Merge remote-tracking branch 'origin' into SPEAR_ECDA

.gitlab-ci.yml

@@ -38,6 +38,10 @@ setup:
     - test -d MOM6-examples/src/LM3 || make -f MRS/Makefile.clone clone_gfdl -s
     - make -f MRS/Makefile.clone MOM6-examples/.datasets -s
     - env > gitlab_session.log
+    # Show hashes for final setup
+    - git show --oneline
+    - git submodule status
+    - (cd MOM6-examples && git submodule status --recursive src)
     # Cache everything under tests to unpack for each subsequent stage
     - cd ../ ; time tar zcf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz tests
 

.testing/Makefile

@@ -193,7 +193,7 @@ endif
 # Rules
 
 .PHONY: all build.regressions
-all: $(foreach b,$(BUILDS),build/$(b)/MOM6)
+all: $(foreach b,$(BUILDS),build/$(b)/MOM6) $(VENV_PATH)
 build.regressions: $(foreach b,symmetric target,build/$(b)/MOM6)
 
 # Executable
@@ -361,6 +361,7 @@ check_mom6_api_mct: build/mct/mom_ocean_model_mct.o
 work/local-env:
 	python3 -m venv $@
 	. $@/bin/activate \
+	  && python3 -m pip install --upgrade pip \
 	  && pip3 install wheel \
 	  && pip3 install cython \
 	  && pip3 install numpy \

ac/configure.ac

@@ -59,6 +59,18 @@ AS_IF([test "x$with_driver" != "x"],
 # used to configure a header based on a template.
 #AC_CONFIG_HEADERS(["$MEM_LAYOUT/MOM_memory.h"])
 
+# Select the model framework (default: FMS1)
+# NOTE: We can phase this out after the FMS1 I/O has been removed from FMS and
+#   replace with a detection test.  For now, it is a user-defined switch.
+MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS1
+AC_ARG_WITH([framework],
+  AS_HELP_STRING([--with-framework=fms1|fms2], [Select the model framework]))
+AS_CASE([with_framework],
+  [fms1], [MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS1],
+  [fms2], [MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS2],
+  [MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS1]
+)
+
 
 # Explicitly assume free-form Fortran
 AC_LANG(Fortran)
@@ -192,6 +204,22 @@ AX_FC_CHECK_LIB([FMS], [fms_init], [fms_mod],
 )
 
 
+# Verify that FMS is at least 2019.01.02
+# NOTE: 2019.01.02 introduced two changes:
+#   - diag_axis_init supports an optional domain_position argument
+#   - position values NORTH, EAST, CENTER were added to diag_axis_mod
+# For our versioning test, we check the second feature.
+AC_MSG_CHECKING([if diag_axis_mod supports domain positions])
+AC_COMPILE_IFELSE(
+  [AC_LANG_PROGRAM([], [use diag_axis_mod, only: NORTH, EAST, CENTER])],
+  [AC_MSG_RESULT([yes])],
+  [
+    AC_MSG_RESULT([no])
+    AC_MSG_ERROR([diag_axis_mod in MOM6 requires FMS 2019.01.02 or newer.])
+  ]
+)
+
+
 # Search for mkmf build tools
 AC_PATH_PROG([LIST_PATHS], [list_paths])
 AS_IF([test -z "$LIST_PATHS"], [
@@ -216,11 +244,14 @@ AS_IF([test -z "$MKMF"], [
 AC_CONFIG_COMMANDS([path_names],
   [list_paths -l \
     ${srcdir}/src \
-    ${srcdir}/config_src/infra/FMS1 \
+    ${MODEL_FRAMEWORK} \
     ${srcdir}/config_src/ext* \
     ${DRIVER_DIR} \
-    ${MEM_LAYOUT}
-], [MEM_LAYOUT=$MEM_LAYOUT DRIVER_DIR=$DRIVER_DIR])
+    ${MEM_LAYOUT}],
+  [MODEL_FRAMEWORK=$MODEL_FRAMEWORK
+    MEM_LAYOUT=$MEM_LAYOUT
+    DRIVER_DIR=$DRIVER_DIR]
+)
 
