Merge pull request #1309 from mvertens/mvertens/scolpr

New single column functionality for NUOPC/CMEPS

Externals.cfg

@@ -37,21 +37,21 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = branch_tags/cime5.8.37_a02
+tag = cime5.8.39
 required = True
 
 [cmeps]
 local_path = cime/src/drivers/nuopc/
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
-hash = c4acaa8
+tag = v0.5.0
 required = True
 
 [cdeps]
 local_path = components/cdeps
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
-hash = 1f02a73
+tag = v0.5.0
 required = True
 
 [doc-builder]
@@ -63,4 +63,3 @@ required = False
 
 [externals_description]
 schema_version = 1.0.0
-

bld/namelist_files/namelist_definition_ctsm.xml

@@ -2003,7 +2003,7 @@ CLM datasets exist for years: 1000 (for testing), 1850, and 2000
 
 <entry id="sim_year_range" type="char*9" category="default_settings"
        group="default_settings" valid_values=
-"constant,1000-1002,1000-1004,850-1850,1850-1855,1850-2000,1850-2005,1850-2100,1980-2015,2000-2100">
+"constant,1000-1002,1000-1004,850-1850,1850-1855,1850-2000,1850-2005,1850-2100,1980-2015,2000-2025,2000-2100">
 Range of years to simulate transitory datasets for (such as dynamic: land-use datasets, aerosol-deposition, Nitrogen deposition rates etc.)
 Constant means simulation will be held at a constant year given in sim_year.
 A sim_year_range of 1000-1002 or 1000-1004 corresponds to data used for testing only, NOT corresponding to any real datasets.

cime_config/testdefs/ExpectedTestFails.xml

@@ -30,13 +30,62 @@
 
   <!-- aux_clm test suite failures -->
 
-  <test name="ERS_Ln9.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.IHistClm50SpGs.cheyenne_intel.clm-clm50cam6LndTuningMode_1979Start">
+  <test name="ERS_Ln12.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.IHistClm50SpGs.cheyenne_intel.clm-clm50cam6LndTuningMode_1979Start">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
       <issue>#1117</issue>
     </phase>
   </test>
 
+  <test name="DAE_N2_D_Lh12_Vnuopc.f10_f10_mg37.I2000Clm50BgcCrop.cheyenne_intel.clm-DA_multidrv">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>ESCOMP/CMEPS#175</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_D_Lm1_Mmpi-serial_Vnuopc.CLM_USRDAT.I1PtClm50SpRs.cheyenne_intel.clm-USUMB">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>ESMCI/cime#3905</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_D_Lm1_Mmpi-serial.CLM_USRDAT.I1PtClm50SpRs.cheyenne_intel.clm-USUMB">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>ESMCI/cime#3905</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_Ld5_D_P48x1_Vnuopc.f10_f10_mg37.IHistClm51Bgc.izumi_nag.clm-decStart">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1317</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_P48x1_D_Ld5_Vnuopc.f10_f10_mg37.I2000Clm50Cn.izumi_nag.clm-default">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1317</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_Vnuopc.f10_f10_mg37.I2000Clm50BgcCrop.izumi_pgi.clm-crop">
+    <phase name="BUILD">
+      <status>FAIL</status>
+      <issue>ESMCI/cime#3496</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_D_Vnuopc.f10_f10_mg37.I2000Clm51BgcCrop.izumi_pgi.clm-crop">
+    <phase name="BUILD">
+      <status>FAIL</status>
+      <issue>ESMCI/cime#3496</issue>
+    </phase>
+  </test>
+
   <!-- fates test suite failures -->
 
   <test name="ERS_Ld60.f45_f45_mg37.I2000Clm45Fates.hobart_nag.clm-Fates">

cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode/shell_commands

@@ -1,4 +1,5 @@
 #!/bin/bash
 
 ./xmlchange LND_TUNING_MODE="clm5_0_cam6.0"
+./xmlchange ROF_NCPL='$ATM_NCPL'
 

cime_config/testdefs/testmods_dirs/clm/pts/shell_commands

@@ -22,3 +22,5 @@
 ./xmlchange NTASKS_ROF=1
 ./xmlchange NTASKS_WAV=1
 ./xmlchange NTASKS_ESP=1
+./xmlchange MOSART_MODE=NULL
+./xmlchange RTM_MODE=NULL

