Merge pull request #1770 from GEOS-ESM/develop

GitFlow: Merge Develop into Main for 2.29 Release

.circleci/config.yml

@@ -147,6 +147,22 @@ workflows:
           baselibs_version: *baselibs_version
           bcs_version: *bcs_version
 
+      # Run Coupled GCM (1 hour, no ExtData)
+      - ci/run_gcm:
+          name: run-coupled-GCM-on-<< matrix.compiler >>
+          context:
+            - docker-hub-creds
+          matrix:
+            parameters:
+              compiler: [ifort]
+          requires:
+            - build-GEOSgcm-on-<< matrix.compiler >>
+          repo: GEOSgcm
+          baselibs_version: *baselibs_version
+          bcs_version: *bcs_version
+          gcm_ocean_type: MOM6
+          change_layout: false
+
       # Run MAPL Tutorials
       - ci/run_mapl_tutorial:
           name: run-<< matrix.tutorial_name >>-Tutorial-with-<< matrix.compiler >>

CHANGELOG.md

@@ -12,12 +12,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 ### Changed
-- Error codes in `shared/MAPL_Error_Handling.F90` are now consistent with `_FAILURE = 1` in `include/MAPL_ErrLog.h`
 
 ### Removed
 
 ### Deprecated
 
+## [2.29.0] - 2022-10-28
+
+### Fixed
+
+- Add define for `-Dsys${CMAKE_SYSTEM_NAME}` to fix build issue with macOS and Intel (#1695)
+- Fix handling of return macros for programs and subroutines (#1194)
+
+### Added
+
+- Add Coupled MOM6 GCM run to CI (ifort only)
+- Added ability to pass in extra options to FLAP CLI arguments
+- Added option to pass vertical metadata to FieldBundleWriter class for output file
+- Expose FileMetaUtilities class MAPL_VerticalDataMod via "use MAPL"
+
+### Changed
+
+- Change argument arrdes of MAPL_Read and Write NC Var 3d to optional
+- Error codes in `shared/MAPL_Error_Handling.F90` are now consistent with `_FAILURE = 1` in `include/MAPL_ErrLog.h`
+- Updated `components.yaml
+  - ESMA_env v4.4.0 → v4.5.0 (Update for GMI builds)
+  - ESMA_cmake v3.18.0 → v3.19.0 (Add `-save-temps` to GNU debug, check if install prefix is writable)
+
 ## [2.28.0] - 2022-10-17
 
 ### Fixed

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_policy (SET CMP0054 NEW)
 
 project (
   MAPL
-  VERSION 2.28.0
+  VERSION 2.29.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the default build type to release
@@ -158,6 +158,8 @@ else ()
   add_subdirectory (pflogger_stub)
 endif ()
 
+add_definitions(-Dsys${CMAKE_SYSTEM_NAME})
+
 # Special case - MAPL_cfio is built twice with two different precisions.
 add_subdirectory (MAPL_cfio MAPL_cfio_r4)
 add_subdirectory (MAPL_cfio MAPL_cfio_r8)

base/Base.F90

@@ -49,6 +49,8 @@ module MAPLBase_Mod
   use MAPL_EtaHybridVerticalCoordinateMod
   use MAPL_ApplicationSupport
   use MAPL_ServerManager
+  use MAPL_FileMetadataUtilsMod
+  use MAPL_VerticalDataMod
   logical, save, private :: mapl_is_initialized = .false.
 
 end module MAPLBase_Mod

base/FileMetadataUtilities.F90

@@ -490,11 +490,14 @@ function get_variable_attribute(this,var_name,attr_name,rc) result(units)
 
    end function get_variable_attribute
 
-   subroutine get_coordinate_info(this,coordinate_name,coordSize,coordUnits,coords,rc)
+   subroutine get_coordinate_info(this,coordinate_name,coordSize,coordUnits,long_name,standard_name,coords,coordinate_attr,rc)
       class (FileMetadataUtils), intent(inout) :: this
       character(len=*), intent(in) :: coordinate_name
       integer, optional, intent(out) :: coordSize
       character(len=*), optional, intent(out) :: coordUnits
+      character(len=*), optional, intent(out) :: long_name
+      character(len=*), optional, intent(out) :: standard_name
+      character(len=*), optional, intent(out) :: coordinate_attr
       real, allocatable, optional,  intent(inout) :: coords(:)
       integer, optional, intent(out) :: rc
 
@@ -522,10 +525,55 @@ subroutine get_coordinate_info(this,coordinate_name,coordSize,coordUnits,coords,
          type is (character(*))
             coordUnits = trim(coordUnitPtr)
          class default
-            _FAIL('coordinate units must be string in '//fname)
+            _FAIL(trim(coordinate_name)//' units must be string in '//fname)
          end select
       end if 
 
