Handmerge develop to release/MAPL-v3 - 2025-Jan-06

.github/actions/deploy-ford-docs/action.yml

@@ -49,14 +49,14 @@ runs:
         repository: Goddard-Fortran-Ecosystem/gFTL
         path: gFTL
         fetch-depth: 1
-        ref: v1.13.0
+        ref: v1.14.0
 
     - name: Build gFTL
       run: |
         cd gFTL
         mkdir -p build
         cd build
-        cmake .. -DCMAKE_Fortran_COMPILER=gfortran-10 -DCMAKE_INSTALL_PREFIX=../install
+        cmake .. -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_INSTALL_PREFIX=../install
         make -j$(nproc) install
       shell: bash
 

CHANGELOG.md

@@ -74,12 +74,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Added optional start_date and start_time to control the output window for each History collection. No output will be written before then. If not specified, these default to the beginning of the experiment.
 - Added utility to prepare inputs for ExtDatDriver.x so that ExtData can simulate a real GEOS run
 - Added loggers when writing or reading weight files
 - Added new option to AGCM.rc `overwrite_checkpoint` to allow checkpoint files to be overwritten. By default still will not overwrite checkpoints
 
 ### Changed
 
+- Changed MAPL_ESMFRegridder to require the dstMaskValues to be added as grid attribute to use fixed masking, fixes UFS issue
 - Increased formatting width of time index in ExtData2G diagnostic print
 
 ### Fixed

base/MAPL_EsmfRegridder.F90

@@ -1431,13 +1431,13 @@ subroutine create_route_handle(this, kind, rc)
      real(real64), pointer :: src_dummy_r8(:,:), dst_dummy_r8(:,:)
      type (ESMF_Field) :: src_field, dst_field
 
-     integer :: srcTermProcessing
+     integer :: srcTermProcessing, num_mask_values
      integer, pointer :: factorIndexList(:,:)
      integer, allocatable :: dstMaskValues(:)
      real(ESMF_KIND_R8), pointer :: factorList(:)
      type(ESMF_RouteHandle) :: dummy_rh
      type(ESMF_UnmappedAction_Flag) :: unmappedaction
-     logical :: global, isPresent, has_mask
+     logical :: global, isPresent, has_mask, has_dstMaskValues
      type(RegridderSpecRouteHandleMap), pointer :: route_handles, transpose_route_handles
      type(ESMF_RouteHandle) :: route_handle, transpose_route_handle
      character(len=ESMF_MAXPATHLEN) :: rh_file,rh_trans_file
@@ -1513,6 +1513,14 @@ subroutine create_route_handle(this, kind, rc)
            end if
            call ESMF_GridGetItem(spec%grid_out,itemflag=ESMF_GRIDITEM_MASK, &
            staggerloc=ESMF_STAGGERLOC_CENTER, isPresent = has_mask, _RC)
+           call ESMF_InfoGetFromHost(spec%grid_out,infoh,_RC)
+           has_dstMaskValues = ESMF_InfoIsPresent(infoh,MAPL_DESTINATIONMASK,_RC)
+           if (has_dstMaskValues) then
+              _ASSERT(has_mask, "masking destination values when no masks is present")
+              call ESMF_InfoGet(infoh,MAPL_DESTINATIONMASK,num_mask_values,_RC)
+              allocate(dstMaskValues(num_mask_values), _STAT)
+              call ESMF_InfoGet(infoh,MAPL_DESTINATIONMASK,dstMaskValues,_RC)
+           end if
 
            counter = counter + 1
 
@@ -1523,7 +1531,6 @@ subroutine create_route_handle(this, kind, rc)
               call ESMF_InfoGet(infoh,'Global',global,_RC)
               if (.not.global) unmappedaction=ESMF_UNMAPPEDACTION_IGNORE
            end if
-           if (has_mask) dstMaskValues = [MAPL_MASK_OUT] ! otherwise unallocated
            select case (spec%regrid_method)
            case (REGRID_METHOD_BILINEAR, REGRID_METHOD_BILINEAR_MONOTONIC)
 

base/MAPL_XYGridFactory.F90

@@ -1020,6 +1020,7 @@ subroutine add_mask(this,grid,rc)
       integer :: status
       type(ESMF_VM) :: vm
       integer :: has_undef, local_has_undef
+      type(ESMF_Info) :: infoh
 
       call ESMF_GridGetCoord(grid, coordDim=1, localDE=0, &
          staggerloc=ESMF_STAGGERLOC_CENTER, farrayPtr=fptr, _RC)
@@ -1041,6 +1042,9 @@ subroutine add_mask(this,grid,rc)
       mask = MAPL_MASK_IN
       where(fptr==MAPL_UNDEF) mask = MAPL_MASK_OUT
 
