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

Author: Jesse Lentz

.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 }}

.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

.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]
 
@@ -15,19 +15,19 @@ jobs:
         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.libyaml-flag }}"
-        EXCLUDE_TESTS: "test_mpp_nesting|test_bc_restart|test_collective_io|test_fms2_io|test_io_with_mask"
+        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 -DOPENMP=on -DUNIT_TESTS=on -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view ..
+        cmake -DOVERSUBSCRIBE_FLAG="--map-by :OVERSUBSCRIBE" $CMAKE_FLAGS -DOPENMP=on -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view -DUNIT_TESTS=on ..
     - name: Build the library
       run: make -C build
     - name: Run the unit tests
@@ -40,10 +40,10 @@ jobs:
         libyaml-flag: [ "", -DWITH_YAML=on ]
         build-type: [ "-DCMAKE_BUILD_TYPE=Release", "-DCMAKE_BUILD_TYPE=Debug" ]
     container:
-      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0-arm
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0-arm-cmake-update
       env:
         CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.libyaml-flag }}"
-        EXCLUDE_TESTS: "test_mpp_nesting|test_bc_restart|test_collective_io|test_fms2_io|test_io_with_mask|test_sat_vapor_pres"
+        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
@@ -52,7 +52,7 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake $CMAKE_FLAGS -DOPENMP=on -DUNIT_TESTS=on -DNetCDF_ROOT=/opt/view -DLIBYAML_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

.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]

CMakeLists.txt

@@ -65,6 +65,9 @@ option(PORTABLE_KINDS        "Enable compiler definition -DPORTABLE_KINDS"
 option(GFS_PHYS              "Enable compiler definition -DGFS_PHYS"              OFF)
 option(WITH_YAML             "Enable compiler definition -Duse_yaml"              OFF)
 
+# Testing-specific options
+set(OVERSUBSCRIBE_FLAG " --oversubscribe " CACHE STRING "Flag for mpirun to use more cores than available")
+
 if(32BIT)
   list(APPEND kinds "r4")
   message(STATUS "Building library with 4-byte real defaults (with mixed precision real support for most modules).")
@@ -586,6 +589,9 @@ 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(OVERSUBSCRIBE "${OVERSUBSCRIBE_FLAG}")
+message(STATUS "Using '${OVERSUBSCRIBE}' flag to oversubscribe ranks in test scripts")
+
 # set the fms library to link tests with based on whats built
 if(NOT kinds)
   set(fmsLibraryName FMS::fms)
@@ -717,6 +723,7 @@ if(UNIT_TESTS)
     test_fms/mpp/test_mpp_domains.F90
     test_fms/mpp/test_mpp.F90
     test_fms/mpp/test_mpp_gatscat.F90
+    test_fms/mpp/test_mpp_pelist_gatscat_gen_ind.F90
     test_fms/mpp/test_mpp_get_ascii_lines.F90
     test_fms/mpp/test_mpp_global_field_ug.F90
     test_fms/mpp/test_mpp_global_sum_ad.F90

configure.ac

@@ -24,7 +24,7 @@ AC_PREREQ([2.69])
 
 # Initialize with name, version, and support email address.
 AC_INIT([GFDL FMS Library],
-  [2026.01.01],
+  [2026.01.01-dev],
   [gfdl.climate.model.info@noaa.gov],
   [FMS],
   [https://www.github.com/NOAA-GFDL/FMS])
@@ -392,9 +392,12 @@ fi
 AC_CHECK_PROGS([MPI_LAUNCHER],[srun aprun mpirun])
 
 # Check if the launcher can oversubscribe the MPI processes
-AS_IF([$MPI_LAUNCHER --oversubscribe hostname >/dev/null 2>&1], \
+AS_IF([$MPI_LAUNCHER --oversubscribe nproc >/dev/null 2>&1], \
       [ AC_SUBST([OVERSUBSCRIBE], [--oversubscribe])])
 
+# newer openmpi versions take a different flag
+AS_IF([$MPI_LAUNCHER --map-by :OVERSUBSCRIBE nproc >/dev/null 2>&1], \
+      [ AC_SUBST([OVERSUBSCRIBE], [--map-by :OVERSUBSCRIBE])])
 
 # Compiler with version information. This consists of the full path
 # name of the compiler and the reported version number.