 
 AC_CONFIG_COMMANDS([Makefile.mkmf],

config_src/drivers/FMS_cap/MOM_surface_forcing_gfdl.F90

@@ -27,7 +27,8 @@ module MOM_surface_forcing_gfdl
 use MOM_grid,             only : ocean_grid_type
 use MOM_interpolate,      only : init_external_field, time_interp_external
 use MOM_interpolate,      only : time_interp_external_init
-use MOM_io,               only : slasher, write_version_number, MOM_read_data, stdout
+use MOM_io,               only : slasher, write_version_number, MOM_read_data
+use MOM_io,               only : stdout_if_root
 use MOM_restart,          only : register_restart_field, restart_init, MOM_restart_CS
 use MOM_restart,          only : restart_init_end, save_restart, restore_state
 use MOM_string_functions, only : uppercase
@@ -110,6 +111,8 @@ module MOM_surface_forcing_gfdl
   logical :: restore_temp       !< If true, the coupled MOM driver adds a term to restore sea
                                 !! surface temperature to a specified value.
   real    :: Flux_const                     !< Piston velocity for surface restoring [Z T-1 ~> m s-1]
+  real    :: Flux_const_salt                !< Piston velocity for surface salt restoring [Z T-1 ~> m s-1]
+  real    :: Flux_const_temp                !< Piston velocity for surface temp restoring [Z T-1 ~> m s-1]
   logical :: salt_restore_as_sflux          !< If true, SSS restore as salt flux instead of water flux
   logical :: adjust_net_srestore_to_zero    !< Adjust srestore to zero (for both salt_flux or vprec)
   logical :: adjust_net_srestore_by_scaling !< Adjust srestore w/o moving zero contour
@@ -290,22 +293,18 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, valid_time, G,
 
     call safe_alloc_ptr(fluxes%salt_flux,isd,ied,jsd,jed)
     call safe_alloc_ptr(fluxes%salt_flux_in,isd,ied,jsd,jed)
-    call safe_alloc_ptr(fluxes%salt_flux_added,isd,ied,jsd,jed)
 
     call safe_alloc_ptr(fluxes%TKE_tidal,isd,ied,jsd,jed)
     call safe_alloc_ptr(fluxes%ustar_tidal,isd,ied,jsd,jed)
 
-    if (CS%allow_flux_adjustments) then
-      call safe_alloc_ptr(fluxes%heat_added,isd,ied,jsd,jed)
-      call safe_alloc_ptr(fluxes%salt_flux_added,isd,ied,jsd,jed)
-    endif
+    call safe_alloc_ptr(fluxes%heat_added,isd,ied,jsd,jed)
+    call safe_alloc_ptr(fluxes%salt_flux_added,isd,ied,jsd,jed)
 
     do j=js-2,je+2 ; do i=is-2,ie+2
       fluxes%TKE_tidal(i,j)   = CS%TKE_tidal(i,j)
       fluxes%ustar_tidal(i,j) = CS%ustar_tidal(i,j)
     enddo ; enddo
 
-    if (CS%restore_temp) call safe_alloc_ptr(fluxes%heat_added,isd,ied,jsd,jed)
 
   endif   ! endif for allocation and initialization
 
@@ -335,10 +334,8 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, valid_time, G,
   fluxes%fluxes_used = .false.
   fluxes%dt_buoy_accum = US%s_to_T*valid_time
 
-  if (CS%allow_flux_adjustments) then
-    fluxes%heat_added(:,:) = 0.0
-    fluxes%salt_flux_added(:,:) = 0.0
-  endif
+  fluxes%heat_added(:,:) = 0.0
+  fluxes%salt_flux_added(:,:) = 0.0
 
