Merge branch 'develop' into feature/ygyu/logging_config_to_extdriver

.circleci/config.yml

@@ -16,7 +16,7 @@ parameters:
 
 # Anchors to prevent forgetting to update a version
 os_version: &os_version ubuntu20
-baselibs_version: &baselibs_version v7.7.0
+baselibs_version: &baselibs_version v7.13.0
 bcs_version: &bcs_version v11.00.0
 tag_build_arg_name: &tag_build_arg_name maplversion
 

.github/workflows/enforce-labels.yml

@@ -8,7 +8,7 @@ jobs:
   require-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v4
+      - uses: mheap/github-action-required-labels@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
@@ -21,7 +21,7 @@ jobs:
   blocking-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v4
+      - uses: mheap/github-action-required-labels@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:

.github/workflows/workflow.yml

@@ -17,7 +17,7 @@ jobs:
     name: Build and Test MAPL GNU
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env-mkl:v7.7.0-openmpi_4.1.4-gcc_12.1.0
+      image: gmao/ubuntu20-geos-env-mkl:v7.13.0-openmpi_4.1.4-gcc_12.1.0
       # Per https://github.com/actions/virtual-environments/issues/1445#issuecomment-713861495
       # It seems like we might not need secrets on GitHub Actions which is good for forked
       # pull requests
@@ -77,7 +77,7 @@ jobs:
     name: Build and Test MAPL Intel
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env:v7.7.0-intelmpi_2021.6.0-intel_2022.1.0
+      image: gmao/ubuntu20-geos-env:v7.13.0-intelmpi_2021.6.0-intel_2022.1.0
       # Per https://github.com/actions/virtual-environments/issues/1445#issuecomment-713861495
       # It seems like we might not need secrets on GitHub Actions which is good for forked
       # pull requests

CHANGELOG.md

@@ -9,8 +9,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Added field utilities to perform basic numeric operations on fields
+- For ExtDataDriver.x only, added logging config to Tests/ExtDataDriverMod.F90 to enable Logger there
+
 ### Changed
 
+- Updated programs using FLAP for command line parsing to use fArgParse instead
+- Updated `components.yaml` to match GEOSgcm v11.1.0
+  - ESMA_env v4.9.1 → v4.17.0
+    - Baselibs 7.13.0
+      - esmf v8.5.0b22
+      - GFE v1.10.0
+      - curl 8.1.1
+      - HDF5 1.10.10
+      - netCDF-C 4.9.2
+      - netCDF-Fortran 4.6.1
+      - CDO 2.2.0
+      - NCO 5.1.5
+    - Move to MPT 2.28 at NAS, and other various changes for TOSS4 at NAS
+  - ESMA_cmake v3.28.0 → v3.29.0
+    - Clean up for TOSS4 changes at NAS
 - Make the GEOSadas CI build separate as it often fails due to race conditions in GSI
 
 ### Fixed
@@ -21,11 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
-## [2.39.3] - 2023-06-07
-
-### Add
-
-- For ExtDataDriver.x only, added logging config to Tests/ExtDataDriverMod.F90 to enable Logger there
+- Deprecate the use of FLAP for command line parsing in favor of fArgParse. FLAP support will be removed in MAPL 3
 
 ## [2.39.2] - 2023-05-30
 

CMakeLists.txt

@@ -1,20 +1,19 @@
 cmake_minimum_required (VERSION 3.17)
-cmake_policy (SET CMP0053 NEW)
-cmake_policy (SET CMP0054 NEW)
+
+get_property(is_multi_config GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
+if(NOT is_multi_config AND NOT (CMAKE_BUILD_TYPE OR DEFINED ENV{CMAKE_BUILD_TYPE}))
+  message (STATUS "Setting build type to 'Release' as none was specified.")
+  set (CMAKE_BUILD_TYPE Release CACHE STRING "Default Release-Choose the type of build.")
+endif ()
 
 project (
   MAPL
   VERSION 2.39.2
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
-# Set the default build type to release
-if (NOT CMAKE_BUILD_TYPE)
-  message (STATUS "Setting build type to 'Release' as none was specified.")
-  set (CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
-  # Set the possible values of build type for cmake-gui
-  set_property (CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
-    "Debug" "Release" "Aggressive")
-endif ()
+# Set the possible values of build type for cmake-gui
+set_property (CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+  "Debug" "Release" "Aggressive")
 