cime_config/testdefs/testmods_dirs/clm/waccmx_offline/shell_commands

@@ -1,4 +1,5 @@
 ./xmlchange USE_ESMF_LIB=TRUE,ATM_NCPL=288,CALENDAR=GREGORIAN,ROF_NCPL='$ATM_NCPL',LND_TUNING_MODE="clm5_0_cam6.0"
 ./xmlchange CLM_BLDNML_OPTS="-megan -drydep" --append
 ./xmlchange RUN_STARTDATE=1979-01-01
+./xmlchange ROF_NCPL='$ATM_NCPL'
 

doc/ChangeLog

@@ -1,4 +1,121 @@
 ===============================================================
+Tag name:  ctsm5.1.dev030
+Originator(s):  mvertens / erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Wed Mar 31 16:46:04 MDT 2021
+One-line Summary: New single column functionality for the NUOPC cap
+
+Purpose and description of changes
+----------------------------------
+
+Implemented new nuopc/cmeps single column functionality.
+
+In config/cesm/config_files.xml - single point domains are only used 
+for mct/cpl7. For cmeps single point meshes are now generated on the 
+fly and component domains files are no longer needed.
+env_run.xml variables PTS_LAT, PTS_LON and PTS_DOMAINFILE are used 
+to determine if there is a single point or single column run.
+If PTS_LAT and PTS_LON are not -999 and PTS_DOMAINFILE is UNSET, 
+then you have a single point run and the exact values of PTS_LAT
+and PTS_LON are used.  If PTS_LAT and PTS_LON are not -999 and 
+PTS_DOMAINFILE is not UNSET, then then the cmeps driver will recognize the nearest neighbor
+values of PTS_LAT and PTS_LON in PTS_DOMAINFILE as the single column lat and lon to use.
+
+
+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
+------------------------
+
+Issues fixed (include CTSM Issue #):
+   Fixes #1312 -- Add NUOPC tests
+   Fixes #1302 -- Setup to allow landuse.timeseries file for high resolution cases for 2000-2025
+   Fixes #1183 -- mkmapdata needs input option for large file support, current defaults unsuitable for high res grids.
+
+Known bugs introduced in this tag (include issue #):
+
+Known bugs found since the previous tag (include issue #):
+   #1317 -- MPI timeout for some izumi_nag tests reading in datm forcing files in NUOPC cap 
+   #1314 -- Send unset value for scol_lat/lon from driver
+
+Notes of particular relevance for users
+---------------------------------------
+
+Notes of particular relevance for developers:
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+  Nine step tests changed so that they have ROF run at same frequency as ATM (like the similar CAM tests)
+  as these will fail with NUOPC since it doesn't allow you to end not on an even time-step for all components.
+  One of these tests changed to a CAM type test from decStart
+
+Changes to tests or testing: Add more NUOPC tests to test list
+
+
+Testing summary: regular
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    cheyenne - PASS
+
+  tools-tests (test/tools) (if tools have been changed):
+
+    cheyenne - OK
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    cheyenne -- FAIL
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- OK
+    izumi ------- OK
+
+  any other testing (give details below): Ran full izumi test list for nuopc driver (failed tests appear above)
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No
+   (List of fields change though)
+
+
+Other details
+-------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, CDEPS, CMEPS
+   cime  to cime5.8.39
+   CDEPS to v0.5.0
+   CMEPS to v0.5.0
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+   #1309 -- New single column functionality for NUOPC/CMEPS
+   #1310 -- run_sys_tests: add --retry option on izumi 
+
+===============================================================
+===============================================================
 Tag name:  ctsm5.1.dev029
 Originator(s):  mvertens (Mariana Vertenstein), sacks (Bill Sacks)
 Date:  Thu Mar 18 21:21:21 MDT 2021