   do j=js,je ; do i=is,ie
     fluxes%salt_flux(i,j) = 0.0
@@ -359,7 +356,7 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, valid_time, G,
       do j=js,je ; do i=is,ie
         delta_sss = data_restore(i,j)- sfc_state%SSS(i,j)
         delta_sss = sign(1.0,delta_sss)*min(abs(delta_sss),CS%max_delta_srestore)
-        fluxes%salt_flux(i,j) = 1.e-3*G%mask2dT(i,j) * (CS%Rho0*CS%Flux_const)* &
+        fluxes%salt_flux(i,j) = 1.e-3*G%mask2dT(i,j) * (CS%Rho0*CS%Flux_const_salt)* &
              (CS%basin_mask(i,j)*open_ocn_mask(i,j)*CS%srestore_mask(i,j)) *delta_sss  ! R Z T-1 ~> kg Salt m-2 s-1
       enddo ; enddo
       if (CS%adjust_net_srestore_to_zero) then
@@ -369,9 +366,10 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, valid_time, G,
           fluxes%saltFluxGlobalAdj = 0.
         else
           work_sum(is:ie,js:je) = US%L_to_m**2*US%RZ_T_to_kg_m2s * &
-                  G%areaT(is:ie,js:je)*fluxes%salt_flux(is:ie,js:je)
+                  G%areaT(is:ie,js:je)*fluxes%salt_flux(is:ie,js:je) * G%mask2dT(is:ie,js:je)
           fluxes%saltFluxGlobalAdj = reproducing_sum(work_sum(:,:), isr,ier, jsr,jer)/CS%area_surf
-          fluxes%salt_flux(is:ie,js:je) = fluxes%salt_flux(is:ie,js:je) - kg_m2_s_conversion * fluxes%saltFluxGlobalAdj
+          fluxes%salt_flux(is:ie,js:je) = fluxes%salt_flux(is:ie,js:je) - &
+                                          kg_m2_s_conversion * fluxes%saltFluxGlobalAdj * G%mask2dT(is:ie,js:je)
         endif
       endif
       fluxes%salt_flux_added(is:ie,js:je) = fluxes%salt_flux(is:ie,js:je) ! Diagnostic
@@ -381,7 +379,7 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, valid_time, G,
           delta_sss = sfc_state%SSS(i,j) - data_restore(i,j)
           delta_sss = sign(1.0,delta_sss)*min(abs(delta_sss),CS%max_delta_srestore)
           fluxes%vprec(i,j) = (CS%basin_mask(i,j)*open_ocn_mask(i,j)*CS%srestore_mask(i,j))* &
-                      (CS%Rho0*CS%Flux_const) * &
+                      (CS%Rho0*CS%Flux_const_salt) * &
                       delta_sss / (0.5*(sfc_state%SSS(i,j) + data_restore(i,j)))
         endif
       enddo ; enddo
@@ -409,7 +407,7 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, valid_time, G,
       delta_sst = data_restore(i,j)- sfc_state%SST(i,j)
       delta_sst = sign(1.0,delta_sst)*min(abs(delta_sst),CS%max_delta_trestore)
       fluxes%heat_added(i,j) = G%mask2dT(i,j) * CS%trestore_mask(i,j) * &
-                               rhoXcp * delta_sst * CS%Flux_const  ! W m-2
+                               rhoXcp * delta_sst * CS%Flux_const_temp  ! W m-2
     enddo ; enddo
   endif
 
@@ -1111,7 +1109,7 @@ subroutine apply_flux_adjustments(G, US, CS, Time, fluxes)
   type(forcing),            intent(inout) :: fluxes !< Surface fluxes structure
 
   ! Local variables
-  real, dimension(SZI_(G),SZJ_(G)) :: temp_at_h ! Various fluxes at h points [W m-2] or [kg m-2 s-1]
+  real, dimension(G%isc:G%iec,G%jsc:G%jec) :: temp_at_h ! Various fluxes at h points [W m-2] or [kg m-2 s-1]
 
   integer :: isc, iec, jsc, jec, i, j
   logical :: overrode_h
@@ -1251,6 +1249,7 @@ subroutine surface_forcing_init(Time, G, US, param_file, diag, CS, wind_stagger)
   character(len=48)  :: flnam
   character(len=240) :: basin_file
   integer :: i, j, isd, ied, jsd, jed
+  real :: unscaled_fluxconst
 