 # mepo can now clone subrepos in three styles
 set (ESMA_CMAKE_DIRS

MAPL/CMakeLists.txt

@@ -3,7 +3,7 @@ esma_set_this()
 
 esma_add_library (${this}
   SRCS MAPL.F90
-  DEPENDENCIES MAPL.base MAPL.generic MAPL.pfio MAPL_cfio_r4 MAPL.gridcomps MAPL.orbit MAPL.griddedio ${EXTDATA_TARGET}
+  DEPENDENCIES MAPL.base MAPL.generic MAPL.pfio MAPL_cfio_r4 MAPL.gridcomps MAPL.orbit MAPL.griddedio MAPL.geom ${EXTDATA_TARGET}
                esmf NetCDF::NetCDF_Fortran MPI::MPI_Fortran
                $<$<BOOL:${BUILD_WITH_FLAP}>:FLAP::FLAP>
   TYPE ${MAPL_LIBRARY_TYPE}

MAPL/MAPL.F90

@@ -15,6 +15,7 @@ module MAPL
    use MAPL_OpenMP_Support, only : MAPL_find_bounds => find_bounds
    use MAPL_OpenMP_Support, only : MAPL_Interval => Interval
    use MAPL_Profiler, initialize_profiler =>initialize, finalize_profiler =>finalize
+   use MAPL_Geom
    implicit none
 end module MAPL
 

Tests/ExtDataDriver.F90

@@ -16,9 +16,9 @@ program ExtData_Driver
   character(len=*), parameter :: Iam="ExtData_Driver"
   type(ExtDataDriver) :: Driver
   type (MAPL_CapOptions) :: cap_options
-  type (MAPL_FlapCLI) :: cli
+  type (MAPL_FargparseCLI) :: cli
 
-  cli = MAPL_FlapCLI(description='extdata driver',authors='gmao')
+  cli = MAPL_FargparseCLI()
   cap_options=MAPL_CapOptions(cli)
 
   driver = ExtDataDriver('ExtDataApp',Root_SetServices,cap_options=cap_options,_RC)

Tests/ExtDataRoot_GridComp.F90

@@ -353,7 +353,7 @@ function evaluate_time(this,currTime,rc) result(dt)
       class(timeVar), intent(in) :: this
       type(ESMF_Time), intent(inout) :: currTime
       integer, optional, intent(out) :: rc
-      real(REAL64) :: dt
+      real(kind=ESMF_KIND_R8) :: dt
 
       integer :: status
 
@@ -482,6 +482,7 @@ subroutine FillState(inState,outState,time,grid,Synth,rc)
       type(ESMF_State) :: pstate
       character(len=:), pointer :: fexpr
       integer :: i1,in,j1,jn,ldims(3),i,j
+      real(kind=ESMF_KIND_R8) :: doy,time_delta
 
       call MAPL_GridGet(grid,localcellcountperdim=ldims,_RC)
       call MAPL_Grid_Interior(grid,i1,in,j1,jn)
@@ -490,9 +491,6 @@ subroutine FillState(inState,outState,time,grid,Synth,rc)
       _VERIFY(status)
       call ESMF_StateGet(outState,itemNameList=outNameList,_RC)
 
-      call MAPL_GetPointer(inState,exPtr2,'time',_RC)
-      exPtr2=synth%tFunc%evaluate_time(Time,_RC)
-
       call MAPL_GetPointer(inState,exPtr2,'i_index',_RC)
       do j = 1,ldims(2)
          do i=1,ldims(1)
@@ -505,15 +503,17 @@ subroutine FillState(inState,outState,time,grid,Synth,rc)
             exPtr2(i,j)=j1+j-1
          enddo
       enddo
-      call MAPL_GetPointer(inState,exPtr2,'doy',_RC)
-      exPtr2 = compute_doy(time,_RC)
 
       call ESMF_StateGet(inState,'time',farray(1),_RC)
+      time_delta = synth%tFunc%evaluate_time(Time,_RC)
+      call FieldSet(farray(1), time_delta,_RC)
       call ESMF_StateGet(inState,'lons',farray(2),_RC)
       call ESMF_StateGet(inState,'lats',farray(3),_RC)
       call ESMF_StateGet(inState,'i_index',farray(4),_RC)
       call ESMF_StateGet(inState,'j_index',farray(5),_RC)
       call ESMF_StateGet(inState,'doy',farray(6),_RC)
+      doy = compute_doy(time,_RC)
+      call FieldSet(farray(6), doy,_RC)
       pstate = ESMF_StateCreate(_RC)
       call ESMF_StateAdd(pstate,farray,_RC)
 
