User/jml/operation fms2 the reckoning

.testing/Makefile

@@ -21,7 +21,7 @@ MKMF := $(abspath $(DEPS)/mkmf/bin/mkmf)
 
 # FMS framework
 FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
-FMS_COMMIT ?= f2e2c86f6c0eb6d389a20509a8a60fa22924e16b
+FMS_COMMIT ?= master
 FMS := $(DEPS)/fms
 
 #---
@@ -111,7 +111,7 @@ $(BUILD)/%/Makefile: $(BUILD)/%/path_names
 	cp $(MKMF_TEMPLATE) $(@D)
 	cd $(@D) && $(MKMF) \
 		-t $(notdir $(MKMF_TEMPLATE)) \
-		-o '-I $(FMS)/build' \
+		-o '-I $(FMS)/build -I $(FMS)/src/include' \
 		-p MOM6 \
 		-l '$(FMS)/lib/libfms.a' \
 		-c $(MKMF_CPP) \

.testing/tc4/build_grid.py

@@ -46,8 +46,8 @@
 areav.units = 'm2'
 f_sg.createVariable('angle_dx', 'f8', ('nyp', 'nxp'))
 f_sg.createVariable('tile', 'S1', ('string'))
-f_sg.variables['y'].units = 'degrees'
-f_sg.variables['x'].units = 'degrees'
+f_sg.variables['y'].units = 'degrees_north'
+f_sg.variables['x'].units = 'degrees_east'
 f_sg.variables['dy'].units = 'meters'
 f_sg.variables['dx'].units = 'meters'
 f_sg.variables['area'].units = 'm2'

config_src/coupled_driver/ocean_model_MOM.F90

@@ -54,6 +54,7 @@ module ocean_model_mod
 use coupler_types_mod, only : coupler_type_set_diags, coupler_type_send_data
 use mpp_domains_mod, only : domain2d, mpp_get_layout, mpp_get_global_domain
 use mpp_domains_mod, only : mpp_define_domains, mpp_get_compute_domain, mpp_get_data_domain
+use mpp_domains_mod, only : mpp_define_io_domain, mpp_get_io_domain_layout
 use atmos_ocean_fluxes_mod, only : aof_set_coupler_flux
 use fms_mod, only : stdout
 use mpp_mod, only : mpp_chksum
@@ -766,7 +767,7 @@ subroutine initialize_ocean_public_type(input_domain, Ocean_sfc, diag, maskmap,
                                               !! in the calculation of additional gas or other
                                               !! tracer fluxes.
 
-  integer :: xsz, ysz, layout(2)
+  integer :: xsz, ysz, layout(2), io_layout(2)
   ! ice-ocean-boundary fields are always allocated using absolute indicies
   ! and have no halos.
   integer :: isc, iec, jsc, jec
@@ -779,6 +780,8 @@ subroutine initialize_ocean_public_type(input_domain, Ocean_sfc, diag, maskmap,
      call mpp_define_domains((/1,xsz,1,ysz/),layout,Ocean_sfc%Domain)
   endif
   call mpp_get_compute_domain(Ocean_sfc%Domain, isc, iec, jsc, jec)
+  io_layout = mpp_get_io_domain_layout(input_domain)
+  call mpp_define_io_domain(Ocean_sfc%Domain, io_layout)
 
   allocate ( Ocean_sfc%t_surf (isc:iec,jsc:jec), &
              Ocean_sfc%s_surf (isc:iec,jsc:jec), &

config_src/ice_solo_driver/ice_shelf_driver.F90

@@ -32,7 +32,7 @@ program SHELF_main
 !   use MOM_grid, only : ocean_grid_type
   use MOM_get_input, only : Get_MOM_Input, directories
   use MOM_io, only : file_exists, open_file, close_file
-  use MOM_io, only : check_nml_error, io_infra_init, io_infra_end
+  use MOM_io, only : check_nml_error, io_infra_init
   use MOM_io, only : APPEND_FILE, ASCII_FILE, READONLY_FILE, SINGLE_FILE
   use MOM_restart, only : save_restart
 !  use MOM_sum_output, only : write_energy, accumulate_net_input
@@ -405,7 +405,7 @@ program SHELF_main
   call diag_mediator_end(Time, ice_shelf_CSp%diag, end_diag_manager=.true.)
   call cpu_clock_end(termClock)
 