   isd = G%isd ; ied = G%ied ; jsd = G%jsd ; jed = G%jed
 
@@ -1374,9 +1373,14 @@ subroutine surface_forcing_init(Time, G, US, param_file, diag, CS, wind_stagger)
     call get_param(param_file, mdl, "FLUXCONST", CS%Flux_const, &
                  "The constant that relates the restoring surface fluxes to the relative "//&
                  "surface anomalies (akin to a piston velocity).  Note the non-MKS units.", &
-                 default=0.0, units="m day-1", scale=US%m_to_Z*US%T_to_s)
+                 default=0.0, units="m day-1", scale=US%m_to_Z*US%T_to_s,unscaled=unscaled_fluxconst)
+    call get_param(param_file, mdl, "FLUXCONST_SALT", CS%Flux_const_salt, &
+                 "The constant that relates the restoring surface salt fluxes to the relative "//&
+                 "surface anomalies (akin to a piston velocity).  Note the non-MKS units.", &
+                 fail_if_missing=.false.,default=unscaled_fluxconst, units="m day-1", scale=US%m_to_Z*US%T_to_s)
     ! Convert CS%Flux_const from m day-1 to m s-1.
     CS%Flux_const = CS%Flux_const / 86400.0
+    CS%Flux_const_salt = CS%Flux_const_salt / 86400.0
     call get_param(param_file, mdl, "SALT_RESTORE_FILE", CS%salt_restore_file, &
                  "A file in which to find the surface salinity to use for restoring.", &
                  default="salt_restore.nc")
@@ -1421,9 +1425,14 @@ subroutine surface_forcing_init(Time, G, US, param_file, diag, CS, wind_stagger)
     call get_param(param_file, mdl, "FLUXCONST", CS%Flux_const, &
                  "The constant that relates the restoring surface fluxes to the relative "//&
                  "surface anomalies (akin to a piston velocity).  Note the non-MKS units.", &
-                 default=0.0, units="m day-1", scale=US%m_to_Z*US%T_to_s)
+                 default=0.0, units="m day-1", scale=US%m_to_Z*US%T_to_s,unscaled=unscaled_fluxconst)
+    call get_param(param_file, mdl, "FLUXCONST_TEMP", CS%Flux_const_temp, &
+                 "The constant that relates the restoring surface temperature fluxes to the relative "//&
+                 "surface anomalies (akin to a piston velocity).  Note the non-MKS units.", &
+                 fail_if_missing=.false.,default=unscaled_fluxconst, units="m day-1", scale=US%m_to_Z*US%T_to_s)
     ! Convert CS%Flux_const from m day-1 to m s-1.
     CS%Flux_const = CS%Flux_const / 86400.0
+    CS%Flux_const_temp = CS%Flux_const_temp / 86400.0
     call get_param(param_file, mdl, "SST_RESTORE_FILE", CS%temp_restore_file, &
                  "A file in which to find the surface temperature to use for restoring.", &
                  default="temp_restore.nc")
@@ -1628,8 +1637,8 @@ subroutine ice_ocn_bnd_type_chksum(id, timestep, iobt)
   logical :: root    ! True only on the root PE
   integer :: outunit ! The output unit to write to
 
-  outunit = stdout
   root = is_root_pe()
+  outunit = stdout_if_root()
 
   if (root) write(outunit,*) "BEGIN CHECKSUM(ice_ocean_boundary_type):: ", id, timestep
   chks = field_chksum( iobt%u_flux         ) ; if (root) write(outunit,100) 'iobt%u_flux         ', chks

config_src/drivers/FMS_cap/ocean_model_MOM.F90

@@ -35,7 +35,7 @@ module ocean_model_mod
 use MOM_forcing_type, only : forcing_diagnostics, mech_forcing_diags
 use MOM_get_input, only : Get_MOM_Input, directories
 use MOM_grid, only : ocean_grid_type
-use MOM_io, only : write_version_number, stdout
+use MOM_io, only : write_version_number, stdout_if_root
 use MOM_marine_ice, only : iceberg_forces, iceberg_fluxes, marine_ice_init, marine_ice_CS
 use MOM_restart, only : MOM_restart_CS, save_restart
 use MOM_string_functions, only : uppercase
@@ -55,7 +55,7 @@ module ocean_model_mod
 use MOM_ice_shelf, only : initialize_ice_shelf, shelf_calc_flux, ice_shelf_CS
 use MOM_ice_shelf, only : add_shelf_forces, ice_shelf_end, ice_shelf_save_restart
 use MOM_wave_interface, only: wave_parameters_CS, MOM_wave_interface_init
-use MOM_wave_interface, only: MOM_wave_interface_init_lite, Update_Surface_Waves
+use MOM_wave_interface, only: Update_Surface_Waves
 use iso_fortran_env, only : int64
 
