Merge pull request #1996 from GEOS-ESM/develop

GitFlow: Merge Develop into main for 2.35 release

.circleci/config.yml

@@ -82,7 +82,7 @@ workflows:
           baselibs_version: *baselibs_version
           repo: MAPL
           mepodevelop: false
-          extra_cmake_options: "-DBUILD_WITH_FLAP=OFF -DBUILD_WITH_PFLOGGER=OFF -DBUILD_SHARED_MAPL=OFF"
+          extra_cmake_options: "-DBUILD_WITH_FLAP=OFF -DBUILD_WITH_PFLOGGER=OFF -DBUILD_WITH_FARGPARSE=OFF -DUSE_EXTDATA2G=OFF -DBUILD_SHARED_MAPL=OFF"
           run_unit_tests: true
           ctest_options: "-LE 'PERFORMANCE|EXTDATA1G_BIG_TESTS|EXTDATA2G_BIG_TESTS' --output-on-failure"
 

.github/workflows/push-to-develop.yml

@@ -11,11 +11,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3.2.0
+        uses: actions/checkout@v3.3.0
         with:
           fetch-depth: 0
       - name: Run the action
-        uses: devops-infra/action-pull-request@v0.5.3
+        uses: devops-infra/action-pull-request@v0.5.5
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           source_branch: develop

.github/workflows/push-to-main.yml

@@ -11,11 +11,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3.2.0
+        uses: actions/checkout@v3.3.0
         with:
           fetch-depth: 0
       - name: Run the action
-        uses: devops-infra/action-pull-request@v0.5.3
+        uses: devops-infra/action-pull-request@v0.5.5
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           source_branch: main

.github/workflows/release-tarball.yml

@@ -10,12 +10,12 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3.2.0
+        uses: actions/checkout@v3.3.0
         with:
           path: ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}
 
       - name: Checkout mepo
-        uses: actions/checkout@v3.2.0
+        uses: actions/checkout@v3.3.0
         with:
           repository: GEOS-ESM/mepo
           path: mepo

.github/workflows/validate_yaml_files.yml

@@ -15,7 +15,7 @@ jobs:
   validate-YAML:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.2.0
+      - uses: actions/checkout@v3.3.0
       - id: yaml-lint
         name: yaml-lint
         uses: ibiqlik/action-yamllint@v3

.github/workflows/workflow.yml

@@ -34,7 +34,7 @@ jobs:
         with:
           access_token: ${{ github.token }}
       - name: Checkout
-        uses: actions/checkout@v3.2.0
+        uses: actions/checkout@v3.3.0
         with:
           fetch-depth: 1
       - name: Set all directories as git safe
@@ -90,7 +90,7 @@ jobs:
         with:
           access_token: ${{ github.token }}
       - name: Checkout
-        uses: actions/checkout@v3.2.0
+        uses: actions/checkout@v3.3.0
         with:
           fetch-depth: 1
       - name: Set all directories as git safe

Apps/Regrid_Util.F90

@@ -171,7 +171,7 @@ subroutine process_command_line(this,rc)
     if (.not.allocated(this%tripolar_file_out)) then
        this%tripolar_file_out = "empty"
     end if
-    this%regridMethod = get_regrid_method(regridMth)
+    this%regridMethod = regrid_method_string_to_int(regridMth)
     _ASSERT(this%regridMethod/=UNSPECIFIED_REGRID_METHOD,"improper regrid method chosen")
 
     this%filenames = split_string(cfilenames,',')

