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ChangeLog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, 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).

[2023.01.01] - 2023-06-06

Changed

  • FMS2_IO: Performance changes for domain_reads_2d and domain_reads_3d:

    • Root pe reads the data
    • Uses mpp_scatter to send the data to the other pes
    • Added unit tests to test all of the domain_read/domain_write interfaces

  • FMS2_IO: Performance changes for compressed_writes_1d/2d/3d

    • Uses mpp_gather to get data for write
    • Added unit tests to test all of the compressed writes interfaces
    • Compressed_writes_4d/5d were unchanged

  • FMS2_IO: Extended mpp_scatter and mpp_gather to work for int8; added a kludge for scatter since the data is assumed to be (x,y,z)

[2023.01] - 2023-04-03

Known Issues

  • If using GCC 10 or higher as well as MPICH, compilation errors will occur unless -fallow-argument-mismatch is included in the Fortran compiler flags(the flag will now be added automatically if building with autotools or CMake).
  • GCC 11.1.0 is unsupported due to compilation issues with select type. The issue is resolved in later GCC releases.
  • When outputting sub-region diagnostics, the current diag_manager does not add "tileX" to the filename when using a cube sphere. This leads to trouble when trying to combine the files and regrid them (if the region is in two different tiles)

Added

  • DIAG_MANAGER: Added code refactored as part of larger diag_manager rewrite for the send_data routines. The refactored code is disabled by default and enabled by setting use_refactored_send to true in the diag_manager_nml, and should mirror current behaviour.
  • FMS2_IO: Added the ability to set deflate_level and shuffle netcdf options in fms2_io_nml. Also added functionality for registering dimensions as unlimited compressed.
  • YAML_PARSER: Added support for emitting multiple tabbed section keys to allow diag manager yaml output

Changed

  • STRING_UTILS: Extended the string interface in fms_string_utils_mod to accept reals of 4 or 8 kind, as well as 1, 2, and 3 dimensional real arrays
  • DIAG_MANAGER: Changed the log_diag_field_info routine to allow for specifying seperator
  • INTERPOLATOR(s): In horiz_interp, amip_interp and interpolator, changed pointers arrays into allocatables

Fixed

  • TRIDIAGONAL: Added OMP directives to prevent race conditions
  • DIAG_MANAGER: Added diag_send_data routine to fix class(*) related compiler issues from the refactor update
  • SAT_VAPOR_PRES_K: Removed implied saves causing issues with class(*) type checking
  • TIME_INTERP: Fixed naming conflicts between module level and local variables
  • YAML_PARSER: Fixed typo in variable name, rename variables to avoid fortran keywords
  • DOCS: Fixed incorrect serial build instructions
  • COMPILER SUPPORT: Fixed compilation errors with Intel's llvm-based compiler and added support for the CMake build. Also fixed mpp_checksum unit test failures with openmpi and nvhpc compilation issues.
  • TIME_MANAGER: Fixed an bug from PR #1169 that was causing answer changes in land models

Tag Commit Hashes

  • 2023.01-beta4 (63626578cb8ed4bed1ce670b88acd6a1ec438e32)
  • 2023.01-beta3 (0ff254e409b74d7d17ab234abe5ecd985967256c)
  • 2023.01-beta2 (74d8e734bd43b0ce043003da74896e5d747afc2f)
  • 2023.01-beta1 (6255971af28381fad22547bdc2c538fc3ea2e8bf)
  • 2023.01-alpha4 (4526cc94a3e19fe8fa151f54b0db432e1fb2f7d0)
  • 2023.01-alpha3 (f0e8cab3d8e58195f7c2663b84fd0bed12fa8b64)
  • 2023.01-alpha2 (91e732473f7cffce070f9ce239f8ffa22c081261)
  • 2023.01-alpha1 (203c8bf464ff26fe0fe39b1451caedd026bbce55)

[2022.04] - 2022-10-13

Known Issues

  • If using GCC 10 or higher as well as MPICH, compilation errors will occur unless -fallow-argument-mismatch is included in the Fortran compiler flags(the flag will now be added automatically if building with autotools or CMake).
  • GCC 11.1.0 is unsupported due to compilation issues with select type. The issue is resolved in later GCC releases.
  • When outputting sub-region diagnostics, the current diag_manager does not add "tileX" to the filename when using a cube sphere. This leads to trouble when trying to combine the files and regrid them (if the region is in two different tiles)

