removed rpointer timestamp, merged to main

.github/workflows/srt.yml

@@ -95,6 +95,8 @@ jobs:
           cd ../components/cdeps
           git checkout main
           git submodule update --init
+          cd ../../share
+          git checkout main
           
       - name: Cache ESMF
         id: cache-esmf
@@ -170,6 +172,6 @@ jobs:
           popd
 #     the following can be used by developers to login to the github server in case of errors
 #     see https://github.com/marketplace/actions/debugging-with-tmate for further details
-#      - name: Setup tmate session
-#        if: ${{ failure() }}
-#        uses: mxschmitt/action-tmate@v3
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3

cesm/driver/esm.F90

@@ -877,6 +877,9 @@ subroutine esm_init_pelayout(driver, maxthreads, rc)
     character(len=5)               :: inst_suffix
     character(CL)                  :: cvalue
     logical                        :: found_comp
+#ifdef ESMF_AWARE_THREADING
+    integer                        :: cnt
+#endif
     integer :: rank, nprocs, ierr
     character(len=*), parameter    :: subname = "(esm_pelayout.F90:esm_init_pelayout)"
     !---------------------------------------

cesm/nuopc_cap_share/seq_drydep_mod.F90

@@ -1,8 +1,6 @@
 module seq_drydep_mod
 
   use shr_drydep_mod, only: seq_drydep_setHCoeff=>shr_drydep_setHCoeff
-  use shr_drydep_mod
-
   implicit none
 