+      call ESMF_InfoGetFromHost(grid,infoh,_RC)
+      call ESMF_InfoSet(infoh,key=MAPL_DESTINATIONMASK,values=[MAPL_MASK_OUT],_RC)
+
       _RETURN(_SUCCESS)
     end subroutine add_mask
 

docs/Ford/docs-with-remote-esmf.md

@@ -7,8 +7,8 @@ coloured_edges: true
 graph_maxdepth: 4
 graph_maxnodes: 32
 include: ../../include/
-         ../../gFTL/install/GFTL-1.13/include/v1
-         ../../gFTL/install/GFTL-1.13/include/v2
+         ../../gFTL/install/GFTL-1.14/include/v1
+         ../../gFTL/install/GFTL-1.14/include/v2
 exclude: **/EsmfRegridder.F90
          **/FieldBLAS_IntrinsicFunctions.F90
          **/GeomManager.F90

docs/Ford/docs-with-remote-esmf.public_private_protected.md

@@ -8,8 +8,8 @@ coloured_edges: true
 graph_maxdepth: 4
 graph_maxnodes: 32
 include: ../../include/
-         ../../gFTL/install/GFTL-1.13/include/v1
-         ../../gFTL/install/GFTL-1.13/include/v2
+         ../../gFTL/install/GFTL-1.14/include/v1
+         ../../gFTL/install/GFTL-1.14/include/v2
 exclude: **/EsmfRegridder.F90
          **/FieldBLAS_IntrinsicFunctions.F90
          **/GeomManager.F90

docs/Ford/ford-ci.md

@@ -8,8 +8,8 @@ coloured_edges: true
 graph_maxdepth: 4
 graph_maxnodes: 32
 include: ../../include/
-         ../../gFTL/install/GFTL-1.13/include/v1
-         ../../gFTL/install/GFTL-1.13/include/v2
+         ../../gFTL/install/GFTL-1.14/include/v1
+         ../../gFTL/install/GFTL-1.14/include/v2
 exclude: **/EsmfRegridder.F90
          **/FieldBLAS_IntrinsicFunctions.F90
          **/GeomManager.F90

docs/Ford/mapl3docs-with-remote-esmf.md

@@ -8,8 +8,8 @@ coloured_edges: true
 graph_maxdepth: 4
 graph_maxnodes: 32
 include: ../../include/
-         ../../gFTL/install/GFTL-1.13/include/v1
-         ../../gFTL/install/GFTL-1.13/include/v2
+         ../../gFTL/install/GFTL-1.14/include/v1
+         ../../gFTL/install/GFTL-1.14/include/v2
 exclude: **/EsmfRegridder.F90
          **/FieldBLAS_IntrinsicFunctions.F90
          **/GeomManager.F90

docs/Ford/mapl3docs-with-remote-esmf.public_private_protected.md

@@ -8,8 +8,8 @@ coloured_edges: true
 graph_maxdepth: 4
 graph_maxnodes: 32
 include: ../../include/
-         ../../gFTL/install/GFTL-1.13/include/v1
-         ../../gFTL/install/GFTL-1.13/include/v2
+         ../../gFTL/install/GFTL-1.14/include/v1
+         ../../gFTL/install/GFTL-1.14/include/v2
 exclude: **/EsmfRegridder.F90
          **/FieldBLAS_IntrinsicFunctions.F90
          **/GeomManager.F90

gridcomps/History/MAPL_HistoryCollection.F90

@@ -47,12 +47,15 @@ module MAPL_HistoryCollectionMod
      integer                            :: acc_offset
      integer                            :: ref_date
      integer                            :: ref_time
+     integer                            :: start_date
+     integer                            :: start_time
      integer                            :: end_date
      integer                            :: end_time
      integer                            :: duration
      type(ESMF_Alarm)                   :: his_alarm ! when to write file
      type(ESMF_Alarm)                   :: seg_alarm ! segment alarm controls when to write to new file
      type(ESMF_Alarm)                   :: mon_alarm
+     type(ESMF_Alarm)                   :: start_alarm
      type(ESMF_Alarm)                   :: end_alarm
      integer,pointer                    :: expSTATE (:)
      integer                            :: unit
@@ -70,6 +73,7 @@ module MAPL_HistoryCollectionMod
      integer                            :: verbose
      integer                            :: xyoffset
      logical                            :: disabled
+     logical                            :: skipWriting
      logical                            :: subVm
      logical                            :: backwards ! Adds support for clock running in reverse direction
      logical                            :: useNewFormat

