Update CMEPS to its ESCOMP/master branch 20220607 commit

.github/workflows/extbuild.yml

@@ -19,12 +19,10 @@ jobs:
       CXX: mpicxx
       CPPFLAGS: "-I/usr/include -I/usr/local/include"
       # Versions of all dependencies can be updated here
-      ESMF_VERSION: ESMF_8_2_0_beta_snapshot_14
-      PNETCDF_VERSION: pnetcdf-1.12.2
+      ESMF_VERSION: v8.3.0b13
+      PNETCDF_VERSION: pnetcdf-1.12.3
       NETCDF_FORTRAN_VERSION: v4.5.2
-      # PIO version is awkward
-      PIO_VERSION_DIR: pio2_5_3
-      PIO_VERSION: pio-2.5.3
+      PIO_VERSION: pio2_5_7
     steps:
       - uses: actions/checkout@v2
         # Build the ESMF library, if the cache contains a previous build
@@ -38,12 +36,19 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install gfortran wget openmpi-bin netcdf-bin libopenmpi-dev libnetcdf-dev
+      - id: checkout-ESMF
+        uses: actions/checkout@v3
+        with:
+          repository: esmf-org/esmf
+          path: esmf-src
+          ref: ${{ env.ESMF_VERSION }}
       - id: build-ESMF
         if: steps.cache-esmf.outputs.cache-hit != 'true'
         run: |
-          wget https://github.com/esmf-org/esmf/archive/${{ env.ESMF_VERSION }}.tar.gz
-          tar -xzvf ${{ env.ESMF_VERSION }}.tar.gz
-          pushd esmf-${{ env.ESMF_VERSION }}
+          #wget https://github.com/esmf-org/esmf/archive/${{ env.ESMF_VERSION }}.tar.gz
+          #tar -xzvf ${{ env.ESMF_VERSION }}.tar.gz
+          #pushd esmf-${{ env.ESMF_VERSION }}
+          pushd esmf-src
           export ESMF_DIR=`pwd`
           export ESMF_COMM=openmpi
           export ESMF_YAMLCPP="internal"
@@ -95,14 +100,18 @@ jobs:
             ${{ runner.os }}-${{ env.NETCDF_FORTRAN_VERSION }}-netcdf-fortran
             ${{ runner.os }}-${{ env.PNETCDF_VERSION }}-pnetcdf
 
+      - id: checkout-PIO
+        uses: actions/checkout@v3
+        with:
+          repository: NCAR/ParallelIO
+          path: parallelio-src
+          ref: ${{ env.PIO_VERSION }}
       - name: Build PIO
         if: steps.cache-PIO.outputs.cache-hit != 'true'
         run: |
-          wget https://github.com/NCAR/ParallelIO/releases/download/${{ env.PIO_VERSION_DIR }}/${{ env.PIO_VERSION }}.tar.gz
-          tar -xzvf ${{ env.PIO_VERSION }}.tar.gz
           mkdir build-pio
           pushd build-pio
-          cmake -Wno-dev -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/usr/include -DCMAKE_PREFIX_PATH=/usr -DCMAKE_INSTALL_PREFIX=$HOME/pio -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On -DPIO_ENABLE_TESTS=Off -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_EXAMPLES=Off -DPIO_ENABLE_TIMING=Off -DNetCDF_Fortran_PATH=$HOME/netcdf-fortran -DPnetCDF_PATH=$HOME/pnetcdf ../${{ env.PIO_VERSION }}
+          cmake -Wno-dev -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/usr/include -DCMAKE_PREFIX_PATH=/usr -DCMAKE_INSTALL_PREFIX=$HOME/pio -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On -DPIO_ENABLE_TESTS=Off -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_EXAMPLES=Off -DPIO_ENABLE_TIMING=Off -DNetCDF_Fortran_PATH=$HOME/netcdf-fortran -DPnetCDF_PATH=$HOME/pnetcdf ../parallelio-src
           make VERBOSE=1
           make install
           popd