Added

  • FIELD MANAGER: Adds support for reading field tables in the yaml format (field_table.yaml). Yaml input only be used if compiled with -Duse_yaml preprocessor flag, otherwise it will default to previous behaviour. The converter script to convert current field tables to the new format is publicly available here although the conversions will also be done automatically in FRE.
  • FMS2_IO: Adds options to enable data compression and chunking for netcdf output in register_restart_field

Changed

  • BUILD: Improves the configuration check for the MPICH/GCC 10+ argument mismatch bug by replacing it with a m4 compile test

Fixed

  • Compiler Support: allows for compilation via the Cray/HP CCE compilers by fixing string concatenation compilation errors

Tag Commit Hashes

  • 2022.04-beta2 163cb3e434dba05933c3d2151dea5d770758a2f3
  • 2022.04-beta1 1099a2890a06d279df0abe1f383b71279643bcdd
  • 2022.04-alpha4 8036d8d8448b0da8416a76ee0820314da27d5711
  • 2022.04-alpha3 7fafa4f7fb7a89c6f22da7ae19dc4e61a8073451
  • 2022.04-alpha2 0c4b3cc98f4bce5b39c6e9f6404ea32f5bf719e5
  • 2022.04-alpha1 ec57a48aeefb62b475a11cad7e30ebe460fa0d9f

[2022.03] - 2022-08-01

Known Issues

  • If using GCC 10 or higher as well as MPICH, compilation errors will occur unless -fallow-argument-mismatch is included in the Fortran compiler flags(the flag will now be added automatically if building with autotools or CMake).
  • GCC 11.1.0 is unsupported due to compilation issues with select type. The issue is resolved in later GCC releases.
  • When outputting sub-region diagnostics, the current diag_manager does not add "tileX" to the filename when using a cube sphere. This leads to trouble when trying to combine the files and regrid them (if the region is in two different tiles)

Added

  • BUILD: Adds checks to autotools and cmake build files to solve compilation issues with GCC 10 and greater. Also adds a debug build type for CMake to allow for overriding compiler flags, and individual override flags for mixed precision routines.
  • DOCS: Additional information added for building and testing FMS with the build systems; renamed and moved autotools build document.
  • YAML: Adds support for writing yaml files through the fms_yaml_output_mod module

Changed

  • MIXED MODE: Expands support for mixed precision reals to the constants files, diag_manager, sat_vapor_pres, time_manager, and tracer_manager
  • FMS_IO: Increased the character length for restart file names to allow for longer paths

Fixed

  • COUPLER: Fixes global checksum being written to stdout by every core instead of just the root
  • DOCS: Fixed parsing issues with include and header files, adds class diagrams and layout improvements

Tag Commit Hashes

  • 2022.03-alpha1 62588548a5ecbdce7dbf857542ed272f7b2c971f
  • 2022.03-beta1 8a4ad847122c7cc597a1f2626290b46af44b143a

[2022.02] - 2022-04-29

Known Issues

  • If using GCC 10 or higher as well as MPICH, compilation errors will occur unless -fallow-argument-mismatch is included in the Fortran compiler flags
  • GCC 11.1.0 is unsupported due to compilation issues with select type. The issue is resolved in later GCC releases.
  • Current diag_manager does not add "tileX" to the filename when using a cube sphere, which leads to trouble when trying to combine the files and regrid them (if the region is in two different tiles)

Added

  • STRING_UTILS: Adds a module, fms_string_utils_mod, for common string operations throughout FMS
  • LIBFMS: makes recently added routines available through the global fms module
  • CMAKE: Adds build option for position independent code
  • CONSTANTS: Adds macros to load constants for different modeling systems/uses between GFDL, GEOS and GFS. Can be selected in cmake with -DCONSTANTS=<GEOS|GFDL|GFS>

Changed

  • STRING_UTILS: Refactored string routine definitions from fms_mod and fms2_io_mod to be located in fms_string_utils_mod
  • CONSTANTS: Makes fmsconstants.F90 contain the constant definitions, with constants_mod refactored to hold the same values
  • MOSAIC2: changes grid 'version' names and documentation to be more descriptive

