fix: add 2025.01.02 patch commits to main (#1659)

Author: rem1776

CHANGELOG.md

@@ -6,6 +6,32 @@ 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`).
 
+## [2025.01.02] - 2025-03-06
+
+### Known Issues
+- 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 this 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.
+- INTEL: The `-check uninit` flag for the Intel Oneapi Fortran compiler (ifx) is unsupported due to a bug causing false positives when using external libraries. If using the `-check all` flag, `-check all,nouninit` should be used instead.
+
+### Changed
+- DIAG_MANAGER: Change name of yaml output file to include the root PE number at the end in order to prevent overwrites (#1654)
+
+## [2025.01.01] - 2025-02-26
+
+### Known Issues
+- 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 this 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.
+- INTEL: The `-check uninit` flag for the Intel Oneapi Fortran compiler (ifx) is unsupported due to a bug causing false positives when using external libraries. If using the `-check all` flag, `-check all,nouninit` should be used instead.
+
+### Changed
+- DIAG_MANAGER: Change name of yaml output file from "diag_out.yaml" to "diag_manifest.yaml" (#1646)
+
+### Added
+- DIAG_MANAGER: Added field to the yaml output file to specify the number of time levels written to a given file (#1648)
+
+
 ## [2025.01] - 2025-01-30
 
 ### Known Issues

CMakeLists.txt

@@ -23,7 +23,7 @@ cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
 # Define the CMake project
 project(FMS
-  VERSION 2025.01.0
+  VERSION 2025.01.02
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)

configure.ac

@@ -25,7 +25,7 @@ AC_PREREQ([2.69])
 
 # Initialize with name, version, and support email address.
 AC_INIT([GFDL FMS Library],
-  [2025.01-dev],
+  [2025.01.02-dev],
   [[email protected]],
   [FMS],
   [https://www.github.com/NOAA-GFDL/FMS])

diag_manager/diag_manager.F90

@@ -3518,6 +3518,7 @@ LOGICAL FUNCTION send_data_4d(diag_field_id, field, time, is_in, js_in, ks_in, &
     call fms_diag_object%fms_diag_accept_data(diag_field_id, field, mask_local, rmask_local, &
                                                           time, is_in, js_in, ks_in, ie_in, je_in, ke_in, weight, &
                                                           err_msg)
+    send_data_4d = .true.
 
     if (present(err_msg)) then
       if (err_msg .ne. "") then

diag_manager/fms_diag_file_object.F90

@@ -99,6 +99,7 @@ module fms_diag_file_object_mod
   logical, allocatable :: time_ops !< .True. if file contains variables that are time_min, time_max, time_average,
                                    !! or time_sum
   integer :: unlim_dimension_level !< The unlimited dimension level currently being written
+  integer :: num_time_levels !< The number of time levels that were actually written to the file
   logical :: data_has_been_written !< .True. if data has been written for the current unlimited dimension level
   logical :: is_static !< .True. if the frequency is -1
   integer :: nz_subaxis !< The number of Z axis currently added to the file
@@ -194,6 +195,7 @@ module fms_diag_file_object_mod
   procedure :: init_unlim_dim
   procedure :: update_current_new_file_freq_index
   procedure :: get_unlim_dimension_level
+  procedure :: get_num_time_levels
   procedure :: flush_diag_file
   procedure :: get_next_output
   procedure :: get_next_next_output
@@ -296,6 +298,7 @@ logical function fms_diag_files_object_init (files_array)
      endif
 
      obj%unlim_dimension_level = 0
+     obj%num_time_levels = 0
      obj%is_static = obj%get_file_freq() .eq. -1
      obj%nz_subaxis = 0
 
@@ -1607,6 +1610,16 @@ subroutine init_unlim_dim(this, output_buffers)
   enddo
 end subroutine init_unlim_dim
 
+!> \brief Get the number of time levels that were actually written to the file
+!! \return Number of time levels that were actually written to the file
+pure function get_num_time_levels(this) &
+result(res)
+  class(fmsDiagFileContainer_type), intent(in), target   :: this            !< The file object
+  integer :: res
+
+  res = this%FMS_diag_file%num_time_levels
+end function
+
 !> \brief Get the unlimited dimension level that is in the file
 !! \return The unlimited dimension
 pure function get_unlim_dimension_level(this) &
@@ -1816,6 +1829,13 @@ subroutine close_diag_file(this, output_buffers, model_end_time, diag_fields)
     call close_file(fms2io_fileobj)
   end select
 