-  call io_infra_end ; call MOM_infra_end
+  call MOM_infra_end
 
   call ice_shelf_end(ice_shelf_CSp)
 

config_src/ice_solo_driver/user_surface_forcing.F90

@@ -51,7 +51,6 @@ module user_surface_forcing
 use MOM_forcing_type, only : forcing, mech_forcing
 use MOM_forcing_type, only : allocate_forcing_type, allocate_mech_forcing
 use MOM_grid, only : ocean_grid_type
-use MOM_io, only : file_exists, read_data
 use MOM_time_manager, only : time_type, operator(+), operator(/), get_time
 use MOM_tracer_flow_control, only : call_tracer_set_forcing
 use MOM_tracer_flow_control, only : tracer_flow_control_CS

config_src/solo_driver/MOM_driver.F90

@@ -42,7 +42,7 @@ program MOM_main
   use MOM_get_input,       only : directories
   use MOM_grid,            only : ocean_grid_type
   use MOM_io,              only : file_exists, open_file, close_file
-  use MOM_io,              only : check_nml_error, io_infra_init, io_infra_end
+  use MOM_io,              only : check_nml_error, io_infra_init
   use MOM_io,              only : APPEND_FILE, ASCII_FILE, READONLY_FILE, SINGLE_FILE
   use MOM_restart,         only : MOM_restart_CS, save_restart
   use MOM_string_functions,only : uppercase
@@ -64,6 +64,7 @@ program MOM_main
 
   use ensemble_manager_mod, only : ensemble_manager_init, get_ensemble_size
   use ensemble_manager_mod, only : ensemble_pelist_setup
+  use fms_affinity_mod, only : get_cpu_affinity=>fms_affinity_get, set_cpu_affinity=>fms_affinity_set
   use mpp_mod, only : set_current_pelist => mpp_set_current_pelist
   use time_interp_external_mod, only : time_interp_external_init
 
@@ -209,7 +210,7 @@ program MOM_main
   integer :: ocean_nthreads = 1
   integer :: ncores_per_node = 36
   logical :: use_hyper_thread = .false.
-  integer :: omp_get_num_threads,omp_get_thread_num,get_cpu_affinity,adder,base_cpu
+  integer :: omp_get_num_threads,omp_get_thread_num,adder,base_cpu
   namelist /ocean_solo_nml/ date_init, calendar, months, days, hours, minutes, seconds,&
                             ocean_nthreads, ncores_per_node, use_hyper_thread
 
@@ -264,7 +265,11 @@ program MOM_main
 !$  else
 !$     adder = omp_get_thread_num()
 !$  endif
-!$  call set_cpu_affinity (base_cpu + adder)
+!$  if (base_cpu + adder >= 1) then
+!$    call set_cpu_affinity(component="MOM_driver", use_hyper_thread=use_hyper_thread, nthreads=base_cpu + adder)
+!$  else
+!$    call set_cpu_affinity(component="MOM_driver", use_hyper_thread=use_hyper_thread, nthreads=1)
+!$  endif
 !$  write(6,*) " ocean ", base_cpu, get_cpu_affinity(), adder, omp_get_thread_num(), omp_get_num_threads()
 !$  call flush(6)
 !$OMP END PARALLEL
@@ -663,7 +668,7 @@ program MOM_main
   call diag_mediator_end(Time, diag, end_diag_manager=.true.)
   call cpu_clock_end(termClock)
 
-  call io_infra_end ; call MOM_infra_end
+  call MOM_infra_end
 
   call MOM_end(MOM_CSp)
   if (use_ice_shelf) call ice_shelf_end(ice_shelf_CSp)

config_src/unit_drivers/MOM_sum_driver.F90

@@ -27,9 +27,9 @@ program MOM_main
   use MOM_file_parser, only : open_param_file, close_param_file
   use MOM_grid, only : MOM_grid_init, ocean_grid_type
   use MOM_grid_initialize, only : set_grid_metrics
-  use MOM_io, only : MOM_io_init, file_exists, open_file, close_file
-  use MOM_io, only : check_nml_error, io_infra_init, io_infra_end
-  use MOM_io, only : APPEND_FILE, ASCII_FILE, READONLY_FILE, SINGLE_FILE
+  use MOM_io, only : MOM_io_init
+  use MOM_io, only : check_nml_error, io_infra_init
+  use MOM_io, only : APPEND_FILE, ASCII_FILE, READONLY_FILE
 
