Merge pull request #132 from jiandewang/feature/update-to-main-20240401

update to MOM6 main repo 20240401 commit

config_src/drivers/nuopc_cap/mom_cap.F90

@@ -16,7 +16,7 @@ module MOM_cap_mod
 use MOM_domains,              only: MOM_infra_init, MOM_infra_end
 use MOM_file_parser,          only: get_param, log_version, param_file_type, close_param_file
 use MOM_get_input,            only: get_MOM_input, directories
-use MOM_domains,              only: pass_var
+use MOM_domains,              only: pass_var, pe_here
 use MOM_error_handler,        only: MOM_error, FATAL, is_root_pe
 use MOM_grid,                 only: ocean_grid_type, get_global_grid_size
 use MOM_ocean_model_nuopc,    only: ice_ocean_boundary_type
@@ -29,6 +29,7 @@ module MOM_cap_mod
 use MOM_cap_methods,          only: med2mod_areacor, state_diagnose
 use MOM_cap_methods,          only: ChkErr
 use MOM_ensemble_manager,     only: ensemble_manager_init
+use MOM_coms,                 only: sum_across_PEs
 
 #ifdef CESMCOUPLED
 use shr_log_mod,             only: shr_log_setLogUnit
@@ -842,6 +843,7 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
   type(ocean_grid_type)        , pointer     :: ocean_grid
   type(ocean_internalstate_wrapper)          :: ocean_internalstate
   integer                                    :: npet, ntiles
+  integer                                    :: npes ! number of PEs (from FMS).
   integer                                    :: nxg, nyg, cnt
   integer                                    :: isc,iec,jsc,jec
   integer, allocatable                       :: xb(:),xe(:),yb(:),ye(:),pe(:)
@@ -868,6 +870,8 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
   integer                                    :: lsize
   integer                                    :: ig,jg, ni,nj,k
   integer, allocatable                       :: gindex(:) ! global index space
+  integer, allocatable                       :: gindex_ocn(:) ! global index space for ocean cells (excl. masked cells)
+  integer, allocatable                       :: gindex_elim(:) ! global index space for eliminated cells
   character(len=128)                         :: fldname
   character(len=256)                         :: cvalue
   character(len=256)                         :: frmt    ! format specifier for several error msgs
@@ -891,6 +895,11 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
   real(ESMF_KIND_R8)                         :: min_areacor_glob(2)
   real(ESMF_KIND_R8)                         :: max_areacor_glob(2)
   character(len=*), parameter                :: subname='(MOM_cap:InitializeRealize)'
+  integer                                    :: niproc, njproc
+  integer                                    :: ip, jp, pe_ix
+  integer                                    :: num_elim_blocks ! number of blocks to be eliminated
+  integer                                    :: num_elim_cells_global, num_elim_cells_local, num_elim_cells_remaining
+  integer, allocatable                       :: cell_mask(:,:)
   real(8)                                    :: MPI_Wtime, timeirls
   !--------------------------------
 
@@ -937,19 +946,19 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
     rc = ESMF_FAILURE
     call ESMF_LogWrite(subname//' ntiles must be 1', ESMF_LOGMSG_ERROR)
   endif
-  ntiles = mpp_get_domain_npes(ocean_public%domain)
-  write(tmpstr,'(a,1i6)') subname//' ntiles = ',ntiles
+  npes = mpp_get_domain_npes(ocean_public%domain)
+  write(tmpstr,'(a,1i6)') subname//' npes = ',npes
   call ESMF_LogWrite(trim(tmpstr), ESMF_LOGMSG_INFO)
 
   !---------------------------------
   ! get start and end indices of each tile and their PET
   !---------------------------------
 
-  allocate(xb(ntiles),xe(ntiles),yb(ntiles),ye(ntiles),pe(ntiles))
+  allocate(xb(npes),xe(npes),yb(npes),ye(npes),pe(npes))
   call mpp_get_compute_domains(ocean_public%domain, xbegin=xb, xend=xe, ybegin=yb, yend=ye)
   call mpp_get_pelist(ocean_public%domain, pe)
   if (dbug > 1) then
-    do n = 1,ntiles
+    do n = 1,npes
       write(tmpstr,'(a,6i6)') subname//' tiles ',n,pe(n),xb(n),xe(n),yb(n),ye(n)
       call ESMF_LogWrite(trim(tmpstr), ESMF_LOGMSG_INFO)
     enddo
@@ -971,17 +980,102 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
     call get_global_grid_size(ocean_grid, ni, nj)
     lsize = ( ocean_grid%iec - ocean_grid%isc + 1 ) * ( ocean_grid%jec - ocean_grid%jsc + 1 )
 
