Merge pull request #250 from COSIMA/209-new-build

Update all components with new versions from upstream per #209

.gitmodules

@@ -1,9 +1,9 @@
 [submodule "MOM6/MOM6"]
 	path = MOM6/MOM6
-	url = https://github.com/ACCESS-NRI/mom6
+	url = https://github.com/ACCESS-NRI/MOM6
 [submodule "CICE6/CICE6"]
 	path = CICE/CICE
-	url = https://github.com/ESCOMP/CICE
+	url = https://github.com/ACCESS-NRI/CICE
 [submodule "CMEPS/CMEPS"]
 	path = CMEPS/CMEPS
 	url = https://github.com/ESCOMP/CMEPS

CDEPS/CMakeLists.txt

@@ -14,9 +14,9 @@ target_sources(OM3_cdeps_common PRIVATE
   CDEPS/streams/dshr_stream_mod.F90
   CDEPS/streams/dshr_tinterp_mod.F90
 
+  CDEPS/dshr/dshr_mod.F90
   CDEPS/dshr/dshr_dfield_mod.F90
   CDEPS/dshr/dshr_fldlist_mod.F90
-  CDEPS/dshr/dshr_mod.F90
 )
 
 ## DATM
@@ -52,6 +52,8 @@ target_sources(OM3_cdeps_docn PRIVATE
   CDEPS/docn/docn_datamode_aquaplanet_mod.F90
   CDEPS/docn/docn_datamode_copyall_mod.F90
   CDEPS/docn/docn_datamode_cplhist_mod.F90
+  CDEPS/docn/docn_datamode_multilev_mod.F90
+  CDEPS/docn/docn_datamode_multilev_dom_mod.F90
   CDEPS/docn/docn_datamode_iaf_mod.F90
   CDEPS/docn/docn_datamode_som_mod.F90
   CDEPS/docn/docn_import_data_mod.F90

CDEPS/extra_sources/datm_datamode_jra55do_mod.F90

@@ -10,7 +10,6 @@ module datm_datamode_jra55do_mod
   use shr_const_mod    , only : shr_const_tkfrz, shr_const_pi, shr_const_rdair
   use dshr_strdata_mod , only : shr_strdata_get_stream_pointer, shr_strdata_type
   use dshr_methods_mod , only : dshr_state_getfldptr, dshr_fldbun_getfldptr, dshr_fldbun_regrid, chkerr
-  use dshr_mod         , only : dshr_restart_read, dshr_restart_write
   use dshr_strdata_mod , only : shr_strdata_type
   use dshr_fldlist_mod , only : fldlist_type, dshr_fldlist_add
 
@@ -20,8 +19,7 @@ module datm_datamode_jra55do_mod
   public  :: datm_datamode_jra55do_advertise
   public  :: datm_datamode_jra55do_init_pointers
   public  :: datm_datamode_jra55do_advance
-  public  :: datm_datamode_jra55do_restart_write
-  public  :: datm_datamode_jra55do_restart_read
+
 
   ! export state pointers
   real(r8), pointer :: Sa_z(:)       => null()
@@ -283,39 +281,4 @@ subroutine datm_datamode_jra55do_advance(exportstate, target_ymd, target_tod, mo
 
   end subroutine datm_datamode_jra55do_advance
 
-  !===============================================================================
-  subroutine datm_datamode_jra55do_restart_write(case_name, inst_suffix, ymd, tod, &
-       logunit, my_task, sdat)
-
-    ! input/output variables
-    character(len=*)            , intent(in)    :: case_name
-    character(len=*)            , intent(in)    :: inst_suffix
-    integer                     , intent(in)    :: ymd       ! model date
-    integer                     , intent(in)    :: tod       ! model sec into model date
-    integer                     , intent(in)    :: logunit
-    integer                     , intent(in)    :: my_task
-    type(shr_strdata_type)      , intent(inout) :: sdat
-    !-------------------------------------------------------------------------------
-
-    call dshr_restart_write(rpfile, case_name, 'datm', inst_suffix, ymd, tod, &
-         logunit, my_task, sdat)
-
-  end subroutine datm_datamode_jra55do_restart_write
-
-  !===============================================================================
-  subroutine datm_datamode_jra55do_restart_read(rest_filem, inst_suffix, logunit, my_task, mpicom, sdat)
-
-    ! input/output arguments
-    character(len=*)            , intent(inout) :: rest_filem
-    character(len=*)            , intent(in)    :: inst_suffix
-    integer                     , intent(in)    :: logunit
-    integer                     , intent(in)    :: my_task
-    integer                     , intent(in)    :: mpicom
-    type(shr_strdata_type)      , intent(inout) :: sdat
-    !-------------------------------------------------------------------------------
-
-    call dshr_restart_read(rest_filem, rpfile, inst_suffix, nullstr, logunit, my_task, mpicom, sdat)
-
-  end subroutine datm_datamode_jra55do_restart_read
-
 end module datm_datamode_jra55do_mod

