Merge branch 'NOAA-GFDL:main' into am5-ci

NOAA-GFDL · Sep 5, 2024 · e84a2b8 · e84a2b8
2 parents fab25d4 + d13c129
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,36 @@ and this project uses `yyyy.rr[.pp]`, where `yyyy` is the year a patch is releas
 `rr` is a sequential release number (starting from `01`), and an optional two-digit
 sequential patch number (starting from `01`).
 
+## [2024.03] - 2024-08-22
+
+### Known Issues
+- Diag Manager Rewrite: See [below](#20240102---2024-06-14) for known output file differences regarding the new diag manager. The new diag_manager is disabled by default, so this differences will only be present if `use_modern_diag` is set to true in the `diag_manager_nml`.
+- BUILD(HDF5): HDF5 version 1.14.3 generates floating point exceptions, and will cause errors if FMS is built with FPE traps enabled. FPE traps are turned on when using the debug target in mkmf.
+- GCC: version 14.1.0 is unsupported due to a bug with strings that has come up previously in earlier versions. This will be caught by the configure script, but will cause compilation errors if using other build systems.
+- INTEL: The `-check uninit` flag for the Intel Oneapi Fortran compiler (ifx) is unsupported due to a bug causing false positives when using external libraries. If using the `-check all` flag, `-check all,nouninit` should be used instead.
+
+### Added
+- DATA_OVERRIDE: Adds a namelist flag `use_center_grid_points` which, if true, enables reading the centroid values from the grid spec for ocean and ice models. This fixes issues with grid files that have longitudes ranges from 0:180 and then -180:0, but will cause answer changes if enabled. (#1566)
+- DATA_OVERRIDE: Adds support for reading external weight files. Currently only supported for fregrid generated files while using the bilinear interpolation method. Documentation for this feature can be found in `data_override/README.md`. (#1556)
+- PLATFORM: Adds two constants `FMS_PATH_LEN` and `FMS_FILE_LEN` and uses it across the code for any file path or file name character strings. They default to 1024 and 255 but can also be set by the `FMS_MAX_PATH_LEN` and `FMS_MAX_FILE_LEN` CPP macros. (#1567)
+- CMAKE: Adds Cmake option to support building shared libraries (#1559)
+
+### Changed
+- DIAG_MANAGER: Simplifies the diag_table.yaml format by allowing `module`, `reduction`, and `kind` to be set on a file level, with the ability to override for a specific field. (#1545)
+- FIELD_MANAGER: Updated and refactored the `fm_yaml_mod` module for a new table format to remove the `subparams` key. (#1547)
+- DATA_OVERRIDE: Updates the yaml format to be improve readablity and to be more consistent in key names. Additional documentation for the new format can be found in `data_override/README.md`. (#1556)
+
+### Fixed
+- PARSER: Adds error code checks to the yaml parser to prevent code from hanging on invalid yamls (#1563)
+- PARSER: Adds ability to read in generic blocks to support `field_manager` updates. (#1519)
+- CRAY COMPILER SUPPORT: Updated any multi-line string literals to be compatible with the cray compiler. (#1554)
+
+### Removed
+- DIAG_MANAGER: Removed diag_table schemas from FMS and moved them to the `gfdl_msd_schemas` repository, and updates the `diag_manager` documentation markdowns. (#1543)
+
+### Tag Commit Hashes
+- 2024.03-beta1 a5de6a54abeb00be2443db4cf07aa267b7faa724
+
 ## [2024.02] - 2024-07-11
 
 ### Known Issues

diff --git a/CMAKE_INSTRUCTIONS.md b/CMAKE_INSTRUCTIONS.md
@@ -50,21 +50,23 @@ make install
 ```
 
 ### User configurable options:
-By default, FMS is built without `OpenMP` and in `single precision (r4)`
+By default, FMS is built without `OpenMP`, in `single precision (r4)` and delivered in static library files.
 
 The 64BIT and 32BIT precision options will build distinct libraries when enabled with the given default
 real size, libfms_r4 or libfms_r8.
 
 The following build options are available:
 ```
--DOPENMP   "Build FMS with OpenMP support"        DEFAULT: OFF
--D32BIT    "Build 32-bit (r4) FMS library"        DEFAULT: ON
--D64BIT    "Build 64-bit (r8) FMS library"        DEFAULT: OFF
--DFPIC     "Build with position independent code" DEFAULT: OFF
+-DOPENMP      "Build FMS with OpenMP support"        DEFAULT: OFF
+-D32BIT       "Build 32-bit (r4) FMS library"        DEFAULT: ON
+-D64BIT       "Build 64-bit (r8) FMS library"        DEFAULT: OFF
+-DFPIC        "Build with position independent code" DEFAULT: OFF
+-DSHARED_LIBS "Build shared/dynamic libraries"       DEFAULT: OFF
 