   ! method specification

cesm/nuopc_cap_share/shr_dust_emis_mod.F90

@@ -0,0 +1,222 @@
+module shr_dust_emis_mod
+
+  !========================================================================
+  ! Module for handling dust emissions.
+  ! This module is shared by land and atmosphere models for the computation of
+  ! dust emissions.
+  !========================================================================
+
+  use shr_sys_mod    , only : shr_sys_abort
+  use shr_kind_mod   , only : CS => SHR_KIND_CS
+  use shr_nl_mod     , only : shr_nl_find_group_name
+  use shr_log_mod    , only : shr_log_getLogUnit, errMsg => shr_log_errMsg
+
+  implicit none
+  private
+
+  ! public member functions
+  public :: shr_dust_emis_readnl           ! Read namelist
+  public :: is_dust_emis_zender            ! If Zender_2003 dust emission method is being used
+  public :: is_dust_emis_leung             ! If Leungr_2023 dust emission method is being used
+  public :: is_zender_soil_erod_from_land  ! If Zender_2003 is being used and soil eroditability is in land
+  public :: is_zender_soil_erod_from_atm   ! If Zender/_2003 is being used and soil eroditability is in atmosphere
+
+  ! The following is only public for the sake of unit testing; it should not be called
+  ! directly outside this module
+  public :: dust_emis_set_options       ! Set the namelist options directory not through the namelist
+  public :: is_NOT_initialized          ! Check if dust emission has NOT been initialized
+
+  ! private data members:
+  private :: check_options_finish_init  ! Check that the options are correct and finish initialization
+
+  ! PRIVATE DATA:
+  character(len=CS) :: dust_emis_method = 'Zender_2003'  ! Dust emisison method to use: Zender_2003 or Leung_2023
+  character(len=CS) :: zender_soil_erod_source = 'none'  ! if calculated in lnd or atm (only when Zender_2003 is used)
+  logical           :: dust_emis_initialized=.false.     ! If dust emissions have been initiatlized yet or not
+
+  character(len=*), parameter :: u_FILE_u = &
+       __FILE__
+
+!===============================================================================
+CONTAINS
+!===============================================================================
+
+  subroutine shr_dust_emis_readnl(mpicom, NLFilename)
+
+    !========================================================================
+    ! reads dust_emis_inparm namelist to determine how dust emissions will
+    ! be handled between the land and atmosphere models
+    !========================================================================
+    use shr_mpi_mod, only : shr_mpi_bcast, shr_mpi_commrank
+
+    character(len=*), intent(in)  :: NLFilename ! Namelist filename
+    integer         , intent(in)  :: mpicom     ! MPI communicator for broadcasting all all tasks
+
+    !----- local -----
+    integer       :: unitn            ! namelist unit number
+    integer       :: ierr             ! error code
+    logical       :: exists           ! if file exists or not
+    integer       :: localPet         ! Local processor rank
+    integer       :: s_logunit        ! Output log unit
+    character(*),parameter :: F00   = "('(shr_dust_emis_read) ',8a)"
+    character(*),parameter :: subName = '(shr_dust_emis_read) '
+    !-----------------------------------------------------------------------------
+
+    namelist /dust_emis_inparm/ dust_emis_method, zender_soil_erod_source
+
+    !-----------------------------------------------------------------------------
+    ! Read namelist, check if namelist file exists first
+    !-----------------------------------------------------------------------------
+
+    !--- Open and read namelist ---
+    if ( len_trim(NLFilename) == 0  )then
+       call shr_sys_abort( subName//'ERROR: nlfilename not set' )
+    end if
+
+    call shr_mpi_commrank( mpicom, localPet )
+
+    call shr_log_getLogUnit(s_logunit)
+    if (localPet==0) then
+       inquire( file=trim(NLFileName), exist=exists)
+       if ( exists ) then
+          open(newunit=unitn, file=trim(NLFilename), status='old' )
+          write(s_logunit,F00) 'Read in dust_emis_inparm namelist from: ', trim(NLFilename)
+          call shr_nl_find_group_name(unitn, 'dust_emis_inparm', ierr)
+          if (ierr == 0) then
+             ! Note that ierr /= 0, no namelist is present.
+             read(unitn, dust_emis_inparm, iostat=ierr)
+             if (ierr > 0) then
+                call shr_sys_abort( subName//'ERROR:: problem on read of dust_emis_inparm ' &
+                                    // 'namelist in shr_dust_emis_readnl')
+             end if
+          endif
+          close( unitn )
+       end if
+    end if
+    call shr_mpi_bcast(dust_emis_method, mpicom)
+    call shr_mpi_bcast(zender_soil_erod_source, mpicom)
+
+    call check_options_finish_init()
+
+  end subroutine shr_dust_emis_readnl
+
+!====================================================================================
+
+  subroutine check_options_finish_init()