CHANGELOG.md

@@ -17,6 +17,53 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
+## [2.35.0] - 2023-03-01
+
+### Added
+
+- Added subroutines to read char type in Netcdf
+- Added a subroutine add_variable to Netcdf4_Fileformatter
+- Add a function to get the area of a spherical polygon to the spherical geometry module
+- Created layout independent version of the "DownBit"/"pFIO_ShaveMantissa" routines when running in MPI codes
+- Added subroutine `MAPL_SunGetLocalSolarHourAngle()` in `base/MAPL_sun_uc.F90`. This
+  provides a convenient local solar hour angle diagnostic which will be used to detect local
+  solar noon via the `EXAMPLE OF USE` in the subroutine header. See `DESCRIPTION` in code
+  for more details. Provides the TRUE local solar hour angle (i.e., with equation of time
+  included), but can also provide the MEAN value (without EOT) via `FORCE_MLSHA=.TRUE.`
+  optional argument.
+- Add `shavemantissa` f2py code. This is used by AeroApps.
+  - NOTE: If you do not have a need for this code, build with `-DUSE_F2PY=OFF`. Note that even if you try to build the f2py code, it might fail anyway due to issues with the Python stack on the machine. ESMA_cmake has code that "tests" if f2py works. If it doesn't, it should failover gracefully.
+
+### Changed
+
+- Changed set_grid method so users have a chance to specify the grid type
+- Renamed `get_regrid_method` and `translate_regrid_method` to `regrid_method_string_to_int` and `regrid_method_int_to_string`
+  respectively in `RegridMethods.F90`. This was done so we could add `get_regrid_method` to the AbstractRegridder. The new names
+  more accurately reflect what the RegridMethods functions do.
+- Changed call to `MAPL_SunOrbitCreate()` inside `MAPL_Generic.F90` to call to new function
+  `MAPL_SunOrbitCreateFromConfig()`, the latter which get the orbital parameters from the MAPL
+  state's Config. In this way no default orbital parameter values need appear in `MAPL_Generic.F90`.
+  Rather, these default values are encapsulated where they belong in `Sun_Mod` in `base/MAPL_sun_uc.F90`
+  and are now explicitly named and commented on at the head of the module. This is a structural
+  zero-diff change.
+- Created `MAPL.profiler` logger and moved throughput, per-component, and global timers to use it
+- Moved most of the MAPL_GetResource generic subroutine to a new module, MAPL_ResourceMod, in base.
+  The specific subroutines remain in MAPL_GenericMod to maintain the interface in one module, but
+  most of the functionality is in MAPL_ResourceMod now.
+- Update "build like UFS" CI test
+- Converted the History Gridded Component to use `_RC` and `_STAT` macros
+
+### Fixed
+
+- Changed the type of output counters to INT64 for large file.
+- Tested optional arguments arrdes in MAPL_WriteVars
+- Added the correct values to halo corner of LatLon grid
+- Fixed range in halo of LatLonGridFactory
+- Corrected issue with native output having metadata saying it was bilinearly regridded. Now sets these files to have
+  `regrid_method: identity`
+- Fix bug in `mapl_acg.cmake` that caused unnecessary rebuilds
+- Fixed error handling for refactored MAPL_GetResource
+
 ## [2.34.3] - 2023-02-14
 
 ### Added

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_policy (SET CMP0054 NEW)
 
 project (
   MAPL
-  VERSION 2.34.3
+  VERSION 2.35.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the default build type to release

MAPL_cfio/CMakeLists.txt

@@ -54,3 +54,23 @@ if (precision MATCHES "r8")
     target_compile_options (${lib} PRIVATE $<$<COMPILE_LANGUAGE:Fortran>:${flag}>)
   endforeach ()
 endif ()
+
+if (USE_F2PY)
+  if (precision STREQUAL "r4")
+    find_package(F2PY2)
+    if (F2PY2_FOUND)
+      esma_add_f2py2_module(ShaveMantissa_
+        SOURCES ShaveMantissa_py.F90 ShaveMantissa.c
+        DESTINATION lib/Python/${this}
+        INCLUDEDIRS ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_BINARY_DIR}/lib ${include_${this}}
+        )
+      add_dependencies(ShaveMantissa_ ${this})
+
+      # Install the Python files
+      install (
+        FILES shavemantissa.py
+        DESTINATION lib/Python/${this}
+        )
+      endif ()
+  endif ()
+endif ()