   implicit none
 
@@ -161,7 +161,7 @@ program MOM_main
     endif
   enddo
 
-  call io_infra_end ; call MOM_infra_end
+  call MOM_infra_end
 
 contains
 

src/ALE/MOM_ALE.F90

@@ -22,7 +22,7 @@ module MOM_ALE
 use MOM_error_handler,    only : callTree_enter, callTree_leave, callTree_waypoint
 use MOM_file_parser,      only : get_param, param_file_type, log_param
 use MOM_io,               only : vardesc, var_desc, fieldtype, SINGLE_FILE
-use MOM_io,               only : create_file, write_field, close_file
+use MOM_io,               only : create_file, write_field
 use MOM_interface_heights,only : find_eta
 use MOM_open_boundary,    only : ocean_OBC_type, OBC_DIRECTION_E, OBC_DIRECTION_W
 use MOM_open_boundary,    only : OBC_DIRECTION_N, OBC_DIRECTION_S
@@ -1270,7 +1270,6 @@ subroutine ALE_writeCoordinateFile( CS, GV, directory )
   character(len=240) :: filepath
   type(vardesc)      :: vars(2)
   type(fieldtype)    :: fields(2)
-  integer            :: unit
   real               :: ds(GV%ke), dsi(GV%ke+1)
 
   filepath    = trim(directory) // trim("Vertical_coordinate")
@@ -1284,10 +1283,9 @@ subroutine ALE_writeCoordinateFile( CS, GV, directory )
   vars(2) = var_desc('ds_interface', getCoordinateUnits( CS%regridCS ), &
                     'Layer Center Coordinate Separation','1','i','1')
 
-  call create_file(unit, trim(filepath), vars, 2, fields, SINGLE_FILE, GV=GV)
-  call write_field(unit, fields(1), ds)
-  call write_field(unit, fields(2), dsi)
-  call close_file(unit)
+  call create_file(trim(filepath), vars, 2, GV=GV)
+  call write_field(trim(filepath), vars(1)%name, ds, "append", var_desc=vars(1), GV=GV)
+  call write_field(trim(filepath), vars(2)%name, dsi, "append", var_desc=vars(2), GV=GV)
 
 end subroutine ALE_writeCoordinateFile
 

src/core/MOM.F90

@@ -39,6 +39,7 @@ module MOM
 use MOM_obsolete_params,      only : find_obsolete_params
 use MOM_restart,              only : register_restart_field, query_initialized, save_restart
 use MOM_restart,              only : restart_init, is_new_run, MOM_restart_CS
+use MOM_restart,              only : write_initial_conditions
 use MOM_spatial_means,        only : global_mass_integral
 use MOM_time_manager,         only : time_type, real_to_time, time_type_to_real, operator(+)
 use MOM_time_manager,         only : operator(-), operator(>), operator(*), operator(/)
@@ -2215,13 +2216,14 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
     call adjustGridForIntegrity(CS%ALE_CSp, G, GV, CS%h )
     call callTree_waypoint("Calling ALE_main() to remap initial conditions (initialize_MOM)")
     if (use_ice_shelf) then
+      filename = ''
       filename = trim(inputdir)//trim(ice_shelf_file)
-      if (.not.file_exists(filename, G%Domain)) call MOM_error(FATAL, &
+      if (.not.file_exists(filename)) call MOM_error(FATAL, &
         "MOM: Unable to open "//trim(filename))
 
       allocate(area_shelf_h(isd:ied,jsd:jed))
       allocate(frac_shelf_h(isd:ied,jsd:jed))
-      call MOM_read_data(filename, trim(area_varname), area_shelf_h, G%Domain)
+      call MOM_read_data(filename, trim(area_varname), area_shelf_h, G%domain)
       ! initialize frac_shelf_h with zeros (open water everywhere)
       frac_shelf_h(:,:) = 0.0
       ! compute fractional ice shelf coverage of h
@@ -2507,13 +2509,13 @@ subroutine finish_MOM_initialization(Time, dirs, CS, restart_CSp)
   if (CS%write_IC) then
     allocate(restart_CSp_tmp)
     restart_CSp_tmp = restart_CSp
+    ! register eta to the temporary control structure for the IC data
     allocate(z_interface(SZI_(G),SZJ_(G),SZK_(G)+1))
     call find_eta(CS%h, CS%tv, G, GV, US, z_interface, eta_to_m=1.0)
     call register_restart_field(z_interface, "eta", .true., restart_CSp_tmp, &
-                                "Interface heights", "meter", z_grid='i')
+                              z_grid='i', longname="Interface heights", units="meter")
 
