Add patch commits to the main (#1846)

Author: vithikashah001

.github/workflows/github_cmake_gnu.yml

@@ -12,13 +12,13 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        omp-flags: [ -DOPENMP=on, -DOPENMP=off ]
         libyaml-flag: [ "", -DWITH_YAML=on ]
         build-type: [ "-DCMAKE_BUILD_TYPE=Release", "-DCMAKE_BUILD_TYPE=Debug" ]
     container:
       image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
       env:
-        CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.omp-flags }} ${{ matrix.libyaml-flag }}"
+        CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.libyaml-flag }}"
+        EXCLUDE_TESTS: "test_mpp_nesting|test_bc_restart|test_collective_io|test_fms2_io|test_io_with_mask"
         PKG_CONFIG_PATH: "/opt/views/view/lib64/pkgconfig:/opt/views/view/lib/pkgconfig:/opt/views/view/share/pkgconfig"
     steps:
     - name: Checkout code
@@ -27,21 +27,23 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake $CMAKE_FLAGS -DNetCDF_ROOT=/opt/view ..
+        cmake $CMAKE_FLAGS -DOPENMP=on -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view ..
     - name: Build the library
       run: make -C build
+    - name: Run the unit tests
+      run: cd build && ctest -E "${EXCLUDE_TESTS}" --output-on-failure
 
   build_arm:
     runs-on: ubuntu-24.04-arm
     strategy:
       matrix:
-        omp-flags: [ -DOPENMP=on, -DOPENMP=off ]
         libyaml-flag: [ "", -DWITH_YAML=on ]
         build-type: [ "-DCMAKE_BUILD_TYPE=Release", "-DCMAKE_BUILD_TYPE=Debug" ]
     container:
       image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0-arm
       env:
-        CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.omp-flags }} ${{ matrix.libyaml-flag }}"
+        CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.libyaml-flag }}"
+        EXCLUDE_TESTS: "test_mpp_nesting|test_bc_restart|test_collective_io|test_fms2_io|test_io_with_mask|test_sat_vapor_pres"
         PKG_CONFIG_PATH: "/opt/views/view/lib64/pkgconfig:/opt/views/view/lib/pkgconfig:/opt/views/view/share/pkgconfig"
     steps:
     - name: Checkout code
@@ -50,6 +52,8 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake $CMAKE_FLAGS -DNetCDF_ROOT=/opt/view ..
+        cmake $CMAKE_FLAGS -DOPENMP=on -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view ..
     - name: Build the library
       run: make -C build
+    - name: Run the unit tests
+      run: cd build && ctest -E "${EXCLUDE_TESTS}" --output-on-failure

CHANGELOG.md

@@ -6,6 +6,13 @@ 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`).
 
+## [2026.01.01] - 2026-03-03
+
+### Fixed
+- Fix: modern diag manager cell measures and associated files (#1837)
+- Avoid integer overflow in mpp_define_unstruct_domain (#1841)
+- Fixes for cmake 32/64bit builds and enable CI testing via ctest (#1787)
+
 ## [2026.01] - 2026-01-26
 
 ### Known Issues

CMakeLists.txt

@@ -22,7 +22,7 @@ cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
 # Define the CMake project
 project(FMS
-  VERSION 2026.01.0
+  VERSION 2026.01.01
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)
@@ -65,18 +65,17 @@ option(PORTABLE_KINDS        "Enable compiler definition -DPORTABLE_KINDS"
 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)
-option(USE_DEPRECATED_IO     "THIS OPTION HAS NO EFFECT AND WILL BE REMOVED IN A FUTURE RELEASE"   OFF)
 
 if(32BIT)
   list(APPEND kinds "r4")
+  message(STATUS "Building library with 4-byte real defaults (with mixed precision real support for most modules).")
 endif()
 if(64BIT)
   list(APPEND kinds "r8")
+  message(STATUS "Building library with 8-byte real defaults (with mixed precision real support for most modules).")
 endif()
 if(NOT kinds)
-  message(STATUS "Single Precision 32BIT: ${32BIT}")
-  message(STATUS "Double Precision 64BIT: ${64BIT}")
-  message(STATUS "No kind specified, building default double precision (with mixed precision support). Real size will not be included in built library name.")
+  message(STATUS "Building library with 8-byte real defaults (with mixed precision 4-byte real support for most modules). Real size will not be included in built library name.")
 endif()
 
