Merge remote-tracking branch 'upstream/main' into hotfix/cesm_so_t

.github/workflows/extbuild.yml

@@ -20,11 +20,11 @@ jobs:
       CPPFLAGS: "-I/usr/include -I/usr/local/include"
 
       # Versions of all dependencies can be updated here
-      ESMF_VERSION: v8.4.2
+      ESMF_VERSION: v8.6.0
       PNETCDF_VERSION: checkpoint.1.12.3
-      NETCDF_FORTRAN_VERSION: v4.6.0
-      PIO_VERSION: pio2_6_0
-      CDEPS_VERSION: cdeps1.0.15
+      NETCDF_FORTRAN_VERSION: v4.6.1
+      PIO_VERSION: pio2_6_2
+      CDEPS_VERSION: cdeps1.0.26
     steps:
       - uses: actions/checkout@v3
         # Build the ESMF library, if the cache contains a previous build
@@ -84,7 +84,7 @@ jobs:
           ref: ${{ env.CDEPS_VERSION }}
       - name: Build CDEPS
         if: steps.cache-cdeps.outputs.cache-hit != 'true'
-        uses: ESCOMP/CDEPS/.github/actions/[email protected].15
+        uses: ESCOMP/CDEPS/.github/actions/[email protected].26
         with:
           esmfmkfile: $HOME/ESMF/lib/libg/Linux.gfortran.64.openmpi.default/esmf.mk
           pio_path: $HOME/pio
@@ -102,6 +102,6 @@ jobs:
           make VERBOSE=1
           popd
 
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
+#      - name: Setup tmate session
+#        if: ${{ failure() }}
+#        uses: mxschmitt/action-tmate@v3

.github/workflows/srt.yml

@@ -26,8 +26,8 @@ jobs:
       CPPFLAGS: "-I/usr/include -I/usr/local/include "
       LDFLAGS: "-L/usr/lib/x86_64-linux-gnu -lnetcdf -lnetcdff -lpnetcdf"     
       # Versions of all dependencies can be updated here
-      ESMF_VERSION: v8.5.0
-      PARALLELIO_VERSION: pio2_6_0
+      ESMF_VERSION: v8.6.0
+      PARALLELIO_VERSION: pio2_6_2
       CIME_MODEL: cesm
       CIME_DRIVER: nuopc
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -79,7 +79,21 @@ jobs:
       - name: checkout externals
         run: |
           pushd cesm
-          ./manage_externals/checkout_externals ccs_config cdeps cime share mct cpl7 parallelio
+          ./manage_externals/checkout_externals ccs_config cdeps share mct cpl7 parallelio
+          cd ccs_config
+          git checkout main 
+          cd ../
+          git clone https://github.com/ESMCI/cime
+          cd cime
+          if [[ ! -e "${PWD}/.gitmodules.bak" ]]
+             then
+              echo "Converting [email protected] to https://github.com urls in ${PWD}/.gitmodules"
+
+              sed -i".bak" "s/[email protected]:/https:\/\/github.com\//g" "${PWD}/.gitmodules"
+          fi
+          git submodule update --init
+          cd ../components/cdeps
+          git checkout main
           
       - name: Cache ESMF
         id: cache-esmf

cesm/driver/ensemble_driver.F90

@@ -145,7 +145,7 @@ subroutine SetModelServices(ensemble_driver, rc)
     integer                :: pio_asyncio_stride
     integer                :: pio_asyncio_rootpe
     integer                :: Global_Comm
-    character(len=CL)          :: start_type     ! Type of startup
+    character(len=CL)      :: start_type     ! Type of startup
     character(len=7)       :: drvrinst
     character(len=5)       :: inst_suffix
     character(len=CX)      :: msgstr
@@ -377,10 +377,8 @@ subroutine SetModelServices(ensemble_driver, rc)
        endif
        call shr_log_setLogUnit (logunit)
        ! Create a clock for each driver instance
-
        call esm_time_clockInit(ensemble_driver, driver, logunit, localpet==petList(1), rc)
        if (chkerr(rc,__LINE__,u_FILE_u)) return
-
     enddo
     inst = localPet/(ntasks_per_member+pio_asyncio_ntasks) + 1
 