-    call save_restart(dirs%output_directory, Time, G, &
-                      restart_CSp_tmp, filename=CS%IC_file, GV=GV)
+    call write_initial_conditions(dirs%output_directory, CS%IC_file, restart_CSp_tmp, G, Time, GV=GV)
     deallocate(z_interface)
     deallocate(restart_CSp_tmp)
   endif
@@ -2616,43 +2618,43 @@ subroutine set_restart_fields(GV, US, param_file, CS, restart_CSp)
 
   if (associated(CS%tv%T)) &
     call register_restart_field(CS%tv%T, "Temp", .true., restart_CSp, &
-                                "Potential Temperature", "degC")
+                                longname="Potential Temperature", units="degC")
   if (associated(CS%tv%S)) &
     call register_restart_field(CS%tv%S, "Salt", .true., restart_CSp, &
-                                "Salinity", "PPT")
+                                longname="Salinity", units="PPT")
 
   call register_restart_field(CS%h, "h", .true., restart_CSp, &
-                              "Layer Thickness", thickness_units)
+                              longname="Layer Thickness", units=thickness_units)
 
   call register_restart_field(CS%u, "u", .true., restart_CSp, &
-                              "Zonal velocity", "m s-1", hor_grid='Cu')
+                              longname="Zonal velocity", units="m s-1", hor_grid='Cu')
 
   call register_restart_field(CS%v, "v", .true., restart_CSp, &
-                              "Meridional velocity", "m s-1", hor_grid='Cv')
+                              longname="Meridional velocity", units="m s-1", hor_grid='Cv')
 
   if (associated(CS%tv%frazil)) &
     call register_restart_field(CS%tv%frazil, "frazil", .false., restart_CSp, &
-                                "Frazil heat flux into ocean", "J m-2")
+                                longname="Frazil heat flux into ocean", units="J m-2")
 
   if (CS%interp_p_surf) then
     call register_restart_field(CS%p_surf_prev, "p_surf_prev", .false., restart_CSp, &
-                                "Previous ocean surface pressure", "Pa")
+                                longname="Previous ocean surface pressure", units="Pa")
   endif
 
   call register_restart_field(CS%ave_ssh_ibc, "ave_ssh", .false., restart_CSp, &
-                              "Time average sea surface height", "meter")
+                              longname="Time average sea surface height", units="meter")
 
   ! hML is needed when using the ice shelf module
   call get_param(param_file, '', "ICE_SHELF", use_ice_shelf, default=.false., &
                  do_not_log=.true.)
   if (use_ice_shelf .and. associated(CS%Hml)) then
     call register_restart_field(CS%Hml, "hML", .false., restart_CSp, &
-                                "Mixed layer thickness", "meter")
+                                longname="Mixed layer thickness", units="meter")
   endif
 
   ! Register scalar unit conversion factors.
   call register_restart_field(US%m_to_Z_restart, "m_to_Z", .false., restart_CSp, &
-                              "Height unit conversion factor", "Z meter-1")
+                              longname="Height unit conversion factor", units="Z meter-1")
   call register_restart_field(GV%m_to_H_restart, "m_to_H", .false., restart_CSp, &
                               "Thickness unit conversion factor", "H meter-1")
   call register_restart_field(US%m_to_L_restart, "m_to_L", .false., restart_CSp, &
@@ -2661,7 +2663,6 @@ subroutine set_restart_fields(GV, US, param_file, CS, restart_CSp)
                               "Time unit conversion factor", "T second-1")
   call register_restart_field(US%kg_m3_to_R_restart, "kg_m3_to_R", .false., restart_CSp, &
                               "Density unit conversion factor", "R m3 kg-1")
-
 end subroutine set_restart_fields
 