@@ -556,8 +556,8 @@ subroutine CompareState(State1,State2,tol,rc)
             call ESMF_StateGet(State2,trim(nameList(i)),field2,_RC)
             call ESMF_FieldGet(field1,rank=rank1,_RC)
             call ESMF_FieldGet(field2,rank=rank2,_RC)
-            all_undef1 = is_field_undef(field1,_RC)
-            all_undef2 = is_field_undef(field2,_RC)
+            all_undef1 = FieldIsConstant(field1,MAPL_UNDEF,_RC)
+            all_undef2 = FieldIsConstant(field2,MAPL_UNDEF,_RC)
             if (all_undef1 .or. all_undef2) then
                exit
             end if

Tests/pfio_MAPL_demo.F90

@@ -10,7 +10,7 @@
 !
 !#### Usage:
 !
-!   If we reserve 2 haswell nodes (28 cores in each), want to run the model on 28 cores 
+!   If we reserve 2 haswell nodes (28 cores in each), want to run the model on 28 cores
 !   and use 1 MultiGroup with 5 backend processes, then the execution command is:
 !```
 ! mpiexec -np 56 pfio_MAPL_demo.x --npes_model 28 --oserver_type multigroup --nodes_output_server 1 --npes_backend_pernode 5
@@ -38,7 +38,7 @@ program main
       integer,           parameter ::              num_dims = 2 ! number of dimension to decompose
 
       ! PFIO specific variables
-      type(MAPL_FlapCLI)      :: cli
+      type(MAPL_FargparseCLI) :: cli
       type(MAPL_CapOptions)   :: cap_options
       type(ServerManager)     :: ioserver_manager
       type(SplitCommunicator) :: split_comm
@@ -85,8 +85,7 @@ program main
 !------------------------------------------------------------------------------
 
       ! Read and parse the command line, and set parameters
-      cli = MAPL_FlapCLI(description = 'GEOS AGCM', &
-                         authors     = 'GMAO')
+      cli = MAPL_FargparseCLI()
       cap_options = MAPL_CapOptions(cli)
 
       ! Initialize MPI if MPI_Init has not been called
@@ -123,22 +122,22 @@ program main
             ! ---> Perform domain decomposition for the model
             !------------------------------------------------
             call perform_domain_deposition()
-   
+
             ! Allocate model variables
             !-------------------------
             ALLOCATE(local_tracer(i1:i2, j1:j2))
             ALLOCATE(local_temp(i1:i2, j1:j2, k1:k2))
-   
+
             ! if there are multiple oserver, split it into large and small pool
             call o_clients%split_server_pools()
-   
+
             call create_file_metada()
-   
+
             !---------------------------------------------
             ! ---> Model time stepping and writing outputs
             !---------------------------------------------
             call run_model()
-   
+
             deallocate(local_temp)
             deallocate(local_tracer)
             deallocate(points_per_procX)
@@ -157,11 +156,11 @@ program main
       call ioserver_manager%finalize()
 
       call MPI_finalize(ierror)
-      
+
 !------------------------------------------------------------------------------
 CONTAINS
 !------------------------------------------------------------------------------
-!> 
+!>
 ! `create_member_subcommunicator` -- Create a subcommunicator
 !
    integer function create_member_subcommunicator(comm, n_members, npes_member, rc) result(subcommunicator)
@@ -183,7 +182,7 @@ integer function create_member_subcommunicator(comm, n_members, npes_member, rc)
 
    end function create_member_subcommunicator
 !------------------------------------------------------------------------------
-!> 
+!>
 ! `initialize_mpi` -- Initialized MPI is MPI_Init has not been called yet.
 !
    subroutine initialize_mpi(comm)
@@ -204,7 +203,7 @@ subroutine initialize_mpi(comm)
 
