Merge branch 'main' into oneapi-broken

Author: rem1776

.github/CODEOWNERS

@@ -25,43 +25,4 @@
 # 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.
-*          @uramirez8707 @bensonr @rem1776 @vithikashah001
-
-# GNU autotools files
-Makefile.am      @uramirez8707 @rem1776
-/configure.ac    @uramirez8707 @rem1776
-/m4/             @uramirez8707 @rem1776
-*.m4             @uramirez8707 @rem1776
-
-# cmake files
-CM*              @mlee03 @rem1776 @vithikashah001
-cmake            @mlee03 @rem1776 @vithikashah001
-
-# Files specific to GitHub or GitLab
-/.github/        @rem1776 @vithikashah001
-
-# Testing files
-/test_fms/       @uramirez8707 @mlee03 @bensonr @rem1776 @vithikashah001
-
-# Specific component directories
-/affinity/          @bensonr
-/test_fms/affinity/ @bensonr @rem1776
-
-/block_control/          @bensonr
-/test_fms/block_control/ @bensonr @rem1776
-
-#/data_override/ Currently no code owner
-/test_fms/data_override/ @rem1776
-
-/diag_manager            @uramirez8707
-/test_fms/diag_manager/  @uramirez8707
-
-/fms/             @uramirez8707 @rem1776
-/test_fms/fms/    @uramirez8707 @rem1776
-/fms2/            @uramirez8707
-/test_fms/fms2/   @uramirez8707
-
-/libFMS/           @uramirez8707 @rem1776
-
-/mpp/              @uramirez8707 @bensonr
-/test_fms/mpp/     @uramirez8707 @bensonr @rem1776
+*          @uramirez8707 @bensonr @rem1776 @vithikashah001

AUTOTOOLS_INSTRUCTIONS.md

@@ -11,7 +11,7 @@ something like:
 
 ./configure && make check install
 
-The configure step queries the system about many things, and contructs
+The configure step queries the system about many things, and constructs
 makefiles.
 
 The make step uses the generated Makefiles to build, test, and install
@@ -33,11 +33,11 @@ been added to .gitignore and should never be added to the repo.
 
 Previously, everyone built FMS by checking out code from git. However,
 with the new build system, only those who want to contribute to the
-code base need check out the code from git.
+code base need to check out the code from git.
 
 ## As an FMS Developer
 
-All FMS developers will need a reasobably reacent version of tools
+All FMS developers will need a reasonably recent version of tools
 autoconf, automake, and libtool. These are available on package
 management systems. (Ex. yum install automake autoconf libtool).
 
@@ -51,7 +51,7 @@ The process of building FMS from the repo is:
 ## As an FMS User
 
 Users start with a tarball, not the git repo. They do not have to have
-any of the autotools installed. Thier build process is:
+any of the autotools installed. Their build process is:
 
 1. Unpack the tarball and cd into the directory.
 2. Run ./configure --prefix=/my/installdir

CHANGELOG.md

@@ -6,6 +6,41 @@ 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`).
 
+## [2025.03] - 2025-06-24
+
+### Known Issues
+- INTEL: Oneapi 2025.1 is currently unsupported due to an internal compiler error. The `-check uninit` flag for intel's LLVM compilers(ifx/icx) is also unsupported, see prior release for more information.
+- Diag Manager Rewrite: See [below](#20240102---2024-06-14) for known output file differences regarding the new diag manager. The new diag_manager is disabled by default, so these differences will only be present if `use_modern_diag` is set to true in the `diag_manager_nml`.
+- BUILD(HDF5): HDF5 version 1.14.3 generates floating point exceptions, and will cause errors if FMS is built with FPE traps enabled. FPE traps are turned on when using the debug target in mkmf.
+- 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
+- LICENSE: added notice about the change to Apache license. (#1685)
+- DIAG_MANAGER: added standard name to diag manifest yaml (#1692)
+- FMS2_IO: added netcdf chunksizes argument to register_field routines (#1696) 
+- DIAG_MANAGER: added more robust diag manager tests for when outputting data at every time step (#1688)
+- FM2_IO: added a test for collective netcdf mpi io (#1647)
+
+### Changed
+- DOCS: style guide update (#1642)
+- DOCS: updates to contributing guide to reflect modern FMS practices (#1708)
+- DOCS: fixed typos throughout the code (#1703)
+- DATA_OVERRIDE: simplify argument lists of subroutines in get_grid_version_mod (#1514)
+
+### Fixed
+- DIAG_MANAGER: fixed the time variable in instantaneous outputs from diag_manager in both  openmp and non-openmp cases (#1690)
+- DIAG_MANAGER: fixed number of time levels in diag manifest yaml for subregional files. (#1698)
+- LIBFMS: fixed missed aliases in libFMS file (#1303)
+- DIAG_MANAGER: fixed new file and file duration in MODERN_DIAG_MANAGER (#1705)
+
+### Removed
+- FMS_IO/MPP_IO: removed fms_io/mpp_io modules (#1669)
+- AMIP_INTERP: removed the sst_anom and sst_ncep varaibles (#1695)
+
+### Tag Commit Hashes
+- 2025.03-beta1  96e97c0e271167dd42700b5ed28fb1fe85d7ecce
+- 2025.03-alpha1 44f182dc459c6a60d3b3f4257cf379c8bd71e797
+
 ## [2025.02] - 2025-04-28
 
