 @@
 ./xmlchange ROF_NCPL=\$ATM_NCPL
-./xmlchange LND_DOMAIN_FILE="domain.lnd.mpasa120_gx1v7.201215.nc"

cime_config/testdefs/testmods_dirs/cam/outfrq1d_physgrid_tem_mpasa120_wcmsc/user_nl_clm

@@ -1,4 +1,3 @@
 hist_nhtfrq = -24
 hist_mfilt  = 1
 hist_ndens  = 1
-fsurdat = '${DIN_LOC_ROOT}/lnd/clm2/surfdata_map/release-clm5.0.34/surfdata_mpasa120_hist_78pfts_CMIP6_simyr2000_c201215.nc'

cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa120/shell_commands

@@ -1,3 +1,2 @@
 ./xmlchange ROF_NCPL=\$ATM_NCPL
 ./xmlchange GLC_NCPL=\$ATM_NCPL
-./xmlchange LND_DOMAIN_FILE="domain.lnd.mpasa120_gx1v7.201215.nc"

cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa120/user_nl_clm

@@ -1,4 +1,3 @@
 hist_nhtfrq = 9
 hist_mfilt  = 1
 hist_ndens  = 1
-fsurdat = '${DIN_LOC_ROOT}/lnd/clm2/surfdata_map/release-clm5.0.34/surfdata_mpasa120_hist_78pfts_CMIP6_simyr2000_c201215.nc'

cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa480/shell_commands

@@ -1,3 +1,2 @@
 ./xmlchange ROF_NCPL=\$ATM_NCPL
 ./xmlchange GLC_NCPL=\$ATM_NCPL
-./xmlchange LND_DOMAIN_FILE="domain.lnd.mpasa480_gx1v7.201001.nc"

cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa480/user_nl_clm

@@ -1,4 +1,3 @@
 hist_nhtfrq = 9
 hist_mfilt  = 1
 hist_ndens  = 1
-fsurdat = '${DIN_LOC_ROOT}/lnd/clm2/surfdata_map/surfdata_mpasa480_hist_78pfts_CMIP6_simyr2000_c201001.nc'

doc/ChangeLog

@@ -1,5 +1,131 @@
 ===============================================================
 
