Merge branch 'mom-ocean:main' into dev/gfdl

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

@@ -13,5 +13,6 @@ runs:
         brew update
         brew install automake
         brew install netcdf
+        brew install netcdf-fortran
         brew install mpich
         echo "::endgroup::"

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

@@ -13,7 +13,7 @@ runs:
         sudo apt-get install netcdf-bin
         sudo apt-get install libnetcdf-dev
         sudo apt-get install libnetcdff-dev
-        sudo apt-get install mpich
-        sudo apt-get install libmpich-dev
+        sudo apt-get install openmpi-bin
+        sudo apt-get install libopenmpi-dev
         sudo apt-get install linux-tools-common
         echo "::endgroup::"

.testing/Makefile

@@ -182,14 +182,25 @@ endif
 SOURCE = \
   $(foreach ext,F90 inc c h,$(wildcard $(1)/*/*.$(ext) $(1)/*/*/*.$(ext)))
 
-MOM_SOURCE = $(call SOURCE,../src) \
-  $(wildcard ../config_src/infra/FMS1/*.F90) \
+MOM_SOURCE = \
+  $(call SOURCE,../src) \
   $(wildcard ../config_src/drivers/solo_driver/*.F90) \
   $(wildcard ../config_src/ext*/*/*.F90)
-TARGET_SOURCE = $(call SOURCE,build/target_codebase/src) \
-  $(wildcard build/target_codebase/config_src/infra/FMS1/*.F90) \
+
+TARGET_SOURCE = \
+  $(call SOURCE,build/target_codebase/src) \
   $(wildcard build/target_codebase/config_src/drivers/solo_driver/*.F90) \
   $(wildcard build/target_codebase/config_src/ext*/*.F90)
+
+# NOTE: Current default framework is FMS1, but this could change.
+ifeq ($(FRAMEWORK), fms2)
+  MOM_SOURCE +=$(wildcard ../config_src/infra/FMS2/*.F90)
+  TARGET_SOURCE += $(wildcard build/target_codebase/config_src/infra/FMS2/*.F90)
+else
+  MOM_SOURCE += $(wildcard ../config_src/infra/FMS1/*.F90)
+  TARGET_SOURCE += $(wildcard build/target_codebase/config_src/infra/FMS1/*.F90)
+endif
+
 FMS_SOURCE = $(call SOURCE,deps/fms/src)
 
 
@@ -602,6 +613,7 @@ report.cov: run.cov codecov
 	  2> build/cov/codecov.err \
 	  && echo -e "${MAGENTA}Report uploaded to codecov.${RESET}" \
 	  || { \
+	    cat build/cov/codecov.err ; \
 	    echo -e "${RED}Failed to upload report.${RESET}" ; \
 		if [ "$(REQUIRE_COVERAGE_UPLOAD)" = true ] ; then false ; fi ; \
 	  }
@@ -740,6 +752,7 @@ report.cov.unit: build/unit/MOM_file_parser_tests.F90.gcov codecov
 	    2> build/unit/codecov.err \
 	  && echo -e "${MAGENTA}Report uploaded to codecov.${RESET}" \
 	  || { \
+	    cat build/unit/codecov.err ; \
 	    echo -e "${RED}Failed to upload report.${RESET}" ; \
 		if [ "$(REQUIRE_COVERAGE_UPLOAD)" = true ] ; then false ; fi ; \
 	  }

ac/configure.ac

@@ -234,21 +234,28 @@ AC_SUBST([SRC_DIRS],
 AC_CONFIG_COMMANDS(Makefile.dep, [make depend])
 
 
-# setjmp verification
+# POSIX verification tests
 AC_LANG_PUSH([C])
 