cesm/driver/esm.F90

@@ -1203,6 +1203,8 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
     use netcdf, only : nf90_inq_dimid, nf90_inquire_dimension, nf90_inq_varid, nf90_get_var
     use NUOPC , only : NUOPC_CompAttributeGet, NUOPC_CompAttributeSet, NUOPC_CompAttributeAdd
     use ESMF  , only : ESMF_GridComp, ESMF_GridCompGet, ESMF_VM, ESMF_VMGet, ESMF_SUCCESS
+    use ESMF  , only : ESMF_Mesh, ESMF_MeshCreate, ESMF_FILEFORMAT_ESMFMESH, ESMF_MeshGet, ESMF_MESHLOC_ELEMENT
+    use ESMF  , only : ESMF_Field, ESMF_FieldCreate, ESMF_FieldGet, ESMF_FieldRegridGetArea, ESMF_TYPEKIND_r8
 
     ! input/output variables
     character(len=*)    , intent(in)    :: compname
@@ -1212,14 +1214,24 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
     ! local variables
     type(ESMF_VM)          :: vm
     character(len=CL)      :: single_column_lnd_domainfile
+    character(len=CL)      :: single_column_global_meshfile
     real(r8)               :: scol_lon
     real(r8)               :: scol_lat
     real(r8)               :: scol_area
     integer                :: scol_lndmask
     real(r8)               :: scol_lndfrac
     integer                :: scol_ocnmask
     real(r8)               :: scol_ocnfrac
-    integer                :: i,j,ni,nj
+    integer                :: scol_mesh_n
+    type(ESMF_Mesh)        :: mesh
+    type(ESMF_Field)       :: lfield
+    integer                :: lsize
+    integer                :: spatialdim
+    real(r8), pointer      :: ownedElemCoords(:)
+    real(r8), pointer      :: latMesh(:)
+    real(r8), pointer      :: lonMesh(:)
+    real(r8), pointer      :: dataptr(:)
+    integer                :: i,j,ni,nj,n
     integer                :: ncid
     integer                :: dimid
     integer                :: varid_xc
@@ -1243,7 +1255,6 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
     character(len=*), parameter :: subname= ' (esm_get_single_column_attributes) '
     !-------------------------------------------------------------------------------
 
-
     rc = ESMF_SUCCESS
 
     ! obtain the single column lon and lat
@@ -1255,6 +1266,8 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
     read(cvalue,*) scol_lat
     call NUOPC_CompAttributeGet(gcomp, name='single_column_lnd_domainfile', value=single_column_lnd_domainfile, rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    call NUOPC_CompAttributeGet(gcomp, name='mesh_atm', value=single_column_global_meshfile, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
     call NUOPC_CompAttributeAdd(gcomp, attrList=(/'scol_spval'/), rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
 
@@ -1349,6 +1362,7 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
           do j = 1,nj
              lats(j) = glob_grid(1,j)
           end do
+
           ! 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
@@ -1388,26 +1402,53 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
                   //' ocean and land mask cannot both be zero')
           end if
 
