Update changelog, version numbers and build info (#873)

Co-authored-by: rem1776 <Ryan.Mulhall@lscamd50-d.gfdl.noaa.gov>

CHANGELOG.md

@@ -5,6 +5,34 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0),
 and this project uses `yyyy.rr[.pp]`, where `yyyy` is the year a patch is released,
 `rr` is a sequential release number (starting from `01`), and an optional two-digit
 sequential patch number (starting from `01`).
+## [2021.04] - 2021-12-23
+### Known Issues
+- GCC 11.1.0 is unsupported due to compilation issues with `select type`. The issue appears to be resolved in later GCC releases
+### Added
+- PARSER: Adds a parser using the libyaml C library to support yaml format input files.
+  Currently implemented in data override and can be enabled with the configure option  `--with-yaml` or with CMake option `-DWITH_YAML`
+- FMS: Adds an interface, `fms_c2f_string`, to convert C strings and C pointers to Fortran strings
+- MPP: Adds a routine `mpp_shift_nest_domains` and a field to `nest_domain_type` to allow for modifying the position of a given nest domain
+- FMS2_IO: Reintroduces the option to flush_nc_files with fms2_io
+### Changed
+- DIAG_MANAGER: Cleans up IO code and replaces any remaining dependencies to mpp_io with fms2_io
+- FMS_IO: Changes to allow for custom paths for namelists, field_table, and the INPUT directory
+- EXCHANGE: Changes real sizes in xgrid and gradient modules to be explicitly r8_kind to prevent runtime issues with mixed precision
+### Deprecated
+- MPP: `get_unit` has been deperecated in favor of the Fortran intrinsic `newunit` and will now generate a warning if used
+### Removed
+- TIME_MANAGER: Removes deprecated array-based gregorian calender calculations that were replaced in 2021.02
+### Fixed
+- DIAG_MANAGER: Fixes issues with 3D diurnal diagnostic output and removes a redundant write_data call
+- TIME_INTERP: Fixes load_record read_data call for 3d variables with fms2_io and eliminates redundant data loading and validity checking for on-grid interpolations.
+- MPP: Fixed a bug with non-blocking domain updates failing on GNU compilers from uninitialized values
+- MPP: Fixed issues with the `mpp_type_free` function causing errors and memory leaks when freeing the `mpp_byte` type
+
+### Tag Commit Hashes
+- 2021.04-alpha1 (e0b998321611f80f2d0c587a13b8c03c173d5520)
+- 2021.04-alpha2 (ab1b0a4cb2beac72d889d94a628e0d02092723b2)
+- 2021.04-alpha3 (90583aeb369831b01296ab4b0e7e6a1b69ed91b1)
+- 2021.04-beta1  (6d179fcdc189070f74d49e0025d072fa304e96d6)
 
 ## [2021.03] - 2021-08-16
 ### Known Issues
@@ -27,6 +55,9 @@ sequential patch number (starting from `01`).
 - MPP: Fixed uninitialized variables for data domains in mpp domains broadcast routines
 - MPP: Minor memory leaks from deallocating domains
 - AXIS_UTILS: Fix PGI related error with string length sizes
+### Tag Commit Hashes
+- 2021.03-alpha1 (87d945d8dba6341f1f56631047ae5d3e5b4ab828)
+- 2021.03-beta1  (6d6ff9595ede12ea0a342ae014442708a27041d2)
 
 ## [2021.02] - 2021-05-20
 ### Added
@@ -74,7 +105,7 @@ sequential patch number (starting from `01`).
 ### Removed
 ### Fixed
 - MPP: Fixed a bug causing mpp_get_UG_domain_tile_pe_inf to seg fault from the incorrect assignment of an optional argument
-- FMS: Fixes issues with FMS unit tests failing from pointer allocations by reworking deallocate_unstruct_pass_type 
+- FMS: Fixes issues with FMS unit tests failing from pointer allocations by reworking deallocate_unstruct_pass_type
 - MPP_IO: Fixes unintentional printing of file attributes
 - An issue with the automake build system causing unnecessary rebuilds of source files
 - Fixes CMake build of the FMS library to install configuration files in the appropriate directories; and for OpenMP dependencies to the private