 # Find dependencies
@@ -181,6 +180,8 @@ list(APPEND fms_fortran_src_files
   mpp/mpp_memutils.F90
   mpp/mpp_parameter.F90
   mpp/mpp_utilities.F90
+  offloading/offloading_io.F90
+  offloading/metadata_transfer.F90
   parser/yaml_parser.F90
   parser/fms_yaml_output.F90
   platform/platform.F90
@@ -276,11 +277,6 @@ if(LARGEFILE)
   list(APPEND fms_defs use_LARGEFILE)
 endif()
 
-# Precision-based compiler definitions
-if(32BIT)
-  list(APPEND r4_defs OVERLOAD_R4 OVERLOAD_R8)
-endif()
-
 # Add platform specific compiler definitions
 if(APPLE)
   list(APPEND fms_defs __APPLE__)
@@ -291,7 +287,7 @@ include(fms_compiler_flags)
 
 # If netCDF was not built with HDF5 parallel I/O features, set up the macro -DNO_NC_PARALLEL4
 IF(NOT NetCDF_PARALLEL)
-  MESSAGE(WARNING "netCDF was not build with HDF5 parallel I/O features, so collective netcdf io is not allowed")
+  MESSAGE(WARNING "netCDF was not build with HDF5 parallel I/O features, so parallel netcdf io is not allowed")
   list(APPEND fms_defs NO_NC_PARALLEL4)
 ENDIF()
 
@@ -347,7 +343,7 @@ foreach(kind ${kinds})
                                                  amip_interp/include)
   target_compile_definitions(${libTgt}_f PRIVATE "${fms_defs}")
   target_compile_definitions(${libTgt}_f PRIVATE "${${kind}_defs}")
-  set_target_properties(${libTgt}_f PROPERTIES COMPILE_FLAGS ${${kind}_flags})
+  set_target_properties(${libTgt}_f PROPERTIES COMPILE_FLAGS "${${kind}_flags}")
   set_target_properties(${libTgt}_f PROPERTIES Fortran_MODULE_DIRECTORY
                                                ${moduleDir})
   target_link_libraries(${libTgt}_f PRIVATE NetCDF::NetCDF_Fortran
@@ -594,6 +590,14 @@ include(CTest)
 set(MPI_LAUNCHER "mpirun")
 # used in the test-lib.sh.in to make it behave differently when parsed by cmake
 set(USING_CMAKE "true")
+# set the fms library to link tests with based on whats built
+if(NOT kinds)
+  set(fmsLibraryName FMS::fms)
+elseif(64BIT)
+  set(fmsLibraryName FMS::fms_r8)
+elseif(32BIT)
+  set(fmsLibraryName FMS::fms_r4)
+endif()
 
 # parse and add build info to test script util file
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/test_fms/test-lib.sh.in ${CMAKE_CURRENT_SOURCE_DIR}/test-lib.sh
@@ -617,7 +621,7 @@ list(APPEND TEST_MODS_SRC
   test_fms/mpp/test_system_clock.F90)
 