 -DCONSTANTS             "Build with <X> constants parameter definitions"     DEFAULT:GFDL  OPTIONS:GFS|GEOS|GFDL
 -DINTERNAL_FILE_NML     "Enable compiler definition -DINTERNAL_FILE_NML"     DEFAULT: ON
 -DENABLE_QUAD_PRECISION "Enable compiler definition -DENABLE_QUAD_PRECISION" DEFAULT: ON
+-DPORTABLE_KINDS        "Enable compiler definition -DPORTABLE_KINDS"        DEFAULT:OFF
 -DGFS_PHYS              "Enable compiler definition -DGFS_PHYS"              DEFAULT:OFF
 -DLARGEFILE             "Enable compiler definition -Duse_LARGEFILE"         DEFAULT:OFF
 -DWITH_YAML             "Enable compiler definition -Duse_yaml"              DEFAULT:OFF

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -23,7 +23,7 @@ cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
 # Define the CMake project
 project(FMS
-  VERSION 2024.02.0
+  VERSION 2024.03.0
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)
@@ -52,14 +52,16 @@ endif()
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 # Build options
-option(OPENMP "Build FMS with OpenMP support"        OFF)
-option(32BIT  "Build 32-bit (r4) FMS library"         ON)
-option(64BIT  "Build 64-bit (r8) FMS library"        OFF)
-option(FPIC   "Build with position independent code" OFF)
+option(OPENMP      "Build FMS with OpenMP support"        OFF)
+option(32BIT       "Build 32-bit (r4) FMS library"         ON)
+option(64BIT       "Build 64-bit (r8) FMS library"        OFF)
+option(FPIC        "Build with position independent code" OFF)
+option(SHARED_LIBS "Build shared/dynamic libraries"       OFF)
 
 # Options for compiler definitions
 option(INTERNAL_FILE_NML     "Enable compiler definition -DINTERNAL_FILE_NML"      ON)
 option(ENABLE_QUAD_PRECISION "Enable compiler definition -DENABLE_QUAD_PRECISION"  ON)
+option(PORTABLE_KINDS        "Enable compiler definition -DPORTABLE_KINDS"        OFF)
 option(GFS_PHYS              "Enable compiler definition -DGFS_PHYS"              OFF)
 option(LARGEFILE             "Enable compiler definition -Duse_LARGEFILE"         OFF)
 option(WITH_YAML             "Enable compiler definition -Duse_yaml"              OFF)
@@ -266,6 +268,10 @@ if(ENABLE_QUAD_PRECISION)
   list(APPEND fms_defs ENABLE_QUAD_PRECISION)
 endif()
 
+if(PORTABLE_KINDS)
+  list(APPEND fms_defs PORTABLE_KINDS)
+endif()
+
 if(LARGEFILE)
   list(APPEND fms_defs use_LARGEFILE)
 endif()
@@ -360,8 +366,15 @@ foreach(kind ${kinds})
   endif()
 
   # FMS (C + Fortran)
-  add_library(${libTgt} STATIC $<TARGET_OBJECTS:${libTgt}_c>
-                               $<TARGET_OBJECTS:${libTgt}_f>)
+  if (SHARED_LIBS)
+      message(STATUS "Shared library target: ${libTgt}")
+      add_library(${libTgt} SHARED $<TARGET_OBJECTS:${libTgt}_c>
+                                   $<TARGET_OBJECTS:${libTgt}_f>)
+  else ()
+      message(STATUS "Static library target: ${libTgt}")
+      add_library(${libTgt} STATIC $<TARGET_OBJECTS:${libTgt}_c>
+                                   $<TARGET_OBJECTS:${libTgt}_f>)
+  endif ()
 
   target_include_directories(${libTgt} PUBLIC
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
@@ -397,7 +410,8 @@ foreach(kind ${kinds})
   target_compile_definitions(${libTgt} PRIVATE "${fms_defs}")
   target_compile_definitions(${libTgt} PRIVATE "${${kind}_defs}")
 
