Merge branch 'main' into commit-doc

.github/CODEOWNERS

@@ -34,15 +34,13 @@ 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
 
 # Specific component directories
@@ -52,18 +50,16 @@ 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
-
-/fv3gfs/          @bensonr
+/diag_manager            @thomas-robinson
+/test_fms/diag_manager/  @thomas-robinson
 
 /fms/             @thomas-robinson @rem1776
 /test_fms/fms/    @thomas-robinson @rem1776
-/fms2/            @uramirez8707 @GFDL-Eric
-/test_fms/fms2/   @uramirez8707 @GFDL-Eric
+/fms2/            @uramirez8707
+/test_fms/fms2/   @uramirez8707
 
 /libFMS/           @thomas-robinson @rem1776
 

.github/workflows/github_autotools_gnu.yml

@@ -14,17 +14,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        conf-flag: [ --disable-openmp, --disable-setting-flags, --with-mpi=no, --disable-r8-defaults]
+        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_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@v4

.github/workflows/github_cmake_gnu.yml

@@ -16,13 +16,24 @@ jobs:
         libyaml-flag: [ "", -DWITH_YAML=on ]
         io-flag: [ "", -DUSE_DEPRECATED_IO=on ]
     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"
     steps:
     - name: Checkout code
       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

@@ -10,7 +10,7 @@ jobs:
   coupler-build:
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:12.3.0
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
       credentials:
         username: ${{ github.actor }}
         password: ${{ secrets.github_token }}

.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

CHANGELOG.md

@@ -6,6 +6,61 @@ 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`).
 
+## [2024.01] - 2024-05-03
+
+### Known Issues
+- Diag Manager Rewrite:
+	- If two empty files are present in the diag_table.yaml file the code will crash with a allocation error (#1506)
+	- Setting an output frequency of '0 days' does not work as expected and may cause an error stating a time_step has been skipped (#1502)
+	- The `flush_nc_files` and `mix_snapshot_average_fields` nml options are not yet functional. The `mix_snapshot_average_fields` option is planned to be deprecated (for the rewritten diag_manager only).
+	- Expected output file changes:
+		- If the model run time is less than the output frequency, old diag_manager would write a specific value (9.96921e+36). The new diag_manager will not, so only fill values will be present.
+		- A `scalar_axis` dimension will not be added to scalar variables
+		- The `average_*` variables will no longer be added as they are non-standard conventions
+ 		- Attributes added via `diag_field_add_attributes` in the old code were saved as `NF90_FLOAT` regardless of precision, but will now be written as the precision that is passed in
+		- Subregional output will have a global attribute `is_subregional = True` set for non-global history files.
+		- The `grid_type` and `grid_tile` global attributes will no longer be added for all files, and some differences may be seen in the exact order of the `associated_files` attribute
+
+- DIAG_MANAGER: When using the `do_diag_field_log` nml option, the output log file may be ovewritten if using a multiple root pe's
+- TESTS: `test_mpp_gatscat.F90` fails to compile with the Intel Oneapi 2024.01's version of ifort
+- BUILD(HDF5): HDF5 version 1.14.3 generates floating point exceptions, and will cause errors if FMS is built with FPE traps enabled.
+
+### Added
+- DIAG_MANAGER: The diag manager has been rewritten with a object oriented design. The old diag_manager code has been kept intact and will be used by default. The rewritten diag manager can be enabled via `use_modern_diag = .true.` to your `diag_manager_nml`. New features include:
+	- Self-describing YAML formatting for diag_table's
+	- Allows 4d variables
+  - Support defining subregions with indices
+  - More flexibility when adding metadata and defining output frequency
+- FMS2_IO: Adds support for collective parallel reads to improve model startup time. The collective reads are disabled by default and enabled via the `use_collective` flag in `netcdf_io_mod`.
+- DATA_OVERRIDE: Adds multifile support for using 3 input netcdf files instead of one. Three keys have been added to the data_table: `is_multi_file` to be set to true to enable the feature, as well as `prev_file_name` and `next_file_name` to set to the names of the additional files.
+- INTERPOLATOR: Adds support for yearly/annual data
+- DATA_OVERRIDE: Adds support for monotonically increasing/decreasing arrays
+- DOCS: Add documentation for the exchange grid (xgrid_mod) and update the contribution guide to add a section on code reviews
+- MPP: MPI sub-communicators for domains are now accessible via `mpp_get_domain_tile_commid` and `mpp_get_domain_commid` in `mpp_domains_mod`
+
+### Changed
+- DATA_OVERRIDE: Changes behavior to crash if both data_table and data_table.yaml are present and adds error checking when reading in yaml files
+- FIELD_MANAGER: Changes behavior to crash if both field_table and field_table.yaml are present as well as adds a namelist flag (`use_field_table_yaml`) to enable support for the yaml input.
+
+### Fixed
+- DATA_OVERRIDE: Fixes allocation error with scalar routine and replaces pointers with allocatables
+- INTERPOLATOR: Increase max string size for file paths
+- AXIS_UTILS: Improves performance of `nearest_index` routine
+- CMAKE: Fixes macOS linking issues with OpenMP
+
+### Tag Commit Hashes
+- 2024.01-beta5  d3bab5a84b6a51eddd46ab6fb65eaa532830c6c7
+- 2024.01-beta4  ac363ddfd3075637cecae30ddfbae7a78751197b
+- 2024.01-alpha6 2ace94564a08aec4d7ab7eca0e57c0289e52d5b1
+- 2024.01-alpha5 5ed0bd373cc59a9681052fa837cb83a67169d102
+- 2024.01-alpha4 8dd90d72b58f0de3632dc62920f8adfb996b2265
+- 2024.01-beta3  f71405a075102aef42f5811dc09e239ddd002637
+- 2024.01-beta2  bb6de937f70a08a440f5e63b8553b047c1921509
+- 2024.01-beta1  913f8aaecca374d5e10280056de862d5e4a7a668
+- 2024.01-alpha3 085c6bfc945a6f1c586b842ca6268fca442884d8
+- 2024.01-alpha2 38bfde30e1cb8bf5222410a9c37e71529567bf69
+- 2024.01-alpha1 ac0d086296ea8b9196552463655cb9a848db39fe
+
 ## [2023.04] - 2023-12-04
 ### Known Issues
 - GCC 9 and below as well as GCC 11.1.0 are unsupported due to compilation issues. See prior releases for more details.