+      if (present(long_name)) then
+         if (this%var_has_attr(coordinate_name,"long_name")) then
+            attr => var%get_attribute('long_name')
+            coordUnitPtr => attr%get_value()
+            select type(coordUnitPtr)
+            type is (character(*))
+               long_name = trim(coordUnitPtr)
+            class default
+               _FAIL(trim(coordinate_name)//' long_name must be string in '//fname)
+            end select
+         else
+             long_name = 'not found'
+         endif
+      end if 
+
+      if (present(standard_name)) then
+         if (this%var_has_attr(coordinate_name,"standard_name")) then
+            attr => var%get_attribute('standard_name')
+            coordUnitPtr => attr%get_value()
+            select type(coordUnitPtr)
+            type is (character(*))
+               standard_name = trim(coordUnitPtr)
+            class default
+               _FAIL(trim(coordinate_name)//' standard_name must be string in '//fname)
+            end select
+         else
+             standard_name = 'not found'
+         endif
+      end if 
+
+      if (present(coordinate_attr)) then
+         if (this%var_has_attr(coordinate_name,"coordinate")) then
+            attr => var%get_attribute('coordinate')
+            coordUnitPtr => attr%get_value()
+            select type(coordUnitPtr)
+            type is (character(*))
+               coordinate_attr = trim(coordUnitPtr)
+            class default
+               _FAIL(trim(coordinate_name)//' name must be string in '//fname)
+            end select
+         else
+             coordinate_attr = 'not found'
+         endif
+      end if 
+
       if (present(coords)) then
          ptr => var%get_coordinate_data()
          _ASSERT(associated(ptr),"coord variable coordinate data not found in "//fname)

base/MAPL_VerticalMethods.F90

@@ -28,6 +28,9 @@ module MAPL_VerticalDataMod
      character(len=:), allocatable :: func
      character(len=:), allocatable :: vvar
      character(len=:), allocatable :: positive
+     character(len=:), allocatable :: long_name
+     character(len=:), allocatable :: standard_name
+     character(len=:), allocatable :: vcoord
      real :: vscale
      real :: pow=0.0
      real, allocatable :: levs(:)
@@ -57,15 +60,19 @@ module MAPL_VerticalDataMod
 
   contains
 
-     function newVerticalData(levels,vcoord,vscale,vunit,positive,rc) result(vdata)
+     function newVerticalData(levels,vcoord,vscale,vunit,positive,long_name,standard_name,force_no_regrid,rc) result(vdata)
         type(VerticalData) :: vData
         real, pointer, intent(in), optional :: levels(:)
         real, intent(in), optional :: vscale
         character(len=*), optional, intent(in) :: vcoord
         character(len=*), optional, intent(in) :: vunit
         character(len=*), optional, intent(in) :: positive
+        character(len=*), optional, intent(in) :: long_name
+        character(len=*), optional, intent(in) :: standard_name
+        logical, optional, intent(in) :: force_no_regrid
         integer, optional, intent(Out) :: rc
 
+        logical :: local_force_no_regrid
 
         if (present(positive)) then
            _ASSERT(trim(positive)=='up'.or.trim(positive)=='down',trim(positive)//" not allowed for positive argument")
@@ -74,43 +81,73 @@ function newVerticalData(levels,vcoord,vscale,vunit,positive,rc) result(vdata)
            vdata%positive='down'
         end if
 
-        if (.not.present(levels)) then
-           if (trim(vdata%positive)=='down') then
-              vdata%regrid_type = VERTICAL_METHOD_NONE
-           else
-              vdata%regrid_type = VERTICAL_METHOD_FLIP
-           end if
-           _RETURN(ESMF_SUCCESS)
+        if (present(long_name)) then
+           vdata%long_name = long_name
+        else
+           vdata%long_name = 'vertical level'
         end if
+        if (present(standard_name)) then
+           vdata%standard_name = standard_name
+        else
+           vdata%standard_name = 'model_layers'
+        end if
+        if (present(vcoord)) then
+           vdata%vcoord = vcoord
+        else
+           vdata%vcoord = 'eta'
+        endif
 