+          status = nf90_close(ncid)
+          if (status /= nf90_noerr) call shr_sys_abort (trim(subname) //': closing '//&
+               trim(single_column_lnd_domainfile))
+
+          ! Now read in mesh file to get exact values of scol_lon and scol_lat that will be used
+          ! by the models - assume that this occurs only on 1 processor
+          mesh = ESMF_MeshCreate(filename=trim(single_column_global_meshfile), fileformat=ESMF_FILEFORMAT_ESMFMESH, rc=rc)
+          if (chkerr(rc,__LINE__,u_FILE_u)) return
+          call ESMF_MeshGet(mesh, spatialDim=spatialDim, numOwnedElements=lsize, rc=rc)
+          if (ChkErr(rc,__LINE__,u_FILE_u)) return
+          allocate(ownedElemCoords(spatialDim*lsize))
+          allocate(lonMesh(lsize), latMesh(lsize))
+          call ESMF_MeshGet(mesh, ownedElemCoords=ownedElemCoords)
+          if (ChkErr(rc,__LINE__,u_FILE_u)) return
+          do n = 1,lsize
+             lonMesh(n) = ownedElemCoords(2*n-1)
+             latMesh(n) = ownedElemCoords(2*n)
+             if (abs(lonMesh(n) - scol_lon) < 1.e-4 .and. abs(latMesh(n) - scol_lat) < 1.e-4) then
+                scol_mesh_n = n
+                scol_mesh_n = n
+                exit
+             end if
+          end do
+          scol_lon  = lonMesh(scol_mesh_n)
+          scol_lat  = latMesh(scol_mesh_n)
+
+          ! Obtain mesh info areas
+          lfield = ESMF_FieldCreate(mesh, ESMF_TYPEKIND_r8, name='area', meshloc=ESMF_MESHLOC_ELEMENT, rc=rc)
+          if (ChkErr(rc,__LINE__,u_FILE_u)) return
+          call ESMF_FieldRegridGetArea(lfield, rc=rc)
+          if (chkerr(rc,__LINE__,u_FILE_u)) return
+          call ESMF_FieldGet(lfield, farrayPtr=dataptr, rc=rc)
+          if (chkerr(rc,__LINE__,u_FILE_u)) return
+          scol_area = dataptr(scol_mesh_n)
+
+          ! Set single column attribute values for all components
           write(cvalue,*) scol_lon
           call NUOPC_CompAttributeSet(gcomp, name='scol_lon', value=trim(cvalue), rc=rc)
           if (chkerr(rc,__LINE__,u_FILE_u)) return
-
           write(cvalue,*) scol_lat
           call NUOPC_CompAttributeSet(gcomp, name='scol_lat', value=trim(cvalue), rc=rc)
           if (chkerr(rc,__LINE__,u_FILE_u)) return
-
-          write(cvalue,*) ni
-          call NUOPC_CompAttributeSet(gcomp, name='scol_ni', value=trim(cvalue), rc=rc)
-          if (chkerr(rc,__LINE__,u_FILE_u)) return
-
-          write(cvalue,*) nj
-          call NUOPC_CompAttributeSet(gcomp, name='scol_nj', value=trim(cvalue), rc=rc)
+          write(cvalue,*) scol_area
+          call NUOPC_CompAttributeSet(gcomp, name='scol_area', value=trim(cvalue), rc=rc)
           if (chkerr(rc,__LINE__,u_FILE_u)) return
 
-          status = nf90_close(ncid)
-          if (status /= nf90_noerr) call shr_sys_abort (trim(subname) //': closing '//&
-               trim(single_column_lnd_domainfile))
-
+          ! Write out diagnostic info
           write(logunit,'(a,2(f13.5,2x))')trim(subname)//' nearest neighbor scol_lon and scol_lat in '&
                //trim(single_column_lnd_domainfile)//' are ',scol_lon,scol_lat
           if (trim(compname) == 'LND') then
@@ -1419,6 +1460,12 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
           else
              write(logunit,'(a)')trim(subname)//' atm point has unit mask and unit fraction '
           end if
+          write(cvalue,*) ni
+          call NUOPC_CompAttributeSet(gcomp, name='scol_ni', value=trim(cvalue), rc=rc)
+          if (chkerr(rc,__LINE__,u_FILE_u)) return
+          write(cvalue,*) nj
+          call NUOPC_CompAttributeSet(gcomp, name='scol_nj', value=trim(cvalue), rc=rc)
+          if (chkerr(rc,__LINE__,u_FILE_u)) return
 
        else
 
@@ -1431,12 +1478,11 @@ subroutine esm_set_single_column_attributes(compname, gcomp, rc)
           scol_ocnfrac = 1._r8
           scol_area = 1.e30
 
