Merge branch 'NOAA-GFDL:main' into fixlibfms

Author: rem1776

.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/am4_regression_parallelWorks_intel_tag.yml

@@ -0,0 +1,45 @@
+# '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
+
+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, --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: 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_horiz_interp2.[23-24]" # TODO (couldn't reproduce outside CI)
+        DEBUG_FLAGS: "-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow" # debug compiler flags taken from the mkmf template
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4.2.2
+    - 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
+      if: ${{ matrix.conf-flag != '--with-mpi=no' }}
+    - name: Build the library (without test suite for serial build)
+      run: make
+      if: ${{ matrix.conf-flag == '--with-mpi=no' }}

.github/workflows/build_cmake_gnu.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:
@@ -17,7 +26,7 @@ jobs:
     steps:
     - name: Cache dependencies
       id: cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4.2.0
       with:
         path: /libs
         key: ${{ runner.os }}-intel-libs
@@ -44,9 +53,12 @@ jobs:
         ./configure --prefix=/libs
         make -j install && cd
     - name: checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4.2.2
     - name: Configure
-      run: autoreconf -if ./configure.ac && ./configure --with-yaml
+      run: |
+        autoreconf -if ./configure.ac
+        export LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH"
+        ./configure --with-yaml ${{ matrix.io-flag }}
     - name: Compile
       run: make -j || make
     - name: Run test suite

.github/workflows/build_ubuntu_gnu.yml

@@ -0,0 +1,40 @@
+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
+    strategy:
+      matrix:
+        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: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
+      env:
+        CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.omp-flags }} ${{ matrix.io-flag  }} ${{ matrix.libyaml-flag }} -D64BIT=on"
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4.2.2
+    - name: Generate makefiles with CMake
+      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/coupler.yml

@@ -0,0 +1,34 @@
+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: 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/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@v4.2.2
+      with:
+        path: FMS
+    - name: Checkout FMScoupler
+      uses: actions/checkout@v4.2.2
+      with:
+        repository: 'NOAA-GFDL/FMScoupler'
+        path: FMScoupler
+    - name: Test Null build
+      run: FMScoupler/t/null_model_build.sh --local-fms

.github/workflows/github_autotools_gnu.yml

@@ -7,10 +7,10 @@ on:
   workflow_dispatch:
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4.2.2
       - name: Setup repo
         run: | # do autotool's job for substitutes since we don't need a full build environement
           mkdir gen_docs
@@ -24,7 +24,7 @@ jobs:
           sudo apt -y install doxygen graphviz
           doxygen gen_docs/Doxyfile
       - name: Upload Pages Artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v3.0.1
         with:
           path: 'gen_docs/html'
   deploy:
@@ -45,4 +45,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v4.0.5