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm5.1.dev030     erik 03/31/2021 New single column functionality for the NUOPC cap
   ctsm5.1.dev029 mvertens 03/18/2021 Rework domain initialization for nuopc
   ctsm5.1.dev028 swensosc 03/17/2021 Change limitation of top layer evaporation/sublimation
   ctsm5.1.dev027    sacks 03/15/2021 Update cime and other externals; includes switch to pio2

src/biogeochem/SatellitePhenologyMod.F90

@@ -17,7 +17,6 @@ module SatellitePhenologyMod
   use shr_log_mod     , only : errMsg => shr_log_errMsg
   use decompMod       , only : bounds_type
   use abortutils      , only : endrun
-  use clm_varctl      , only : scmlat,scmlon,single_column
   use clm_varctl      , only : iulog, use_lai_streams, inst_name
   use clm_varcon      , only : grlnd
   use controlMod      , only : NLFilename
@@ -501,7 +500,6 @@ subroutine readAnnualVegetation (bounds, canopystate_inst)
     use domainMod   , only : ldomain
     use fileutils   , only : getfil
     use clm_varctl  , only : fsurdat
-    use shr_scam_mod, only : shr_scam_getCloseLatLon
     !
     ! !ARGUMENTS:
     type(bounds_type), intent(in) :: bounds
@@ -511,7 +509,6 @@ subroutine readAnnualVegetation (bounds, canopystate_inst)
     type(file_desc_t) :: ncid             ! netcdf id
     real(r8), pointer :: annlai(:,:)      ! 12 months of monthly lai from input data set
     real(r8), pointer :: mlai(:,:)        ! lai read from input files
-    real(r8):: closelat,closelon          ! single column vars
     integer :: ier                        ! error code
     integer :: g,k,l,m,n,p                ! indices
     integer :: ni,nj,ns                   ! indices
@@ -520,7 +517,6 @@ subroutine readAnnualVegetation (bounds, canopystate_inst)
     integer :: nlon_i                     ! number of input data longitudes
     integer :: nlat_i                     ! number of input data latitudes
     integer :: npft_i                     ! number of input data patch types
-    integer :: closelatidx,closelonidx    ! single column vars
     logical :: isgrid2d                   ! true => file is 2d
     character(len=256) :: locfn           ! local file name
     character(len=32) :: subname = 'readAnnualVegetation'
@@ -553,11 +549,6 @@ subroutine readAnnualVegetation (bounds, canopystate_inst)
     end if
     call check_dim_size(ncid, 'lsmpft', maxsoil_patches)
 
-    if (single_column) then
-       call shr_scam_getCloseLatLon(locfn, scmlat, scmlon, &
-            closelat, closelon, closelatidx, closelonidx)
-    endif
-
     do k=1,12   !! loop over months and read vegetated data
 
        call ncd_io(ncid=ncid, varname='MONTHLY_LAI', flag='read', data=mlai, &
@@ -600,7 +591,6 @@ subroutine readMonthlyVegetation (bounds, &
     use pftconMod        , only : noveg
     use fileutils        , only : getfil
     use spmdMod          , only : masterproc, mpicom, MPI_REAL8, MPI_INTEGER
-    use shr_scam_mod     , only : shr_scam_getCloseLatLon
     use clm_time_manager , only : get_nstep
     use netcdf
     !
@@ -620,8 +610,6 @@ subroutine readMonthlyVegetation (bounds, &
     integer :: nlat_i                     ! number of input data latitudes
     integer :: npft_i                     ! number of input data patch types
     integer :: ier                        ! error code
-    integer :: closelatidx,closelonidx
-    real(r8):: closelat,closelon
     logical :: readvar
     real(r8), pointer :: mlai(:,:)        ! lai read from input files
     real(r8), pointer :: msai(:,:)        ! sai read from input files
@@ -651,11 +639,6 @@ subroutine readMonthlyVegetation (bounds, &
     call getfil(fveg, locfn, 0)
     call ncd_pio_openfile (ncid, trim(locfn), 0)
 