+Tag name: cam6_3_142
+Originator(s): jedwards, ekluzek, goldy, bstephens82, eaton
+Date: 13 December 2023
+One-line Summary: Resolve miscellaneous issues
+Github PR URL: https://github.com/ESCOMP/CAM/pull/937
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+
+. https://github.com/ESCOMP/CAM/issues/863 - Incorrect error message
+  - remove the code in cam_history that was checking fincl input for the
+    names of zonal mean fields and writing a message to the atm log file if
+    the dycore was not FV.  These messages are now incorrect and have been
+    removed. 
+
+. https://github.com/ESCOMP/CAM/issues/837 - Remove setting of CTSM fsurdat
+  file and LND_DOMAIN_FILE in mpas testmods 
+  - The LND_DOMAIN_FILE is no longer needed.  The fsurdat file is now
+    appropriately set by CTSM.
+
+. https://github.com/ESCOMP/CAM/pull/792 - changes to fix single-exe option
+  for PLB tests
+  - Fix from jedwards
+
+. https://github.com/ESCOMP/CAM/issues/931 - Bad outfld calls in
+  cam_development?
+  - Fix several bad outfld calls.  The size of the 1st dimension of the
+    passed data did not match the size passed as a separate argument.
+
+. https://github.com/ESCOMP/CAM/pull/855 - Bug fix for SILHS history output
+  being garbled.
+  - Fix from bstephens82.
+
+. resolves #863
+. resolves #837
+. resolves #792
+. resolves #931
+. resolves #855
+
+
+Describe any changes made to build system: none
+
+Describe any changes made to the namelist: none
+
+List any changes to the defaults for the boundary datasets: none for cam, but
+. The fsurdat file has changed for mpasa grids.
+
+Describe any substantial timing or memory changes: none
+
+Code reviewed by: cacraigucar, nusbaume
+
+List all files eliminated: none
+
+List all files added and what they do: none
+
+List all existing files that have been modified, and describe the changes:
+
+bld/namelist_files/use_cases/waccmx_ma_2000_cam6.xml
+. add dyn="fv" attribute to fincl7 element so that zonal mean output is only
+  requested for the FV dycore.
+
+cime_config/buildnml
+cime_config/config_tests.xml
+. fix single-exe option for PLB tests (from Jim Edwards)
+
+cime_config/testdefs/testmods_dirs/cam/outfrq1d_physgrid_tem_mpasa120_wcmsc/shell_commands
+cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa120/shell_commands
+cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa480/shell_commands
+. remove xmlchange for LND_DOMAIN_FILE.
+
+cime_config/testdefs/testmods_dirs/cam/outfrq1d_physgrid_tem_mpasa120_wcmsc/user_nl_clm
+cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa120/user_nl_clm
+cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa480/user_nl_clm
+. remove setting for fsurdat
+
+src/control/cam_history.F90
+. subroutine fldlst
+  - remove code that inspects the fincl lists for the zonal mean fields
+    that used to only be available when using FV dycore.  This code removed
+    these fields from the fincl list and printed a message to the atm log
+    file.  These messages are no longer correct and have been removed.
+. subroutine addfld_nd
+  - fix conditional so that is_subcol gets set correctly for fields
+    representing subcolumns.
+
+src/physics/cam/cam_diagnostics.F90
+src/physics/cam/vertical_diffusion.F90
+src/physics/rrtmg/rrtmg_state.F90
+src/physics/spcam/spcam_drivers.F90
+src/physics/waccm/mo_aurora.F90
+. fix several outfld calls - make sure 1st dimension of the data array matches
+  the value passed as the size of the 1st dimension
+
+If there were any failures reported from running test_driver.sh on any test
+platform, and checkin with these failures has been OK'd by the gatekeeper,
+then copy the lines from the td.*.status files for the failed tests to the
+appropriate machine below.  All failed tests must be justified.
+
+derecho/intel/aux_cam:
+  ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.derecho_intel.cam-outfrq9s_mg3 (Overall: PEND) details:
+  ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+- pre-existing failures
+
+  ERS_Ln9_P288x1_Vnuopc.mpasa120_mpasa120.F2000climo.derecho_intel.cam-outfrq9s_mpasa120 (Overall: DIFF) details:
+  ERS_Ln9_P36x1_Vnuopc.mpasa480_mpasa480.F2000climo.derecho_intel.cam-outfrq9s_mpasa480 (Overall: DIFF) details:
+- fsurdat file changed resulting in baseline comparison failures
+
+  SMS_D_Ln9_Vnuopc.ne16_ne16_mg17.FX2000.derecho_intel.cam-outfrq9s (Overall: NLFAIL) details:
+- use_case file modified to exclude the fincl7 list of zonal mean fields.
+  Previous code was ignoring these fields and printing a message to the
+  atm.log file.
+
+izumi/nag/aux_cam:
+  DAE_Vnuopc.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL) details:
+- pre-existing failure
+
+izumi/gnu/aux_cam: All PASS
+
+CAM tag used for the baseline comparison tests if different than previous
+tag:
+
+Summarize any changes to answers: BFB except for MPAS tests due to a change
+in the fsurdat file specified by CTSM.
+
+===============================================================
+===============================================================
+
 Tag name: cam6_3_141
 Originator(s): eaton
 Date: 8 December 2023

src/control/cam_history.F90

@@ -2584,16 +2584,6 @@ subroutine fldlst ()
     !    on that grid.
     integer, allocatable        :: gridsontape(:,:)
 