Removed

  • FMS_MOD: Removes fms_c.c and fms_c.h files from the fms directory

Fixed

  • FMS2_IO: Fixed bug casuing non-root pe's to fail during the flush_file routine

Tag Commit Hashes

  • 2022.02-alpha1 270c2a4e1a94229a2ae6b1e431c473589b6e15c3
  • 2022.02-alpha2 7768ad1d4941b92ec8f40d34b1b517f5bde3df4e
  • 2022.02-beta1 689579eea6bf7a25c64e8b823551ec588be90984

[2022.01] - 2022-03-25

Known Issues

  • The MPICH MPI implementation is unsupported when used alongside GCC 10 or 11 due to compilation issues with the mixed precision reals. MPICH can still be used to compile FMS with GCC 9 or earlier, or with other compilers.
  • GCC 11.1.0 is unsupported due to compilation issues with select type. The issue appears to be resolved in later GCC releases

Added

  • FMS2_IO: Added a macro MAX_NUM_RESTART_VARS_ to allow the max amount of restart variables to be set at compile time
  • TESTING: Adds a configure option, --enable-code-coverage, to build a code coverage report using intel's codecov
  • AFFINITY: Adds an initialization check to fms_affinity_set, and updates test program with init/end routines
  • FMS2_IO: Adds an optional argument to ignore embedded checksum checks when reading restart files

Changed

  • TESTING: Changes the testing suite scripts for various improvements such improved output, tests with input files, and adding/fixing new tests
  • MPP: Change variable names in mpp to use more inclusive language
  • DOCS: Updates to correct branch name and doxygen guide for functions, and adds CI information page

Fixed

  • Fixes compilation warnings throughout the code, mainly for uninitialized or unused variables
  • Fixed any code not adhering to the projects style guide (mainly line length fixes) so that all future changes can be checked with a linter
  • MOSAIC2: Adds r8_kind casts to calls to C routines in order match precision of doubles
  • TESTS: Fixes crashes in fms2_io tests from namelist read errors

Tag Commit Hashes

  • 2022.01-alpha1 516a5efa681e5ae954c11c0c90677b4444e28ec4
  • 2022.01-beta1 12da12884f8dc8bde47b478c997b0e5d49260a1c
  • 2022.01-alpha2 28e8e3e751a6d5d81b640fb779304329f3edb82d
  • 2022.01-beta2 7b78a73a5ba7acf5d3d932ecfe081e5040e2c778

[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

  • DIAG_MANAGER: 3D diurnal diagnostic variables are not supported in this version of FMS

Added

  • FMS2_IO: Documentation was added for FMS2_io to help users convert from fms_io/mpp_io

Changed

  • FMS2_IO: The error messages in FMS2_io were updated to give more useful information
  • TEST_FMS: The unit tests in mosaic, axis_utils, and time_interp_external were updated to use the FMS2_io version of these routines and are no longer skipped
  • DOCS: The doxygen generated documentation has been improved with more doxygen comments added and a more cohesive layout
  • TEST_FMS: Unit tests for time_manager were updated to use the new get/set_date_gregorian routines

Removed

  • MPP_IO: The namelist variable use_mpp_io was removed from interpolator, amip_interp, diag_manager, topography, xgrid, and data_override
  • MPP_IO: Any remaining fms_io/mpp_io calls from the source and test code were removed
  • FMS: Removes the hardcoded path for input.nml, path now may be specified in the call to fms_init

Fixed

  • MPP: Fixes algorithm used with nested grid updates to properly coalesce x-dir and y-dir pelists for vector quantities
  • CMAKE/AUTOTOOLS: Fixes for minor issues with filenames in both the CMake and autotools build systems
  • MPP: Restored deleted pset functionality needed by GFDL SCM by reinstating mpp_pset.F90
  • 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