-        allocate(vData%levs,source=levels)
-        allocate(vData%scaled_levels,source=levels)
         if (present(vunit)) then
            vdata%vunit=vunit
          else
-           vdata%vunit=""
+           vdata%vunit="layer"
         end if
-        if (present(vscale)) then
-           vdata%vscale=vscale
-           vData%scaled_levels = vData%scaled_levels*vdata%vscale
-        end if
-        if (present(vcoord)) then
-           allocate(vData%interp_levels(size(vData%levs)))
-           vdata%regrid_type = VERTICAL_METHOD_ETA2LEV
-           vdata%VVAR = adjustl(vcoord)
-           vdata%Func = vdata%Vvar(1:3)
-           if    (vdata%Func=='log') then
-              vdata%Vvar = adjustl(vdata%Vvar(index(vdata%Vvar,'(')+1:index(vdata%Vvar,')')-1))
-              vdata%interp_levels = log(vdata%scaled_levels)
-           elseif(vdata%Func=='pow') then
-              read( vdata%Vvar(index(vdata%Vvar,',')+1:index(vdata%Vvar,')')-1) , *) vdata%pow
-              vdata%Vvar = adjustl(vdata%Vvar(index(vdata%Vvar,'(')+1:index(vdata%Vvar,',')-1))
-              vdata%interp_levels =  (vdata%levs*vdata%scaled_levels)**vdata%pow
+
+        if (present(force_no_regrid)) then
+           local_force_no_regrid = force_no_regrid
+        else
+           local_force_no_regrid = .false. 
+        end if 
+
+        if (.not.present(levels)) then
+           if (trim(vdata%positive)=='down') then
+              vdata%regrid_type = VERTICAL_METHOD_NONE
            else
-              vdata%interp_levels = vdata%scaled_levels
-           endif
+              vdata%regrid_type = VERTICAL_METHOD_FLIP
+           end if
         else
-           vdata%regrid_type = VERTICAL_METHOD_SELECT
+           allocate(vData%levs,source=levels)
+           if (local_force_no_regrid) then
+              if (trim(vdata%positive)=='down') then
+                 vdata%regrid_type = VERTICAL_METHOD_NONE
+              else
+                 vdata%regrid_type = VERTICAL_METHOD_FLIP
+              end if
+              _RETURN(_SUCCESS)
+           end if
+           allocate(vData%scaled_levels,source=levels)
+           if (present(vscale)) then
+              vdata%vscale=vscale
+              vData%scaled_levels = vData%scaled_levels*vdata%vscale
+           end if
+           if (present(vcoord)) then
+              allocate(vData%interp_levels(size(vData%levs)))
+              vdata%regrid_type = VERTICAL_METHOD_ETA2LEV
+              vdata%VVAR = adjustl(vcoord)
+              vdata%Func = vdata%Vvar(1:3)
+              if    (vdata%Func=='log') then
+                 vdata%Vvar = adjustl(vdata%Vvar(index(vdata%Vvar,'(')+1:index(vdata%Vvar,')')-1))
+                 vdata%interp_levels = log(vdata%scaled_levels)
+              elseif(vdata%Func=='pow') then
+                 read( vdata%Vvar(index(vdata%Vvar,',')+1:index(vdata%Vvar,')')-1) , *) vdata%pow
+                 vdata%Vvar = adjustl(vdata%Vvar(index(vdata%Vvar,'(')+1:index(vdata%Vvar,',')-1))
+                 vdata%interp_levels =  (vdata%levs*vdata%scaled_levels)**vdata%pow
+              else
+                 vdata%interp_levels = vdata%scaled_levels
+              endif
+           else
+              vdata%regrid_type = VERTICAL_METHOD_SELECT
+           end if
         end if
      end function newVerticalData
 
@@ -470,11 +507,11 @@ subroutine append_vertical_metadata(this,metadata,bundle,rc)
               else
                  call metadata%add_dimension('lev', lm, rc=status)
                  v = Variable(type=PFIO_REAL64, dimensions='lev')
-                 call v%add_attribute('long_name','vertical level')
-                 call v%add_attribute('units','layer')
+                 call v%add_attribute('long_name',this%long_name)
+                 call v%add_attribute('units',this%vunit)
                  call v%add_attribute('positive',trim(this%positive))
-                 call v%add_attribute('coordinate','eta')
-                 call v%add_attribute('standard_name','model_layers')
+                 call v%add_attribute('coordinate',this%vcoord)
+                 call v%add_attribute('standard_name',this%standard_name)
                  call v%add_const_value(UnlimitedEntity(this%levs))
                  call metadata%add_variable('lev',v,rc=status)
                  _VERIFY(status)

base/NCIO.F90

@@ -664,7 +664,7 @@ subroutine MAPL_VarWriteNCpar_R4_3d(formatter, name, A, ARRDES, oClients, RC)
     type(Netcdf4_Fileformatter)           , intent(IN   ) :: formatter
     character(len=*)            , intent(IN   ) :: name
     real(kind=ESMF_KIND_R4)     , intent(IN   ) :: A(:,:,:)
-    type(ArrDescr)              , intent(INOUT) :: ARRDES
+    type(ArrDescr), optional    , intent(INOUT) :: ARRDES
     type (ClientManager), optional, intent(inout)  :: oClients
     integer,           optional , intent(  OUT) :: RC
 
