Merge pull request #16 from NOAA-GFDL/dev/gfdl

Merge in latest dev/gfdl commits

.gitlab-ci.yml

@@ -32,8 +32,9 @@ setup:
     - git clone --recursive http://gitlab.gfdl.noaa.gov/ogrp/Gaea-stats-MOM6-examples.git tests && cd tests
     # Install / update testing scripts
     - git clone https://github.com/adcroft/MRS.git MRS
+    - (cd MRS ; git checkout 9badc63acefbf038)
     # Update MOM6-examples and submodules
-    - (cd MOM6-examples && git checkout . && git checkout dev/gfdl && git pull && git submodule init && git submodule update)
+    - (cd MOM6-examples && git checkout . && git checkout dev/gfdl && git pull && git checkout cf73a9ad63f8ccf7 && git submodule init && git submodule update)
     - (cd MOM6-examples/src/MOM6 && git submodule update)
     - test -d MOM6-examples/src/LM3 || make -f MRS/Makefile.clone clone_gfdl -s
     - make -f MRS/Makefile.clone MOM6-examples/.datasets -s
@@ -73,7 +74,7 @@ gnu:ice-ocean-nolibs:
     - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
     - make -f MRS/Makefile.build build/gnu/env && cd build/gnu
     # mkdir -p build/gnu/repro/symmetric_dynamic/ocean_only && cd build/gnu/repro/symmetric_dynamic/ocean_only
-    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{coupled_driver,dynamic} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_ocean_extras,land_null,atmos_null}
+    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{coupled_driver,dynamic} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_param,land_null,atmos_null}
     - ../../MOM6-examples/src/mkmf/bin/mkmf -t ../../MOM6-examples/src/mkmf/templates/ncrc-gnu.mk -p MOM6 -c"-Duse_libMPI -Duse_netCDF -D_USE_LEGACY_LAND_ -Duse_AM3_physics" path_names
     - time (source ./env ; make NETCDF=3 REPRO=1 MOM6 -s -j)
 

src/diagnostics/MOM_sum_output.F90

@@ -3,6 +3,7 @@ module MOM_sum_output
 
 ! This file is part of MOM6. See LICENSE.md for the license.
 
+use iso_fortran_env, only : int64
 use MOM_coms, only : sum_across_PEs, PE_here, root_PE, num_PEs, max_across_PEs
 use MOM_coms, only : reproducing_sum, EFP_to_real, real_to_EFP
 use MOM_coms, only : EFP_type, operator(+), operator(-), assignment(=)
@@ -24,6 +25,7 @@ module MOM_sum_output
 use MOM_unit_scaling, only : unit_scale_type
 use MOM_variables, only : surface, thermo_var_ptrs
 use MOM_verticalGrid, only : verticalGrid_type
+use mpp_mod, only : mpp_chksum
 
 use netcdf
 
@@ -39,6 +41,13 @@ module MOM_sum_output
 ! vary with the Boussinesq approximation, the Boussinesq variant is given first.
 
 integer, parameter :: NUM_FIELDS = 17 !< Number of diagnostic fields
+character (*), parameter :: depth_chksum_attr = "bathyT_checksum"
+                                      !< Checksum attribute name of G%bathyT
+                                      !! over the compute domain
+character (*), parameter :: area_chksum_attr = "mask2dT_areaT_checksum"
+                                      !< Checksum attribute of name of
+                                      !! G%mask2dT * G%areaT over the compute
+                                      !! domain
 