  • FMS2_IO: Added fms2_io support for boundary condition restarts. register_restart_region_2d and register_restart_region_3d were added to fms2_io’s register_restart_field interface and read_restart_bc and write_restart_bc subroutines were added to read and write boundary conditions restarts. See test_fms/fms2_io/test_bc_restart.F90 for sample usage.
  • FMS2_IO: Added fms2_io’s version of set_filename_appendix. The string sent in will be appended to the filename of a restart/history file before the *.nc or before *.tile if tile is in the filename.
  • FMS2_IO: Added workarounds to get fms2_io code working with pgi
  • COUPLER_TYPES: Added fms2_io’s version of register_restarts_2/3d and CT_restore_state_2/3d to the coupler_type_register_restarts and coupler_type_restore_state interfaces in coupler_types. The fms_io’s versions were renamed as mpp_io_* and both versions may still be used. See test_fms/coupler/test_coupler_*d.F90 for sample usage.
  • MPP_DOMAINS: Added a subroutine mpp_create_super_grid_domain, which sets the indices of the input domain to match the supergrid domain.
  • MOSAIC2/GRID2: Added a version of grid.F90 that is suitable for use with fms2_io called grid2.F90, and moved it into the mosaic2 folder along with mosaic2.F90
  • FMS_MOD: Added grid_init and grid_end calls for use with grid2.F90
  • TIME_MANAGER: New set_date_gregorian and get_date_gregorian function/subroutine that do not use coded_date and date_to_day arrays are added and set as default. The original get_date_gregorian and set_date_gregorian have been renamed to get_date_gregorian_old and set_date_gregorian_old and can be used by adding old_method=.true. optional argument to set_date and get_date subroutine calls. This is the first step out of three to remove the memory-consuming coded_date and date_to_day arrays from the time_manager_mod.
  • FMS GLOBAL MODULE: Adds a new module (libFMS.F90) to be used as a global import for all supported routines/types/variables within FMS. Also adds a separate module (fmsconstants.F90) to be used for constant values from constants_mod.

Changed

  • FMS2_IO: Adds logic so that the domain decomposition variable attribute is only added if the io_layout is not 1,1.
  • FMS_IO: Moved get_great_circle_algorithm from fms_io to grid2.F90
  • FMS_IO: Moved routines and submodules that were not IO related to fms_mod ###Removed
  • DIAG_MANAGER: Removed the variable attributes _FillValue and missing_value from the time_bounds variable to be cf compliant
  • FV3GFS: Removes the unused fv3gfs directory
  • MOSAIC/GRID: Removed references in grid.F90 to fms_mod(replaced with mpp_mod direct calls)
  • MOSAIC/GRID: Moved mosaic/mosaic2.F90 to mosaic2 folder ###Fixed
  • DIAG_MANAGER: Fixed a bug where the variable type of Time and Time_bounds were different (float vs double) when compiling with 32 bit reals
  • FMS2_IO: Fixed a bug where the code was crashing when you were trying to read/write scalar variables with the domain decomposed fileobj

Tag Commit Hashes

  • 2021.02-alpha1 (1a653fcb86a826251e6c8d0a90db897377acc49e)
  • 2021.02-alpha2 (81a5b6ea2559e2c31edbcab32a3230dfc31287be)
  • 2021.02-beta1 (d7e564adee07073febeb263b89158f768d665689)
  • 2021.02-beta2 (9d55115a331685e4c6e01f2dfb3b770a9f80fa37)

[2021.01] - 2021-03-08

Added

  • MPP: A counter for timers to report how many times a timer section is run
  • MPP: Adds missing interfaces to be consistent with interfaces that use the OVERLOAD and no_8byte_integer macros in order to allow building without MPI
  • MPP: Extends interfaces for read and write routines to include 32-bit and 64-bit real data arrays
  • MPP: Adds unit tests for mpp and mpp_io for all public routines with mixed-precision interfaces and expands on existing tests for mixed-precision
  • Adds an .editorconfig file with the project's preferred editor configuration
  • A variable MODDIR in configure.ac for use in Makefiles to find required Fortran module files
  • Adds FMS description web page as a markdown file

Changed

  • DOCS: Updates various modules to doxygen style comments and makes adjustments to correctly generate doxygen documentation through the build system
  • PLATFORM: changes usage of platform.h to platform_mod and it's associated data types
  • Changes all previous uses of flush subroutine calls to function calls
  • Changes travis CI to Github actions CI and removed all trailing whitespace

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
  • 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

Tag Commit Hashes

  • 2021.01-alpha1 (dbe8a1060fb33167c2d12239484226b40fb01fd0)
  • 2021.01-alpha2 (b94eb18fe8e686c5958cbbacc4cf9130873afc85)
  • 2021.01-beta1 (4dcc9a795d9ba0cc959ebd93dda5be5f8473545c)

