Merge remote-tracking branch 'origin/main' into fm_interface_cleanup

.github/CODEOWNERS

@@ -25,7 +25,7 @@
 # These owners will be the default owners for all the files in the
 # repository.  Unless a later match is found, these owners
 # will be requested for a review when a PR is opened.
-*          @thomas-robinson @bensonr @rem1776
+*          @uramirez8707 @bensonr @rem1776
 
 # GNU autotools files
 Makefile.am      @uramirez8707 @rem1776
@@ -34,16 +34,14 @@ Makefile.am      @uramirez8707 @rem1776
 *.m4             @uramirez8707 @rem1776
 
 # cmake files
-CM*              @mlee03 @ngs333
-cmake            @mlee03 @ngs333
+CM*              @mlee03
+cmake            @mlee03
 
 # Files specific to GitHub or GitLab
-/.github/        @GFDL-Eric @rem1776
-/.gitlab/        @GFDL-Eric @rem1776
+/.github/        @rem1776
 
 # Testing files
-/.gitlab-ci.yml  @uramirez8707 @mlee03 @bensonr @thomas-robinson @rem1776
-/test_fms/       @uramirez8707 @mlee03 @bensonr @thomas-robinson @rem1776
+/test_fms/       @uramirez8707 @mlee03 @bensonr @rem1776
 
 # Specific component directories
 /affinity/          @bensonr
@@ -52,20 +50,18 @@ cmake            @mlee03 @ngs333
 /block_control/          @bensonr
 /test_fms/block_control/ @bensonr @rem1776
 
-/data_override/          @GFDL-Eric
-/test_fms/data_override/ @GFDL-Eric @rem1776
+#/data_override/ Currently no code owner
+/test_fms/data_override/ @rem1776
 
-/diag_manager            @thomas-robinson @ngs333
-/test_fms/diag_manager/  @thomas-robinson @ngs333
+/diag_manager            @uramirez8707
+/test_fms/diag_manager/  @uramirez8707
 
-/fv3gfs/          @bensonr
+/fms/             @uramirez8707 @rem1776
+/test_fms/fms/    @uramirez8707 @rem1776
+/fms2/            @uramirez8707
+/test_fms/fms2/   @uramirez8707
 
-/fms/             @thomas-robinson @rem1776
-/test_fms/fms/    @thomas-robinson @rem1776
-/fms2/            @uramirez8707 @GFDL-Eric
-/test_fms/fms2/   @uramirez8707 @GFDL-Eric
+/libFMS/           @uramirez8707 @rem1776
 
-/libFMS/           @thomas-robinson @rem1776
-
-/mpp/              @thomas-robinson @bensonr
-/test_fms/mpp/     @thomas-robinson @bensonr @rem1776
+/mpp/              @uramirez8707 @bensonr
+/test_fms/mpp/     @uramirez8707 @bensonr @rem1776

.github/workflows/github_autotools_gnu.yml

@@ -4,25 +4,30 @@ name: Build libFMS test with autotools
 
 on: [push, pull_request]
 
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        conf-flag: [ --disable-openmp, --enable-mixed-mode, --disable-setting-flags, --with-mpi=no]
+        conf-flag: [ --disable-openmp, --disable-setting-flags, --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: noaagfdl/fms-ci-rocky-gnu:12.3.0
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
       env:
         TEST_VERBOSE: 1
         DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }} ${{ matrix.io-flag }}"
-        SKIP_TESTS: "test_mpp_domains2.14 test_horiz_interp2.9 test_horiz_interp2.10 test_yaml_parser.5" # temporary till fixes are in
+        SKIP_TESTS: "test_horiz_interp2.[23-24]" # TODO (couldn't reproduce outside CI)
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Prepare GNU autoconf for build
       run: autoreconf -if
     - name: Configure the build

.github/workflows/github_autotools_intel.yml

@@ -1,7 +1,16 @@
 on: pull_request
+
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   intel-autotools:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        io-flag: ["--disable-deprecated-io", "--enable-deprecated-io"]
     container:
       image: intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04
       env:
@@ -44,9 +53,12 @@ jobs:
         ./configure --prefix=/libs
         make -j install && cd
     - name: checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Configure
-      run: autoreconf -if ./configure.ac && ./configure --with-yaml
+      run: |
+        autoreconf -if ./configure.ac
+        export LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH"
+        ./configure --with-yaml ${{ matrix.io-flag }}
     - name: Compile
       run: make -j || make
     - name: Run test suite