MAPL_cfio/ShaveMantissa_py.F90

@@ -0,0 +1,26 @@
+subroutine Shave32 ( a_shaved, a, n, xbits, has_undef, undef, chunksize, rc )
+
+!
+!  Simple cover for f2py.
+!
+   use iso_fortran_env, only: REAL32
+   implicit NONE
+   integer,           intent(in) :: n              ! array size
+   real(kind=REAL32), intent(in) :: a(n)           ! array to be shaved, usually 2D
+   integer,           intent(in) :: xbits          ! number of mantissa bits to zero (out of 24)
+   integer,           intent(in) :: has_undef      ! set to 1 if undef is present, 0 otherwise
+   real(kind=REAL32), intent(in) :: undef          ! undef value
+   integer,           intent(in) :: chunksize      ! find mid-range over chunksizes
+
+   real(kind=REAL32), intent(out) :: a_shaved(n)  ! shaved array
+   integer,           intent(out) :: rc            ! error code
+
+!                            ---
+
+   integer, external :: ShaveMantissa32
+
+   rc = ShaveMantissa32(a_shaved,a,n,xbits,has_undef,undef,chunksize)
+
+end subroutine Shave32
+
+

MAPL_cfio/shavemantissa.py

@@ -0,0 +1,36 @@
+"""
+  SImple python interface to the ShaveMantissa function
+"""
+
+MISSING = 1.0E15
+
+from ShaveMantissa_ import shave32
+
+def shave(a,xbits=12,has_undef=0,undef=MISSING,chunksize=-1):
+    """
+    Shaves bits from mantissa of float point array for better netCDF4 compression
+    using gzip.
+
+    a_shaved = shave(a,...)
+
+    xbits      ---  number of bits to shave
+    has_undef  ---  set to 1 if undefs are present
+    undef      ---  undef value
+    chunksize  ---  for scaling of array to be shaved: find mid-range value
+                    over chunksizes. If negative, set to len(a)
+
+    Typically this function is used for a single vertical slice at time.
+
+
+    """
+
+    n = len(a)
+    if chunksize<0: chunksize = n
+
+    a_shaved, rc = shave32(a,xbits,has_undef,undef,chunksize)
+
+    if rc:
+        raise ValueError, 'shave: error on return from ShaveMantissa_.shave32: %d'%rc
+
+    return a_shaved
+

Python/MAPL/constants.py

@@ -6,12 +6,15 @@
 MAPL_DEGREES_TO_RADIANS = MAPL_PI / 180.0
 MAPL_RADIANS_TO_DEGREES = 180.0 / MAPL_PI
 
+MAPL_UNDEF   = 1.0e15
 
 MAPL_PSDRY   = 98305.0                # dry surface pressure [Pa]
 MAPL_SECONDS_PER_SIDEREAL_DAY = 86164.0 #s
 MAPL_GRAV    = 9.80665                # m^2/s
 MAPL_RADIUS  = 6371.0E3               # m
 MAPL_OMEGA   = 2.0*MAPL_PI/MAPL_SECONDS_PER_SIDEREAL_DAY    # 1/s
+MAPL_RUNIV   = 8314.47                # J/(Kmole K)
+MAPL_H2OMW   = 18.015                 # kg/Kmole
 MAPL_EARTH_ECCENTRICITY = 8.1819190842622E-2 # --
 MAPL_EARTH_SEMIMAJOR_AXIS = 6378137 # m
 MAPL_KM_PER_DEG = (1.0/(MAPL_RADIUS/1000.)) * MAPL_RADIANS_TO_DEGREES
@@ -48,9 +51,7 @@
 
 MAPL_STFBOL  = 5.6734E-8              # W/(m^2 K^4)
 MAPL_AVOGAD  = 6.023E26               # 1/kmol
-MAPL_RUNIV   = 8314.47                # J/(Kmole K)
 