-    ! Create the global index space for the computational domain
-    allocate(gindex(lsize))
-    k = 0
-    do j = ocean_grid%jsc, ocean_grid%jec
-      jg = j + ocean_grid%jdg_offset
-      do i = ocean_grid%isc, ocean_grid%iec
-        ig = i + ocean_grid%idg_offset
-        k = k + 1 ! Increment position within gindex
-        gindex(k) = ni * (jg - 1) + ig
+    num_elim_blocks = 0
+    num_elim_cells_global = 0
+    num_elim_cells_local = 0
+    num_elim_cells_remaining = 0
+
+    ! Compute the number of eliminated blocks (specified in MOM_mask_table)
+    if (associated(ocean_grid%Domain%maskmap)) then
+      njproc = size(ocean_grid%Domain%maskmap, 1)
+      niproc = size(ocean_grid%Domain%maskmap, 2)
+
+      do ip = 1, niproc
+        do jp = 1, njproc
+          if (.not. ocean_grid%Domain%maskmap(jp,ip)) then
+            num_elim_blocks = num_elim_blocks+1
+          endif
+        enddo
       enddo
-    enddo
+    endif
+
+    ! Apply land block elimination to ESMF gindex
+    ! (Here we assume that each processor gets assigned a single tile. If multi-tile implementation is to be added
+    ! in MOM6 NUOPC cap in the future, below code must be updated accordingly.)
+    if (num_elim_blocks>0) then
+
+      allocate(cell_mask(ni, nj), source=0)
+      allocate(gindex_ocn(lsize))
+      k = 0
+      do j = ocean_grid%jsc, ocean_grid%jec
+        jg = j + ocean_grid%jdg_offset
+        do i = ocean_grid%isc, ocean_grid%iec
+          ig = i + ocean_grid%idg_offset
+          k = k + 1 ! Increment position within gindex
+          gindex_ocn(k) = ni * (jg - 1) + ig
+          cell_mask(ig, jg) = 1
+        enddo
+      enddo
+      call sum_across_PEs(cell_mask, ni*nj)
+
+      if (maxval(cell_mask) /= 1 ) then
+        call MOM_error(FATAL, "Encountered cells shared by multiple PEs while attempting to determine masked cells.")
+      endif
+
+      num_elim_cells_global = ni * nj - sum(cell_mask)
+      num_elim_cells_local = num_elim_cells_global / npes
+
+      if (pe_here() == pe(npes)) then
+        ! assign all remaining cells to the last PE.
+        num_elim_cells_remaining = num_elim_cells_global - num_elim_cells_local * npes
+        allocate(gindex_elim(num_elim_cells_local+num_elim_cells_remaining))
+      else
+        allocate(gindex_elim(num_elim_cells_local))
+      endif
+
+      ! Zero-based PE index.
+      pe_ix = pe_here() - pe(1)
+
+      k = 0
+      do jg = 1, nj
+        do ig = 1, ni
+          if (cell_mask(ig, jg) == 0) then
+            k = k + 1
+            if (k > pe_ix * num_elim_cells_local .and.  &
+                    k <= ((pe_ix+1) * num_elim_cells_local + num_elim_cells_remaining)) then
+              gindex_elim(k - pe_ix * num_elim_cells_local) = ni * (jg -1) + ig
+            endif
+          endif
+        enddo
+      enddo
+
+      allocate(gindex(lsize + num_elim_cells_local + num_elim_cells_remaining))
+      do k = 1, lsize
+        gindex(k) = gindex_ocn(k)
+      enddo
+      do k = 1, num_elim_cells_local + num_elim_cells_remaining
+        gindex(k+lsize) = gindex_elim(k)
+      enddo
+
+      deallocate(cell_mask)
+      deallocate(gindex_ocn)
+      deallocate(gindex_elim)
+
+    else ! no eliminated land blocks
+
+      ! Create the global index space for the computational domain
+      allocate(gindex(lsize))
+      k = 0
+      do j = ocean_grid%jsc, ocean_grid%jec
+        jg = j + ocean_grid%jdg_offset
+        do i = ocean_grid%isc, ocean_grid%iec
+          ig = i + ocean_grid%idg_offset
+          k = k + 1 ! Increment position within gindex
+          gindex(k) = ni * (jg - 1) + ig
+        enddo
+      enddo
+
+    endif
 