cesm/driver/esm.F90

@@ -1224,13 +1224,17 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
     real (r8), allocatable :: lats(:)        ! temporary
     real (r8), allocatable :: lons(:)        ! temporary
     real (r8), allocatable :: pos_lons(:)    ! temporary
+    real (r8), allocatable :: pos_lats(:)    ! temporary
+    real (r8), allocatable :: cols(:)        ! temporary
     real (r8), allocatable :: glob_grid(:,:) ! temporary
     real (r8)              :: pos_scol_lon   ! temporary
+    real (r8)              :: pos_scol_lat   ! temporary
     real (r8)              :: scol_data(1)
     integer                :: iscol_data(1)
     integer                :: petcount
     character(len=CL)      :: cvalue
     character(len=*), parameter :: subname= ' (esm_get_single_column_attributes) '
+    logical                :: unstructured = .false.
     !-------------------------------------------------------------------------------
 
     rc = ESMF_SUCCESS
@@ -1324,7 +1328,15 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
           if (status /= nf90_noerr) call shr_sys_abort (subname//' inq_varid frac')
 
           ! Read in domain file for single column
-          allocate(lats(nj))
+          ! Check for unstructured data ni>1 and nj==1
+          if (ni.gt.1 .and. nj == 1) unstructured=.true.
+
+          if (unstructured) then
+             allocate(lats(ni))
+             allocate(pos_lats(ni))
+          else
+             allocate(lats(nj))
+          end if
           allocate(lons(ni))
           allocate(pos_lons(ni))
           allocate(glob_grid(ni,nj))
@@ -1334,28 +1346,37 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
           count3=(/ni,nj,1/)
           status = nf90_get_var(ncid, varid_xc, glob_grid, start3, count3)
           if (status /= nf90_noerr) call shr_sys_abort (subname//' get_var xc')
-          do i = 1,ni
-             lons(i) = glob_grid(i,1)
-          end do
+          lons(1:ni) = glob_grid(1:ni,1)
           status = nf90_get_var(ncid, varid_yc, glob_grid, start3, count3)
           if (status /= nf90_noerr) call shr_sys_abort (subname//' get_var yc')
-          do j = 1,nj
-             lats(j) = glob_grid(1,j)
-          end do
-
+          if (unstructured) then
+             lats(1:ni) = glob_grid(1:ni,1)
+          else
+             lats(1:nj) = glob_grid(1,1:nj)
+          end if
           ! find nearest neighbor indices of scol_lon and scol_lat in single_column_lnd_domain file
           ! convert lons array and scol_lon to 0,360 and find index of value closest to 0
           ! and obtain single-column longitude/latitude indices to retrieve
-          pos_lons(:)  = mod(lons(:)  + 360._r8, 360._r8)
-          pos_scol_lon = mod(scol_lon + 360._r8, 360._r8)
-          start(1) = (MINLOC(abs(pos_lons - pos_scol_lon), dim=1))
-          start(2) = (MINLOC(abs(lats      -scol_lat    ), dim=1))
-
+          if (unstructured) then
+             allocate(cols(ni))
+             pos_lons(:)  = mod(lons(:)  + 360._r8, 360._r8)
+             pos_scol_lon = mod(scol_lon + 360._r8, 360._r8)
+             pos_lats(:)  = lats(:)  + 90._r8
+             pos_scol_lat = scol_lat + 90._r8
+             cols=abs(pos_lons - pos_scol_lon)+abs(pos_lats - pos_scol_lat)
+             start(1) = MINLOC(cols, dim=1)
+             start(2) = 1
+             deallocate(cols)
+          else
+             pos_lons(:)  = mod(lons(:)  + 360._r8, 360._r8)
+             pos_scol_lon = mod(scol_lon + 360._r8, 360._r8)
+             start(1) = (MINLOC(abs(pos_lons - pos_scol_lon), dim=1))
+             start(2) = (MINLOC(abs(lats      -scol_lat    ), dim=1))
+          end if
           deallocate(lats)
           deallocate(lons)
           deallocate(pos_lons)
           deallocate(glob_grid)
-
           ! read in value of nearest neighbor lon and RESET scol_lon and scol_lat
           ! also get area of gridcell, mask and frac
           status = nf90_get_var(ncid, varid_xc, scol_lon, start)
@@ -1517,6 +1538,7 @@ subroutine esm_finalize(driver, rc)
 