CDEPS/patches/atm_comp_nuopc.F90.patch

@@ -1,27 +1,27 @@
---- CDEPS/datm/atm_comp_nuopc.F90	2023-08-31 10:49:23.508874000 +1000
-+++ extra_sources/atm_comp_nuopc.F90	2023-08-31 10:48:55.428272000 +1000
-@@ -52,6 +52,12 @@
-   use datm_datamode_jra_mod     , only : datm_datamode_jra_restart_write
-   use datm_datamode_jra_mod     , only : datm_datamode_jra_restart_read
+diff --git a/datm/atm_comp_nuopc.F90 b/datm/atm_comp_nuopc.F90
+index b74e0d3..bb31c22 100644
+--- a/datm/atm_comp_nuopc.F90
++++ b/datm/atm_comp_nuopc.F90
+@@ -48,6 +48,10 @@ module cdeps_datm_comp
+   use datm_datamode_jra_mod     , only : datm_datamode_jra_init_pointers
+   use datm_datamode_jra_mod     , only : datm_datamode_jra_advance
 
 +  use datm_datamode_jra55do_mod , only : datm_datamode_jra55do_advertise
 +  use datm_datamode_jra55do_mod , only : datm_datamode_jra55do_init_pointers
 +  use datm_datamode_jra55do_mod , only : datm_datamode_jra55do_advance
-+  use datm_datamode_jra55do_mod , only : datm_datamode_jra55do_restart_write
-+  use datm_datamode_jra55do_mod , only : datm_datamode_jra55do_restart_read
 +
    use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_advertise
    use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_init_pointers
    use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_advance
-@@ -342,6 +348,7 @@
+@@ -357,6 +361,7 @@ contains
      if ( trim(datamode) == 'CORE2_NYF'    .or. &
           trim(datamode) == 'CORE2_IAF'    .or. &
           trim(datamode) == 'CORE_IAF_JRA' .or. &
-+         trim(datamode) == 'JRA55do'.or. &
++         trim(datamode) == 'JRA55do'      .or. &
           trim(datamode) == 'CLMNCEP'      .or. &
           trim(datamode) == 'CPLHIST'      .or. &
           trim(datamode) == 'GEFS'         .or. &
-@@ -361,6 +368,10 @@
+@@ -377,6 +382,10 @@ contains
         call datm_datamode_jra_advertise(exportState, fldsExport, flds_scalar_name, &
              flds_co2, flds_wiso, flds_presaero, flds_presndep, rc)
         if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -32,7 +32,7 @@
      case ('CLMNCEP')
         call datm_datamode_clmncep_advertise(exportState, fldsExport, flds_scalar_name, &
              flds_co2, flds_wiso, flds_presaero, flds_presndep, flds_preso3, rc)
-@@ -606,6 +617,9 @@
+@@ -627,6 +636,9 @@ contains
         case('CORE_IAF_JRA')
            call datm_datamode_jra_init_pointers(exportState, sdat, rc)
            if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -42,16 +42,16 @@
         case('CLMNCEP')
            call datm_datamode_clmncep_init_pointers(importState, exportState, sdat, rc)
            if (ChkErr(rc,__LINE__,u_FILE_u)) return
-@@ -630,6 +644,8 @@
-              call datm_datamode_core2_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-           case('CORE_IAF_JRA')
-              call datm_datamode_jra_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-+          case('JRA55do')
-+             call datm_datamode_jra55do_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-           case('CLMNCEP')
-              call datm_datamode_clmncep_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-           case('CPLHIST')
-@@ -677,6 +693,9 @@
+@@ -652,7 +664,7 @@ contains
+           call shr_get_rpointer_name(gcomp, 'atm', target_ymd, target_tod, rpfile, 'read', rc)
+           if (ChkErr(rc,__LINE__,u_FILE_u)) return
+           select case (trim(datamode))
+-          case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','CLMNCEP','CPLHIST','ERA5','GEFS','CFSR','SIMPLE')
++          case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','JRA55do','CLMNCEP','CPLHIST','ERA5','GEFS','CFSR','SIMPLE')
+              call dshr_restart_read(restfilm, rpfile, logunit, my_task, mpicom, sdat, rc)
+              if (ChkErr(rc,__LINE__,u_FILE_u)) return
+           case default
+@@ -694,6 +706,9 @@ contains
      case('CORE_IAF_JRA')
         call datm_datamode_jra_advance(exportstate, target_ymd, target_tod, sdat%model_calendar, rc)
         if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -61,13 +61,12 @@
      case('CLMNCEP')
         call datm_datamode_clmncep_advance(mainproc, logunit, mpicom,  rc)
         if (ChkErr(rc,__LINE__,u_FILE_u)) return
-@@ -705,6 +724,9 @@
-        case('CORE_IAF_JRA')
-           call datm_datamode_jra_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-                logunit, my_task, sdat)
-+       case('JRA55do')
-+          call datm_datamode_jra55do_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-+               logunit, my_task, sdat)
-        case('CLMNCEP')
-           call datm_datamode_clmncep_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-                logunit, my_task, sdat)
+@@ -722,7 +737,7 @@ contains
+        call shr_get_rpointer_name(gcomp, 'atm', target_ymd, target_tod, rpfile, 'write', rc)
+        if (ChkErr(rc,__LINE__,u_FILE_u)) return
+        select case (trim(datamode))
+-       case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','CLMNCEP','CPLHIST','ERA5','GEFS','CFSR','SIMPLE')
++       case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','JRA55do','CLMNCEP','CPLHIST','ERA5','GEFS','CFSR','SIMPLE')
+           call dshr_restart_write(rpfile, case_name, 'datm', inst_suffix, target_ymd, target_tod, logunit, &
+                my_task, sdat, rc)
+           if (ChkErr(rc,__LINE__,u_FILE_u)) return

