Matt's changes to drivers

Merge branch 'revert_drivers' of https://github.com/MJHarrison-GFDL/MOM6 into matts-revert-drivers

.gitignore

@@ -4,19 +4,7 @@
 html
 
 
-# Build output
-*.o
-*.mod
-MOM6
-build/
-_build/
-deps/
-MOM6.tags
-bib*.aux
-citelist.doc*
-
-
-# Autoconf
+# Autoconf output
 aclocal.m4
 autom4te.cache/
 config.log

ac/configure.ac

@@ -83,25 +83,56 @@ AX_FC_CHECK_MODULE([mpi],
 
 # netCDF configuration
 
-# NOTE: `nf-config --flibs` combines library paths (-L) and libraries (-l),
-#   even though these ought to be separated in the invocation of `ld`.
-#
-# We use `sed` to strip the -l and pass the -L to LDFLAGS, and rely on autoconf
-#   to configure the -l flags.
-AC_PROG_SED
-
-AC_PATH_PROG([NF_CONFIG], [nf-config])
-AS_IF([test -n "$NF_CONFIG"],
-  [CPPFLAGS="$CPPFLAGS $($NF_CONFIG --fflags)"
-  FCFLAGS="$FCFLAGS $($NF_CONFIG --fflags)"
-  LDFLAGS="$LDFLAGS $($NF_CONFIG --flibs | $SED -e 's/-l[[^ 	]]*//g')"],
-  [AC_MSG_ERROR([Could not find nf-config.])])
-
-AX_FC_CHECK_MODULE([netcdf],
-  [], [AC_MSG_ERROR([Could not find netcdf module.])])
-AX_FC_CHECK_LIB([netcdff], [nf_create], [netcdf],
-  [], [AC_MSG_ERROR([Could not link netcdff library.])]
-)
+# Search for the Fortran netCDF module, fallback to nf-config.
+AX_FC_CHECK_MODULE([netcdf], [], [
+  AS_UNSET([ax_fc_cv_mod_netcdf])
+  AC_PATH_PROG([NF_CONFIG], [nf-config])
+  AS_IF([test -n "$NF_CONFIG"], [
+    AC_SUBST([FCFLAGS], ["$FCFLAGS -I$($NF_CONFIG --includedir)"])
+    ], [AC_MSG_ERROR([Could not find nf-config.])]
+  )
+  AX_FC_CHECK_MODULE([netcdf], [], [
+    AC_MSG_ERROR([Could not find netcdf module.])
+  ])
+])
+
+# FMS may invoke netCDF C calls, so we link to libnetcdf.
+AC_LANG_PUSH([C])
+AC_CHECK_LIB([netcdf], [nc_create], [], [
+  AS_UNSET([ac_cv_lib_netcdf_nc_create])
+  AC_PATH_PROG([NC_CONFIG], [nc-config])
+  AS_IF([test -n "$NC_CONFIG"], [
+    AC_SUBST([LDFLAGS],
+      ["$LDFLAGS -L$($NC_CONFIG --libdir)"]
+    )
+    ], [AC_MSG_ERROR([Could not find nc-config.])]
+  )
+  AC_CHECK_LIB([netcdf], [nc_create], [], [
+    AC_MSG_ERROR([Could not find libnetcdf.])
+  ])
+])
+AC_LANG_POP([C])
+
+# NOTE: We test for nf_create, rather than nf90_create, because AX_FC_CHECK_LIB
+#   is currently not yet able to properly probe inside modules.
+#   Testing of the nf90_* functions will require a macro update.
+# NOTE: nf-config does not have a --libdir flag, so we use --prefix and assume
+#   that libraries are in the $prefix/lib directory.
+
+# Link to Fortran netCDF library, netcdff
+AX_FC_CHECK_LIB([netcdff], [nf_create], [], [], [
+  AS_UNSET([ax_fc_cv_lib_netcdff_nf_create])
+  AC_PATH_PROG([NF_CONFIG], [nf-config])
+  AS_IF([test -n "$NF_CONFIG"], [
+    AC_SUBST([LDFLAGS],
+      ["$LDFLAGS -L$($NF_CONFIG --prefix)/lib"]
+    )
+    ], [AC_MSG_ERROR([Could not find nf-config.])]
+  )
+  AX_FC_CHECK_LIB([netcdff], [nf_create], [], [], [
+    AC_MSG_ERROR([Could not find libnetcdff.])
+  ])
+])
 