     call ESMF_LogWrite(trim(subname)//": called", ESMF_LOGMSG_INFO)
     rc = ESMF_SUCCESS
+
     call shr_log_setLogunit(logunit)
     call ESMF_GridCompGet(driver, vm=vm, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return

cesm/driver/esm_time_mod.F90

@@ -282,7 +282,6 @@ subroutine esm_time_clockInit(ensemble_driver, instance_driver, logunit, maintas
     call ESMF_TimeSet( RefTime, yy=yr, mm=mon, dd=day, s=ref_tod, rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-
     call ESMF_TimeIntervalSet( TimeStep, s=dtime_drv, rc=rc )
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 

cesm/flux_atmocn/shr_flux_mod.F90

@@ -133,15 +133,18 @@ end subroutine shr_flux_adjust_constants
   !                   Thomas Toniazzo (Bjerknes Centre, Bergen) ”
   !===============================================================================
   SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
-       &               qbot  ,s16O  ,sHDO  ,s18O  ,rbot,  &
+       &               qbot,  rainc ,s16O  ,sHDO  ,s18O  ,rbot,  &
        &               tbot  ,us    ,vs,  pslv,  &
        &               ts    ,mask  , seq_flux_atmocn_minwind, &
        &               sen   ,lat   ,lwup  ,   &
        &               r16O, rhdo, r18O, &
        &               evap  ,evap_16O, evap_HDO, evap_18O, &
        &               taux  ,tauy  ,tref  ,qref  ,   &
        &               ocn_surface_flux_scheme, &
-       &               duu10n,  ustar_sv ,re_sv ,ssq_sv,   &
+       &               add_gusts, & 
+       &               duu10n, & 
+       &               ugust_out, & 
+       &               ustar_sv ,re_sv ,ssq_sv,   &
        &               missval)
 
     ! !USES:
@@ -156,11 +159,13 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
     integer(IN),intent(in) :: nMax        ! data vector length
     integer(IN),intent(in) :: mask (nMax) ! ocn domain mask       0 <=> out of domain
     integer(IN),intent(in) :: ocn_surface_flux_scheme
+    logical ,intent(in)    :: add_gusts
     real(R8)   ,intent(in) :: zbot (nMax) ! atm level height      (m)
     real(R8)   ,intent(in) :: ubot (nMax) ! atm u wind            (m/s)
     real(R8)   ,intent(in) :: vbot (nMax) ! atm v wind            (m/s)
     real(R8)   ,intent(in) :: thbot(nMax) ! atm potential T       (K)
     real(R8)   ,intent(in) :: qbot (nMax) ! atm specific humidity (kg/kg)
+    real(R8)   ,intent(in) :: rainc(nMax) ! atm precip for convective gustiness (kg/m^3) - RBN 24Nov2008/MDF 31Jan2022
     real(R8)   ,intent(in) :: s16O (nMax) ! atm H216O tracer conc. (kg/kg)
     real(R8)   ,intent(in) :: sHDO (nMax) ! atm HDO tracer conc.  (kg/kg)
     real(R8)   ,intent(in) :: s18O (nMax) ! atm H218O tracer conc. (kg/kg)
@@ -188,6 +193,7 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
     real(R8),intent(out)  ::  tref (nMax) ! diag:  2m ref height T     (K)
     real(R8),intent(out)  ::  qref (nMax) ! diag:  2m ref humidity (kg/kg)
     real(R8),intent(out)  :: duu10n(nMax) ! diag: 10m wind speed squared (m/s)^2
+    real(R8),intent(out)  :: ugust_out(nMax) ! diag: gustiness addition to U10 (m/s)
 