 ### Known Issues
@@ -156,7 +191,7 @@ sequential patch number (starting from `01`).
 - COUPLER: Adds optional argument to `coupler_types_send_data` routine that contains the return statuses for any calls made to the diag_manager's `send_data` routine. (#1530)
 - MPP: Adds a separate error log file `warnfile.<root pe num>.out` that only holds output from any `mpp_error` calls made during a run (#1544)
 ### Changed
-- DIAG_MANAGER: The `diag_field_log.out` output file of all registered fields will now include the PE number of the root PE at the time of writing (ie. diag_field_log.out.0). This is to prevent overwritting the file in cases where the root PE may change. (#1497)
+- DIAG_MANAGER: The `diag_field_log.out` output file of all registered fields will now include the PE number of the root PE at the time of writing (ie. diag_field_log.out.0). This is to prevent overwriting the file in cases where the root PE may change. (#1497)
 
 ### Fixed
 - CMAKE: Fixes real kind flags being overwritten when using the Debug release type (#1532)
@@ -208,7 +243,7 @@ sequential patch number (starting from `01`).
 - 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.
+- FMS2_IO: Changed `register_unlimited_compressed_axis` to use a collective gather rather than send and receives 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.

CMakeLists.txt

@@ -23,7 +23,7 @@ cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
 # Define the CMake project
 project(FMS
-  VERSION 2025.02.0
+  VERSION 2025.03.0
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)
@@ -284,6 +284,12 @@ endif()
 # Obtain compiler-specific flags
 include(fms_compiler_flags)
 
+# If netCDF was not built with HDF5 parallel I/O features, set up the macro -DNO_NC_PARALLEL4
+IF(NOT NetCDF_PARALLEL)
+  MESSAGE(WARNING "netCDF was not build with HDF5 parallel I/O features, so collective netcdf io is not allowed")
+  list(APPEND fms_defs NO_NC_PARALLEL4)
+ENDIF()
+
 foreach(kind ${kinds})
 
   set(libTgt fms_${kind})

CONTRIBUTING.md

@@ -2,9 +2,9 @@
 
 Thank you for taking time to contribute.
 
-libFMS is a software framework for supporting the efficient development,
+libFMS is a software framework for supporting the **seamless** development,
 construction, execution, and scientific interpretation of atmospheric, oceanic,
-and climate system models.
+and land models across timescales.
 
 Contributions to this project are released to the public under the
 [projects open source license](LICENSE.md).
@@ -123,7 +123,7 @@ Comments on pull requests should be courteous and constructive, giving useful fe
 
 ## Tests
 
-FMS uses TravisCI and gitlab-CI to run build tests for libFMS.  Users may create
+FMS uses github actons to run build tests for libFMS.  Users should create
 unit tests, code coverage tests, and regression tests for new and existing code
 in yaml (.yml) files.  Github provides a guide
 (https://help.github.com/en/articles/about-continuous-integration) for
@@ -138,7 +138,8 @@ Code updates should follow the coding style for the project, contained in
 Releases will be tagged using the format `yyyy.rr[.pp]`, where `yyyy` is the
 4-digit year, `rr` is the 2-digit release number, and `pp` is the 2-digit patch
 number.  Preliminary releases mean for testing (i.e., code that is still under
-development) will be marked `yyyy.rr.alpha.pp` or `yyyy.rr.beta.pp`. Alpha tags
+development) will be marked `yyyy.rr-alpha#` or `yyyy.rr-beta#` where `#` is
+the incremented number of the testing tag. Alpha tags
 mark code updates that are intended for developers to include in their baseline
 regression tests to determine whether the code contains bugs not encountered
 during baseline testing. Beta tags are intended for a wider audience of

README.md

@@ -4,7 +4,7 @@ FMS will switch to the
 [Apache License, Version 2.0](https://www.apache.org/licenses/LICENSE-2.0.txt)
 with the 2025.04 or 2026.01 release.  Please refer to
 [issue 1683 on changing the license](https://github.com/NOAA-GFDL/FMS/issues/1683)
-to participate in or follow any dicussion on the topic.
+to participate in or follow any discussion on the topic.
 