@@ -673,24 +673,26 @@ subroutine MAPL_VarWriteNCpar_R4_3d(formatter, name, A, ARRDES, oClients, RC)
     integer ::  i1, j1, in, jn,  global_dim(3)
     type(ArrayReference)     :: ref
 
-    if (arrdes%write_restart_by_oserver) then
-       _ASSERT(present(oClients), "output server is needed")
-       call MAPL_GridGet(arrdes%grid,globalCellCountPerDim=global_dim,rc=status)
-        _VERIFY(status)
-       call MAPL_Grid_interior(arrdes%grid,i1,in,j1,jn)
-       _ASSERT( i1 == arrdes%I1(arrdes%NX0), "interior starting i not match")
-       _ASSERT( j1 == arrdes%j1(arrdes%NY0), "interior starting j not match")
-       ref = ArrayReference(A)
-       _ASSERT( size(a,1) == in-i1+1, "size not match")
-       _ASSERT( size(a,2) == jn-j1+1, "size not match")
-       call oClients%collective_stage_data(arrdes%collection_id,trim(arrdes%filename),trim(name), &
+    if (present(arrdes)) then
+       if (arrdes%write_restart_by_oserver) then
+          _ASSERT(present(oClients), "output server is needed")
+          call MAPL_GridGet(arrdes%grid,globalCellCountPerDim=global_dim,rc=status)
+          _VERIFY(status)
+          call MAPL_Grid_interior(arrdes%grid,i1,in,j1,jn)
+          _ASSERT( i1 == arrdes%I1(arrdes%NX0), "interior starting i not match")
+          _ASSERT( j1 == arrdes%j1(arrdes%NY0), "interior starting j not match")
+          ref = ArrayReference(A)
+          _ASSERT( size(a,1) == in-i1+1, "size not match")
+          _ASSERT( size(a,2) == jn-j1+1, "size not match")
+          call oClients%collective_stage_data(arrdes%collection_id,trim(arrdes%filename),trim(name), &
                       ref,start=[i1,j1,1], &
                       global_start=[1,1,1], global_count=[global_dim(1),global_dim(2),size(a,3)])
-       _RETURN(_SUCCESS)
+          _RETURN(_SUCCESS)
+       endif
     endif
 
     do l=1,size(a,3)
-       call MAPL_VarWrite(formatter,name,A(:,:,l),arrdes,lev=l, rc=status)
+       call MAPL_VarWrite(formatter,name,A(:,:,l), arrdes=arrdes,lev=l, rc=status)
        _VERIFY(status)
     enddo
 
@@ -704,14 +706,14 @@ subroutine MAPL_VarReadNCpar_R4_3d(formatter, name, A, ARRDES, RC)
     type (Netcdf4_Fileformatter)          , intent(IN   ) :: formatter
     character(len=*)            , intent(IN   ) :: name
     real(kind=ESMF_KIND_R4)     , intent(INOUT) :: A(:,:,:)
-    type(ArrDescr)              , intent(INOUT) :: ARRDES
+    type(ArrDescr), optional    , intent(INOUT) :: ARRDES
     integer,           optional , intent(  OUT) :: RC
 
     integer                               :: status
     integer :: l
 
     do l=1,size(a,3)
-       call MAPL_VarRead(formatter,name,A(:,:,l),arrdes,lev=l, rc=status)
+       call MAPL_VarRead(formatter,name,A(:,:,l), arrdes=arrdes, lev=l, rc=status)
        _VERIFY(status)
     enddo
 

base/cub2latlon_regridder.F90

@@ -1186,7 +1186,6 @@ end module SupportMod
 ! throw an exception and RETURN.
 
 ! The main program.   Misleadingly simple.
-#undef MAPL_ErrLog_DONE
 #define I_AM_MAIN
 #include "MAPL_Generic.h"
 program main
@@ -1253,6 +1252,8 @@ program main
 contains
 
 
+#undef I_AM_MAIN
+#include "MAPL_Generic.h"
 
    subroutine check_resources(rc)
       use SupportMod

base/tests/mapl_bundleio_test.F90

@@ -172,7 +172,6 @@ end module BundleTestSupport
 ! This is how you can "reset" the MAPL_Generic.h verify bits for a program.
 ! Program must be at the end of the file to do this and everything else in a module
 
-#undef MAPL_ErrLog_DONE
 #define I_AM_MAIN
 #include "MAPL_Generic.h"