Merge branch 'NOAA-GFDL:main' into feature/general-indices-gatscat

Author: abrooks1085

.github/workflows/github_autotools_gnu.yml

@@ -1,6 +1,4 @@
-# 'main' required ci, does a distcheck (builds, tests, check install)
-# image created off dockerfile in repo, compile/link flags are set there
-name: Build libFMS test with autotools
+name: Autotools build and unit testing with GCC
 
 on: [push, pull_request]
 
@@ -14,31 +12,38 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        conf-flag: [ --disable-openmp, --disable-setting-flags, --with-mpi=no, --disable-r8-default]
+        conf-flag: [ --disable-openmp, --with-mpi=no, --disable-r8-default]
         input-flag: [--with-yaml, --enable-test-input=/home/unit_tests_input]
         exclude:
           - conf-flag: --with-mpi=no
             input-flag: --enable-test-input=/home/unit_tests_input
     container:
-      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:15.1.0
       env:
-        TEST_VERBOSE: 1
-        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }} ${{ matrix.io-flag }}"
+        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }}"
         DEBUG_FLAGS: "-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow" # debug compiler flags taken from the mkmf template
+        # diag manager openmp + logical mask tests fail with gcc, these are reproducible outside the CI
+        # test_mpp_clock_begin_end_id is an expected fail that is passing, only happens in the CI
+        # test_time_interp2 tests fail from file issues, only happens in the CI
+        SKIP_TESTS: "test_time_none.10 test_time_sum.10 test_time_avg.10 test_time_min.10 test_time_max.10 test_time_pow.10 test_time_rms.10 test_mpp_clock_begin_end_id.10 test_time_interp2.7 test_time_interp2.8"
     steps:
     - name: Checkout code
-      uses: actions/checkout@v4.2.2
+      uses: actions/checkout@v6.0.1
     - name: Prepare GNU autoconf for build
       run: autoreconf -if
     - name: Configure the build
-      if: ${{ matrix.conf-flag != '--disable-setting-flags' }}
-      run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} FCFLAGS="$FCFLAGS $DEBUG_FLAGS"
-    - name: Configure the build with compiler flags
-      if: ${{ matrix.conf-flag == '--disable-setting-flags' }}
-      run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} FCFLAGS="-fdefault-real-8 -fdefault-double-8 -fcray-pointer -ffree-line-length-none -I/usr/include $FCFLAGS $DEBUG_FLAGS" || cat config.log
-    - name: Build the library
-      run: make distcheck
+      run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} FCFLAGS="$FCFLAGS $DEBUG_FLAGS" || cat config.log
+    - name: Run distcheck (compiles, tests, and packages)
+      run: make distcheck 2>&1 > distcheck.log
       if: ${{ matrix.conf-flag != '--with-mpi=no' }}
+    - name: Output errors on failure
+      run: grep -E "^FAIL:|^XPASS:" distcheck.log
+      if: failure()
+    - name: Upload log on failure
+      uses: actions/upload-artifact@v7.0.0
+      if: failure()
+      with:
+        path: distcheck.log
     - name: Build the library (without test suite for serial build)
       run: make
       if: ${{ matrix.conf-flag == '--with-mpi=no' }}

.github/workflows/github_autotools_intel_classic.yml

@@ -1,8 +1,9 @@
+name: Autotools build and unit testing with Intel Classic (weekly)
+
 on:
   schedule:
     - cron: '0 0 * * 0' # sundays @ midnight
 
-
 # cancel running jobs if theres a newer push
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -21,8 +22,6 @@ 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

@@ -1,3 +1,5 @@
+name: Autotools build and unit testing with Intel Oneapi
+
 on: pull_request
 
 # cancel running jobs if theres a newer push
@@ -18,8 +20,6 @@ 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

@@ -1,4 +1,4 @@
-name: Build libFMS with cmake
+name: CMake build and unit testing with GCC
 
 on: [push, pull_request]
 
@@ -12,36 +12,38 @@ 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
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:15.1.0
       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_mpp_clock_begin_end_id|test_time_*"
         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
+      uses: actions/checkout@v6.0.1
     - name: Generate makefiles with CMake
       run: |
         mkdir build
         cd build
-        cmake $CMAKE_FLAGS -DNetCDF_ROOT=/opt/view ..
+        cmake -DOVERSUBSCRIBE_FLAG="--map-by :OVERSUBSCRIBE" $CMAKE_FLAGS -DOPENMP=on -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view -DUNIT_TESTS=on ..
     - name: Build the library
       run: make -C build
+    - name: Run the unit tests
+      run: cd build && ctest -E "${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
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0-arm-cmake-update
       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_sat_vapor_pres|test_mpp_clock_begin_end_id"
         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 $CMAKE_FLAGS -DOVERSUBSCRIBE_FLAG="" -DOPENMP=on -DUNIT_TESTS=on -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view ..
     - name: Build the library
       run: make -C build
+    - name: Run the unit tests
+      run: cd build && ctest -E "${EXCLUDE_TESTS}" --output-on-failure

.github/workflows/github_coupler_gnu.yml

@@ -1,4 +1,4 @@
-name: Test coupler build
+name: FMScoupler null model build with GCC
 on: [pull_request]
 
 # cancel running jobs if theres a newer push
@@ -10,7 +10,7 @@ jobs:
   coupler-build:
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:15.1.0
       credentials:
         username: ${{ github.actor }}
         password: ${{ secrets.github_token }}

.github/workflows/github_linter.yml

@@ -1,4 +1,4 @@
-name: libFMS lint tests
+name: Line length and whitespace linter
 
 on: [push, pull_request]
 

.github/workflows/github_mom_gnu.yml

@@ -1,4 +1,4 @@
-name: Run MOM6 test suite
+name: MOM6 test suite with GCC
 
 # runs on PR's or when manually triggered
 on: [workflow_dispatch, pull_request]
@@ -11,17 +11,14 @@ concurrency:
 jobs:
   build:
     runs-on: ubuntu-latest
-    container:
-      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
-      credentials:
-        username: ${{ github.actor }}
-        password: ${{ secrets.github_token }}
     steps:
     - name: Checkout MOM6 repository
       uses: actions/checkout@v4.2.2
       with:
         repository: 'NOAA-GFDL/MOM6'
         submodules: recursive
+    - name: Install dependency packages
+      uses: ./.github/actions/ubuntu-setup/
     - name: Checkout FMS into MOM build
       uses: actions/checkout@v4.2.2
       with:

.github/workflows/version.yml

@@ -1,5 +1,5 @@
-# appends -dev to the version upon release and opens pr
 # CI won't run on generated PR, easiest workaround is to close + reopen
+name: Append version number and create PR
 on:
   release:
     types: [published]

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

CMAKE_INSTRUCTIONS.md

@@ -77,12 +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