 !> Apply a correction to the sea surface height to compensate

src/core/MOM_barotropic.F90

@@ -4459,38 +4459,39 @@ subroutine register_barotropic_restarts(HI, GV, param_file, CS, restart_CS)
                 hor_grid='u', z_grid='1')
   vd(3) = var_desc("vbtav","m s-1","Time mean barotropic meridional velocity",&
                 hor_grid='v', z_grid='1')
-  call register_restart_field(CS%ubtav, vd(2), .false., restart_CS)
-  call register_restart_field(CS%vbtav, vd(3), .false., restart_CS)
-
-  vd(2) = var_desc("ubt_IC", "m s-1", &
-              longname="Next initial condition for the barotropic zonal velocity", &
-              hor_grid='u', z_grid='1')
-  vd(3) = var_desc("vbt_IC", "m s-1", &
-              longname="Next initial condition for the barotropic meridional velocity",&
-              hor_grid='v', z_grid='1')
-  call register_restart_field(CS%ubt_IC, vd(2), .false., restart_CS)
-  call register_restart_field(CS%vbt_IC, vd(3), .false., restart_CS)
+  call register_restart_field(CS%ubtav, vd(2)%name, .false., restart_CS, longname = vd(2)%longname, &
+                              units=vd(2)%units, hor_grid=vd(2)%hor_grid, z_grid=vd(2)%z_grid)
+
+  call register_restart_field(CS%vbtav, vd(3)%name, .false., restart_CS, longname=vd(3)%longname, &
+                              units=vd(3)%units, hor_grid=vd(3)%hor_grid, z_grid=vd(3)%z_grid)
+  vd(2) = var_desc("ubt_IC", "m s-1", longname="Next initial condition for the barotropic zonal velocity", &
+                   hor_grid='u', z_grid='1')
+  vd(3) = var_desc("vbt_IC", "m s-1", longname="Next initial condition for the barotropic meridional velocity", &
+                   hor_grid='v', z_grid='1')
+  call register_restart_field(CS%ubt_IC, vd(2)%name, .false., restart_CS, longname = vd(2)%longname, &
+                              units=vd(2)%units, hor_grid=vd(2)%hor_grid, z_grid=vd(2)%z_grid)
+
+  call register_restart_field(CS%vbt_IC, vd(3)%name, .false., restart_CS, longname = vd(3)%longname, &
+                              units=vd(3)%units, hor_grid=vd(3)%hor_grid, z_grid=vd(3)%z_grid)
 
   if (GV%Boussinesq) then
-    vd(2) = var_desc("uhbt_IC", "m3 s-1", &
-                longname="Next initial condition for the barotropic zonal transport", &
+    vd(2) = var_desc("uhbt_IC", "m3 s-1", longname="Next initial condition for the barotropic zonal transport", &
                 hor_grid='u', z_grid='1')
-    vd(3) = var_desc("vhbt_IC", "m3 s-1", &
-                longname="Next initial condition for the barotropic meridional transport",&
+    vd(3) = var_desc("vhbt_IC", "m3 s-1", longname="Next initial condition for the barotropic meridional transport", &
                 hor_grid='v', z_grid='1')
   else
-    vd(2) = var_desc("uhbt_IC", "kg s-1", &
-                longname="Next initial condition for the barotropic zonal transport", &
+    vd(2) = var_desc("uhbt_IC", "kg s-1", longname="Next initial condition for the barotropic zonal transport", &
                 hor_grid='u', z_grid='1')
-    vd(3) = var_desc("vhbt_IC", "kg s-1", &
-                longname="Next initial condition for the barotropic meridional transport",&
+    vd(3) = var_desc("vhbt_IC", "kg s-1", longname="Next initial condition for the barotropic meridional transport", &
                 hor_grid='v', z_grid='1')
   endif
-  call register_restart_field(CS%uhbt_IC, vd(2), .false., restart_CS)
-  call register_restart_field(CS%vhbt_IC, vd(3), .false., restart_CS)
+  call register_restart_field(CS%uhbt_IC, vd(2)%name, .false., restart_CS, longname = vd(2)%longname, &
+                              units=vd(2)%units, hor_grid=vd(2)%hor_grid, z_grid=vd(2)%z_grid)
+
+  call register_restart_field(CS%vhbt_IC, vd(3)%name, .false., restart_CS, longname = vd(3)%longname, &
+                              units=vd(3)%units, hor_grid=vd(3)%hor_grid, z_grid=vd(3)%z_grid)
 
-  call register_restart_field(CS%dtbt, "DTBT", .false., restart_CS, &
-                              longname="Barotropic timestep", units="seconds")
+  call register_restart_field(CS%dtbt, "DTBT", .false., restart_CS, longname="Barotropic timestep", units="seconds")
 
 end subroutine register_barotropic_restarts