+   ! Some error checking and mark initialization as finished
+   integer :: s_logunit        ! Output log unit
+   character(*),parameter :: subName = '(check_options_finish_init) '
+
+   call shr_log_getLogUnit(s_logunit)
+   if (trim(dust_emis_method) == 'Leung_2023') then
+      if ( trim(zender_soil_erod_source) /= 'none' )then
+         write(s_logunit,*) 'ERROR: '//errMsg(u_FILE_u, __LINE__)
+         call shr_sys_abort(subName//"ERROR: zender_soil_erod_source should NOT be set, when dust_emis_method=Leung_2023" )
+         return
+      end if
+   else if (trim(dust_emis_method) == 'Zender_2003') then
+      if ( (trim(zender_soil_erod_source) /= 'lnd') .and. (trim(zender_soil_erod_source) /= 'atm') )then
+         write(s_logunit,*) 'zender_soil_erod_source is NOT valid = ', trim(zender_soil_erod_source)
+         write(s_logunit,*) 'ERROR: '//errMsg(u_FILE_u, __LINE__)
+         call shr_sys_abort(subName//"ERROR: zender_soil_erod_source can only be lnd or atm" )
+         return
+      end if
+   else
+      write(s_logunit,*) 'dust_emis_method not recognized = ', trim(dust_emis_method)
+      write(s_logunit,*) 'ERROR: '//errMsg(u_FILE_u, __LINE__)
+      call shr_sys_abort(subName//"ERROR: dust_emis_method namelist item is not valid" )
+      return
+   end if
+
+   dust_emis_initialized = .true.
+
+  end subroutine check_options_finish_init
+
+!====================================================================================
+
+  logical function is_dust_emis_zender()
+     ! is_dust_emis_zender – Logical function, true if the Zender 2003 scheme is being used
+     if ( is_NOT_initialized() ) return
+     if (trim(dust_emis_method) == 'Zender_2003') then
+        is_dust_emis_zender = .true.
+     else
+        is_dust_emis_zender = .false.
+     end if
+  end function is_dust_emis_zender
+
+!===============================================================================
+
+  logical function is_dust_emis_leung()
+     ! is_dust_emis_leung – Logical function, true if the Leung 2023 scheme is being used
+     if ( is_NOT_initialized() ) return
+     if (trim(dust_emis_method) == 'Leung_2023') then
+        is_dust_emis_leung = .true.
+     else
+        is_dust_emis_leung = .false.
+     end if
+  end function is_dust_emis_leung
+
+!===============================================================================
+
+  logical function is_zender_soil_erod_from_land()
+     ! is_zender_soil_erod_from_land – Logical function, true if the Zender method is being used and soil erodibility is in CTSM
+     if ( is_NOT_initialized() ) return
+     if ( is_dust_emis_zender() )then
+        if (trim(zender_soil_erod_source) == 'lnd') then
+           is_zender_soil_erod_from_land = .true.
+        else
+           is_zender_soil_erod_from_land = .false.
+        end if
+     else
+        is_zender_soil_erod_from_land = .false.
+     end if
+  end function is_zender_soil_erod_from_land
+
+!===============================================================================
+
+  logical function is_zender_soil_erod_from_atm()
+     !is_zender_soil_erod_from_atm – Logical function, true if the Zender method is being used and soil erodibility is in CAM
+     if ( is_NOT_initialized() ) return
+     if ( is_dust_emis_zender() )then
+        if ( trim(zender_soil_erod_source) == 'atm') then
+           is_zender_soil_erod_from_atm = .true.
+        else
+           is_zender_soil_erod_from_atm = .false.
+        end if
+     else
+        is_zender_soil_erod_from_atm = .false.
+     end if
+  end function is_zender_soil_erod_from_atm
+
+!===============================================================================
+
+  logical function is_NOT_initialized()
+     ! Check if this is NOT initialized and return true if so (false if initialized)
+     ! Will abort with an error when using in the model
+     ! For unit testing will return the logical state
+     integer       :: s_logunit        ! Output log unit
+
+     if ( dust_emis_initialized )then
+        is_NOT_initialized = .false.
+        return
+     else
+        is_NOT_initialized = .true.
+        call shr_log_getLogUnit(s_logunit)
+        write(s_logunit,*) 'ERROR: '//errMsg(u_FILE_u, __LINE__)
+        call shr_sys_abort( 'ERROR: dust emission namelist has NOT been read in yet,' // &
+                            ' shr_dust_emis_mod is NOT initialized ' )
+     end if
+   end function is_NOT_initialized
+
+  subroutine dust_emis_set_options( dust_emis_method_in, zender_soil_erod_source_in)
+    character(len=*), intent(IN) :: dust_emis_method_in         ! Dust emisison method to use: Zender_2003 or Leung_2023
+    character(len=*), intent(IN) :: zender_soil_erod_source_in  ! if calculed in lnd or atm (only when Zender_2003 is used)
+
+    dust_emis_method = dust_emis_method_in
+    zender_soil_erod_source = zender_soil_erod_source_in
+    call check_options_finish_init()
+  end subroutine dust_emis_set_options
+
+!===============================================================================
+
+end module shr_dust_emis_mod