 add_library(testLibs "${TEST_MODS_SRC}")
-target_link_libraries(testLibs FMS::fms)
+target_link_libraries(testLibs ${fmsLibraryName})
 target_compile_definitions(testLibs PRIVATE TEST_MOS_KIND_=r8_kind)
 target_include_directories(testLibs PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/include
                                     PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test_fms/common/include
@@ -701,6 +705,7 @@ list(APPEND TEST_SRC_SINGLE_TARGET
   test_fms/fms2_io/test_domain_io.F90
   test_fms/fms2_io/test_collective_io.F90
   test_fms/fms2_io/test_generalized_indices.F90
+  test_fms/fms2_io/test_parallel_writes.F90
   test_fms/fms/test_fms.F90
   test_fms/interpolator/test_interpolator.F90
   test_fms/mpp/test_clock_init.F90
@@ -754,6 +759,8 @@ list(APPEND TEST_SRC_SINGLE_TARGET
   test_fms/parser/generic_blocks.F90
   test_fms/string_utils/test_string_utils.F90
   test_fms/time_manager/test_time_manager.F90
+  test_fms/offloading/test_metadata_transfer.F90
+  test_fms/offloading/test_io_offloading.F90
   )
 # list any test sources that are used for two executables (r4 and r8)
 list(APPEND TEST_SRC_TWO_TARGETS
@@ -778,6 +785,7 @@ list(APPEND TEST_SRC_TWO_TARGETS
   test_fms/sat_vapor_pres/test_sat_vapor_pres.F90
   test_fms/time_interp/test_time_interp.F90
   test_fms/time_interp/test_time_interp_external.F90
+  test_fms/time_interp/test_time_interp_conservative_hi.F90
   test_fms/topography/test_topography.F90
   test_fms/tracer_manager/test_tracer_manager.F90
   test_fms/tridiagonal/test_tridiagonal.F90
@@ -789,14 +797,17 @@ list(APPEND TEST_SRC_FOUR_TARGETS
 
 # add all the test executables and set up linking + compile flags
 foreach (testFile ${TEST_SRC_SINGLE_TARGET})
-  get_filename_component (TName ${testFile} NAME_WE)
 
+  get_filename_component (TName ${testFile} NAME_WE)
   add_executable(${TName} ${testFile})
-  target_compile_definitions(${TName} PRIVATE "${r8_defs}")
-  set_target_properties(${TName} PROPERTIES COMPILE_FLAGS ${r8_flags})
-  target_link_libraries(${TName} PUBLIC FMS::fms
-                                 PRIVATE testLibs
-                                   )
+  target_link_libraries(${TName} PUBLIC ${fmsLibraryName}
+                                 PRIVATE testLibs)
+  if(32BIT)
+    target_compile_definitions(${TName} PRIVATE "${r4_defs} ${fms_defs}")
+  else()
+    target_compile_definitions(${TName} PRIVATE "${r8_defs} ${fms_defs} ")
+    set_target_properties(${TName} PROPERTIES COMPILE_FLAGS ${r8_flags})
+  endif()
 
   if(WITH_YAML)
     target_link_libraries(${TName} PRIVATE PkgConfig::YAML)
@@ -820,18 +831,16 @@ foreach (testFile ${TEST_SRC_TWO_TARGETS})
   get_filename_component (TName ${testFile} NAME_WE)
 
   add_executable(${TName}_r8 ${testFile})
-  target_compile_definitions(${TName}_r8 PRIVATE "${r8_defs}")
+  target_compile_definitions(${TName}_r8 PRIVATE "${r8_defs} ${fms_defs}")
   set_target_properties(${TName}_r8 PROPERTIES COMPILE_FLAGS ${r8_flags})
-  target_link_libraries(${TName}_r8 PUBLIC FMS::fms
-                                    PRIVATE testLibs
-                                    )
-
+  target_link_libraries(${TName}_r8 PUBLIC ${fmsLibraryName}
+                                    PRIVATE testLibs)
   add_executable(${TName}_r4 ${testFile})
-  target_compile_definitions(${TName}_r4 PRIVATE "${r4_defs}")
+  target_compile_definitions(${TName}_r4 PRIVATE "${r4_defs} ${fms_defs}")
   # seems counterintuitive but r4 tests use r8 default
   # they specify kind values explicitly with the preprocessor where needed (TEST_FMS_KIND_)
   set_target_properties(${TName}_r4 PROPERTIES COMPILE_FLAGS ${r8_flags})
-  target_link_libraries(${TName}_r4 PUBLIC FMS::fms
+  target_link_libraries(${TName}_r4 PUBLIC ${fmsLibraryName}
                                     PRIVATE testLibs
                                     )
 
@@ -984,8 +993,16 @@ foreach (testScript ${TEST_SCRIPTS})
         ENVIRONMENT "parser_skip=skip"
     )
   endif()
+
 endforeach()
 