-    ! The following list of field names are only valid for the FV dycore.  They appear
-    ! in fincl settings of WACCM use case files which are not restricted to the FV dycore.
-    ! To avoid duplicating long fincl lists in use case files to provide both FV and non-FV
-    ! versions this short list of fields is checked for and removed from fincl lists when
-    ! the dycore is not FV.
-    integer, parameter :: n_fv_only = 10
-    character(len=6) :: fv_only_flds(n_fv_only) = &
-       [ 'VTHzm ', 'WTHzm ', 'UVzm  ', 'UWzm  ', 'Uzm   ', 'Vzm   ', 'Wzm   ', &
-         'THzm  ', 'TH    ', 'MSKtem' ]
-
     integer :: n_vec_comp, add_fincl_idx
     integer, parameter :: nvecmax = 50 ! max number of vector components in a fincl list
     character(len=2) :: avg_suffix
@@ -2610,25 +2600,9 @@ subroutine fldlst ()
       n_vec_comp       = 0
       vec_comp_names   = ' '
       vec_comp_avgflag = ' '
-fincls: do while (fld < pflds .and. fincl(fld,t) /= ' ')
+      do while (fld < pflds .and. fincl(fld,t) /= ' ')
         name = getname (fincl(fld,t))
 
-        if (.not. dycore_is('FV')) then
-           ! filter out fields only provided by FV dycore
-           do i = 1, n_fv_only
-              if (name == fv_only_flds(i)) then
-                 write(errormsg,'(3a,2(i0,a))')'FLDLST: ', trim(name), &
-                    ' in fincl(', fld,', ',t, ') only available with FV dycore'
-                 if (masterproc) then
-                    write(iulog,*) trim(errormsg)
-                    call shr_sys_flush(iulog)
-                 end if
-                 fld = fld + 1
-                 cycle fincls
-              end if
-           end do
-        end if
-
         mastername=''
         listentry => get_entry_by_name(masterlinkedlist, name)
         if (associated(listentry)) mastername = listentry%field%name
@@ -2656,7 +2630,7 @@ subroutine fldlst ()
            end if
         end if
         fld = fld + 1
-      end do fincls
+      end do
 
       ! Interpolation of vector components requires that both be present.  If the fincl
       ! specifier contains any vector components, then the complement was saved in the
@@ -6121,8 +6095,8 @@ subroutine addfld_nd(fname, dimnames, avgflag, units, long_name,            &
           write(errormsg, *) "Cannot add ", trim(fname),                      &
                "Subcolumn history output only allowed on physgrid"
           call endrun("ADDFLD: "//errormsg)
-          listentry%field%is_subcol = .true.
         end if
+        listentry%field%is_subcol = .true.
       end if
     end if
     ! Levels

src/physics/cam/cam_diagnostics.F90

@@ -1407,7 +1407,7 @@ subroutine diag_phys_writeout_moist(state, pbuf, p_surf_t)
     do k=2,pver
       ftem(:ncol,1) = ftem(:ncol,1) + ftem(:ncol,k)
     end do
-    call outfld ('ATMEINT   ',ftem(:ncol,1)  ,pcols   ,lchnk     )
+    call outfld ('ATMEINT   ', ftem(:ncol,1), ncol, lchnk)
 
     !! Boundary layer atmospheric stability, temperature, water vapor diagnostics
 

src/physics/cam/vertical_diffusion.F90

@@ -1108,9 +1108,9 @@ subroutine vertical_diffusion_tend( &
      call outfld( 'slv_pre_PBL  ', slv_prePBL,                pcols, lchnk )
      call outfld( 'u_pre_PBL    ', state%u,                   pcols, lchnk )
      call outfld( 'v_pre_PBL    ', state%v,                   pcols, lchnk )
-     call outfld( 'qv_pre_PBL   ', state%q(:ncol,:,1),        pcols, lchnk )
-     call outfld( 'ql_pre_PBL   ', state%q(:ncol,:,ixcldliq), pcols, lchnk )
-     call outfld( 'qi_pre_PBL   ', state%q(:ncol,:,ixcldice), pcols, lchnk )
+     call outfld( 'qv_pre_PBL   ', state%q(:,:,1),            pcols, lchnk )
+     call outfld( 'ql_pre_PBL   ', state%q(:,:,ixcldliq),     pcols, lchnk )
+     call outfld( 'qi_pre_PBL   ', state%q(:,:,ixcldice),     pcols, lchnk )
      call outfld( 't_pre_PBL    ', state%t,                   pcols, lchnk )
      call outfld( 'rh_pre_PBL   ', ftem_prePBL,               pcols, lchnk )
 