-MAPL_H2OMW   = 18.015                 # kg/Kmole
 MAPL_O3MW    = 47.9982                # kg/Kmole
 MAPL_ALHL    = 2.4665E6               # J/kg @15C
 MAPL_ALHF    = 3.3370E5               # J/kg

base/ApplicationSupport.F90

@@ -23,7 +23,7 @@ subroutine MAPL_Initialize(unusable,comm,logging_config,rc)
 
       character(:), allocatable :: logging_configuration_file
       integer :: comm_world,status
-     
+
       _UNUSED_DUMMY(unusable)
 
       if (present(logging_config)) then
@@ -55,7 +55,7 @@ subroutine MAPL_Finalize(unusable,comm,rc)
       integer :: comm_world,status
 
       _UNUSED_DUMMY(unusable)
-      
+
       if (present(comm)) then
          comm_world = comm
       else
@@ -137,7 +137,7 @@ subroutine initialize_pflogger(unusable,comm,logging_config,rc)
 
          if (rank == 0) then
             lgr => logging%get_logger('MAPL')
-            call lgr%warning('No configure file specified for logging layer.  Using defaults.')            
+            call lgr%warning('No configure file specified for logging layer.  Using defaults.')
          end if
 
       end if
@@ -158,6 +158,7 @@ subroutine report_global_profiler(unusable,comm,rc)
       integer :: npes, my_rank, ierror
       character(1) :: empty(0)
       class (BaseProfiler), pointer :: t_p
+      type(Logger), pointer :: lgr
 
       _UNUSED_DUMMY(unusable)
       if (present(comm)) then
@@ -185,13 +186,14 @@ subroutine report_global_profiler(unusable,comm,rc)
       call MPI_Comm_Rank(world_comm, my_rank, ierror)
 
       if (my_rank == 0) then
-            report_lines = reporter%generate_report(t_p)
-            write(*,'(a,1x,i0)')'Report on process: ', my_rank
-            do i = 1, size(report_lines)
-               write(*,'(a)') report_lines(i)
-            end do
-       end if
-       call MPI_Barrier(world_comm, ierror)
+         report_lines = reporter%generate_report(t_p)
+         lgr => logging%get_logger('MAPL.profiler')
+         call lgr%info('Report on process: %i0', my_rank)
+         do i = 1, size(report_lines)
+            call lgr%info('%a', report_lines(i))
+         end do
+      end if
+      call MPI_Barrier(world_comm, ierror)
 
    end subroutine report_global_profiler
 

base/Base.F90

@@ -52,6 +52,7 @@ module MAPLBase_Mod
   use MAPL_FileMetadataUtilsMod
   use MAPL_VerticalDataMod
   use MAPL_FieldUtilities
+  use MAPL_SphericalGeometry
   logical, save, private :: mapl_is_initialized = .false.
 
 end module MAPLBase_Mod

base/CMakeLists.txt

@@ -53,14 +53,16 @@ set (srcs
   TimeStringConversion.F90
   MAPL_ISO8601_DateTime_ESMF.F90
   FieldUtilities.F90
+  MAPL_Resource.F90
   # Orphaned program: should not be in this library.
   # tstqsat.F90
   )
 
 
 esma_add_library(
   ${this} SRCS ${srcs}
-  DEPENDENCIES MAPL.shared MAPL.constants MAPL.profiler MAPL.pfio MAPL_cfio_r4 PFLOGGER::pflogger GFTL_SHARED::gftl-shared
+  DEPENDENCIES MAPL.shared MAPL.constants MAPL.profiler MAPL.pfio MAPL_cfio_r4 PFLOGGER::pflogger 
+               GFTL_SHARED::gftl-shared-v2 GFTL_SHARED::gftl-shared-v1  GFTL::gftl-v2 GFTL::gftl-v1
                esmf NetCDF::NetCDF_Fortran MPI::MPI_Fortran
   TYPE ${MAPL_LIBRARY_TYPE})