 !> A list of depths and corresponding globally integrated ocean area at each
 !! depth and the ocean volume below each depth.
@@ -64,6 +73,12 @@ module MOM_sum_output
   character(len=200) :: depth_list_file  !< The name of the depth list file.
   real    :: D_list_min_inc     !<  The minimum increment [Z ~> m], between the depths of the
                                 !! entries in the depth-list file, 0 by default.
+  logical :: require_depth_list_chksum
+                                !< Require matching checksums in Depth_list.nc when reading
+                                !! the file.
+  logical :: update_depth_list_chksum
+                                !< Automatically update the Depth_list.nc file if the
+                                !! checksums are missing or do not match current values.
   logical :: use_temperature    !<   If true, temperature and salinity are state variables.
   real    :: fresh_water_input  !<   The total mass of fresh water added by surface fluxes
                                 !! since the last time that write_energy was called [kg].
@@ -226,6 +241,17 @@ subroutine MOM_sum_output_init(G, US, param_file, directory, ntrnc, &
                    "The name of the depth list file.", default="Depth_list.nc")
       if (scan(CS%depth_list_file,'/') == 0) &
         CS%depth_list_file = trim(slasher(directory))//trim(CS%depth_list_file)
+
+      call get_param(param_file, mdl, "REQUIRE_DEPTH_LIST_CHECKSUMS", &
+                     CS%require_depth_list_chksum, &
+                 "Require that matching checksums be in Depth_list.nc\n" // &
+                 "when reading the file.", default=.true.)
+      if (.not. CS%require_depth_list_chksum) &
+        call get_param(param_file, mdl, "UPDATE_DEPTH_LIST_CHECKSUMS", &
+                     CS%update_depth_list_chksum, &
+                 "Automatically update the Depth_list.nc file if the\n" // &
+                 "checksums are missing or do not match current values.", &
+                 default=.false.)
     endif
 
     allocate(CS%lH(G%ke))
@@ -1102,7 +1128,7 @@ subroutine create_depth_list(G, CS)
 
     list_pos = (j_global-1)*G%Domain%niglobal + i_global
     Dlist(list_pos) = G%bathyT(i,j)
-    Arealist(list_pos) = G%mask2dT(i,j)*G%areaT(i,j)
+    Arealist(list_pos) = G%mask2dT(i,j) * G%areaT(i,j)
   enddo ; enddo
 
   ! These sums reproduce across PEs because the arrays are only nonzero on one PE.
@@ -1203,6 +1229,10 @@ subroutine write_depth_list(G, US, CS, filename, list_size)
   ! Local variables
   real, allocatable :: tmp(:)
   integer :: ncid, dimid(1), Did, Aid, Vid, status, k
+  character(len=16) :: depth_chksum, area_chksum
+
+  ! All ranks are required to compute the global checksum
+  call get_depth_list_checksums(G, depth_chksum, area_chksum)
 
   if (.not.is_root_pe()) return
 
@@ -1248,6 +1278,15 @@ subroutine write_depth_list(G, US, CS, filename, list_size)
   if (status /= NF90_NOERR) call MOM_error(WARNING, &
       filename//" vol_below "//trim(NF90_STRERROR(status)))
 
+  ! Dependency checksums
+  status = NF90_PUT_ATT(ncid, NF90_GLOBAL, depth_chksum_attr, depth_chksum)
+  if (status /= NF90_NOERR) call MOM_error(WARNING, &
+      filename//" "//depth_chksum_attr//" "//trim(NF90_STRERROR(status)))
+
+  status = NF90_PUT_ATT(ncid, NF90_GLOBAL, area_chksum_attr, area_chksum)
+  if (status /= NF90_NOERR) call MOM_error(WARNING, &
+      filename//" "//area_chksum_attr//" "//trim(NF90_STRERROR(status)))
+
   status = NF90_ENDDEF(ncid)
   if (status /= NF90_NOERR) call MOM_error(WARNING, &
       filename//trim(NF90_STRERROR(status)))
@@ -1287,6 +1326,9 @@ subroutine read_depth_list(G, US, CS, filename)
   real, allocatable :: tmp(:)
   integer :: ncid, status, varid, list_size, k
   integer :: ndim, len, var_dim_ids(NF90_MAX_VAR_DIMS)
+  character(len=16) :: depth_file_chksum, depth_grid_chksum
+  character(len=16) :: area_file_chksum, area_grid_chksum
+  integer :: depth_attr_status, area_attr_status
 
   mdl = "MOM_sum_output read_depth_list:"
 
@@ -1296,6 +1338,60 @@ subroutine read_depth_list(G, US, CS, filename)
         " - "//trim(NF90_STRERROR(status)))
   endif
 
