Merge branch 'main' of github.com:NOAA-GFDL/FMS

Author: uramirez8707

.github/workflows/github_autotools_intel_classic.yml

@@ -21,8 +21,6 @@ jobs:
         LDFLAGS: "-L/libs/lib"
         TEST_VERBOSE: 1
         I_MPI_FABRICS: "shm" # needed for mpi in image
-        # intel bug causes some failures with shm option(required in container)
-        SKIP_TESTS: "test_mpp_update_domains.1 test_update_domains_performance.1 test_diag_manager2.23"
     steps:
     - name: Cache dependencies
       id: cache

.github/workflows/github_autotools_intel_oneapi.yml

@@ -6,7 +6,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  intel-oneapi-2025.3:
+  intel-oneapi-2025-3:
     runs-on: ubuntu-latest
     container:
       image: intel/oneapi-hpckit:2025.3.0-0-devel-ubuntu22.04
@@ -18,8 +18,6 @@ jobs:
         LDFLAGS: "-L/libs/lib"
         TEST_VERBOSE: 1
         I_MPI_FABRICS: "shm" # needed for mpi in image
-        # intel bug causes some failures with shm option(required in container)
-        SKIP_TESTS: "test_mpp_update_domains.1 test_update_domains_performance.1 test_diag_manager2.23"
     steps:
     - name: Cache dependencies
       id: cache

.github/workflows/github_cmake_gnu.yml

@@ -12,42 +12,48 @@ 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
       uses: actions/checkout@v4.2.2
     - name: Generate makefiles with CMake
       run: |
         mkdir build
         cd build
-        cmake $CMAKE_FLAGS -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view ..
+        cmake $CMAKE_FLAGS -DOPENMP=on -DUNIT_TESTS=on -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view ..
     - name: Build the library
       run: make -C build
+    - name: Run the unit tests
+      run: cd build && ctest -E "${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
       uses: actions/checkout@v4.2.2
     - name: Generate makefiles with CMake
       run: |
         mkdir build
         cd build
-        cmake $CMAKE_FLAGS -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view ..
+        cmake $CMAKE_FLAGS -DOPENMP=on -DUNIT_TESTS=on -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view ..
     - name: Build the library
       run: make -C build
+    - name: Run the unit tests
+      run: cd build && ctest -E "${EXCLUDE_TESTS}" --output-on-failure

CHANGELOG.md

@@ -6,6 +6,41 @@ 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
+- - INTEL: Oneapi 2025.1 is currently unsupported due to an internal compiler error. The `-check uninit` flag for intel's LLVM compilers(ifx/icx) is also unsupported, see prior release for more information.
+- 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 these 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.
+
+### Added
+- Modifed and added tests for future generalized indices updates (#1763)
+- OFFLOAD: Added a prototype for offloading io to a smaller set of PE's `offloading_io_mod` (#1774)
+
+### Changed
+- Legacy field_table and data_table ASCII formats are now deprecated and will output a warning if used (#1802)
+- MPP: Replaced point-to-point communication with collective mode in `mpp_gather` routines (#1775)
+- FMS2_IO: Refactored API for enabling MPI-IO support (#1789)
+- DIAG_MANAGER: The updated diag manager will now add the experiment title as a global attribute (#1817)
+
+### Fixed
+- Fixed multiple compiler warnings raised from GCC 15 (#1765)
+- Fixed GNU warnings with the -DPORTABLE_KINDS flag (#1792)
+- DIAG_MANAGER: Fixed issue with not getting correct output name when adding the cell_measure attribute (#1815)
+- DIAG_MANAGER: Fixed error when setting zbounds for more than one variable (#1813)
+- CMAKE: Fixed handling of libyaml dependency when using a r4/r8 option (#1822)
+
+### Removed
+- EXCHANGE: Removed cray pointer usage from `xgrid.F90` (#1778)
+
 ## [2025.04] - 2025-09-29
 
 ### Known Issues

CMAKE_INSTRUCTIONS.md

@@ -22,11 +22,6 @@ MPI compiler wrappers may be named different on your system, so its best to ensu
 export NetCDF_ROOT=`nc-config --prefix`
 ```
 
-#### If building with yaml parser (-DWITH_YAML)
-```
-export LIBYAML_ROOT=<your libyaml install directory>
-```
-
 ### Running CMake
 It's best to create a build directory inside of the FMS folder to avoid building on top of the source code.
 Once that is done, CMake can be ran to generate the necessary build files:
@@ -82,12 +77,12 @@ The following build options are available:
 -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
+-DUNIT_TESTS            "Toggle on build of unit tests"                      DEFAULT:OFF
 ```
 
 ## 3. Installation structure