 
 # Force 8-byte reals

ac/deps/Makefile

@@ -13,7 +13,7 @@ MKMF_COMMIT ?= master
 
 # FMS framework
 FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
-FMS_COMMIT ?= 2019.01.03
+FMS_COMMIT ?= 2020.04
 
 
 # List of source files to link this Makefile's dependencies to model Makefiles

ac/deps/configure.fms.ac

@@ -15,6 +15,7 @@ AC_PROG_CC
 AX_MPI
 CC=$MPICC
 
+
 # FMS configuration
 
 # Linux and macOS have a gettid system call, but it is not implemented in older
@@ -74,25 +75,38 @@ AC_DEFINE([use_libMPI])
 
 # netCDF configuration
 
-# NOTE: `nf-config --flibs` combines library paths (-L) and libraries (-l),
-#   even though these ought to be separated in the invocation of `ld`.
-#
-# We use `sed` to strip the -l and pass the -L to LDFLAGS, and rely on autoconf
-#   to configure the -l flags.
-AC_PROG_SED
-
-AC_PATH_PROG([NF_CONFIG], [nf-config])
-AS_IF([test -n "$NF_CONFIG"],
-  [CPPFLAGS="$CPPFLAGS $($NF_CONFIG --fflags)"
-  FCFLAGS="$FCFLAGS $($NF_CONFIG --fflags)"
-  LDFLAGS="$LDFLAGS $($NF_CONFIG --flibs | $SED -e 's/-l[[^ 	]]*//g')"],
-  [AC_MSG_ERROR([Could not find nf-config.])])
-
-AX_FC_CHECK_MODULE([netcdf],
-  [], [AC_MSG_ERROR([Could not find netcdf module.])])
-AX_FC_CHECK_LIB([netcdff], [nf_create], [netcdf],
-  [], [AC_MSG_ERROR([Could not link netcdff library.])]
-)
+# Check for netcdf.h header function declarations.
+# If unavailable, then try to invoke nc-create.
+AC_LANG_PUSH([C])
+AC_CHECK_HEADERS([netcdf.h], [], [
+  AS_UNSET([ac_cv_header_netcdf_h])
+  AC_PATH_PROG([NC_CONFIG], [nc-config])
+  AS_IF([test -n "$NC_CONFIG"], [
+      AC_SUBST([CPPFLAGS], ["$CPPFLAGS -I$($NC_CONFIG --includedir)"])
+    ],
+    [AC_MSG_ERROR([Could not find nc-config.])]
+  )
+  AC_CHECK_HEADERS([netcdf.h], [], [
+    AC_MSG_ERROR([Could not find netcdf.h])
+  ])
+])
+AC_LANG_POP([C])
+
+# Search for the Fortran netCDF module, fallback to nf-config.
+AX_FC_CHECK_MODULE([netcdf], [], [
+  AS_UNSET([ax_fc_cv_mod_netcdf])
+  AC_PATH_PROG([NF_CONFIG], [nf-config])
+  AS_IF([test -n "$NF_CONFIG"], [
+      AC_SUBST([FCFLAGS], ["$FCFLAGS -I$($NF_CONFIG --includedir)"])
+    ],
+    [AC_MSG_ERROR([Could not find nf-config.])]
+  )
+  AX_FC_CHECK_MODULE([netcdf], [], [
+    AC_MSG_ERROR([Could not find netcdf module.])
+  ])
+])
+
+# FMS requires this macro to signal netCDF support.
 AC_DEFINE([use_netCDF])
 