     DistGrid = ESMF_DistGridCreate(arbSeqIndexList=gindex, rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -1005,6 +1099,10 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
     call ESMF_MeshGet(Emesh, spatialDim=spatialDim, numOwnedElements=numOwnedElements, rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
+    if (lsize /= numOwnedElements - num_elim_cells_local - num_elim_cells_remaining) then
+      call MOM_error(FATAL, "Discrepancy detected between ESMF mesh and internal MOM6 domain sizes. Check mask table.")
+    endif
+
     allocate(ownedElemCoords(spatialDim*numOwnedElements))
     allocate(lonMesh(numOwnedElements), lon(numOwnedElements))
     allocate(latMesh(numOwnedElements), lat(numOwnedElements))
@@ -1036,7 +1134,7 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
     end do
 
     eps_omesh = get_eps_omesh(ocean_state)
-    do n = 1,numOwnedElements
+    do n = 1,lsize
       diff_lon = abs(mod(lonMesh(n) - lon(n),360.0))
       if (diff_lon > eps_omesh) then
         frmt = "('ERROR: Difference between ESMF Mesh and MOM6 domain coords is "//&
@@ -1140,11 +1238,11 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
 
     ! generate delayout and dist_grid
 
-    allocate(deBlockList(2,2,ntiles))
-    allocate(petMap(ntiles))
-    allocate(deLabelList(ntiles))
+    allocate(deBlockList(2,2,npes))
+    allocate(petMap(npes))
+    allocate(deLabelList(npes))
 
-    do n = 1, ntiles
+    do n = 1, npes
       deLabelList(n) = n
       deBlockList(1,1,n) = xb(n)
       deBlockList(1,2,n) = xe(n)
@@ -1727,7 +1825,7 @@ subroutine ModelAdvance(gcomp, rc)
         rpointer_filename = 'rpointer.ocn'//trim(inst_suffix)
 
         write(restartname,'(A,".mom6.r.",I4.4,"-",I2.2,"-",I2.2,"-",I5.5)') &
-             trim(casename), year, month, day, seconds
+             trim(casename), year, month, day, hour * 3600 + minute * 60 + seconds
         call ESMF_LogWrite("MOM_cap: Writing restart :  "//trim(restartname), ESMF_LOGMSG_INFO)
         ! write restart file(s)
         call ocean_model_restart(ocean_state, restartname=restartname, num_rest_files=num_rest_files)

config_src/drivers/nuopc_cap/mom_cap_methods.F90

@@ -853,7 +853,7 @@ subroutine State_SetExport(state, fldname, isc, iec, jsc, jec, input, ocean_grid
 
   ! local variables
   type(ESMF_StateItem_Flag)     :: itemFlag
-  integer                       :: n, i, j, i1, j1, ig,jg
+  integer                       :: n, i, j, k, i1, j1, ig,jg
   integer                       :: lbnd1,lbnd2
   real(ESMF_KIND_R8), pointer   :: dataPtr1d(:)
   real(ESMF_KIND_R8), pointer   :: dataPtr2d(:,:)
@@ -889,6 +889,13 @@ subroutine State_SetExport(state, fldname, isc, iec, jsc, jec, input, ocean_grid
         enddo
       end if
 