-# Verify that either sigsetjmp (POSIX) or __sigsetjmp (glibc) are available.
-AC_CHECK_FUNC([sigsetjmp])
-AS_IF([test "$ac_cv_func_sigsetjmp" == "yes"], [
-  SIGSETJMP_NAME="sigsetjmp"
-], [
-  AC_CHECK_FUNC([__sigsetjmp], [
-    SIGSETJMP_NAME="__sigsetjmp"
-  ], [
-    AC_MSG_ERROR([Could not find a symbol for sigsetjmp.])
+# These symbols may be defined as macros, making them inaccessible by Fortran.
+# The following exist in BSD and Linux, so we just test for them.
+AC_CHECK_FUNC([setjmp], [], [AC_MSG_ERROR([Could not find setjmp.])])
+AC_CHECK_FUNC([longjmp], [], [AC_MSG_ERROR([Could not find longjmp.])])
+AC_CHECK_FUNC([siglongjmp], [], [AC_MSG_ERROR([Could not find siglongjmp.])])
+
+# Determine the sigsetjmp symbol.  If missing, then point to sigsetjmp_missing.
+#
+# Supported symbols:
+#   sigsetjmp       POSIX, BSD libc (MacOS)
+#   __sigsetjmp     glibc (Linux)
+SIGSETJMP="sigsetjmp_missing"
+for sigsetjmp_fn in sigsetjmp __sigsetjmp; do
+  AC_CHECK_FUNC([${sigsetjmp_fn}], [
+    SIGSETJMP=${sigsetjmp_fn}
+    break
   ])
-])
-AC_DEFINE_UNQUOTED([SIGSETJMP_NAME], ["$SIGSETJMP_NAME"])
+done
+AC_DEFINE_UNQUOTED([SIGSETJMP_NAME], ["${SIGSETJMP}"])
 
 # Determine the size of jmp_buf and sigjmp_buf
 AC_CHECK_SIZEOF([jmp_buf], [], [#include <setjmp.h>])

config_src/drivers/FMS_cap/ocean_model_MOM.F90

@@ -53,6 +53,7 @@ module ocean_model_mod
 use MOM_variables, only : surface
 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 : initialize_ice_shelf_fluxes, initialize_ice_shelf_forces
 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: Update_Surface_Waves
@@ -274,9 +275,13 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
   if (.not.OS%is_ocean_pe) return
 
   OS%Time = Time_in ; OS%Time_dyn = Time_in
+  ! Call initialize MOM with an optional Ice Shelf CS which, if present triggers
+  ! initialization of ice shelf parameters and arrays.
+
   call initialize_MOM(OS%Time, Time_init, param_file, OS%dirs, OS%MOM_CSp, &
                       OS%restart_CSp, Time_in, offline_tracer_mode=OS%offline_tracer_mode, &
-                      diag_ptr=OS%diag, count_calls=.true., waves_CSp=OS%Waves)
+                      diag_ptr=OS%diag, count_calls=.true., ice_shelf_CSp=OS%ice_shelf_CSp, &
+                      waves_CSp=OS%Waves)
   call get_MOM_state_elements(OS%MOM_CSp, G=OS%grid, GV=OS%GV, US=OS%US, C_p=OS%C_p, &
                               C_p_scaled=OS%fluxes%C_p, use_temp=use_temperature)
 
@@ -372,9 +377,10 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
   endif
 
   if (OS%use_ice_shelf)  then
-    call initialize_ice_shelf(param_file, OS%grid, OS%Time, OS%ice_shelf_CSp, &
-                              OS%diag, OS%forces, OS%fluxes)
+    call initialize_ice_shelf_fluxes(OS%ice_shelf_CSp, OS%grid, OS%US, OS%fluxes)
+    call initialize_ice_shelf_forces(OS%ice_shelf_CSp, OS%grid, OS%US, OS%forces)
   endif
+
   if (OS%icebergs_alter_ocean)  then
     call marine_ice_init(OS%Time, OS%grid, param_file, OS%diag, OS%marine_ice_CSp)
     if (.not. OS%use_ice_shelf) &

config_src/drivers/nuopc_cap/mom_cap.F90

@@ -98,8 +98,6 @@ module MOM_cap_mod
 use NUOPC_Model, only: model_label_Finalize       => label_Finalize
 use NUOPC_Model, only: SetVM
 
-!$use omp_lib             , only : omp_set_num_threads
-
 implicit none; private
 
 public SetServices
@@ -149,7 +147,6 @@ module MOM_cap_mod
 integer              :: scalar_field_count = 0
 integer              :: scalar_field_idx_grid_nx = 0
 integer              :: scalar_field_idx_grid_ny = 0
-integer              :: nthrds  !< number of openmp threads per task
 character(len=*),parameter :: u_FILE_u = &
      __FILE__
 