CMakeLists.txt

@@ -26,7 +26,7 @@ set(CMAKE_Fortran_FLAGS_DEBUG)
 
 # Define the CMake project
 project(FMS
-  VERSION 2023.04.0
+  VERSION 2024.01.0
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)
@@ -125,11 +125,20 @@ list(APPEND fms_fortran_src_files
   diag_manager/diag_output.F90
   diag_manager/diag_table.F90
   diag_manager/diag_util.F90
+  diag_manager/fms_diag_time_utils.F90
+  diag_manager/fms_diag_object.F90
+  diag_manager/fms_diag_yaml.F90
+  diag_manager/fms_diag_file_object.F90
+  diag_manager/fms_diag_field_object.F90
+  diag_manager/fms_diag_axis_object.F90
+  diag_manager/fms_diag_output_buffer.F90
+  diag_manager/fms_diag_input_buffer.F90
   diag_manager/fms_diag_time_reduction.F90
   diag_manager/fms_diag_outfield.F90
   diag_manager/fms_diag_elem_weight_procs.F90
   diag_manager/fms_diag_fieldbuff_update.F90
   diag_manager/fms_diag_bbox.F90
+  diag_manager/fms_diag_reduction_methods.F90
   drifters/cloud_interpolator.F90
   drifters/drifters.F90
   drifters/drifters_comm.F90
@@ -345,9 +354,12 @@ foreach(kind ${kinds})
     target_link_libraries(${libTgt}_f PRIVATE OpenMP::OpenMP_Fortran)
   endif()
 
