Automated Runtime Land Block Elimination (#263)

* Enhancements for adding land block elimination to NUOPC cap:
 - Add sum_across_PEs_int4_2d to the sum_across_PEs interface
 - Allow mask_table file to be placed in run directory (now,
the first dir that is looked at).

* Enhance NUOPC cap to support MOM_mask_table.

- Determine masked blocks.
- Evenly distribute eliminated cells.
- Fill ESMF gindex array accordingly.
- During Export phase, set fields of eliminated cells to zero.

* set %label in register_netcdf_field and register_netcdf_axis

* first working version of an automated mask table generator

* While determining masked blocks, take reentrancy and tripolar stitch into account

* apply tripolar stitch fix in auto mask_table generation

* add AUTO_IO_LAYOUT_FAC parameter to control IO_LOAYUT when AUTO_MASKTABLE is on

* Miscellaneous auto masking fixes to address reviews:

- Dimensionalize topographic depth variables used to determine cell masks in auto masktable routine.
- Raise error if the user provided PE layout is inconsistent with auto masktable generation.
- Save the masktable parameter description to a string variable to avoid repetition.
- Fix typos, whitespaces, use modern array syntax.

* Disable FPEs in MacOS testing

Due to poor handling of floating point in HDF5 1.14.3, it is currently
not possible to use floating point exceptions (FPEs) whenever this
version is present.

The GitHub Actions CI nodes would randomly select either 1.14.2 or
1.14.3, and would raise an FPE error if 1.14.3 was selected.
Additionally, the homebrew installation does not provide a clean method
for selecting a different version of HDF5.

Thus, for now we disable FPEs in the MacOS testing, and hope to catch
any legitimate FP errors in the Ubuntu version.  We will restore these
tests as soon as this has been fixed in an easily-accessible version of
HDF5.

As part of this PR, I have also moved the FCFLAGS configuration to the
platform specific Actions files, allowing for independent compiler
configuration for each platform.

---------

Co-authored-by: Marshall Ward <marshall.ward@noaa.gov>

.github/actions/macos-setup/action.yml

@@ -16,3 +16,18 @@ runs:
         brew install netcdf-fortran
         brew install mpich
         echo "::endgroup::"
+
+    # NOTE: Floating point exceptions are currently disabled due to an error in
+    # HDF5 1.4.3.  They will be re-enabled when the default brew version has
+    # been updated to a working version.
+
+    - name: Set compiler flags
+      shell: bash
+      run: |
+        cd .testing
+        echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
+        cat config.mk
+        echo "::endgroup::"

.github/actions/testing-setup/action.yml

@@ -31,17 +31,6 @@ runs:
         REPORT_ERROR_LOGS=true make deps/lib/libFMS.a -s -j
         echo "::endgroup::"
 
-    - name: Store compiler flags used in Makefile
-      shell: bash
-      run: |
-        echo "::group::config.mk"
-        cd .testing
-        echo "FCFLAGS_DEBUG=-g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
-        echo "FCFLAGS_REPRO=-g -O2 -fbacktrace" >> config.mk
-        echo "FCFLAGS_INIT=-finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
-        cat config.mk
-        echo "::endgroup::"
-
     - name: Compile MOM6 in symmetric memory mode
       shell: bash
       run: |

.github/actions/ubuntu-setup/action.yml

@@ -17,3 +17,15 @@ runs:
         sudo apt-get install libopenmpi-dev
         sudo apt-get install linux-tools-common
         echo "::endgroup::"
+
+    - name: Store compiler flags used in Makefile
+      shell: bash
+      run: |
+        echo "::group::config.mk"
+        cd .testing
+        echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
+        cat config.mk
+        echo "::endgroup::"

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
@@ -826,6 +827,7 @@ 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(:)
@@ -852,6 +854,8 @@ 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
@@ -875,6 +879,11 @@ 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(:,:)
   !--------------------------------
 
   rc = ESMF_SUCCESS
@@ -919,19 +928,19 @@ 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
@@ -953,17 +962,102 @@ 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
@@ -987,6 +1081,10 @@ 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))
@@ -1018,7 +1116,7 @@ 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 "//&
@@ -1122,11 +1220,11 @@ 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)

config_src/drivers/nuopc_cap/mom_cap_methods.F90

@@ -852,7 +852,7 @@ 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(:,:)
@@ -888,6 +888,13 @@ 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.