[2020.04] - 2020-12-07

Added

  • DIAG_MANAGER: A namelist flag called use_mpp_io if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
  • DIAG_MANAGER: A check is added before a time axis is registered to check if the time axis is registered as a variable
  • DIAG_MANAGER: A unit test was added to test the optional new_file_freq functionality
  • XGRID: A namelist flag called use_mpp_io if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
  • INTERPOLATOR: A namelist flag called use_mpp_io if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
  • AMIP_INTERP: A namelist flag called use_mpp_io if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
  • TOPOGRAPHY: A namelist flag called use_mpp_io if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
  • DATA_OVERRIDE: A namelist flag called use_mpp_bug if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
  • DATA_OVERRIDE: A namelist flag called reproduce_null_char_bug_flag if set to .true. and fms2_io is being used, it will reproduce the mpp_io bug where the axis bounds were calculated instead of read. The default is .false. A unit test was added to test the functionality of get_grid_version_1
  • FMS2_IO: A unit test was added to test the functionality of get_valid and is_valid

Changed

  • The autotools build has been changed to copy each subdirectory module (.mod) files to a common .mod directory located at the top of the source directory. This change simplifies the include path specifications.
  • Use F90 module files for external libraries (MPI and NetCDF) for improved interface checking, thereby removing the reliance on library header include files.
  • FMS2_IO: Changed how nest file names are created to be consistent with mpp_io
  • CMAKE: Changed visibility of FMS OpenMP libraries to private in order to avoid conflicts with model libraries

Removed

  • LIBFMS: The flag -Duse_mpp_io should not be used and will cause a crash
  • LIBFMS: Macros and logic for interfacing to the Flexible File I/O library
  • LIBFMS: Macros for SGI MIPSpro compilers, including: mpp_node function and SGI Irix specific high resolution timer
  • LIBFMS: Macros for IBM AIX compilers
  • LIBFMS: Files in mpp supporting the CRAY SHMEM communications library
  • LIBFMS: Files in mpp for the SGI PSET approach for communication via GSM
  • MPP_IO: removed left over #ifdefs from backwards compatibility changes

Fixed

  • DATA_OVERRIDE: Fixed a bug in get_grid_version_1 where the variable_size calls were not correct
  • FMS2_IO: Fixed a bug in get_valid where the mpp_broadcast calls were done inside if (root_pe) blocks The fms2_io unit tests were modified so they can work with the AOCC compiler
  • XGRID: Fixed a bug in load_xgrid by checking if a dimension exists before calling get_dimension_size to avoid FATAL: NetCDF: Invalid dimension ID or name crashes
  • DIAG_MANAGER: Fixed a bug where files were getting written with redundant time_bounds data
  • CMAKE: Fixed a bug causing the build to fail on latest versions of Ubuntu
  • CMAKE: Fixed a bug that caused the build to fail from incorrect source paths

Tag Commit Hashes

  • 2020.04-alpha1 (2428bb182133b8062432ee1b15974739753ca470)
  • 2020.04-alpha2 (ad9915d83a2f34610cd748fd85889ba1f0f1fc02)
  • 2020.04-alpha3 (e7e48839ab25cc9405abe5d8418e1b6ee6fb2d69)
  • 2020.04-beta1 (6d3ac620423e7ede412e4bb1b36c338775d95193)

[2020.03] - 2020-10-08

Added

  • FMS2_IO: Adds header_buffer_val to the fms2io namelist which sets the netcdf header size in bytes. The default value is 16kb
  • FMS2_IO: Adds netcdf_default_format to the fms2io namelist which allows the user to change the netcdf file type. The default value is 64bit.
  • FMS2_IO: Adds support to read netcdf string global attributes
  • FMS2_IO: Adds an optional argument to open_file, dont_add_res_to_filename, which indicates that the filename should not be modified (default adds .res to restart file name)
  • FMS2_IO: Modifies the register_variable_attribute and register_global_attribute interfaces by adding str_len as an argument. This is a workaround to get fms2io to work with PGI because they don't support class () with len=.
  • FMS2_IO: Adds unit test that tests write_data and read_data when using a domain with a mask table
  • FMS2_IO: Adds fms2io’s version of get_mosaic_tile_grid
  • MPP_IO: Adds -Duse_mpp_io compile option for data_override, interpolator, amip_interp, diag_manager, topography, and xgrid to select using mpp_io instead of fms2_io
  • MPP_INIT: Adds unit tests for routines/functions that are called in mpp_init
  • CMAKE: A cmake build system has been added with a CI build using cmake