    end subroutine initialize_mpi
 !------------------------------------------------------------------------------
-!> 
+!>
 ! `initialize_ioserver` -- Initialize the IO Server using the command line options
 !
    subroutine initialize_ioserver(comm)
@@ -224,7 +223,7 @@ subroutine initialize_ioserver(comm)
       _VERIFY(status)
    end subroutine initialize_ioserver
 !------------------------------------------------------------------------------
-!> 
+!>
 ! `perform_domain_deposition` -- Perfom the domain decomposition
 !
    subroutine perform_domain_deposition()
@@ -267,7 +266,7 @@ subroutine perform_domain_deposition()
       print '(a7,i5,a5,4i5)', 'pe_id: ', pe_id, '-->', i1, i2, j1, j2
    end subroutine perform_domain_deposition
 !------------------------------------------------------------------------------
-!> 
+!>
 ! `create_file_metada` -- Create the file metada using PFIO methods and the file collection identifier
 !
    subroutine create_file_metada()
@@ -348,7 +347,7 @@ subroutine create_file_metada()
       hist_id = o_clients%add_hist_collection(fmd)
    end subroutine create_file_metada
 !------------------------------------------------------------------------------
-!> 
+!>
 ! `run_model` -- Run the model and write out the data
 !
    subroutine run_model()
@@ -415,7 +414,7 @@ subroutine run_model()
       enddo
    end subroutine run_model
 !------------------------------------------------------------------------------
-!> 
+!>
 ! `add_fvar` -- PFIO utility routine to create a variable and set attributes
 !
    subroutine add_fvar(cf, vname, vtype, dims, units, long_name ,rc)
@@ -449,10 +448,10 @@ subroutine add_fvar(cf, vname, vtype, dims, units, long_name ,rc)
       _VERIFY(status)
    end subroutine add_fvar
 !------------------------------------------------------------------------------
-!> 
-! `decompose_dim` -- 
-! For a given number of grid points along a dimension and a number of 
-! available processors for that diemsion,, !! determine the number of 
+!>
+! `decompose_dim` --
+! For a given number of grid points along a dimension and a number of
+! available processors for that diemsion,, !! determine the number of
 ! grid points assigned to each processor.
 !
    subroutine decompose_dim(dim_world, dim_array, num_procs )
@@ -472,7 +471,7 @@ subroutine decompose_dim(dim_world, dim_array, num_procs )
    end subroutine decompose_dim
 !------------------------------------------------------------------------------
 !>
-! `decompose_proc` -- 
+! `decompose_proc` --
 !  Given the total number of available processors and the number of dimensions,
 ! determine the number of processors along each dimension.
 !
@@ -491,10 +490,10 @@ subroutine decompose_proc(num_procs, proc_sizes)
       END DO
    end subroutine decompose_proc
 !------------------------------------------------------------------------------
-!> 
-! `mapping_domain` -- 
+!>
+! `mapping_domain` --
 ! Determime the indices of the local domain corners
-! with respect to the global domain. 
+! with respect to the global domain.
 !
    subroutine mapping_domain(map_proc, map_domainX, map_domainY, &
                         points_per_procX, points_per_procY, NX, NY, &
@@ -550,7 +549,7 @@ subroutine mapping_domain(map_proc, map_domainX, map_domainY, &
       enddo
    end subroutine mapping_domain
 !------------------------------------------------------------------------------
-!> 
+!>
 ! `set_tracer` -- Arbitrary set values for a field
 !
    subroutine set_tracer(var)
@@ -566,7 +565,7 @@ subroutine set_tracer(var)
 
    end subroutine set_tracer
 !------------------------------------------------------------------------------
-!> 
+!>
 ! `set_temperature` -- Arbitrary set values for the temperature field.
 !
    subroutine set_temperature(var)

base/Base.F90

@@ -51,7 +51,6 @@ module MAPLBase_Mod
   use MAPL_ServerManager
   use MAPL_FileMetadataUtilsMod
   use MAPL_VerticalDataMod
-  use MAPL_FieldUtilities
   use MAPL_SphericalGeometry
   logical, save, private :: mapl_is_initialized = .false.
 

base/CMakeLists.txt

@@ -52,7 +52,6 @@ set (srcs
   Base/Base_Base.F90 Base/Base_Base_implementation.F90
   TimeStringConversion.F90
   MAPL_ISO8601_DateTime_ESMF.F90
-  FieldUtilities.F90
   MAPL_Resource.F90
   MAPL_XYGridFactory.F90
   MAPL_NetCDF.F90