.github/workflows/github_cmake_gnu.yml

@@ -2,6 +2,11 @@ name: Build libFMS with cmake
 
 on: [push, pull_request]
 
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -10,14 +15,26 @@ jobs:
         omp-flags: [ -DOPENMP=on, -DOPENMP=off ]
         libyaml-flag: [ "", -DWITH_YAML=on ]
         io-flag: [ "", -DUSE_DEPRECATED_IO=on ]
+        build-type: [ "-DCMAKE_BUILD_TYPE=Release", "-DCMAKE_BUILD_TYPE=Debug" ]
     container:
-      image: noaagfdl/hpc-me.ubuntu-minimal:cmake
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
       env:
-        CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.io-flag  }} ${{ matrix.libyaml-flag }} -D64BIT=on"
+        CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.omp-flags }} ${{ matrix.io-flag  }} ${{ matrix.libyaml-flag }} -D64BIT=on"
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Generate makefiles with CMake
-      run: cmake $CMAKE_FLAGS .
+      run: cmake $CMAKE_FLAGS -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view
     - name: Build the library
       run: make
+    - name: Link with basic executable
+      run: |
+        echo "program test" > test.F90
+        echo "    use fms_mod" >> test.F90
+        echo "    call fms_init" >> test.F90
+        echo "    call fms_end" >> test.F90
+        echo "end program" >> test.F90
+        mpifort -L/opt/view/lib -fopenmp `nf-config --flibs` -Iinclude_r4 -Iinclude_r8 test.F90 libfms_r4.a libfms_r8.a -o test.x
+        touch input.nml
+    - name: Run executable
+      run: ./test.x

.github/workflows/github_coupler_gnu.yml

@@ -1,25 +1,32 @@
 name: Test coupler build
 on: [pull_request]
 
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   coupler-build:
     runs-on: ubuntu-latest
     container:
-      image: ryanmulhall/hpc-me.ubuntu-minimal:coupler
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.github_token }}
       env:
         CC: mpicc
         FC: mpif90
-        CPPFLAGS: '-I/usr/include -Duse_LARGEFILE -DMAXFIELDMETHODS_=500'
-        FCFLAGS: '-fcray-pointer -fdefault-double-8 -fdefault-real-8 -Waliasing -ffree-line-length-none -fno-range-check -I/usr/include'
-        LDFLAGS: '-L/usr/lib'
-        VERBOSE: 1
+        CPPFLAGS: '-I/opt/view/include'
+        FFLAGS: '-fallow-argument-mismatch' # mkmf uses FFLAGS instead of FC
+        LDFLAGS: '-L/opt/view/lib'
     steps:
     - name: Checkout FMS
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         path: FMS
     - name: Checkout FMScoupler
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: 'NOAA-GFDL/FMScoupler'
         path: FMScoupler

.github/workflows/github_doc_site.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Setup repo
         run: | # do autotool's job for substitutes since we don't need a full build environement
           mkdir gen_docs

.github/workflows/github_linter.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Run Lint
         uses: NOAA-GFDL/simple_lint@f5aa1fe976bd4c231db0536ba00cbfdc26708253
         with:

.github/workflows/github_mom_gnu.yml

@@ -0,0 +1,32 @@
+name: Run MOM6 test suite
+
+# runs on PR's or when manually triggered
+on: [workflow_dispatch, pull_request]
+
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+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
+      with:
+        repository: 'NOAA-GFDL/MOM6'
+        submodules: recursive
+    - name: Checkout FMS into MOM build
+      uses: actions/checkout@v4
+      with:
+        path: .testing/deps/fms/src
+    - name: Build FMS and MOM test suite
+      run: make -C .testing -j
+    - name: Run MOM tests
+      run: make -C .testing -j test

.github/workflows/version.yml

@@ -7,7 +7,7 @@ jobs:
   add-dev-to-version:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Append version with dev
       run: sed -i '/20[0-9][0-9]\.[0-9][0-9]/ s/]/-dev]/' configure.ac
     - name: Create pull request