-  target_link_libraries(${libTgt} PUBLIC NetCDF::NetCDF_Fortran
+  target_link_libraries(${libTgt} PUBLIC NetCDF::NetCDF_C
+                                         NetCDF::NetCDF_Fortran
                                          MPI::MPI_Fortran)
 
   if(OpenMP_Fortran_FOUND)

diff --git a/amip_interp/amip_interp.F90 b/amip_interp/amip_interp.F90
@@ -135,10 +135,11 @@ module amip_interp_mod
                              NOTE, mpp_error, fms_error_handler
 
 use     constants_mod, only: TFREEZE, pi
-use      platform_mod, only: r4_kind, r8_kind, i2_kind
+use      platform_mod, only: r4_kind, r8_kind, i2_kind, FMS_FILE_LEN
 use mpp_mod,           only: input_nml_file
 use fms2_io_mod,       only: FmsNetcdfFile_t, fms2_io_file_exists=>file_exists, open_file, close_file, &
                              get_dimension_size, fms2_io_read_data=>read_data
+use netcdf,            only: NF90_MAX_NAME
 
 implicit none
 private
@@ -302,9 +303,8 @@ module amip_interp_mod
 
 !  ---- global unit & date ----
 
-   integer, parameter :: maxc = 128
    integer :: iunit
-   character(len=maxc) :: file_name_sst, file_name_ice
+   character(len=FMS_FILE_LEN) :: file_name_sst, file_name_ice
    type(FmsNetcdfFile_t), target :: fileobj_sst, fileobj_ice
 
    type (date_type) :: Curr_date = date_type( -99, -99, -99 )

diff --git a/amip_interp/include/amip_interp.inc b/amip_interp/include/amip_interp.inc
@@ -46,7 +46,7 @@ subroutine GET_AMIP_SST_ (Time, Interp, sst, err_msg, lon_model, lat_model)
     integer, dimension(:), allocatable :: ryr, rmo, rdy
     character(len=30) :: time_unit
     real(FMS_AMIP_INTERP_KIND_), dimension(:), allocatable :: timeval
-    character(len=maxc) :: ncfilename
+    character(len=FMS_FILE_LEN) :: ncfilename
     type(FmsNetcdfFile_t) :: fileobj
     logical :: the_file_exists
 ! end add by JHC
@@ -652,7 +652,8 @@ endif
      integer(I2_KIND) :: idat(mobs,nobs)
      integer :: nrecords, yr, mo, dy, ierr, k
      integer, dimension(:), allocatable :: ryr, rmo, rdy
-     character(len=maxc) :: ncfilename, ncfieldname
+     character(len=FMS_FILE_LEN)  :: ncfilename
+     character(len=NF90_MAX_NAME) :: ncfieldname
      type(FmsNetcdfFile_t), pointer :: fileobj
      integer, parameter :: lkind = FMS_AMIP_INTERP_KIND_
 

diff --git a/column_diagnostics/column_diagnostics.F90 b/column_diagnostics/column_diagnostics.F90
@@ -32,7 +32,7 @@ module column_diagnostics_mod
                                    get_date, time_type
 use constants_mod,          only:  constants_init, PI, RADIAN
 use mpp_mod,                only:  input_nml_file
-use platform_mod,           only:  r4_kind, r8_kind
+use platform_mod,           only:  r4_kind, r8_kind, FMS_FILE_LEN
 !-------------------------------------------------------------------
 
 implicit none

diff --git a/column_diagnostics/include/column_diagnostics.inc b/column_diagnostics/include/column_diagnostics.inc
@@ -99,7 +99,7 @@ integer, dimension(:), intent(out)   :: diag_units            !< unit number for
       real(FMS_CD_KIND_) ::  ref_lat
       real(FMS_CD_KIND_) ::  current_distance
       character(len=8)   ::  char         !< character string for diaganostic column index
-      character(len=32)  ::  filename     !< filename for output file for diagnostic column
+      character(len=FMS_FILE_LEN)  ::  filename     !< filename for output file for diagnostic column
       logical            ::  allow_ij_input
       logical            ::  open_file
       integer            ::  io

diff --git a/configure.ac b/configure.ac
@@ -25,7 +25,7 @@ AC_PREREQ([2.69])
 