-  # Check if gnu 10 or higher with mpich
+  # Check if gnu 10 or higher
+  # this should only be needed with mpich, but wasn't able to find a good way to find the MPI flavor consistently
   if ( CMAKE_Fortran_COMPILER_VERSION MATCHES "1[0-9]\.[0-9]*\.[0-9]*" AND CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
-    if(MPI_C_COMPILER MATCHES ".*mpich.*" )
+    include(CheckFortranCompilerFlag)
+    check_fortran_compiler_flag("-fallow-argument-mismatch" _arg_mismatch_flag)
+    if(_arg_mismatch_flag)
       message(STATUS "Adding -fallow-argument-mismatch flag to compile with GCC >=10 and MPICH")
       target_compile_options(${libTgt}_f PRIVATE "-fallow-argument-mismatch;-w")
     endif()

CONTRIBUTING.md

@@ -103,6 +103,33 @@ Descriptive commit messages within PR’s should still be used, and some project
 The commit message on the main branch must follow the guidelines of [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/), meaning it includes a ‘type’ prefix (ie. usually fix or feat(ure)) and a footer for any API-breaking changes.
 Additionally, commits should include the number of the pull request in parentheses (this is automatically added on github) to allow easier tracking of each commit.
 
+## Reviewing Pull Requests
+
+When reviewing a pull request, members of MSD should look for the following:
+
+- Design
+  - Does the code change belong in the FMS library or does it better belong elsewhere such as a component repository or the FMScoupler?
+  - Could existing routines/modules be utilized to reduce redundancy?
+  - Temporary changes/fixes meant to be removed should be avoided whenever possible
+- Functionality
+  - Does this PR do what is intended (and stated)
+  - Are the changes good for both end-users and developers?
+  - Will the code change impact existing end-users needlessly?
+- Complexity
+  - Are the changes easily understood by the reader / reviewer?
+- Testing
+  - Code changes should include a test program or a modification to a test program to ensure the code is covered by the test suite
+- Comments
+  - Inline comments for complex code segments or intricacies to make the purpose of the code reasonably clear
+- Style and Consistency
+  - Code should follow the syle guide in general, but should also be consistent to the file the change is made in
+- Documentation
+  - If a PR changes the behaviour or instructions, accompanying documentation should also change
+- Thoroughness
+  - Reviews should be done line by line, and the surrounding context/file should be taken into account
+
+Comments on pull requests should be courteous and constructive, giving useful feedback and explanations for why changes should be made. See the [code of conduct](CODE_OF_CONDUCT.md) for more information.
+
 ## Tests
 
 FMS uses github actions workflows to run build, runtime, and code linting tests for libFMS.  Users may be required to create

Makefile.am

@@ -45,6 +45,7 @@ SUBDIRS = \
   mosaic2 \
   fms \
   parser \
+  string_utils \
   affinity \
   mosaic \
   time_manager \
@@ -125,10 +126,10 @@ check-code-coverage: check
 .PHONY: check-code-coverage
 
 clean-local:
-	-rm -rf .mods coverage-data coverage-report
+	-rm -rf .mods coverage-data coverage-report test.nc
 else
 clean-local:
-	-rm -rf .mods
+	-rm -rf .mods test.nc
 endif
 
 install-data-hook:

cmake/Findlibyaml.cmake

@@ -3,8 +3,8 @@
 #    LIBYAML_INCLUDE_DIR
 #    LIBYAML_LIBRARIES
 
-FIND_PATH(LIBYAML_INCLUDE_DIR  NAMES yaml.h  PATHS $ENV{LIBYAML_ROOT}/include )
-FIND_LIBRARY(LIBYAML_LIBRARIES NAMES yaml    PATHS $ENV{LIBYAML_ROOT}/lib )
+FIND_PATH(LIBYAML_INCLUDE_DIR  NAMES yaml.h  PATHS ${LIBYAML_ROOT}/include $ENV{LIBYAML_ROOT}/include )
+FIND_LIBRARY(LIBYAML_LIBRARIES NAMES yaml    PATHS ${LIBYAML_ROOT}/lib     $ENV{LIBYAML_ROOT}/lib )
 if(NOT LIBYAML_INCLUDE_DIR OR NOT LIBYAML_LIBRARIES)
   message(SEND_ERROR "libyaml library/include file not found, set LIBYAML_ROOT")
 endif()