[pull] main from NOAA-GFDL:main

.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

@@ -16,10 +16,7 @@ jobs:
         libyaml-flag: [ "", -DWITH_YAML=on ]
         io-flag: [ "", -DUSE_DEPRECATED_IO=on ]
     container:
-      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:12.3.0
-      credentials:
-        username: ${{ github.actor }}
-        password: ${{ secrets.github_token }}
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
       env:
         CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.io-flag  }} ${{ matrix.libyaml-flag }} -D64BIT=on"
     steps:

.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 +6,99 @@ 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`).
 
+## [2024.01.01] - 2024-05-30
+
+### Known Issues
+- Diag Manager Rewrite:
+	- 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
+- BUILD(HDF5): HDF5 version 1.14.3 generates floating point exceptions, and will cause errors if FMS is built with FPE traps enabled.
+- GCC: version 14.1.0 is unsupported due to a bug with strings that has come up previously in earlier versions. This will be caught by the configure script, but will cause compilation errors if using other build systems.
+
+### Added
+- DIAG_MANAGER: Implements `flush_nc_files` functionality from legacy diag_manager.
+
+### Changed
+- FMS2_IO: Changed `register_unlimited_compressed_axis` to use a collective gather rather than send and recieves to improve efficiency when reading in iceberg restarts.
+
+### Fixed
+- DIAG_MANAGER: Fixes 0 day output frequencies causing error stating a time_step was skipped. Also adds checks to crash if averaged fields have -1 or 0 day frequencies or if mixing averaged and non-averaged fields in the same file.
+- DIAG_MANAGER: Fixes issue with the weight argument not getting passed through to reduction methods.
+- DIAG_MANAGER: Allocation errors when using two empty files.
+- DIAG_MANAGER: `time` and `time_bnds` being larger than expected when running for 1 day and using daily data.
+- DIAG_MANAGER: Allows for mixing static and non-static fields when frequency is 0 days.
+- TESTS: Fixes compile failure with ifort 2024.01 from test_mpp_gatscat.F90.
+
+### Removed
+- DIAG_MANAGER: The `mix_snapshot_average_fields` option is deprecated for the rewritten diag_manager only.
+
+### Tag Commit Hashes
+- 2024.01.01-beta2 c00367fa810960e87610162f0f012c5da724c5a9
+- 2024.01.01-beta1 42f8506512e1b5b43982320f5b9d4ca1ca9cbebd
+
+## [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 option to use multiple data files for one field within data_override in order to use annual data files in yearly runs without having to append/prepend timesteps from previous and next year. With the legacy data_table, filenames  can be set in order and separated with `:` ie. `prev_year.nc:curr_year.nc:next_year.nc`. With the data_table.yaml format, the key `is_multi_file` enables the functionality and `prev_file_name` and `next_file_name` sets the file paths.
+
+- INTERPOLATOR: Adds support for yearly/annual data
+- DATA_OVERRIDE: Adds support for monotonically decreasing arrays for `nearest_index`, `axis_edges`, `horiz_interp`(bilinear), and `data_override` (#1388)
+- 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 2024.01.01
   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

CONTRIBUTING.md

@@ -94,6 +94,33 @@ long-term, portability, and the scope of the impact on the code base. Therefore,
 Modeling Systems does not guarantee that all pull requests will be accepted,
 even if the changes pass the initial testing phases, and are otherwise correct.
 
+## 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 TravisCI and gitlab-CI to run build tests for libFMS.  Users may 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: