Merge branch 'dev/gfdl' into ke_from_GV

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

@@ -22,6 +22,7 @@ runs:
       shell: bash
       run: |
         echo "::group::Install linux packages"
+        sudo apt-get update
         sudo apt-get install netcdf-bin libnetcdf-dev libnetcdff-dev mpich libmpich-dev
         echo "::endgroup::"
 

.github/workflows/regression.yml

@@ -23,5 +23,5 @@ jobs:
     - name: Create validation data
       run: make run.symmetric -k -s
 
-    - name: Regression test 
+    - name: Regression test
       run: make test.regressions DO_REGRESSION_TESTS=true -k -s

.gitignore

@@ -4,13 +4,7 @@
 html
 
 
-# Build output
-*.o
-*.mod
-MOM6
-
-
-# Autoconf
+# Autoconf output
 aclocal.m4
 autom4te.cache/
 config.log

.readthedocs.yml

@@ -1,8 +1,9 @@
 version: 2
 
 # Extra formats
-formats:
-  - pdf
+# PDF generation is failing for now; disabled on 2020-12-02
+#formats:
+#  - pdf
 
 # Build documentation
 sphinx:

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/MOM_surface_forcing_gfdl.F90

@@ -1664,7 +1664,8 @@ subroutine check_mask_val_consistency(val, mask, i, j, varname, G)
 
   real, intent(in) :: val  !< value of flux/variable passed by IOB
   real, intent(in) :: mask !< value of ocean mask
-  integer, intent(in) :: i, j !< model grid cell indices
+  integer, intent(in) :: i !< model grid cell indices
+  integer, intent(in) :: j !< model grid cell indices
   character(len=*), intent(in) :: varname !< variable name
   type(ocean_grid_type), intent(in) :: G !< The ocean's grid structure
   ! Local variables

config_src/external/GFDL_ocean_BGC/FMS_coupler_util.F90

@@ -12,23 +12,31 @@ module FMS_coupler_util
 subroutine extract_coupler_values(BC_struc, BC_index, BC_element, array_out, ilb, jlb, &
                                   is, ie, js, je, conversion)
   real, dimension(ilb:,jlb:),intent(out) :: array_out !< The array being filled with the input values
-  integer,                   intent(in)  :: ilb, jlb !< Lower bounds
+  integer,                   intent(in)  :: ilb !< Lower bounds
+  integer,                   intent(in)  :: jlb !< Lower bounds
   type(coupler_2d_bc_type),  intent(in)  :: BC_struc !< The type from which the data is being extracted
   integer,                   intent(in)  :: BC_index !< The boundary condition number being extracted
   integer,                   intent(in)  :: BC_element !< The element of the boundary condition being extracted
-  integer,        optional,  intent(in)  :: is, ie, js, je !< The i- and j- limits of array_out to be filled
+  integer,        optional,  intent(in)  :: is !< The i- limits of array_out to be filled
+  integer,        optional,  intent(in)  :: ie !< The i- limits of array_out to be filled
+  integer,        optional,  intent(in)  :: js !< The j- limits of array_out to be filled
+  integer,        optional,  intent(in)  :: je !< The j- limits of array_out to be filled
   real,           optional,  intent(in)  :: conversion !< A number that every element is multiplied by
 end subroutine extract_coupler_values
 
 !> Set element and index of a boundary condition
 subroutine set_coupler_values(array_in, BC_struc, BC_index, BC_element, ilb, jlb,&
                               is, ie, js, je, conversion)
   real, dimension(ilb:,jlb:), intent(in)  :: array_in !< The array containing the values to load into the BC
-  integer,                  intent(in)    :: ilb, jlb !< Lower bounds
+  integer,                  intent(in)    :: ilb !< Lower bounds
+  integer,                  intent(in)    :: jlb !< Lower bounds
   type(coupler_2d_bc_type), intent(inout) :: BC_struc !< The type into which the data is being loaded
   integer,                  intent(in)    :: BC_index !< The boundary condition number being set
   integer,                  intent(in)    :: BC_element !< The element of the boundary condition being set
-  integer,        optional, intent(in)    :: is, ie, js, je !< The i- and j- limits of array_out to be filled
+  integer,        optional, intent(in)    :: is !< The i- limits of array_out to be filled
+  integer,        optional, intent(in)    :: ie !< The i- limits of array_out to be filled
+  integer,        optional, intent(in)    :: js !< The j- limits of array_out to be filled
+  integer,        optional, intent(in)    :: je !< The j- limits of array_out to be filled
   real,           optional, intent(in)    :: conversion !< A number that every element is multiplied by
 end subroutine set_coupler_values
 

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

config_src/mct_driver/mom_surface_forcing_mct.F90

@@ -34,10 +34,10 @@ module MOM_surface_forcing_mct
 use coupler_types_mod,    only : coupler_type_initialized, coupler_type_spawn
 use coupler_types_mod,    only : coupler_type_copy_data
 use data_override_mod,    only : data_override_init, data_override
-use fms_mod,              only : stdout
 use mpp_mod,              only : mpp_chksum
 use time_interp_external_mod, only : init_external_field, time_interp_external
 use time_interp_external_mod, only : time_interp_external_init
+use MOM_io,               only: stdout
 
 implicit none ; private
 
@@ -1361,37 +1361,35 @@ subroutine ice_ocn_bnd_type_chksum(id, timestep, iobt)
                                          !! ocean in a coupled model whose checksums are reported
 
   ! local variables
-  integer ::   n,m, outunit
-
-  outunit = stdout()
-
-  write(outunit,*) "BEGIN CHECKSUM(ice_ocean_boundary_type):: ", id, timestep
-  write(outunit,100) 'iobt%u_flux         '   , mpp_chksum( iobt%u_flux         )
-  write(outunit,100) 'iobt%v_flux         '   , mpp_chksum( iobt%v_flux         )
-  write(outunit,100) 'iobt%t_flux         '   , mpp_chksum( iobt%t_flux         )
-  write(outunit,100) 'iobt%q_flux         '   , mpp_chksum( iobt%q_flux         )
-  write(outunit,100) 'iobt%salt_flux      '   , mpp_chksum( iobt%salt_flux      )
-  write(outunit,100) 'iobt%seaice_melt_heat'  , mpp_chksum( iobt%seaice_melt_heat)
-  write(outunit,100) 'iobt%seaice_melt    '   , mpp_chksum( iobt%seaice_melt    )
-  write(outunit,100) 'iobt%lw_flux        '   , mpp_chksum( iobt%lw_flux        )
-  write(outunit,100) 'iobt%sw_flux_vis_dir'   , mpp_chksum( iobt%sw_flux_vis_dir)
-  write(outunit,100) 'iobt%sw_flux_vis_dif'   , mpp_chksum( iobt%sw_flux_vis_dif)
-  write(outunit,100) 'iobt%sw_flux_nir_dir'   , mpp_chksum( iobt%sw_flux_nir_dir)
-  write(outunit,100) 'iobt%sw_flux_nir_dif'   , mpp_chksum( iobt%sw_flux_nir_dif)
-  write(outunit,100) 'iobt%lprec          '   , mpp_chksum( iobt%lprec          )
-  write(outunit,100) 'iobt%fprec          '   , mpp_chksum( iobt%fprec          )
-  write(outunit,100) 'iobt%runoff         '   , mpp_chksum( iobt%runoff         )
-  write(outunit,100) 'iobt%calving        '   , mpp_chksum( iobt%calving        )
-  write(outunit,100) 'iobt%p              '   , mpp_chksum( iobt%p              )
+  integer ::   n,m
+
+  write(stdout,*) "BEGIN CHECKSUM(ice_ocean_boundary_type):: ", id, timestep
+  write(stdout,100) 'iobt%u_flux         '   , mpp_chksum( iobt%u_flux         )
+  write(stdout,100) 'iobt%v_flux         '   , mpp_chksum( iobt%v_flux         )
+  write(stdout,100) 'iobt%t_flux         '   , mpp_chksum( iobt%t_flux         )
+  write(stdout,100) 'iobt%q_flux         '   , mpp_chksum( iobt%q_flux         )
+  write(stdout,100) 'iobt%salt_flux      '   , mpp_chksum( iobt%salt_flux      )
+  write(stdout,100) 'iobt%seaice_melt_heat'  , mpp_chksum( iobt%seaice_melt_heat)
+  write(stdout,100) 'iobt%seaice_melt    '   , mpp_chksum( iobt%seaice_melt    )
+  write(stdout,100) 'iobt%lw_flux        '   , mpp_chksum( iobt%lw_flux        )
+  write(stdout,100) 'iobt%sw_flux_vis_dir'   , mpp_chksum( iobt%sw_flux_vis_dir)
+  write(stdout,100) 'iobt%sw_flux_vis_dif'   , mpp_chksum( iobt%sw_flux_vis_dif)
+  write(stdout,100) 'iobt%sw_flux_nir_dir'   , mpp_chksum( iobt%sw_flux_nir_dir)
+  write(stdout,100) 'iobt%sw_flux_nir_dif'   , mpp_chksum( iobt%sw_flux_nir_dif)
+  write(stdout,100) 'iobt%lprec          '   , mpp_chksum( iobt%lprec          )
+  write(stdout,100) 'iobt%fprec          '   , mpp_chksum( iobt%fprec          )
+  write(stdout,100) 'iobt%runoff         '   , mpp_chksum( iobt%runoff         )
+  write(stdout,100) 'iobt%calving        '   , mpp_chksum( iobt%calving        )
+  write(stdout,100) 'iobt%p              '   , mpp_chksum( iobt%p              )
   if (associated(iobt%ustar_berg)) &
-    write(outunit,100) 'iobt%ustar_berg     ' , mpp_chksum( iobt%ustar_berg )
+    write(stdout,100) 'iobt%ustar_berg     ' , mpp_chksum( iobt%ustar_berg )
   if (associated(iobt%area_berg)) &
-    write(outunit,100) 'iobt%area_berg      ' , mpp_chksum( iobt%area_berg  )
+    write(stdout,100) 'iobt%area_berg      ' , mpp_chksum( iobt%area_berg  )
   if (associated(iobt%mass_berg)) &
-    write(outunit,100) 'iobt%mass_berg      ' , mpp_chksum( iobt%mass_berg  )
+    write(stdout,100) 'iobt%mass_berg      ' , mpp_chksum( iobt%mass_berg  )
 100 FORMAT("   CHECKSUM::",A20," = ",Z20)
 
-  call coupler_type_write_chksums(iobt%fluxes, outunit, 'iobt%')
+  call coupler_type_write_chksums(iobt%fluxes, stdout, 'iobt%')
 
 end subroutine ice_ocn_bnd_type_chksum