@@ -465,30 +462,6 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
   CALL ESMF_TimeIntervalGet(TINT, S=DT_OCEAN, RC=rc)
   if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-  !---------------------------------
-  ! openmp threads
-  !---------------------------------
-
-  call ESMF_VMGet(vm, pet=localPet, peCount=localPeCount, rc=rc)
-  if (ChkErr(rc,__LINE__,u_FILE_u)) return
-
-  if (localPeCount == 1) then
-    call NUOPC_CompAttributeGet(gcomp, name="nthreads", value=cvalue, &
-         isPresent=isPresent, isSet=isSet, rc=rc)
-    if (ChkErr(rc,__LINE__,u_FILE_u)) return
-    if (isPresent .and. isSet) then
-      read(cvalue,*) nthrds
-    else
-      nthrds = localPeCount
-    endif
-  else
-    nthrds = localPeCount
-  endif
-  write(logmsg,*) nthrds
-  call ESMF_LogWrite(trim(subname)//': nthreads = '//trim(logmsg), ESMF_LOGMSG_INFO)
-
-!$  call omp_set_num_threads(nthrds)
-
   call fms_init(mpi_comm_mom)
   call constants_init
   call field_manager_init
@@ -781,23 +754,10 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
     if (wave_method == "EFACTOR") then
       call fld_list_add(fldsToOcn_num, fldsToOcn, "Sw_lamult"                 , "will provide")
     else if (wave_method == "SURFACE_BANDS") then
-      if (cesm_coupled) then
-        call fld_list_add(fldsToOcn_num, fldsToOcn, "Sw_pstokes_x", "will provide", &
-          ungridded_lbound=1, ungridded_ubound=Ice_ocean_boundary%num_stk_bands)
-        call fld_list_add(fldsToOcn_num, fldsToOcn, "Sw_pstokes_y", "will provide", &
-          ungridded_lbound=1, ungridded_ubound=Ice_ocean_boundary%num_stk_bands)
-      else ! below is the old approach of importing partitioned stokes drift components. after the planned ww3 nuopc
-           ! cap unification, this else block should be removed in favor of the more flexible import approach above.
-        if (Ice_ocean_boundary%num_stk_bands > 3) then
-          call MOM_error(FATAL, "Number of Stokes Bands > 3, NUOPC cap not set up for this")
-        endif
-        call fld_list_add(fldsToOcn_num, fldsToOcn, "eastward_partitioned_stokes_drift_1" , "will provide")
-        call fld_list_add(fldsToOcn_num, fldsToOcn, "northward_partitioned_stokes_drift_1", "will provide")
-        call fld_list_add(fldsToOcn_num, fldsToOcn, "eastward_partitioned_stokes_drift_2" , "will provide")
-        call fld_list_add(fldsToOcn_num, fldsToOcn, "northward_partitioned_stokes_drift_2", "will provide")
-        call fld_list_add(fldsToOcn_num, fldsToOcn, "eastward_partitioned_stokes_drift_3" , "will provide")
-        call fld_list_add(fldsToOcn_num, fldsToOcn, "northward_partitioned_stokes_drift_3", "will provide")
-      endif
+      call fld_list_add(fldsToOcn_num, fldsToOcn, "Sw_pstokes_x", "will provide", &
+        ungridded_lbound=1, ungridded_ubound=Ice_ocean_boundary%num_stk_bands)
+      call fld_list_add(fldsToOcn_num, fldsToOcn, "Sw_pstokes_y", "will provide", &
+        ungridded_lbound=1, ungridded_ubound=Ice_ocean_boundary%num_stk_bands)
     else
       call MOM_error(FATAL, "Unsupported WAVE_METHOD encountered in NUOPC cap.")
     endif
@@ -936,28 +896,6 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
   call ESMF_VMGet(vm, petCount=npet, mpiCommunicator=mpicom, localPet=localPet, rc=rc)
   if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-  !---------------------------------
-  ! openmp threads
-  !---------------------------------
-
-  call ESMF_VMGet(vm, pet=localPet, peCount=localPeCount, rc=rc)
-  if (ChkErr(rc,__LINE__,u_FILE_u)) return
-
-  if (localPeCount == 1) then
-    call NUOPC_CompAttributeGet(gcomp, name="nthreads", value=cvalue, &
-         isPresent=isPresent, isSet=isSet, rc=rc)
-    if (ChkErr(rc,__LINE__,u_FILE_u)) return
-    if (isPresent .and. isSet) then
-      read(cvalue,*) nthrds
-    else
-      nthrds = localPeCount
-    endif
-  else
-    nthrds = localPeCount
-  endif
-
-!$  call omp_set_num_threads(nthrds)
-
   !---------------------------------
   ! global mom grid size
   !---------------------------------
@@ -1570,8 +1508,6 @@ subroutine ModelAdvance(gcomp, rc)
 
   call shr_file_setLogUnit (logunit)
 