     real(R8),intent(out),optional :: ustar_sv(nMax) ! diag: ustar
     real(R8),intent(out),optional :: re_sv   (nMax) ! diag: sqrt of exchange coefficient (water)
@@ -257,14 +263,16 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
     real(R8)    :: tdiff(nMax)               ! tbot - ts
     real(R8)    :: vscl
 
+    real(R8)    :: ugust      ! function: gustiness as a function of convective rainfall.  
+    real(R8)    :: gprec   ! convective rainfall argument for ugust
 
     qsat(Tk)   = 640380.0_R8 / exp(5107.4_R8/Tk)
 
     ! Large and Yeager 2009
     cdn(Umps)  =  0.0027_R8 / min(33.0000_R8,Umps) + 0.000142_R8 + &
          0.0000764_R8 * min(33.0000_R8,Umps) - 3.14807e-13_r8 * min(33.0000_R8,Umps)**6
     ! Capped Large and Pond by wind
-    !   cdn(Umps)  =   0.0027_R8 / min(30.0_R8,Umps) + 0.000142_R8 + 0.0000764_R8 * min(30.0_R8,Umps) 
+    !   cdn(Umps)  =   0.0027_R8 / min(30.0_R8,Umps) + 0.000142_R8 + 0.0000764_R8 * min(30.0_R8,Umps)
     ! Capped Large and Pond by Cd
     !   cdn(Umps) = min(0.0025_R8, (0.0027_R8 / Umps + 0.000142_R8 + 0.0000764_R8 * Umps ))
     ! Large and Pond
@@ -273,6 +281,13 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
     psimhu(xd) = log((1.0_R8+xd*(2.0_R8+xd))*(1.0_R8+xd*xd)/8.0_R8) - 2.0_R8*atan(xd) + 1.571_R8
     psixhu(xd) = 2.0_R8 * log((1.0_R8 + xd*xd)/2.0_R8)
 
+    ! Convective gustiness appropriate for input precipitation.
+    ! Following Regelsperger et al. (2000, J. Clim)
+    ! Ug = log(1.0+6.69R-0.476R^2)
+    ! Coefficients X by 8640 for mm/s (from cam) -> cm/day (for above forumla)
+    ugust(gprec) = log(1._R8+57801.6_r8*gprec-3.55332096e7_r8*(gprec**2))
+
+
     !--- formats ----------------------------------------
     character(*),parameter :: subName = '(flux_atmOcn) '
     character(*),parameter ::   F00 = "('(flux_atmOcn) ',4a)"
@@ -327,7 +342,14 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
           if (mask(n) /= 0) then
 
              !--- compute some needed quantities ---
-             vmag   = max(seq_flux_atmocn_minwind, sqrt( (ubot(n)-us(n))**2 + (vbot(n)-vs(n))**2) )
+             if (add_gusts) then 
+                vmag   = max(seq_flux_atmocn_minwind, sqrt( (ubot(n)-us(n))**2 + (vbot(n)-vs(n))**2) + ugust(min(rainc(n),6.94444e-4_r8)) )
+                ugust_out(n) = ugust(min(rainc(n),6.94444e-4_r8))
+             else 
+                vmag   = max(seq_flux_atmocn_minwind, sqrt( (ubot(n)-us(n))**2 + (vbot(n)-vs(n))**2) )
+                ugust_out(n) = 0.0_r8
+             end if
+
              if (use_coldair_outbreak_mod) then
                 ! Cold Air Outbreak Modification:
                 ! Increase windspeed for negative tbot-ts
@@ -462,6 +484,7 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
              tref  (n) = spval  !  2m reference height temperature (K)
              qref  (n) = spval  !  2m reference height humidity (kg/kg)
              duu10n(n) = spval  ! 10m wind speed squared (m/s)^2
+             ugust_out(n) = spval ! gustiness addition (m/s) 
 