+# skip parallel netcdf tests if its not enabled in given install
+IF(NOT NetCDF_PARALLEL)
+  set_tests_properties(test_collective_io PROPERTIES
+      ENVIRONMENT "parallel_skip=skip"
+  )
+endif()
+
 set(CMAKE_CTEST_ARGUMENTS "--output-on-failure")
 
 ### Package config

cmake/compiler_flags_GNU_Fortran.cmake

@@ -1,6 +1,6 @@
 # Precision-based Fortran compiler flags
 set(r8_flags "-fdefault-real-8 -fdefault-double-8") # Fortran flags for 64BIT precision
-set(r4_flags "-fdefault-real-4") # Fortran flags for 32BIT precision
+set(r4_flags "") # 4 byte reals is default for gfortran
 
 # GNU Fortran
 set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fcray-pointer -fallow-argument-mismatch -ffree-line-length-none")

configure.ac

@@ -24,7 +24,7 @@ AC_PREREQ([2.69])
 
 # Initialize with name, version, and support email address.
 AC_INIT([GFDL FMS Library],
-  [2026.01-dev],
+  [2026.01.01],
   [gfdl.climate.model.info@noaa.gov],
   [FMS],
   [https://www.github.com/NOAA-GFDL/FMS])
@@ -97,17 +97,6 @@ AS_IF([test ${enable_8byte_int:-no} = yes],
   [enable_8byte_int=yes],
   [enable_8byte_int=no])
 
-AC_ARG_ENABLE([deprecated-io],
-  [AS_HELP_STRING([--enable-deprecated-io],
-    [THIS OPTION HAS BEEN DEPRECATED!!!])])
-AS_IF([test ${enable_deprecated_io:-no} = yes],
-  [enable_deprecated_io=yes],
-  [enable_deprecated_io=no])
-
-if test $enable_deprecated_io = yes; then
-  AC_MSG_ERROR(FMS_IO HAS BEEN REMOVED! PLEASE UPDATE TO USE FMS2_IO AND REMOVE --enable-deprecated-io FROM YOUR CONFIGURE OPTIONS OR REVERT TO VERSION 2025.02)
-fi
-
 AC_ARG_ENABLE([r8-default],
   [AS_HELP_STRING([--disable-r8-default],
     [Disables the build from adding the 8 byte default real kind flag during compilation (default no)])])

diag_manager/fms_diag_field_object.F90

@@ -2001,10 +2001,13 @@ function get_field_file_name(this) &
 end function get_field_file_name
 
 !> @brief Generate the associated files attribute
-subroutine generate_associated_files_att(this, att, start_time)
-  class(fmsDiagField_type)        ,  intent(in)            :: this       !< diag_field_object for the area/volume field
-  character(len=*),                  intent(inout)         :: att        !< associated_files_att
-  type(time_type),                   intent(in)            :: start_time !< The start_time for the field's file
+subroutine generate_associated_files_att(this, att, start_time, var_output_name)
+  class(fmsDiagField_type)        ,  intent(in)            :: this             !< diag_field_object for the
+                                                                               !! area/volume field
+  character(len=*),                  intent(inout)         :: att              !< associated_files_att
+  type(time_type),                   intent(in)            :: start_time       !< The start_time for the field's file
+  character(len=*),                  intent(out)           :: var_output_name  !< output name of the area/volume field
+
 
   character(len=:), allocatable :: field_name !< Name of the area/volume field
   character(len=FMS_FILE_LEN) :: file_name !< Name of the file the area/volume field is in!
@@ -2026,6 +2029,9 @@ subroutine generate_associated_files_att(this, att, start_time)
   endif
 
   att = trim(att)//" "//trim(field_name)//": "//trim(file_name)//".nc"
+
+  ! Save the outputname of the area/volume so it can be added correctly to the cell_measures attribute
+  var_output_name = field_name
 end subroutine generate_associated_files_att
 