 

ac/m4/ax_fc_check_lib.m4

@@ -18,7 +18,7 @@ dnl    library with different -L flags, or perhaps other ld configurations.
 dnl
 dnl Results are cached in the ax_fc_cv_lib_LIBRARY_FUNCTION variable.
 dnl
-AC_DEFUN([AX_FC_CHECK_LIB],[dnl
+AC_DEFUN([AX_FC_CHECK_LIB],[
   AS_VAR_PUSHDEF([ax_fc_Lib], [ax_fc_cv_lib_$1_$2])
   m4_ifval([$6],
     [ax_fc_lib_msg_LDFLAGS=" with $6"],
@@ -29,14 +29,15 @@ AC_DEFUN([AX_FC_CHECK_LIB],[dnl
     LDFLAGS="$6 $LDFLAGS"
     ax_fc_check_lib_save_LIBS=$LIBS
     LIBS="-l$1 $7 $LIBS"
-    AS_IF([test -n $3],
+    AS_IF([test -n "$3"],
       [ax_fc_use_mod="use $3"],
       [ax_fc_use_mod=""])
-    AC_LINK_IFELSE([
-        AC_LANG_PROGRAM([], [dnl
+    AC_LINK_IFELSE([dnl
+dnl Begin 7-column code block
+AC_LANG_PROGRAM([], [dnl
         $ax_fc_use_mod
-        call $2]dnl
-        )
+        call $2])dnl
+dnl End code block
       ],
       [AS_VAR_SET([ax_fc_Lib], [yes])],
       [AS_VAR_SET([ax_fc_Lib], [no])]

config_src/coupled_driver/ocean_model_MOM.F90

@@ -48,7 +48,6 @@ module ocean_model_mod
 use MOM_verticalGrid, only : verticalGrid_type
 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_IS_diag_mediator, only : diag_IS_ctrl => diag_ctrl, diag_mediator_IS_end=>diag_mediator_end
 use coupler_types_mod, only : coupler_1d_bc_type, coupler_2d_bc_type
 use coupler_types_mod, only : coupler_type_spawn, coupler_type_write_chksums
 use coupler_types_mod, only : coupler_type_initialized, coupler_type_copy_data
@@ -182,13 +181,13 @@ module ocean_model_mod
                               !! processes before time stepping the dynamics.
 
   type(directories) :: dirs   !< A structure containing several relevant directory paths.
-  type(mech_forcing), pointer :: forces => NULL() !< A structure with the driving mechanical surface forces
-  type(forcing), pointer      :: fluxes => NULL()   !< A structure containing pointers to
+  type(mech_forcing)          :: forces  !< A structure with the driving mechanical surface forces
+  type(forcing)               :: fluxes  !< A structure containing pointers to
                                                     !! the thermodynamic ocean forcing fields.
-  type(forcing), pointer      :: flux_tmp => NULL() !< A secondary structure containing pointers to the
+  type(forcing)               :: flux_tmp !< A secondary structure containing pointers to the
                               !! ocean forcing fields for when multiple coupled
                               !! timesteps are taken per thermodynamic step.
-  type(surface), pointer      :: sfc_state => NULL() !< A structure containing pointers to
+  type(surface)               :: sfc_state   !< A structure containing pointers to
                               !! the ocean surface state fields.
   type(ocean_grid_type), pointer :: &
     grid => NULL()            !< A pointer to a grid structure containing metrics
@@ -217,9 +216,6 @@ module ocean_model_mod
                               !! that will be used for MOM restart files.
   type(diag_ctrl), pointer :: &
     diag => NULL()            !< A pointer to the diagnostic regulatory structure
-  type(diag_IS_ctrl), pointer :: &
-    diag_IS => NULL()         !< A pointer to the diagnostic regulatory structure
-                              !! for the ice shelf module.
 end type ocean_state_type
 
 contains
@@ -273,9 +269,9 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
   endif
   allocate(OS)
 
-  allocate(OS%fluxes)
-  allocate(OS%forces)
-  allocate(OS%flux_tmp)
+!  allocate(OS%fluxes)
+!  allocate(OS%forces)
+!  allocate(OS%flux_tmp)
 
   OS%is_ocean_pe = Ocean_sfc%is_ocean_pe
   if (.not.OS%is_ocean_pe) return
@@ -365,7 +361,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
     use_melt_pot=.false.
   endif
 
-  allocate(OS%sfc_state)
+  !allocate(OS%sfc_state)
   call allocate_surface_state(OS%sfc_state, OS%grid, use_temperature, do_integrals=.true., &
                               gas_fields_ocn=gas_fields_ocn, use_meltpot=use_melt_pot)
 