 # Modeling Framework: Flexible Modeling System (FMS)
 
@@ -110,7 +110,7 @@ Compilers used in our Github continuous integration testing are in bold.
 Source code documentation for the FMS code base is available at http://noaa-gfdl.github.io/FMS.
 The documentation is generated by doxygen and updated upon releases, and a copy of the site
 can be obtained through the `gh-pages` branch or generated manually with
-`./configure --enable-docs && make -C docs`. For more information on documentating the code
+`./configure --enable-docs && make -C docs`. For more information on documenting the code
 with doxygen please see the
 [documentation style guide](http://noaa-gfdl.github.io/FMS/md_docs_doxygenGuide.html).
 

TESTING.md

@@ -24,7 +24,7 @@ This will compile any code not already compiled and then proceed to run the test
 ### Debugging Output and Test Options
 
 Setting the environment variable TEST_VERBOSE will direct output to stdout as the test runs, while setting VERBOSE will only output on failure.
-Logs are created for each test as well, with the name \<test script name\>.log in it's corresponding test_fms/ directory.
+Logs are created for each test as well, with the name \<test script name\>.log in its corresponding test_fms/ directory.
 
 To run an individual test:
 ```
@@ -43,4 +43,4 @@ for the build system:
      If enabled a coverage report can be generated with `make check-code-coverage`
 -    `--enable-test-input=/path/to/input` turns on test scripts that require input netcdf files (interpolator, xgrid, data_override).
      This option is mainly used internally and in automated testing since we do not host the input data publicly.
--    `--with-yaml` compile with yaml input and enable it's associated tests
+-    `--with-yaml` compile with yaml input and enable its associated tests

configure.ac

@@ -25,7 +25,7 @@ AC_PREREQ([2.69])
 
 # Initialize with name, version, and support email address.
 AC_INIT([GFDL FMS Library],
-  [2025.02-dev],
+  [2025.03-dev],
   [[email protected]],
   [FMS],
   [https://www.github.com/NOAA-GFDL/FMS])
@@ -447,6 +447,22 @@ else
   AC_MSG_RESULT([no])
 fi
 
+AC_MSG_CHECKING([if netCDF was built with HDF5 parallel I/O features])
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[
+#include <netcdf_meta.h>
+#if !defined(NC_HAS_PARALLEL4) || NC_HAS_PARALLEL4 == 0
+      choke me
+#endif]])], [nc_has_parallel4=yes], [nc_has_parallel4=no])
+AC_MSG_RESULT([$nc_has_parallel4])
+
+if test $nc_has_parallel4 = no; then
+  AC_MSG_WARN(netCDF was not build with HDF5 parallel I/O features, so collective netcdf io is not allowed)
+  AC_DEFINE([NO_NC_PARALLEL4], [1], [HDF5 parallel I/O features not allowed])
+  AM_CONDITIONAL([SKIP_PARALLEL_TEST], true)
+else
+  AM_CONDITIONAL([SKIP_PARALLEL_TEST], false)
+fi
+
 #####
 # Create output variables from various
 # shell variables, for use in generating

coupler/atmos_ocean_fluxes.F90

@@ -737,7 +737,7 @@ subroutine atmos_ocean_fluxes_init(gas_fluxes, gas_fields_atm, gas_fields_ice, v
         gas_fields_atm%bc(n)%pass_through_ice = gas_fluxes%bc(n)%pass_through_ice
         gas_fields_ice%bc(n)%pass_through_ice = gas_fluxes%bc(n)%pass_through_ice
       !! mixed precision support
-      !! if use_r4_kind is present and true will intialize to the r4_kind type
+      !! if use_r4_kind is present and true will initialize to the r4_kind type
       else
         ! Save and check the flux_type.
         gas_fluxes%bc_r4(n)%flux_type = fm_util_get_string('flux_type', scalar = .true.)