 !> @brief Determines if the compute domain has been divide further into slices (i.e openmp blocks)

diag_manager/fms_diag_file_object.F90

@@ -1827,6 +1827,7 @@ subroutine write_field_metadata(this, diag_field, diag_axis)
   character(len=255) :: cell_measures !< cell_measures attributes for the field
   logical            :: need_associated_files !< .True. if the 'associated_files' global attribute is needed
   character(len=FMS_FILE_LEN) :: associated_files !< Associated files attribute to add
+  character(len=FMS_FILE_LEN) :: field_outputname !< Output name of the area/volume field
 
   is_regional = this%is_regional()
 
@@ -1841,26 +1842,30 @@ subroutine write_field_metadata(this, diag_field, diag_axis)
 
     cell_measures = ""
     if (field_ptr%has_area()) then
-      cell_measures = "area: "//diag_field(field_ptr%get_area())%get_varname(to_write=.true., &
-        filename=diag_file%get_file_fname())
-
       !! Determine if the area field is already in the file. If it is not create the "associated_files" attribute
       !! which contains the file name of the file the area field is in. This is needed for PP/fregrid.
       if (.not. diag_field(field_ptr%get_area())%is_variable_in_file(diag_file%id)) then
         need_associated_files = .true.
-        call diag_field(field_ptr%get_area())%generate_associated_files_att(associated_files, diag_file%start_time)
+        call diag_field(field_ptr%get_area())%generate_associated_files_att(associated_files, diag_file%start_time, &
+          field_outputname)
+        cell_measures = "area: "//trim(field_outputname)
+      else
+        cell_measures = "area: "//diag_field(field_ptr%get_area())%get_varname(to_write=.true., &
+          filename=diag_file%get_file_fname())
       endif
     endif
 
     if (field_ptr%has_volume()) then
-      cell_measures = trim(cell_measures)//" volume: "//diag_field(field_ptr%get_volume())%get_varname(&
-        to_write=.true., filename=diag_file%get_file_fname())
-
       !! Determine if the volume field is already in the file. If it is not create the "associated_files" attribute
       !! which contains the file name of the file the volume field is in. This is needed for PP/fregrid.
       if (.not. diag_field(field_ptr%get_volume())%is_variable_in_file(diag_file%id)) then
         need_associated_files = .true.
-        call diag_field(field_ptr%get_volume())%generate_associated_files_att(associated_files, diag_file%start_time)
+        call diag_field(field_ptr%get_volume())%generate_associated_files_att(associated_files, diag_file%start_time, &
+          field_outputname)
+        cell_measures = trim(cell_measures)//" volume: "//trim(field_outputname)
+      else
+        cell_measures = trim(cell_measures)//" volume: "//diag_field(field_ptr%get_volume())%get_varname(&
+          to_write=.true., filename=diag_file%get_file_fname())
       endif
     endif
 

fms/fms.F90

@@ -320,9 +320,9 @@ subroutine maximize_system_stacksize_limit() bind(C)
     call mpp_domains_init()
     call fms2_io_init()
 #ifdef use_deprecated_io
-      call mpp_error(NOTE, "fms_io_init: fms_io HAS BEEN DEPRECATED! "//&
+      call mpp_error(ERROR, "fms_io_init: fms_io/mpp_io was removed in the 2025.03 release of FMS! "//&
                            "PLEASE REMOVE -Duse_deprecated_io FROM YOUR COMPILE FLAGS "// &
-                           "AND MOVE TO FMS2_IO. CONTACT YOUR MODEL LIASISON IF YOU NEED "// &
+                           "AND MOVE TO FMS2_IO. CONTACT YOUR GFDL MODEL LIAISON IF YOU NEED "// &
                            "ASSISTANCE")
 #endif
     logunitnum = stdlog()

libFMS/Makefile.am

@@ -27,7 +27,7 @@ lib_LTLIBRARIES = libFMS.la
 # These linker flags specify libtool version info.
 # See http://www.gnu.org/software/libtool/manual/libtool.html#Libtool-versioning
 # for information regarding incrementing `-version-info`.
-libFMS_la_LDFLAGS = -version-info 26:0:0
+libFMS_la_LDFLAGS = -version-info 27:0:0
 
 # Add the convenience libraries to the FMS library.
 libFMS_la_LIBADD = $(top_builddir)/platform/libplatform.la