+      ! if a maskmap is provided, set exports of all eliminated cells to zero.
+      if (associated(ocean_grid%Domain%maskmap)) then
+        do k = n+1, size(dataPtr1d)
+          dataPtr1d(k) = 0.0
+        enddo
+      endif
+
     else if (geomtype == ESMF_GEOMTYPE_GRID) then
 
       call state_getfldptr(state, trim(fldname), dataptr2d, rc)

config_src/infra/FMS1/MOM_domain_infra.F90

@@ -16,7 +16,7 @@ module MOM_domain_infra
 use mpp_domains_mod, only : mpp_create_group_update, mpp_do_group_update
 use mpp_domains_mod, only : mpp_reset_group_update_field, mpp_group_update_initialized
 use mpp_domains_mod, only : mpp_start_group_update, mpp_complete_group_update
-use mpp_domains_mod, only : mpp_compute_block_extent
+use mpp_domains_mod, only : mpp_compute_block_extent, mpp_compute_extent
 use mpp_domains_mod, only : mpp_broadcast_domain, mpp_redistribute, mpp_global_field
 use mpp_domains_mod, only : AGRID, BGRID_NE, CGRID_NE, SCALAR_PAIR, BITWISE_EXACT_SUM
 use mpp_domains_mod, only : CYCLIC_GLOBAL_DOMAIN, FOLD_NORTH_EDGE
@@ -40,7 +40,7 @@ module MOM_domain_infra
 public :: domain2D, domain1D, group_pass_type
 ! These interfaces are actually implemented or have explicit interfaces in this file.
 public :: create_MOM_domain, clone_MOM_domain, get_domain_components, get_domain_extent
-public :: deallocate_MOM_domain, get_global_shape, compute_block_extent
+public :: deallocate_MOM_domain, get_global_shape, compute_block_extent, compute_extent
 public :: pass_var, pass_vector, fill_symmetric_edges, rescale_comp_data
 public :: pass_var_start, pass_var_complete, pass_vector_start, pass_vector_complete
 public :: create_group_pass, do_group_pass, start_group_pass, complete_group_pass
@@ -1945,6 +1945,17 @@ subroutine compute_block_extent(isg, ieg, ndivs, ibegin, iend)
   call mpp_compute_block_extent(isg, ieg, ndivs, ibegin, iend)
 end subroutine compute_block_extent
 
+!> Get the array ranges in one dimension for the divisions of a global index space
+subroutine compute_extent(isg, ieg, ndivs, ibegin, iend)
+  integer,               intent(in)  :: isg    !< The starting index of the global index space
+  integer,               intent(in)  :: ieg    !< The ending index of the global index space
+  integer,               intent(in)  :: ndivs  !< The number of divisions
+  integer, dimension(:), intent(out) :: ibegin !< The starting index of each division
+  integer, dimension(:), intent(out) :: iend   !< The ending index of each division
+
+  call mpp_compute_extent(isg, ieg, ndivs, ibegin, iend)
+end subroutine compute_extent
+
 !> Broadcast a 2-d domain from the root PE to the other PEs
 subroutine broadcast_domain(domain)
   type(domain2d),  intent(inout) :: domain !< The domain2d type that will be shared across PEs.

config_src/infra/FMS2/MOM_coms_infra.F90

@@ -42,6 +42,7 @@ module MOM_coms_infra
 interface sum_across_PEs
   module procedure sum_across_PEs_int4_0d
   module procedure sum_across_PEs_int4_1d
+  module procedure sum_across_PEs_int4_2d
   module procedure sum_across_PEs_int8_0d
   module procedure sum_across_PEs_int8_1d
   module procedure sum_across_PEs_int8_2d
@@ -357,6 +358,15 @@ subroutine sum_across_PEs_int4_1d(field, length, pelist)
   call mpp_sum(field, length, pelist)
 end subroutine sum_across_PEs_int4_1d
 
+!> Find the sum of the values in corresponding positions of field across PEs, and return these sums in field.
+subroutine sum_across_PEs_int4_2d(field, length, pelist)
+  integer(kind=int32), dimension(:,:), intent(inout) :: field     !< The values to add, the sums upon return
+  integer,                             intent(in)    :: length    !< Number of elements in field to add
+  integer,                 optional,   intent(in)    :: pelist(:) !< List of PEs to work with
+
+  call mpp_sum(field, length, pelist)
+end subroutine sum_across_PEs_int4_2d
+
 !> Find the sum of field across PEs, and return this sum in field.
 subroutine sum_across_PEs_int8_0d(field, pelist)
   integer(kind=int64), intent(inout) :: field     !< Value on this PE, and the sum across PEs upon return