Changed

  • FMS2_IO: Improves performance of previous release by gathering the domain decomposed data into one global buffer and doing one write rather than doing multiple reads
  • DATA_OVERRIDE: Changes line in time_interp_external2 to enable 3D overrides

Fixed

  • DATA_OVERRIDE[2]: Fixes a crash when doing ongrid data_override calls with a domain with halos
  • DIAG_MANAGER[2]: Fixes an issue where time_bnds were written incorrectly for the last time stamp
  • DIAG_MANAGER: Regional diagnostics with a mask table now work
  • FMS2_IO: Unit test includes fms2io_init call to improve functionality
  • MPP: BOZ literals that are used in variable declaration are converted to integers using the int() function.
  • MPP_DOMAINS2: Fixed unit test
  • FMS_IO: Changes the logic in get_tile_string to fix bug where tile numbers 9 and 99 produce an inappropriate error

Tag Commit Hashes

  • 2020.03-beta4 (4d38679c1e18e920feb03d69f8a9762eb6a047aa)
  • 2020.03-beta3 (521a15135a99d1f2da7d82f238353945f82ce1dd)
  • 2020.03-beta2 (3dae0dfa405d555ecc09bbd2d60a1be24461f69e)
  • 2020.03-beta1 (f7f1c1c73c1f478a53e84caee6aff2fa840ad086)
  • 2020.03-alpha1 (2dd30b7ca0ac75a4a38b969e4a6d446eb395b4dd)

[2020.02] - 2020-05-01

Added

  • FMS2_IO: An fms2_io_nml namelist has been created. It includes the variable ncchksz. This is the replacement for the environment variable NC_BLKSZ set in model run scripts and used by mpp_io. The default value is 64 KB. Any time a file is opened in fms2_io (nf90_open or nf90_create), the optional argument chunksize=ncchksz is passed to the NetCDF library. NetCDF attempts to use this value to control the blocksize utilized for reads and writes of data from the filesystem.
  • FMS2_IO: Adds support to compute_global_cheksum.inc for real32, assuming the flag -DOVERLOAD_R4 is used when compiling.

Changed

  • MPP_DOMAINS - nesting: The logic supporting nested domains for mosaic grids has been overhauled and extended. FMS now supports multiple nests and telescoping nests (nest embedded within a nest). The requirement for a nest to lie wholly within a single tile has been relaxed and a first-level nest may cross tile boundaries, but may not contain a tile corner. Communications for two-way nesting have also been improved. The 2019 December Public Release and 2020.02 GFDL Release within the [GFDL_atmos_cubed_sphere] (https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere) have been updated and are compatible with this release of FMS.
  • FMS2_IO: The intent of fileobj is changed from (in) to (inout) in netcdf_restore_state_wrap, restore_domain_state, and netcdf_restore_state because the file object type has a pointer that is being reassigned in one of the routines lower in the call stack.

Deprecated

  • MPP_DOMAINS - nesting: The initial nesting implementation is no longer supported. Please see the Changed::MPP_DOMAINS sub-entry under.

Removed

  • GENERAL: References to the macro _ALLOCATABLE have been replaced with “allocatable”, _ALLOCATED has been replaced with “allocated”, and _NULL has been removed. It is now assumed that all compilers support the Fortran 2003 standard. The macros still exist in fms_platforms.h for compatibility within other components.
  • DIAG_MANAGER: “fms_platform.h” is no longer included in any of the diag_manager routines. Instead, fms_platform_mod is now being use-associated where necessary. This fixes an issue for debuggers not providing correct line numbers.

Tag Commit Hashes

  • 2020.02-beta1 (bbc6f8d33cfb75a411bbcd3f8423fa74b8b7cdfd)
  • 2020.02-beta2 (6242941a632f6e261234f3a575e59efa1bfb1b36)
  • 2020.02-beta3 (e6fd03b070eb1ba8ffbca740fd69681ee16d6be7)