-    if (single_column) then
-       call shr_scam_getCloseLatLon (ncid, scmlat, scmlon, closelat, closelon,&
-            closelatidx, closelonidx)
-    endif
-
     do k=1,2   !loop over months and read vegetated data
 
        call ncd_io(ncid=ncid, varname='MONTHLY_LAI', flag='read', data=mlai, dim1name=grlnd, &

src/biogeophys/SoilMoistureStreamMod.F90

@@ -23,8 +23,7 @@ module SoilMoistureStreamMod
   use shr_log_mod     , only : errMsg => shr_log_errMsg
   use decompMod       , only : bounds_type
   use abortutils      , only : endrun
-  use clm_varctl      , only : scmlat,scmlon,single_column, inst_name
-  use clm_varctl      , only : iulog, use_soil_moisture_streams
+  use clm_varctl      , only : iulog, use_soil_moisture_streams, inst_name
   use clm_varcon      , only : grlnd
   use controlMod      , only : NLFilename
   use decompMod       , only : gsMap_lnd2Dsoi_gdc2glo

src/cpl/lilac/lnd_import_export.F90

@@ -275,7 +275,7 @@ subroutine check_atm_landfrac(importState, bounds, rc)
     !---------------------------------------------------------------------------
 
     ! Implementation notes: The CTSM decomposition is set up so that ocean points appear
-    ! at the end of the vectors received from the coupler. Thus, in order to check if
+    ! at the end of the vectors received from the atm. Thus, in order to check if
     ! there are any points that the atmosphere considers land but CTSM considers ocean,
     ! it is sufficient to check the points following the typical ending bounds in the
     ! vectors received from the coupler.
@@ -291,7 +291,6 @@ subroutine check_atm_landfrac(importState, bounds, rc)
        if (atm_landfrac(n) > 0._r8) then
           write(iulog,*) 'At point ', n, ' atm landfrac = ', atm_landfrac(n)
           write(iulog,*) 'but CTSM thinks this is ocean.'
-          write(iulog,*) "Make sure the mask on CTSM's fatmlndfrc file agrees with the atmosphere's land mask"
           call shr_sys_abort( subname//&
                ' ERROR: atm landfrac > 0 for a point that CTSM thinks is ocean')
        end if

src/cpl/mct/lnd_comp_mct.F90

@@ -9,6 +9,7 @@ module lnd_comp_mct
   ! !uses:
   use shr_kind_mod     , only : r8 => shr_kind_r8
   use shr_sys_mod      , only : shr_sys_flush
+  use shr_log_mod      , only : errMsg => shr_log_errMsg
   use mct_mod          , only : mct_avect, mct_gsmap, mct_gGrid
   use decompmod        , only : bounds_type, ldecomp
   use lnd_import_export, only : lnd_import, lnd_export
@@ -28,6 +29,9 @@ module lnd_comp_mct
   private :: lnd_domain_mct    ! set the land model domain information
   private :: lnd_handle_resume ! handle pause/resume signals from the coupler
 
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+
 !====================================================================================
 contains
 !====================================================================================
@@ -44,7 +48,7 @@ subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename )
     use clm_time_manager , only : get_nstep, set_timemgr_init, set_nextsw_cday
     use clm_initializeMod, only : initialize1, initialize2
     use clm_instMod      , only : water_inst, lnd2atm_inst, lnd2glc_inst
-    use clm_varctl       , only : finidat,single_column, clm_varctl_set, iulog
+    use clm_varctl       , only : finidat, single_column, clm_varctl_set, iulog
     use clm_varctl       , only : inst_index, inst_suffix, inst_name
     use clm_varorb       , only : eccen, obliqr, lambm0, mvelpp
     use controlMod       , only : control_setNL
@@ -105,6 +109,7 @@ subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename )
     type(bounds_type) :: bounds                      ! bounds
     logical :: noland
     integer :: ni,nj
+    real(r8)         , parameter :: rundef = -9999999._r8
     character(len=32), parameter :: sub = 'lnd_init_mct'
     character(len=*),  parameter :: format = "('("//trim(sub)//") :',A)"
     !-----------------------------------------------------------------------
@@ -173,6 +178,12 @@ subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename )
                               start_type=starttype, model_version=version,      &
                               hostname=hostname, username=username )
 
+    ! Single Column
+    if ( single_column .and. (scmlat == rundef  .or. scmlon == rundef ) ) then
+       call endrun(msg=' ERROR:: single column mode on -- but scmlat and scmlon are NOT set'//&
+            errMsg(sourcefile, __LINE__))
+    end if
+
     ! Note that we assume that CTSM's internal dtime matches the coupling time step.
     ! i.e., we currently do NOT allow sub-cycling within a coupling time step.
     call set_timemgr_init( calendar_in=calendar, start_ymd_in=start_ymd, start_tod_in=start_tod, &