config_src/infra/FMS2/MOM_domain_infra.F90

@@ -16,7 +16,7 @@ module MOM_domain_infra
 use mpp_domains_mod, only : mpp_create_group_update, mpp_do_group_update
 use mpp_domains_mod, only : mpp_reset_group_update_field, mpp_group_update_initialized
 use mpp_domains_mod, only : mpp_start_group_update, mpp_complete_group_update
-use mpp_domains_mod, only : mpp_compute_block_extent
+use mpp_domains_mod, only : mpp_compute_block_extent, mpp_compute_extent
 use mpp_domains_mod, only : mpp_broadcast_domain, mpp_redistribute, mpp_global_field
 use mpp_domains_mod, only : AGRID, BGRID_NE, CGRID_NE, SCALAR_PAIR, BITWISE_EXACT_SUM
 use mpp_domains_mod, only : CYCLIC_GLOBAL_DOMAIN, FOLD_NORTH_EDGE
@@ -38,7 +38,7 @@ module MOM_domain_infra
 public :: domain2D, domain1D, group_pass_type
 ! These interfaces are actually implemented or have explicit interfaces in this file.
 public :: create_MOM_domain, clone_MOM_domain, get_domain_components, get_domain_extent
-public :: deallocate_MOM_domain, get_global_shape, compute_block_extent
+public :: deallocate_MOM_domain, get_global_shape, compute_block_extent, compute_extent
 public :: pass_var, pass_vector, fill_symmetric_edges, rescale_comp_data
 public :: pass_var_start, pass_var_complete, pass_vector_start, pass_vector_complete
 public :: create_group_pass, do_group_pass, start_group_pass, complete_group_pass
@@ -1936,7 +1936,7 @@ subroutine get_global_shape(domain, niglobal, njglobal)
   njglobal = domain%njglobal
 end subroutine get_global_shape
 
-!> Get the array ranges in one dimension for the divisions of a global index space
+!> Get the array ranges in one dimension for the divisions of a global index space (alternative to compute_extent)
 subroutine compute_block_extent(isg, ieg, ndivs, ibegin, iend)
   integer,               intent(in)  :: isg    !< The starting index of the global index space
   integer,               intent(in)  :: ieg    !< The ending index of the global index space
@@ -1947,6 +1947,17 @@ subroutine compute_block_extent(isg, ieg, ndivs, ibegin, iend)
   call mpp_compute_block_extent(isg, ieg, ndivs, ibegin, iend)
 end subroutine compute_block_extent
 
+!> Get the array ranges in one dimension for the divisions of a global index space
+subroutine compute_extent(isg, ieg, ndivs, ibegin, iend)
+  integer,               intent(in)  :: isg    !< The starting index of the global index space
+  integer,               intent(in)  :: ieg    !< The ending index of the global index space
+  integer,               intent(in)  :: ndivs  !< The number of divisions
+  integer, dimension(:), intent(out) :: ibegin !< The starting index of each division
+  integer, dimension(:), intent(out) :: iend   !< The ending index of each division
+
+  call mpp_compute_extent(isg, ieg, ndivs, ibegin, iend)
+end subroutine compute_extent
+
 !> Broadcast a 2-d domain from the root PE to the other PEs
 subroutine broadcast_domain(domain)
   type(domain2d),  intent(inout) :: domain !< The domain2d type that will be shared across PEs.

src/core/MOM.F90

@@ -2539,12 +2539,12 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, &
   G_in => CS%G_in
 #ifdef STATIC_MEMORY_
   call MOM_domains_init(G_in%domain, param_file, symmetric=symmetric, &
-            static_memory=.true., NIHALO=NIHALO_, NJHALO=NJHALO_, &
-            NIGLOBAL=NIGLOBAL_, NJGLOBAL=NJGLOBAL_, NIPROC=NIPROC_, &
-            NJPROC=NJPROC_)
+                        static_memory=.true., NIHALO=NIHALO_, NJHALO=NJHALO_, &
+                        NIGLOBAL=NIGLOBAL_, NJGLOBAL=NJGLOBAL_, NIPROC=NIPROC_, &
+                        NJPROC=NJPROC_, US=US)
 #else
   call MOM_domains_init(G_in%domain, param_file, symmetric=symmetric, &
-                        domain_name="MOM_in")
+                        domain_name="MOM_in", US=US)
 #endif
 
   ! Copy input grid (G_in) domain to active grid G