 # Initialize with name, version, and support email address.
 AC_INIT([GFDL FMS Library],
-  [2024.02-dev],
+  [2024.03-dev],
   [[email protected]],
   [FMS],
   [https://www.github.com/NOAA-GFDL/FMS])
@@ -112,6 +112,13 @@ AS_IF([test ${enable_r8_default:-yes} = yes],
   [enable_r8_default=yes],
   [enable_r8_default=no])
 
+AC_ARG_ENABLE([portable-kinds],
+  [AS_HELP_STRING([--enable-portable-kinds],
+    [Enables compilation with -DPORTABLE_KINDS with iso_c_binding KIND type parameters])])
+AS_IF([test ${enable_portable_kinds:-no} = yes],
+  [enable_portable_kinds=yes],
+  [enable_portable_kinds=no])
+
 # user enabled testing with input files
 AC_MSG_CHECKING([whether to enable tests with input files])
 AC_ARG_ENABLE([test-input],
@@ -273,6 +280,13 @@ if test $hdf5_fpe_bug = yes; then
 NetCDF must be built with a HDF5 version other than 1.14.3 to support floating point exception traps.])
 fi
 
+rm -f test.nc
+
+# Check if we need a flag to not capitalize module output (needed with cray compiler)
+GX_FC_MOD_CASE_FLAG([FCFLAGS="$FCFLAGS $FC_MOD_CASE_FLAG"])
+
+# Check if new unit is supported
+GX_FC_08_OPEN_NEWUNIT([], [AC_MSG_ERROR([Compiler support for use of newunit argument is required to build FMS])])
 
 # Check if Fortran compiler has the Class, Character array assign bug
 GX_FC_CLASS_CHAR_ARRAY_BUG_CHECK()
@@ -342,6 +356,11 @@ if test $enable_setting_flags = yes; then
     AC_DEFINE([no_8byte_integers], [1], [Set to disable 8 byte integer Fortran routines])
   fi
 
+  # Builds with C data types
+  if test $enable_portable_kinds = yes; then
+    AC_DEFINE([PORTABLE_KINDS], [1], [Set to define KIND parameters to iso_c_binding KIND parameters])
+  fi
+
   # Add Cray Pointer support flag
   if test ! -z "$FC_CRAY_POINTER_FLAG"; then
     FCFLAGS="$FCFLAGS $FC_CRAY_POINTER_FLAG"

diff --git a/coupler/atmos_ocean_fluxes.F90 b/coupler/atmos_ocean_fluxes.F90
@@ -48,7 +48,7 @@ module  atmos_ocean_fluxes_mod
   use coupler_types_mod, only: ind_runoff
   use coupler_types_mod, only: ind_flux, ind_deltap, ind_kw, ind_flux0
 
-  use field_manager_mod, only: fm_path_name_len, fm_string_len, fm_exists, fm_get_index
+  use field_manager_mod, only: fm_string_len, fm_exists, fm_get_index
   use field_manager_mod, only: fm_new_list, fm_get_current_list, fm_change_list
   use field_manager_mod, only: fm_field_name_len, fm_type_name_len, fm_dump_list
   use field_manager_mod, only: fm_loop_over_list
@@ -63,7 +63,7 @@ module  atmos_ocean_fluxes_mod
   use fm_util_mod,       only: fm_util_get_real_array, fm_util_get_real, fm_util_get_integer
   use fm_util_mod,       only: fm_util_get_logical, fm_util_get_logical_array
   use fms_io_utils_mod,  only: get_data_type_string
-  use platform_mod,      only: r4_kind, r8_kind
+  use platform_mod,      only: r4_kind, r8_kind, FMS_PATH_LEN
 
   implicit none
   private
@@ -135,8 +135,8 @@ function aof_set_coupler_flux(name, flux_type, implementation, atm_tr_index, par
     integer                                                 :: length
     integer                                                 :: num_parameters
     integer                                                 :: outunit
-    character(len=fm_path_name_len)                         :: coupler_list
-    character(len=fm_path_name_len)                         :: current_list
+    character(len=FMS_PATH_LEN)                            :: coupler_list
+    character(len=FMS_PATH_LEN)                            :: current_list
     character(len=fm_string_len)                            :: flux_type_test
     character(len=fm_string_len)                            :: implementation_test
     character(len=256)                                      :: error_header