gridcomps/History/MAPL_HistoryGridComp.F90

@@ -56,7 +56,7 @@ module MAPL_HistoryGridCompMod
   use MaskSamplerGeosatMod
   use MAPL_StringTemplate
   use regex_module
-  use MAPL_TimeUtilsMod, only: is_valid_time, is_valid_date
+  use MAPL_TimeUtilsMod, only: is_valid_time, is_valid_date, MAPL_UndefInt
   use gFTL_StringStringMap
   !use ESMF_CFIOMOD
   use MAPL_EpochSwathMod
@@ -812,16 +812,19 @@ subroutine Initialize ( gc, import, dumexport, clock, rc )
                                       label=trim(string) // 'ref_time:',_RC )
        _ASSERT(is_valid_time(list(n)%ref_time),'Invalid ref_time')
 
-       call ESMF_ConfigGetAttribute ( cfg, list(n)%end_date, default=-999, &
+       call ESMF_ConfigGetAttribute ( cfg, list(n)%start_date, default=MAPL_UndefInt, &
+                                      label=trim(string) // 'start_date:',_RC )
+       _ASSERT(is_valid_date(list(n)%start_date),'Invalid start_date')
+       call ESMF_ConfigGetAttribute ( cfg, list(n)%start_time, default=MAPL_UndefInt, &
+                                      label=trim(string) // 'start_time:',_RC )
+       _ASSERT(is_valid_time(list(n)%start_time),'Invalid start_time')
+
+       call ESMF_ConfigGetAttribute ( cfg, list(n)%end_date, default=MAPL_UndefInt, &
                                       label=trim(string) // 'end_date:',_RC )
-       if (list(n)%end_date /= -999) then
-          _ASSERT(is_valid_date(list(n)%end_date),'Invalid end_date')
-       end if
-       call ESMF_ConfigGetAttribute ( cfg, list(n)%end_time, default=-999, &
+       _ASSERT(is_valid_date(list(n)%end_date),'Invalid end_date')
+       call ESMF_ConfigGetAttribute ( cfg, list(n)%end_time, default=MAPL_UndefInt, &
                                       label=trim(string) // 'end_time:',_RC )
-       if (list(n)%end_time /= -999) then
-          _ASSERT(is_valid_time(list(n)%end_time),'Invalid end_time')
-       end if
+       _ASSERT(is_valid_time(list(n)%end_time),'Invalid end_time')
 
        call ESMF_ConfigGetAttribute ( cfg, list(n)%duration, default=list(n)%frequency, &
                                       label=trim(string) // 'duration:'  ,_RC )
@@ -1350,9 +1353,41 @@ subroutine Initialize ( gc, import, dumexport, clock, rc )
           intState%stampOffset(n) = Frequency ! we go to the beginning of the month
        end if
 