-!$  call omp_set_num_threads(nthrds)
-
   ! query the Component for its clock, importState and exportState
   call ESMF_GridCompGet(gcomp, clock=clock, importState=importState, &
     exportState=exportState, rc=rc)
@@ -1763,16 +1699,10 @@ subroutine ModelAdvance(gcomp, rc)
           close(writeunit)
         endif
       else  ! not cesm_coupled
-        ! write the final restart without a timestamp
-        if (ESMF_AlarmIsRinging(stop_alarm, rc=rc)) then
-          write(restartname,'(A)')"MOM.res"
-          write(stoch_restartname,'(A)')"ocn_stoch.res.nc"
-        else
-          write(restartname,'(A,I4.4,"-",I2.2,"-",I2.2,"-",I2.2,"-",I2.2,"-",I2.2)') &
-                "MOM.res.", year, month, day, hour, minute, seconds
-          write(stoch_restartname,'(A,I4.4,"-",I2.2,"-",I2.2,"-",I2.2,"-",I2.2,"-",I2.2,A)') &
-                "ocn_stoch.res.", year, month, day, hour, minute, seconds,".nc"
-        endif
+         write(restartname,'(i4.4,2(i2.2),A,3(i2.2),A)') year, month, day,".", hour, minute, seconds, &
+              ".MOM.res"
+         write(stoch_restartname,'(i4.4,2(i2.2),A,3(i2.2),A)') year, month, day,".", hour, minute, seconds, &
+              ".ocn_stoch.res.nc"
         call ESMF_LogWrite("MOM_cap: Writing restart :  "//trim(restartname), ESMF_LOGMSG_INFO)
 
         ! write restart file(s)
@@ -1932,7 +1862,7 @@ subroutine ModelSetRunClock(gcomp, rc)
                  line=__LINE__, file=__FILE__, rcToReturn=rc)
             return
           endif
-          ! not used in nems
+          ! not used in ufs
           call NUOPC_CompAttributeGet(gcomp, name="restart_ymd", value=cvalue, &
                isPresent=isPresent, isSet=isSet, rc=rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return

config_src/drivers/nuopc_cap/mom_cap_methods.F90

@@ -1,4 +1,4 @@
-!> Contains import/export methods for both NEMS and CMEPS.
+!> Contains import/export methods for CMEPS.
 module MOM_cap_methods
 