+          write(cvalue,*) 1
           call NUOPC_CompAttributeSet(gcomp, name='scol_ni', value=trim(cvalue), rc=rc)
           if (chkerr(rc,__LINE__,u_FILE_u)) return
-          write(cvalue,*) 1
           call NUOPC_CompAttributeSet(gcomp, name='scol_nj', value=trim(cvalue), rc=rc)
           if (chkerr(rc,__LINE__,u_FILE_u)) return
-          write(cvalue,*) 1
 
           write(logunit,'(a)')' single point mode is active'
           write(logunit,'(a,f13.5,a,f13.5,a)')' scol_lon is ',scol_lon,' and scol_lat is '

cime_config/buildnml

@@ -62,11 +62,15 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     config['lnd_grid'] = lnd_grid
     config['ice_grid'] = ice_grid
     config['ocn_grid'] = ocn_grid
-    config['samegrid_atm_lnd'] = 'true' if atm_grid == lnd_grid else 'false'
-    config['samegrid_atm_ice'] = 'true' if atm_grid == ice_grid else 'false'
-    config['samegrid_atm_ocn'] = 'true' if atm_grid == ocn_grid else 'false'
-    config['samegrid_atm_wav'] = 'true' if atm_grid == wav_grid else 'false'
-    config['samegrid_lnd_rof'] = 'true' if lnd_grid == rof_grid else 'false'
+
+    atm_mesh = case.get_value("ATM_DOMAIN_MESH")
+    lnd_mesh = case.get_value("LND_DOMAIN_MESH")
+    rof_mesh = case.get_value("ROF_DOMAIN_MESH")
+    config['samegrid_atm_lnd'] = 'true' if atm_mesh == case.get_value("LND_DOMAIN_MESH") else 'false'
+    config['samegrid_atm_ocn'] = 'true' if atm_mesh == case.get_value("OCN_DOMAIN_MESH") else 'false'
+    config['samegrid_atm_ice'] = 'true' if atm_mesh == case.get_value("ICE_DOMAIN_MESH") else 'false'
+    config['samegrid_atm_wav'] = 'true' if atm_mesh == case.get_value("WAV_DOMAIN_MESH") else 'false'
+    config['samegrid_lnd_rof'] = 'true' if lnd_mesh == rof_mesh else 'false'
 
     # determine if need to set atm_domainfile
     scol_lon = float(case.get_value('PTS_LON'))
@@ -102,6 +106,12 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     #----------------------------------------------------
     nmlgen.init_defaults(infile, config, skip_default_for_groups=["modelio"])
 
+    #--------------------------------
+    # Overwrite: wav-ice coupling (assumes cice6 as the ice component
+    #--------------------------------
+    if (case.get_value("COMP_WAV") == 'ww3dev' and case.get_value("COMP_ICE") == 'cice'):
+        nmlgen.set_value('wavice_coupling', value='.true.')
+
     #--------------------------------
     # Overwrite: set brnch_retain_casename
     #--------------------------------
@@ -307,7 +317,7 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
             model = model.lower()
             config = {}
             config['component'] = model
-            nmlgen.init_defaults(infile, config, skip_entry_loop=True)
+            nmlgen.init_defaults([], config, skip_entry_loop=True)
             if model == 'cpl':
                 newgroup = "MED_modelio"
             else:
@@ -340,16 +350,14 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
                 nmlgen.set_value("diro", case.get_value('RUNDIR'))
                 if model == 'cpl':
                     logfile = 'med' + inst_string + ".log." + str(lid)
+                elif model == 'drv':
+                    logfile = model + ".log." + str(lid)
                 else:
                     logfile = model + inst_string + ".log." + str(lid)
                 nmlgen.set_value("logfile", logfile)
                 inst_index = inst_index + 1
             nmlgen.write_nuopc_config_file(conffile)
 
-
-
-
-
     #--------------------------------
     # Update nuopc.runconfig file if component needs it
     #--------------------------------