[2020.01] - 2020-03-13

Added

  • Adds the modules axis_utils2, mosaic2, and time_interp_external2 that use fms2_io
  • Adds unit tests for thread affinity in test_fms/affinity
  • Autotools unit tests are now run with srun, mpirun, or aprun (whichever is present on your system)
  • fms2_io provides three new derived types, which target the different I/O paradigms used in GFDL GCMs:
    • type(FmsNetcdfFile_t) - This type provides a thin wrapper over the netCDF4 library, but allows the user to assign a “pelist” to the file. If a pelist is assigned, only the first rank on the list directly interacts with the netCDF library, and performs broadcasts to relay the information to the rest of the ranks on the list. This derived type also allows the user to perform “compressed” reads/writes and restart variable “registration” (i.e. the ability to store pointers to user-defined/allocated buffers) and reads/writes in a manner similar to the existing calls in fms_io.
    • type(FmsNetcdfUnstructuredDomainFile_t) - This type extends the FmsNetcdfFile_t type to support “domain-decomposed” reads/writes on a user defined mpp_domains unstructured grid. Users are required to inform the FMS2_io module which dimensions correspond to the unstructured grid using the appropriate register_axis call before any domain-decomposed reads/writes can be performed.
    • type(FmsNetcdfDomainFile_t) - This type extends the FmsNetcdfFile_t type to support “domain-decomposed” reads/writes on a user-defined mpp_domains two-dimensional lon-lat or cubed-sphere grid. Users are required to inform the fms2_io module which dimensions (‘x’ or ‘y’) correspond to the two-dimensional grid using the appropriate register_axis calls before any domain-decomposed reads/writes can be performed.
  • fms2_io requires the user to manage objects of the types described above. Calls to open_file (close_file) act as constructors (destructors) for each of the objects, and must be explicitly made by the user. Each object must be constructed before any I/O can be performed. Examples describing how to use these new types are available in test_fms/fms2_io
  • fms2_io treats _FillValue attributes as valid_max or valid_min range specifiers if none of valid_range, valid_min, and valid_max are specified as described in these netcdf conventions

Changed

  • The diag_manager IO is handled by fms2_io instead of mpp_io. Default behavior assumes that the mpp_io namelist variable is set to cf_compliant = .true.
  • The user must specify the diagnostic attributes that they want to write to the output files. Example: If there is no units attribute, then the variable metadata will not include units, and it will not automatically add units = “none”.
  • Calls to register_diag_axis for an X or Y axis that is shifted from the CENTER position need to include the optional argument domain_position and should be equal to EAST or NORTH based on the position relative to the domain. EAST and NORTH are exposed through diag_manager_mod.
  • Changed the handling of average_T and time_bnds variables so that they are set to values that are sent in and are not manipulated as was the case in mpp_io.
  • interpolator, xgrid, data_override, and amip_interp now call fms2_io routines
  • Support for enabling/disabling quad-precision (used in certain calculations) has been changed to a hard on/off switch. Default behavior is quad-precision disabled. To enable, add the following CPP macro -DENABLE_QUAD_PRECISION. This change was necessary to remove guessing at the proper setting via a mix of compiler vendor and system-defined environment variables which resulted in different behaviors on machines unbeknownst to the user.

Deprecated

  • fms2_io does NOT use the scale_factor, add_offset, or other attributes to manipulate the data. The variable/data is returned to the caller as it appears in the file. All post-read data manipulations should be handled by the caller.

Removed

  • Removes the use of bats when running unit tests

Tag Commit Hashes

  • 2020.01-alpha1 (09dc8e9e0f1c852e9e9190834176d16943cd3729)
  • 2020.01-beta1 (e1c0d9d01d844938adc0d18afa09532f336bcdfe)
  • 2020.01-beta2 (b68de5382a5ce631ddd6167de8d85f7c9ae54351)

[2019.01] - 2019-11-26

Added

  • switch from "city" versioning style to yyyy.<2_digit_version_number>[.<2-digit-patch number>] style
  • main development branch is master instead of dev/master
  • affinity handling moved to the affinity directory
  • support for building with autotools
  • fms_platform.h contains directives that support building on macOS
  • unit and build tests are available in the test_fms directory
  • updated fv3gfs/makefile for use with current EMC build system

Fixed

  • Fixed time_interp_missing parameter in time_interp/time_interp_external.F90 to be within range when compiled in mixed-mode.
  • reverted QUAD_PRECISION cpp macro behavior to pre-Xanadu behavior in include/fms_platform.h
  • Fixed a GNU compiler issue with the logical check to set the netCDF fill value in mpp_io_write by separating the logical .AND. into nested if statements.