cime_config/buildnml

@@ -50,8 +50,9 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     config["continue_run"] = ".true." if case.get_value("CONTINUE_RUN") else ".false."
     config["flux_epbal"] = "ocn" if case.get_value("CPL_EPBAL") == "ocn" else "off"
     config["mask_grid"] = case.get_value("MASK_GRID")
-    config["rest_option"] = case.get_value("REST_OPTION")
-
+    for val in ("HIST", "REST", "STOP"):
+        config[val.lower()+"_option"] = case.get_value(val+"_OPTION")
+
 
     config["comp_ocn"] = case.get_value("COMP_OCN")
 
@@ -100,7 +101,7 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     else:
         config["single_column"] = "false"
 
-    # needed for determining the run sequence as well as glc_renormalize_smb
+    # needed for determining the run sequence
     config["COMP_ATM"] = case.get_value("COMP_ATM")
     config["COMP_ICE"] = case.get_value("COMP_ICE")
     config["COMP_GLC"] = case.get_value("COMP_GLC")
@@ -189,6 +190,8 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     # determine coupling intervals
     comps = case.get_values("COMP_CLASSES")
     mindt = basedt
+
+
     coupling_times = {}
     for comp in comps:
         ncpl = case.get_value(comp.upper() + "_NCPL")
@@ -201,6 +204,19 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
             coupling_times[comp.lower() + "_cpl_dt"] = cpl_dt
             mindt = min(mindt, cpl_dt)
 
+    # Here we convert "nsteps" to "nseconds", this simplifies the fortran
+
+    for val in ("REST", "HIST", "STOP"):
+        if case.get_value(val+"_OPTION") == "nsteps":
+            nsteps = case.get_value(val+"_N")
+            if val == "REST":
+                nmlgen.set_value("restart_n", value=mindt*nsteps)
+            elif val == "HIST":
+                nmlgen.set_value("history_n", value=mindt*nsteps)
+            else:
+                nmlgen.set_value("stop_n", value=mindt*nsteps)
+
+
     # sanity check
     comp_atm = case.get_value("COMP_ATM")
     if comp_atm is not None and comp_atm not in ("datm", "xatm", "satm"):

cime_config/config_component.xml

@@ -1986,15 +1986,15 @@
     https://www.unidata.ucar.edu/software/netcdf/docs/data_type.html
     </desc>
     <values>
-      <value compclass="ATM">64bit_offset</value>
-      <value compclass="CPL">64bit_offset</value>
-      <value compclass="OCN">64bit_offset</value>
-      <value compclass="WAV">64bit_offset</value>
-      <value compclass="GLC">64bit_offset</value>
-      <value compclass="ICE">64bit_offset</value>
-      <value compclass="ROF">64bit_offset</value>
-      <value compclass="LND">64bit_offset</value>
-      <value compclass="ESP">64bit_offset</value>
+      <value compclass="ATM">64bit_data</value>
+      <value compclass="CPL">64bit_data</value>
+      <value compclass="OCN">64bit_data</value>
+      <value compclass="WAV">64bit_data</value>
+      <value compclass="GLC">64bit_data</value>
+      <value compclass="ICE">64bit_data</value>
+      <value compclass="ROF">64bit_data</value>
+      <value compclass="LND">64bit_data</value>
+      <value compclass="ESP">64bit_data</value>
     </values>
   </entry>
 
@@ -2412,6 +2412,19 @@
  </entry>
 
   <!-- ===================================================================== -->
+  <!-- optionally connect the case to a remote git repository,               -->
+  <!-- the branch is the case name and must be unique in remote              -->
+  <!-- ===================================================================== -->
+
+ <entry id="CASE_GIT_REPOSITORY">
+   <type>char</type>
+   <default_value></default_value>
+   <group>case_git</group>
+   <file>env_build.xml</file>
+   <desc>Remote git repository used for this case</desc>
+ </entry>
+
+<!-- ===================================================================== -->
   <!-- Include the AOFLUX calculation for this compset -->
   <!-- ===================================================================== -->