+  !< Keep track of the number of time levels that were written to the file
+  !! If the file is using the new_file_freq key, it will be closing the file multiple
+  !! time, so this ensures that we keep a running count
+  !! This is going be written to the output yaml, after all the files are closed
+  this%FMS_diag_file%num_time_levels = this%FMS_diag_file%num_time_levels + &
+                                       this%FMS_diag_file%unlim_dimension_level
+
   !< Reset the unlimited dimension level back to 0, in case the fms2io_fileobj is re-used
   this%FMS_diag_file%unlim_dimension_level = 0
   this%FMS_diag_file%is_file_open = .false.

diag_manager/fms_diag_object.F90

@@ -99,6 +99,7 @@ module fms_diag_object_mod
     procedure :: allocate_diag_field_output_buffers
     procedure :: fms_diag_compare_window
     procedure :: set_time_end
+    procedure :: get_ntimes_per_file
 #ifdef use_yaml
     procedure :: get_diag_buffer
 #endif
@@ -154,24 +155,49 @@ subroutine fms_diag_object_init (this,diag_subset_output, time_init)
 #endif
 end subroutine fms_diag_object_init
 
+!> @brief Determines the number of time levels that were written each file
+!! @return The number of time levels that were written each file
+function get_ntimes_per_file(this) &
+  result(ntimes)
+  class(fmsDiagObject_type) :: this !< Diag object
+  integer, allocatable :: ntimes(:)
+
+  integer :: i !< For looping through the files
+
+#ifdef use_yaml
+  allocate(ntimes(size(this%FMS_diag_files)))
+  do i = 1, size(this%FMS_diag_files)
+    ntimes(i) = this%FMS_diag_files(i)%get_num_time_levels()
+  enddo
+#else
+  allocate(ntimes(1))
+  ntimes = diag_null
+  call mpp_error(FATAL, "You must compile with -Duse_yaml to call fms_diag_object%get_ntimes_per_file!")
+#endif
+
+end function get_ntimes_per_file
+
 !> \description Loops through all files and does one final write.
 !! Closes all files
 !! Deallocates all buffers, fields, and files
 !! Uninitializes the fms_diag_object
 subroutine fms_diag_object_end (this, time)
   class(fmsDiagObject_type) :: this
   TYPE(time_type), INTENT(in) :: time
+  integer, allocatable :: ntimes(:) !< Number of time steps per file
 
   integer                   :: i
 #ifdef use_yaml
   !TODO: loop through files and force write
   if (.not. this%initialized) return
 
-  ! write output yaml
-  call fms_diag_yaml_out()
-
   call this%do_buffer_math()
   call this%fms_diag_do_io(end_time=time)
+
+  ! write output yaml
+  ntimes = this%get_ntimes_per_file()
+  call fms_diag_yaml_out(ntimes)
+
   !TODO: Deallocate diag object arrays and clean up all memory
   do i=1, size(this%FMS_diag_output_buffers)
     call this%FMS_diag_output_buffers(i)%flush_buffer()

diag_manager/fms_diag_yaml.F90

@@ -1645,7 +1645,8 @@ subroutine dump_diag_yaml_obj( filename )
 !> Writes an output yaml with all available information on the written files.
 !! Will only write with root pe.
 !! Global attributes are limited to 16 per file.
-subroutine fms_diag_yaml_out()
+subroutine fms_diag_yaml_out(ntimes)
+  integer, intent(in) :: ntimes(:) !< The number of time levels that were written for each file
   type(diagYamlFiles_type), pointer :: fileptr !< pointer for individual variables
   type(diagYamlFilesVar_type), pointer :: varptr !< pointer for individual variables
   type (fmsyamloutkeys_type), allocatable :: keys(:), keys2(:), keys3(:)
@@ -1714,6 +1715,7 @@ subroutine fms_diag_yaml_out()
     call fms_f2c_string(keys2(i)%key8, 'start_time')
     call fms_f2c_string(keys2(i)%key9, 'file_duration')
     call fms_f2c_string(keys2(i)%key10, 'file_duration_units')
+    call fms_f2c_string(keys2(i)%key11, 'number_of_timelevels')
 
