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CHANGELOG.md

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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).

[2021.02] - 2021-05-19

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.