CMAKE_INSTRUCTIONS.md

@@ -22,6 +22,10 @@ export CC=mpiicc
 export NetCDF_ROOT=`nc-config --prefix`
 ```
 
+### If building with yaml parser (-DWITH_YAML)
+```
+export LIBYAML_ROOT=<your libyaml install directory>
+```
 
 ## 2. Build and install FMS with CMake
 `<prefix>` is the full install directory for FMS provided by user
@@ -47,6 +51,7 @@ The following build options are available:
 -DENABLE_QUAD_PRECISION "Enable compiler definition -DENABLE_QUAD_PRECISION" DEFAULT: ON
 -DGFS_PHYS              "Enable compiler definition -DGFS_PHYS"              DEFAULT:OFF
 -DLARGEFILE             "Enable compiler definition -Duse_LARGEFILE"         DEFAULT:OFF
+-DWITH_YAML             "Enable compiler definition -Duse_yaml"              DEFAULT:OFF
 ```
 
 ## 3. Installation structure

CMakeLists.txt

@@ -23,7 +23,7 @@ cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
 # Define the CMake project
 project(FMS
-  VERSION 2021.03.0
+  VERSION 2021.04.0
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)

INSTALL.md

@@ -9,6 +9,7 @@ The following external libraries are required when building libFMS
 * Fortran 2003 standard compiler
 * Fortran compiler that supports Cray Pointer
 * MPI C and Fortran headers and libraries (optional)
+* Libyaml header and libraries (optional)
 * Linux or Unix style system
 
 ## Supported Compilers
@@ -56,10 +57,13 @@ configure option will require the user to give all required flags.
 
 Run `./configure --help` to see other available configure options.
 
+For more information on building with autotools and build options please see
+ [BUILD_SYSTEM.md](https://github.com/NOAA-GFDL/FMS/blob/main/libFMS/BUILD_SYSTEM.md)
+
 ### CMake
 
 To build using CMake, follow the instructions in
-[CMAKE_INSTRUCTIONS.mk](https://github.com/NOAA-GFDL/FMS/blob/master/CMAKE_INSTRUCTIONS.md).
+[CMAKE_INSTRUCTIONS.mk](https://github.com/NOAA-GFDL/FMS/blob/main/CMAKE_INSTRUCTIONS.md).
 Currently the CMake configuration is the most restrictive build option as the
 compiler flags are immutable.
 

README.md

@@ -63,6 +63,20 @@ infrastructural changes to enable such developments are within the scope of FMS.
 The collaborative software review process of contributed models is therefore an
 essential facet of FMS.
 
+## Dependencies and installation
+
+The following external libraries are required when building libFMS
+
+* NetCDF C and Fortran (77/90) headers and libraries
+* Fortran 2003 standard compiler
+* Fortran compiler that supports Cray Pointer
+* MPI C and Fortran headers and libraries (optional)
+* Libyaml header and libraries (optional)
+* Linux or Unix style system
+
+Please see the [Build and Installation page](http://noaa-gfdl.github.io/FMS/build.html)
+for more information on building with each build system.
+
 ## Documentation
 
 Source code documentation for the FMS code base is available at http://noaa-gfdl.github.io/FMS.

configure.ac

@@ -25,7 +25,7 @@ AC_PREREQ([2.69])
 
 # Initialize with name, version, and support email address.
 AC_INIT([GFDL FMS Library],
-  [2021.04.0-dev],
+  [2021.04.0],
   [gfdl.climate.model.info@noaa.gov],
   [FMS],
   [https://www.gfdl.noaa.gov/fms])

libFMS/BUILD_SYSTEM.md

@@ -80,8 +80,11 @@ The configure script has some standard options, including:
 
 ## FMS Configure Options
 
-Currently there are not FMS specific configure options, but probably
-we will add some.
+Configure build options for FMS:
+* `--with-yaml` : Build with support for yaml input files(requires the libyaml library and headers)
+* `--enable-mixed-mode` : Build in mixed precision mode, with default 4 byte reals and 8 byte real overloads
+* `--disable-setting-flags` : Build without automatically setting flags during configuration
+* `--with-mpi` : Build with MPI support, enabled by default
 
 ## Standard Make Targets
 

libFMS/Makefile.am

@@ -28,7 +28,7 @@ lib_LTLIBRARIES = libFMS.la
 # These linker flags specify libtool version info.
 # See http://www.gnu.org/software/libtool/manual/libtool.html#Libtool-versioning
 # for information regarding incrementing `-version-info`.
-libFMS_la_LDFLAGS = -version-info 9:0:0
+libFMS_la_LDFLAGS = -version-info 10:0:0
 
 # Add the convenience libraries to the FMS library.
 libFMS_la_LIBADD = $(top_builddir)/platform/libplatform.la