+  ! Check bathymetric consistency
+  depth_attr_status = NF90_GET_ATT(ncid, NF90_GLOBAL, depth_chksum_attr, &
+                                   depth_file_chksum)
+  area_attr_status = NF90_GET_ATT(ncid, NF90_GLOBAL, area_chksum_attr, &
+                                  area_file_chksum)
+
+  if (any([depth_attr_status, area_attr_status] == NF90_ENOTATT)) then
+    var_msg = trim(CS%depth_list_file) // " checksums are missing;"
+    if (CS%require_depth_list_chksum) then
+      call MOM_error(FATAL, trim(var_msg) // " aborting.")
+    elseif (CS%update_depth_list_chksum) then
+      call MOM_error(WARNING, trim(var_msg) // " updating file.")
+      call create_depth_list(G, CS)
+      call write_depth_list(G, US, CS, CS%depth_list_file, CS%list_size+1)
+      return
+    else
+      call MOM_error(WARNING, &
+        trim(var_msg) // " some diagnostics may not be reproducible.")
+    endif
+  else
+    ! Validate netCDF call
+    if (depth_attr_status /= NF90_NOERR) then
+      var_msg = mdl // "Failed to read " // trim(filename) // ":" &
+                // depth_chksum_attr
+      call MOM_error(FATAL, &
+        trim(var_msg) // " - " // NF90_STRERROR(depth_attr_status))
+    endif
+
+    if (area_attr_status /= NF90_NOERR) then
+      var_msg = mdl // "Failed to read " // trim(filename) // ":" &
+                // area_chksum_attr
+      call MOM_error(FATAL, &
+        trim(var_msg) // " - " // NF90_STRERROR(area_attr_status))
+    endif
+
+    call get_depth_list_checksums(G, depth_grid_chksum, area_grid_chksum)
+
+    if (depth_grid_chksum /= depth_file_chksum &
+            .or. area_grid_chksum /= area_file_chksum) then
+      var_msg = trim(CS%depth_list_file) // " checksums do not match;"
+      if (CS%require_depth_list_chksum) then
+        call MOM_error(FATAL, trim(var_msg) // " aborting.")
+      elseif (CS%update_depth_list_chksum) then
+        call MOM_error(WARNING, trim(var_msg) // " updating file.")
+        call create_depth_list(G, CS)
+        call write_depth_list(G, US, CS, CS%depth_list_file, CS%list_size+1)
+        return
+      else
+        call MOM_error(WARNING, &
+          trim(var_msg) // " some diagnostics may not be reproducible.")
+      endif
+    endif
+  endif
+
   var_name = "depth"
   var_msg = trim(var_name)//" in "//trim(filename)//" - "
   status = NF90_INQ_VARID(ncid, var_name, varid)
@@ -1363,6 +1459,42 @@ subroutine read_depth_list(G, US, CS, filename)
 
 end subroutine read_depth_list
 
+
+!> Return the checksums required to verify DEPTH_LIST_FILE contents.
+!!
+!! This function computes checksums for the bathymetry (G%bathyT) and masked
+!! area (mask2dT * areaT) fields of the model grid G, which are used to compute
+!! the depth list.  A difference in checksum indicates that a different method
+!! was used to compute the grid data, and that any results using the depth
+!! list, such as APE, will not be reproducible.
+!!
+!! Checksums are saved as hexadecimal strings, in order to avoid potential
+!! datatype issues with netCDF attributes.
+subroutine get_depth_list_checksums(G, depth_chksum, area_chksum)
+  type(ocean_grid_type), intent(in) :: G          !< Ocean grid structure
+  character(len=16), intent(out) :: depth_chksum  !< Depth checksum hexstring
+  character(len=16), intent(out) :: area_chksum   !< Area checksum hexstring
+
+  integer :: i, j
+  real, allocatable :: field(:,:)
+
+  allocate(field(G%isc:G%iec, G%jsc:G%jec))
+
+  ! Depth checksum
+  do j=G%jsc,G%jec ; do i=G%isc,G%iec
+    field(i,j) = G%bathyT(i,j)
+  enddo ; enddo
+  write(depth_chksum, '(Z16)') mpp_chksum(field(:,:))
+
+  ! Area checksum
+  do j=G%jsc,G%jec ; do i=G%isc,G%iec
+    field(i,j) = G%mask2dT(i,j) * G%areaT(i,j)
+  enddo ; enddo
+  write(area_chksum, '(Z16)') mpp_chksum(field(:,:))
+
+  deallocate(field)
+end subroutine get_depth_list_checksums
+
 !> \namespace mom_sum_output
 !!
 !! By Robert Hallberg, April 1994 - June 2002