+! End Alarm based on start_date and start_time
+! ----------------------------------------
+       if( list(n)%start_date.ne.MAPL_UndefInt .and. list(n)%start_time.ne.MAPL_UndefInt ) then
+          REF_TIME(1) =     list(n)%start_date/10000
+          REF_TIME(2) = mod(list(n)%start_date,10000)/100
+          REF_TIME(3) = mod(list(n)%start_date,100)
+          REF_TIME(4) =     list(n)%start_time/10000
+          REF_TIME(5) = mod(list(n)%start_time,10000)/100
+          REF_TIME(6) = mod(list(n)%start_time,100)
+
+          call ESMF_TimeSet( RingTime, YY = REF_TIME(1), &
+                                       MM = REF_TIME(2), &
+                                       DD = REF_TIME(3), &
+                                       H  = REF_TIME(4), &
+                                       M  = REF_TIME(5), &
+                                       S  = REF_TIME(6), calendar=cal, rc=rc )
+       else
+          RingTime = CurrTime
+       end if
+       list(n)%start_alarm = ESMF_AlarmCreate( clock=clock, RingTime=RingTime, sticky=.false., _RC )
+
+       list(n)%skipWriting = .true.
+       if (RingTime == CurrTime) then
+          call  ESMF_AlarmRingerOn(list(n)%start_alarm, _RC )
+          list(n)%skipWriting = .false.
+       else
+          if (RingTime < CurrTime .NEQV. list(n)%backwards) then
+             list(n)%skipWriting = .false.
+          endif
+       end if
+
+
 ! End Alarm based on end_date and end_time
 ! ----------------------------------------
-       if( list(n)%end_date.ne.-999 .and. list(n)%end_time.ne.-999 ) then
+       if( list(n)%end_date.ne.MAPL_UndefInt .and. list(n)%end_time.ne.MAPL_UndefInt ) then
            REF_TIME(1) =     list(n)%end_date/10000
            REF_TIME(2) = mod(list(n)%end_date,10000)/100
            REF_TIME(3) = mod(list(n)%end_date,100)
@@ -2532,9 +2567,13 @@ subroutine Initialize ( gc, import, dumexport, clock, rc )
          else
             print *, '    Duration: ',       list(n)%duration
          end if
-         if( list(n)%end_date.ne.-999 ) then
-         print *, '    End_Date: ',       list(n)%end_date
-         print *, '    End_Time: ',       list(n)%end_time
+         if( list(n)%start_date.ne.MAPL_UndefInt ) then
+            print *, '    Start_Date: ',       list(n)%start_date
+            print *, '    Start_Time: ',       list(n)%start_time
+         endif
+         if( list(n)%end_date.ne.MAPL_UndefInt ) then
+            print *, '    End_Date: ',       list(n)%end_date
+            print *, '    End_Time: ',       list(n)%end_time
          endif
          if (trim(list(n)%output_grid_label)/='') then
             print *, ' Regrid Mthd: ',       regrid_method_int_to_string(list(n)%regrid_method)
@@ -3433,6 +3472,14 @@ subroutine Run ( gc, import, export, clock, rc )
 
   ! decide if we are writing based on alarms
 
+   do n=1,nlist
+      if (list(n)%skipWriting) then
+         if (ESMF_AlarmIsRinging(list(n)%start_alarm)) then
+            list(n)%skipWriting = .false.
+         endif
+      endif
+   end do
+
    do n=1,nlist
       if (list(n)%disabled .or. ESMF_AlarmIsRinging(list(n)%end_alarm) ) then
          list(n)%disabled = .true.
@@ -3460,6 +3507,8 @@ subroutine Run ( gc, import, export, clock, rc )
          end if
       end if
 
+      if (list(n)%skipWriting) writing(n) = .false.
+
        if (writing(n) .and. .not.IntState%average(n)) then
           ! R8 to R4 copy (if needed!)
           do m=1,list(n)%field_set%nfields

shared/Constants/InternalConstants.F90

@@ -23,6 +23,7 @@ module MAPL_InternalConstantsMod
    character(len=*), parameter  :: MAPL_GRID_NAME_DEFAULT       = 'UNKNOWN'
    character(len=*), parameter  :: MAPL_GRID_FILE_NAME_DEFAULT  = 'UNKNOWN'
    character(len=*), parameter  :: MAPL_CF_COMPONENT_SEPARATOR  = '.'
+   character(len=*), parameter  :: MAPL_DESTINATIONMASK         = "MAPL_DestinationMask"
 
    enum, bind(c)
       enumerator MAPL_TimerModeOld

shared/TimeUtils.F90

@@ -7,6 +7,8 @@ module MAPL_TimeUtilsMod
    public :: is_valid_time
    public :: is_valid_datetime
 
+   integer, public, parameter :: MAPL_UndefInt = -999
+
 contains
 
    logical function is_valid_date(date) result(is_valid)
@@ -19,6 +21,11 @@ logical function is_valid_date(date) result(is_valid)
       integer :: year, month, day
       logical :: is_leap_year
 
+      if (date == MAPL_UndefInt) then
+         is_valid = .true.
+         return
+      end if
+
       year  = date/10000
       month = mod(date,10000)/100
       day   = mod(date,100)
@@ -66,6 +73,11 @@ logical function is_valid_time(time) result(is_valid)
 
       integer :: hours, minutes, seconds
 
+      if (time == MAPL_UndefInt) then
+         is_valid = .true.
+         return
+      end if
+
       hours   = time/10000
       minutes = mod(time,10000)/100
       seconds = mod(time,100)