@@ -379,7 +375,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
 
   if (OS%use_ice_shelf)  then
     call initialize_ice_shelf(param_file, OS%grid, OS%Time, OS%ice_shelf_CSp, &
-                              OS%diag_IS, OS%forces, OS%fluxes)
+                              OS%diag, OS%forces, OS%fluxes)
   endif
   if (OS%icebergs_alter_ocean)  then
     call marine_ice_init(OS%Time, OS%grid, param_file, OS%diag, OS%marine_ice_CSp)
@@ -728,8 +724,6 @@ subroutine ocean_model_end(Ocean_sfc, Ocean_state, Time)
 
   call ocean_model_save_restart(Ocean_state, Time)
   call diag_mediator_end(Time, Ocean_state%diag)
-  if (Ocean_state%use_ice_shelf) &
-    call diag_mediator_IS_end(Time, Ocean_state%diag_IS)
   call MOM_end(Ocean_state%MOM_CSp)
   if (Ocean_state%use_ice_shelf) call ice_shelf_end(Ocean_state%Ice_shelf_CSp)
 end subroutine ocean_model_end

config_src/mct_driver/mom_ocean_model_mct.F90

@@ -56,7 +56,7 @@ module MOM_ocean_model_mct
 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 fms_mod,                  only : stdout
+use MOM_io,                   only : stdout
 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
@@ -409,10 +409,6 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
 
   call close_param_file(param_file)
   call diag_mediator_close_registration(OS%diag)
-
-  if (is_root_pe()) &
-    write(*,'(/12x,a/)') '======== COMPLETED MOM INITIALIZATION ========'
-
   call callTree_leave("ocean_model_init(")
 end subroutine ocean_model_init
 
@@ -1053,20 +1049,18 @@ subroutine ocean_public_type_chksum(id, timestep, ocn)
   integer,                 intent(in) :: timestep !< The number of elapsed timesteps
   type(ocean_public_type), intent(in) :: ocn !< A structure containing various publicly
                                              !! visible ocean surface fields.
-  integer :: n, m, outunit
-
-  outunit = stdout()
-
-  write(outunit,*) "BEGIN CHECKSUM(ocean_type):: ", id, timestep
-  write(outunit,100) 'ocean%t_surf   ',mpp_chksum(ocn%t_surf )
-  write(outunit,100) 'ocean%s_surf   ',mpp_chksum(ocn%s_surf )
-  write(outunit,100) 'ocean%u_surf   ',mpp_chksum(ocn%u_surf )
-  write(outunit,100) 'ocean%v_surf   ',mpp_chksum(ocn%v_surf )
-  write(outunit,100) 'ocean%sea_lev  ',mpp_chksum(ocn%sea_lev)
-  write(outunit,100) 'ocean%frazil   ',mpp_chksum(ocn%frazil )
-  write(outunit,100) 'ocean%melt_potential  ',mpp_chksum(ocn%melt_potential)
-
-  call coupler_type_write_chksums(ocn%fields, outunit, 'ocean%')
+  integer :: n, m
+
+  write(stdout,*) "BEGIN CHECKSUM(ocean_type):: ", id, timestep
+  write(stdout,100) 'ocean%t_surf   ',mpp_chksum(ocn%t_surf )
+  write(stdout,100) 'ocean%s_surf   ',mpp_chksum(ocn%s_surf )
+  write(stdout,100) 'ocean%u_surf   ',mpp_chksum(ocn%u_surf )
+  write(stdout,100) 'ocean%v_surf   ',mpp_chksum(ocn%v_surf )
+  write(stdout,100) 'ocean%sea_lev  ',mpp_chksum(ocn%sea_lev)
+  write(stdout,100) 'ocean%frazil   ',mpp_chksum(ocn%frazil )
+  write(stdout,100) 'ocean%melt_potential  ',mpp_chksum(ocn%melt_potential)
+
+  call coupler_type_write_chksums(ocn%fields, stdout, 'ocean%')
 100 FORMAT("   CHECKSUM::",A20," = ",Z20)
 
 end subroutine ocean_public_type_chksum