 use ESMF,                      only: ESMF_Clock, ESMF_ClockGet, ESMF_time, ESMF_TimeGet
@@ -87,8 +87,6 @@ subroutine mom_import(ocean_public, ocean_grid, importState, ice_ocean_boundary,
   character(len=128)              :: fldname
   real(ESMF_KIND_R8), allocatable :: taux(:,:)
   real(ESMF_KIND_R8), allocatable :: tauy(:,:)
-  real(ESMF_KIND_R8), allocatable :: stkx1(:,:),stkx2(:,:),stkx3(:,:)
-  real(ESMF_KIND_R8), allocatable :: stky1(:,:),stky2(:,:),stky3(:,:)
   real(ESMF_KIND_R8), allocatable :: stkx(:,:,:)
   real(ESMF_KIND_R8), allocatable :: stky(:,:,:)
   character(len=*)  , parameter   :: subname = '(mom_import)'
@@ -329,8 +327,6 @@ subroutine mom_import(ocean_public, ocean_grid, importState, ice_ocean_boundary,
   ! Partitioned Stokes Drift Components
   !----
   if ( associated(ice_ocean_boundary%ustkb) ) then
-
-    if (cesm_coupled) then
       nsc = Ice_ocean_boundary%num_stk_bands
       allocate(stkx(isc:iec,jsc:jec,1:nsc))
       allocate(stky(isc:iec,jsc:jec,1:nsc))
@@ -358,52 +354,6 @@ subroutine mom_import(ocean_public, ocean_grid, importState, ice_ocean_boundary,
         enddo
       enddo
       deallocate(stkx,stky)
-
-    else ! below is the old approach of importing partitioned stokes drift components. after the planned ww3 nuopc
-         ! cap unification, this else block should be removed in favor of the more flexible import approach above.
-      allocate(stkx1(isc:iec,jsc:jec))
-      allocate(stky1(isc:iec,jsc:jec))
-      allocate(stkx2(isc:iec,jsc:jec))
-      allocate(stky2(isc:iec,jsc:jec))
-      allocate(stkx3(isc:iec,jsc:jec))
-      allocate(stky3(isc:iec,jsc:jec))
-
-      call state_getimport(importState,'eastward_partitioned_stokes_drift_1' , isc, iec, jsc, jec, stkx1,rc=rc)
-      if (ChkErr(rc,__LINE__,u_FILE_u)) return
-      call state_getimport(importState,'northward_partitioned_stokes_drift_1', isc, iec, jsc, jec, stky1,rc=rc)
-      if (ChkErr(rc,__LINE__,u_FILE_u)) return
-      call state_getimport(importState,'eastward_partitioned_stokes_drift_2' , isc, iec, jsc, jec, stkx2,rc=rc)
-      if (ChkErr(rc,__LINE__,u_FILE_u)) return
-      call state_getimport(importState,'northward_partitioned_stokes_drift_2', isc, iec, jsc, jec, stky2,rc=rc)
-      if (ChkErr(rc,__LINE__,u_FILE_u)) return
-      call state_getimport(importState,'eastward_partitioned_stokes_drift_3' , isc, iec, jsc, jec, stkx3,rc=rc)
-      if (ChkErr(rc,__LINE__,u_FILE_u)) return
-      call state_getimport(importState,'northward_partitioned_stokes_drift_3', isc, iec, jsc, jec, stky3,rc=rc)
-      if (ChkErr(rc,__LINE__,u_FILE_u)) return
-
-      ! rotate from true zonal/meridional to local coordinates
-      do j = jsc, jec
-        jg = j + ocean_grid%jsc - jsc
-        do i = isc, iec
-          ig = i + ocean_grid%isc - isc
-          ice_ocean_boundary%ustkb(i,j,1) = ocean_grid%cos_rot(ig,jg)*stkx1(i,j) &
-               - ocean_grid%sin_rot(ig,jg)*stky1(i,j)
-          ice_ocean_boundary%vstkb(i,j,1) = ocean_grid%cos_rot(ig,jg)*stky1(i,j) &
-               + ocean_grid%sin_rot(ig,jg)*stkx1(i,j)
-
-          ice_ocean_boundary%ustkb(i,j,2) = ocean_grid%cos_rot(ig,jg)*stkx2(i,j) &
-               - ocean_grid%sin_rot(ig,jg)*stky2(i,j)
-          ice_ocean_boundary%vstkb(i,j,2) = ocean_grid%cos_rot(ig,jg)*stky2(i,j) &
-               + ocean_grid%sin_rot(ig,jg)*stkx2(i,j)
-
-          ice_ocean_boundary%ustkb(i,j,3) = ocean_grid%cos_rot(ig,jg)*stkx3(i,j) &
-               - ocean_grid%sin_rot(ig,jg)*stky3(i,j)
-          ice_ocean_boundary%vstkb(i,j,3) = ocean_grid%cos_rot(ig,jg)*stky3(i,j) &
-               + ocean_grid%sin_rot(ig,jg)*stkx3(i,j)
-        enddo
-      enddo
-      deallocate(stkx1,stkx2,stkx3,stky1,stky2,stky3)
-    endif
   endif
 
 end subroutine mom_import

config_src/drivers/nuopc_cap/mom_surface_forcing_nuopc.F90

@@ -769,7 +769,6 @@ subroutine convert_IOB_to_forces(IOB, forces, index_bounds, Time, G, US, CS)
   endif
   forces%accumulate_p_surf = .true. ! Multiple components may contribute to surface pressure.
 
-  ! TODO: this does not seem correct for NEMS
 #ifdef CESMCOUPLED
   wind_stagger = AGRID
 #else