 #include <MOM_memory.h>
@@ -205,7 +205,7 @@ module ocean_model_mod
     marine_ice_CSp => NULL()  !< A pointer to the control structure for the
                               !! marine ice effects module.
   type(wave_parameters_cs), pointer :: &
-    Waves !< A structure containing pointers to the surface wave fields
+    Waves => NULL()           !< A pointer to the surface wave control structure
   type(surface_forcing_CS), pointer :: &
     forcing_CSp => NULL()     !< A pointer to the MOM forcing control structure
   type(MOM_restart_CS), pointer :: &
@@ -382,11 +382,9 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
 
   call get_param(param_file, mdl, "USE_WAVES", OS%Use_Waves, &
        "If true, enables surface wave modules.", default=.false.)
-  if (OS%use_waves) then
-    call MOM_wave_interface_init(OS%Time, OS%grid, OS%GV, OS%US, param_file, OS%Waves, OS%diag)
-  else
-    call MOM_wave_interface_init_lite(param_file)
-  endif
+  ! MOM_wave_interface_init is called regardless of the value of USE_WAVES because
+  ! it also initializes statistical waves.
+  call MOM_wave_interface_init(OS%Time, OS%grid, OS%GV, OS%US, param_file, OS%Waves, OS%diag)
 
   call initialize_ocean_public_type(OS%grid%Domain, Ocean_sfc, OS%diag, &
                                     gas_fields_ocn=gas_fields_ocn)
@@ -1107,8 +1105,8 @@ subroutine ocean_public_type_chksum(id, timestep, ocn)
   logical :: root    ! True only on the root PE
   integer :: outunit ! The output unit to write to
 
-  outunit = stdout
   root = is_root_pe()
+  outunit = stdout_if_root()
 
   if (root) write(outunit,*) "BEGIN CHECKSUM(ocean_type):: ", id, timestep
   chks = field_chksum(ocn%t_surf ) ; if (root) write(outunit,100) 'ocean%t_surf   ', chks

config_src/drivers/mct_cap/mom_ocean_model_mct.F90

@@ -61,7 +61,7 @@ module MOM_ocean_model_mct
 use mpp_mod,                  only : mpp_chksum
 use MOM_EOS,                  only : gsw_sp_from_sr, gsw_pt_from_ct
 use MOM_wave_interface,       only : wave_parameters_CS, MOM_wave_interface_init
-use MOM_wave_interface,       only : MOM_wave_interface_init_lite, Update_Surface_Waves
+use MOM_wave_interface,       only : Update_Surface_Waves
 use time_interp_external_mod, only : time_interp_external_init
 
 ! MCT specfic routines
@@ -205,7 +205,7 @@ module MOM_ocean_model_mct
     marine_ice_CSp => NULL()  !< A pointer to the control structure for the
                               !! marine ice effects module.
   type(wave_parameters_cs), pointer :: &
-    Waves !< A structure containing pointers to the surface wave fields
+    Waves => NULL()           !< A pointer to the surface wave control structure
   type(surface_forcing_CS), pointer :: &
     forcing_CSp => NULL()     !< A pointer to the MOM forcing control structure
   type(MOM_restart_CS), pointer :: &
@@ -383,11 +383,9 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
 
   call get_param(param_file, mdl, "USE_WAVES", OS%Use_Waves, &
        "If true, enables surface wave modules.", default=.false.)
-  if (OS%use_waves) then
-    call MOM_wave_interface_init(OS%Time, OS%grid, OS%GV, OS%US, param_file, OS%Waves, OS%diag)
-  else
-    call MOM_wave_interface_init_lite(param_file)
-  endif
+  ! MOM_wave_interface_init is called regardless of the value of USE_WAVES because
+  ! it also initializes statistical waves.
+  call MOM_wave_interface_init(OS%Time, OS%grid, OS%GV, OS%US, param_file, OS%Waves, OS%diag)
 
   if (associated(OS%grid%Domain%maskmap)) then
     call initialize_ocean_public_type(OS%grid%Domain%mpp_domain, Ocean_sfc, &