              if (present(ustar_sv)) ustar_sv(n) = spval
              if (present(re_sv   )) re_sv   (n) = spval

cime_config/buildnml

@@ -15,6 +15,7 @@ from CIME.case import Case
 from CIME.nmlgen import NamelistGenerator
 from CIME.utils import expect
 from CIME.utils import get_model, get_time_in_seconds, get_timestamp
+from CIME.namelist import literal_to_python_value
 from CIME.buildnml import create_namelist_infile, parse_input
 from CIME.XML.files import Files
 
@@ -105,7 +106,8 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     config["COMP_OCN"] = case.get_value("COMP_OCN")
     config["COMP_ROF"] = case.get_value("COMP_ROF")
     config["COMP_WAV"] = case.get_value("COMP_WAV")
-
+    config["CAMDEV"] = "True" if "CAM%DEV" in case.get_value("COMPSET") else "False"
+
     if (
         (
             case.get_value("COMP_ROF") == "mosart"
@@ -144,6 +146,11 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     if config["COMP_OCN"] == "docn" and "aqua" in case.get_value("DOCN_MODE"):
         nmlgen.set_value("aqua_planet", value=".true.")
 
+    # make sure that variable add_gusts is only set to true if compset includes cam_dev
+    add_gusts = literal_to_python_value(nmlgen.get_value("add_gusts"), type_="logical")
+    if add_gusts:
+        expect("CAM%DEV" in case.get_value("COMPSET"),"ERROR: add_gusts can only be set if CAM%DEV in compset {}".format(case.get_value("COMPSET")))
+
     # --------------------------------
     # Overwrite: set component coupling frequencies
     # --------------------------------
@@ -658,6 +665,7 @@ def buildnml(case, caseroot, component):
     create_namelist_infile(case, user_nl_file, namelist_infile, infile_text)
     infile = [namelist_infile]
 
+
     # create the files nuopc.runconfig, nuopc.runseq, drv_in and drv_flds_in
     _create_drv_namelists(case, infile, confdir, nmlgen, files)
 

cime_config/config_component.xml

@@ -821,15 +821,6 @@
     different MPI ranks to different GPUs within the same compute node</desc>
   </entry>
 
-  <entry id="SMP_PRESENT">
-    <type>logical</type>
-    <valid_values>TRUE,FALSE</valid_values>
-    <default_value>FALSE</default_value>
-    <group>build_def</group>
-    <file>env_build.xml</file>
-    <desc>TRUE implies that at least one of the components is built threaded (DO NOT EDIT)</desc>
-  </entry>
-
   <entry id="ESMF_AWARE_THREADING">
     <type>logical</type>
     <valid_values>TRUE,FALSE</valid_values>
@@ -1035,23 +1026,6 @@
     this to work.</desc>
   </entry>
 
-  <entry id="ESMF_LOGFILE_KIND">
-    <type>char</type>
-    <valid_values>ESMF_LOGKIND_SINGLE,ESMF_LOGKIND_MULTI,ESMF_LOGKIND_NONE</valid_values>
-    <default_value>ESMF_LOGKIND_NONE</default_value>
-    <group>run_flags</group>
-    <file>env_run.xml</file>
-    <desc>
-      Determines what ESMF log files (if any) are generated when
-          USE_ESMF_LIB is TRUE.
-      ESMF_LOGKIND_SINGLE: Use a single log file, combining messages from
-          all of the PETs. Not supported on some platforms.
-      ESMF_LOGKIND_MULTI: Use multiple log files -- one per PET.
-      ESMF_LOGKIND_NONE: Do not issue messages to a log file.
-      By default, no ESMF log files are generated.
-    </desc>
-  </entry>
-
   <entry id="ESMF_VERBOSITY_LEVEL">
     <type>char</type>
     <valid_values>off,low,high,max</valid_values>