CICE/CMakeLists.txt

@@ -26,6 +26,7 @@ target_sources(OM3_cice PRIVATE
   CICE/cicecore/shared/ice_arrays_column.F90
   CICE/cicecore/shared/ice_calendar.F90
   CICE/cicecore/shared/ice_constants.F90
+  CICE/cicecore/shared/ice_distribution.F90
   CICE/cicecore/shared/ice_domain_size.F90
   CICE/cicecore/shared/ice_fileunits.F90
   CICE/cicecore/shared/ice_init_column.F90
@@ -61,11 +62,13 @@ target_sources(OM3_cice PRIVATE
   CICE/cicecore/cicedyn/general/ice_flux_bgc.F90
   CICE/cicecore/cicedyn/general/ice_forcing.F90
   CICE/cicecore/cicedyn/general/ice_forcing_bgc.F90
+  CICE/cicecore/cicedyn/general/ice_init.F90
   CICE/cicecore/cicedyn/general/ice_state.F90
   CICE/cicecore/cicedyn/general/ice_step_mod.F90
 
   # Infrastructure
   CICE/cicecore/cicedyn/infrastructure/ice_blocks.F90
+  CICE/cicecore/cicedyn/infrastructure/ice_domain.F90
   CICE/cicecore/cicedyn/infrastructure/ice_grid.F90
   CICE/cicecore/cicedyn/infrastructure/ice_memusage.F90
   CICE/cicecore/cicedyn/infrastructure/ice_memusage_gptl.c
@@ -152,10 +155,6 @@ elseif(OM3_CICE_IO MATCHES "Binary")
   )
 endif()
 
-add_patched_source(OM3_cice CICE/cicecore/cicedyn/infrastructure/ice_domain.F90)
-add_patched_source(OM3_cice CICE/cicecore/shared/ice_distribution.F90)
-add_patched_source(OM3_cice CICE/cicecore/cicedyn/general/ice_init.F90)
-
 ### Install and Export
 
 ## Library

CMEPS/CMakeLists.txt

@@ -12,6 +12,7 @@ if(OpenMP_Fortran_FOUND)
 endif()
 target_sources(OM3_cmeps PRIVATE
   CMEPS/cesm/flux_atmocn/shr_flux_mod.F90
+  CMEPS/mediator/med_phases_history_mod.F90
   CMEPS/mediator/med_phases_restart_mod.F90
   CMEPS/mediator/med_map_mod.F90
   CMEPS/mediator/med_methods_mod.F90
@@ -31,7 +32,6 @@ target_sources(OM3_cmeps PRIVATE
   CMEPS/mediator/med_phases_prep_ocn_mod.F90
   CMEPS/mediator/esmFlds.F90
   CMEPS/mediator/med.F90
-  CMEPS/mediator/med_time_mod.F90
   CMEPS/mediator/med_phases_ocnalb_mod.F90
   CMEPS/mediator/med_phases_prep_wav_mod.F90
   CMEPS/mediator/med_utils_mod.F90
@@ -48,8 +48,6 @@ target_sources(OM3_cmeps PRIVATE
   CMEPS/mediator/med_phases_post_wav_mod.F90
 )
 
-add_patched_source(OM3_cmeps CMEPS/mediator/med_phases_history_mod.F90)
-
 ## NUOPC cap share
 add_fortran_library(OM3_nuopc_cap_share mod/nuopc_cap_share STATIC)
 add_library(AccessOM3::nuopc_cap_share ALIAS OM3_nuopc_cap_share)
@@ -61,7 +59,6 @@ target_sources(OM3_nuopc_cap_share PRIVATE
   CMEPS/cesm/nuopc_cap_share/driver_pio_mod.F90
   CMEPS/cesm/nuopc_cap_share/esm_utils_mod.F90
   CMEPS/cesm/nuopc_cap_share/glc_elevclass_mod.F90
-  CMEPS/cesm/nuopc_cap_share/nuopc_shr_methods.F90
 )