@@ -1472,11 +1472,11 @@ subroutine vertical_diffusion_tend( &
      call outfld( 'vflx_cg_PBL'  , vflx_cg,                   pcols, lchnk )
      call outfld( 'slten_PBL'    , slten,                     pcols, lchnk )
      call outfld( 'qtten_PBL'    , qtten,                     pcols, lchnk )
-     call outfld( 'uten_PBL'     , ptend%u(:ncol,:),          pcols, lchnk )
-     call outfld( 'vten_PBL'     , ptend%v(:ncol,:),          pcols, lchnk )
-     call outfld( 'qvten_PBL'    , ptend%q(:ncol,:,1),        pcols, lchnk )
-     call outfld( 'qlten_PBL'    , ptend%q(:ncol,:,ixcldliq), pcols, lchnk )
-     call outfld( 'qiten_PBL'    , ptend%q(:ncol,:,ixcldice), pcols, lchnk )
+     call outfld( 'uten_PBL'     , ptend%u,                   pcols, lchnk )
+     call outfld( 'vten_PBL'     , ptend%v,                   pcols, lchnk )
+     call outfld( 'qvten_PBL'    , ptend%q(:,:,1),            pcols, lchnk )
+     call outfld( 'qlten_PBL'    , ptend%q(:,:,ixcldliq),     pcols, lchnk )
+     call outfld( 'qiten_PBL'    , ptend%q(:,:,ixcldice),     pcols, lchnk )
      call outfld( 'tten_PBL'     , tten,                      pcols, lchnk )
      call outfld( 'rhten_PBL'    , rhten,                     pcols, lchnk )
 

src/physics/rrtmg/rrtmg_state.F90

@@ -233,7 +233,7 @@ subroutine rrtmg_state_update(pstate,pbuf,icall,rstate)
       chi_eff(:) = chi_eff(:) / 2.1415e-5_r8             ! O3 column above in DU
     endwhere
 
-    call outfld('O3colAbove', chi_eff(:ncol), pcols, lchnk)
+    call outfld('O3colAbove', chi_eff(:ncol), ncol, lchnk)
 
   end subroutine rrtmg_state_update
 

src/physics/spcam/spcam_drivers.F90

@@ -2053,7 +2053,7 @@ subroutine spcam_radiation_finalize_sam1mom(cam_in, state, pbuf, rad_avgdata, ca
     call outfld('FSN200  ',rad_avgdata%fsn200_m(:),pcols,lchnk)
     call outfld('FSN200C ',rad_avgdata%fsn200c_m(:),pcols,lchnk)
     call outfld('FSNR'    ,rad_avgdata%fsnr_m(:)  ,pcols,lchnk)
-    call outfld('SWCF    ',rad_avgdata%fsntoa_m(:ncol)-rad_avgdata%fsntoac_m(:ncol)  ,pcols,lchnk)
+    call outfld('SWCF    ',rad_avgdata%fsntoa_m(:ncol)-rad_avgdata%fsntoac_m(:ncol)  ,ncol,lchnk)
 
     do i=1, Nday
        do k=1, pver

src/physics/waccm/mo_aurora.F90

@@ -476,8 +476,8 @@ subroutine aurora_prod( tn, o2, o1, mbar, rlats, &
 !-----------------------------------------------------------------------
 ! 	... output mag lons, lats
 !-----------------------------------------------------------------------
-      call outfld( 'ALONM', r2d*alonm(:ncol,lchnk), pcols, lchnk )
-      call outfld( 'ALATM', r2d*alatm(:ncol,lchnk), pcols, lchnk )
+      call outfld( 'ALONM', r2d*alonm(:ncol,lchnk), ncol, lchnk )
+      call outfld( 'ALATM', r2d*alatm(:ncol,lchnk), ncol, lchnk )
 
       if (indxQTe>0) then
         call pbuf_get_field(pbuf, indxQTe, qteaur)