     call fms_f2c_string(vals2(i)%val1, fileptr%file_fname)
     call fms_f2c_string(vals2(i)%val5, fileptr%file_unlimdim)
@@ -1750,6 +1752,7 @@ subroutine fms_diag_yaml_out()
     enddo
     call fms_f2c_string(vals2(i)%val9, adjustl(tmpstr1))
     call fms_f2c_string(vals2(i)%val10, get_diag_unit_string(fileptr%file_duration_units))
+    call fms_f2c_string(vals2(i)%val11, string(ntimes(i)))
 
     !! tier 3 - varlists, subregion, global metadata
     call yaml_out_add_level2key('varlist', keys2(i))
@@ -1976,7 +1979,7 @@ subroutine fms_diag_yaml_out()
   enddo
   tier2size = i
 
-  call write_yaml_from_struct_3( 'diag_out.yaml'//c_null_char,  1, keys, vals,          &
+  call write_yaml_from_struct_3( 'diag_manifest.yaml.'//string(mpp_pe())//c_null_char,  1, keys, vals, &
                                  SIZE(diag_yaml%diag_files), keys2, vals2, &
                                  tier3size, tier3each, keys3, vals3,       &
                                  (/size(diag_yaml%diag_files), 0, 0, 0, 0, 0, 0, 0/))

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 22:0:0
+libFMS_la_LDFLAGS = -version-info 22:2:0
 
 # Add the convenience libraries to the FMS library.
 libFMS_la_LIBADD = $(top_builddir)/platform/libplatform.la

test_fms/diag_manager/test_diag_manager2.sh

@@ -898,6 +898,7 @@ diag_files:
   start_time:
   file_duration:
   file_duration_units:
+  number_of_timelevels: 1
   varlist:
   - module: atm_mod
     var_name: var7
@@ -930,6 +931,7 @@ diag_files:
   start_time:
   file_duration:
   file_duration_units:
+  number_of_timelevels: 3
   varlist:
   - module: ocn_mod
     var_name: var1
@@ -972,6 +974,7 @@ diag_files:
   start_time:
   file_duration:
   file_duration_units:
+  number_of_timelevels: 3
   varlist:
   - module: atm_mod
     var_name: var3
@@ -1036,6 +1039,7 @@ diag_files:
   start_time:
   file_duration:
   file_duration_units:
+  number_of_timelevels: 3
   varlist:
   - module: lnd_mod
     var_name: var5
@@ -1078,6 +1082,7 @@ diag_files:
   start_time:
   file_duration:
   file_duration_units:
+  number_of_timelevels: 3
   varlist:
   - module: lnd_mod
     var_name: var1
@@ -1109,6 +1114,7 @@ diag_files:
   start_time:
   file_duration:
   file_duration_units:
+  number_of_timelevels: 3
   varlist:
   - module: atm_mod
     var_name: var4
@@ -1140,6 +1146,7 @@ diag_files:
   start_time: 00020101.000000
   file_duration: 12
   file_duration_units: hours
+  number_of_timelevels: 2
   varlist:
   - module: ocn_mod
     var_name: var1
@@ -1171,6 +1178,7 @@ diag_files:
   start_time:
   file_duration:
   file_duration_units:
+  number_of_timelevels: 3
   varlist:
   - module: ocn_mod
     var_name: var1
@@ -1202,6 +1210,7 @@ diag_files:
   start_time: 00020101.000000
   file_duration: 12 3 9
   file_duration_units: hours hours hours
+  number_of_timelevels: 24
   varlist:
   - module: ocn_mod
     var_name: var1
@@ -1233,6 +1242,7 @@ diag_files:
   start_time: 00020101.000000
   file_duration: 12 3 9
   file_duration_units: hours hours hours
+  number_of_timelevels: 24
   varlist:
   - module: ocn_mod
     var_name: var1
@@ -1264,6 +1274,7 @@ diag_files:
   start_time:
   file_duration:
   file_duration_units:
+  number_of_timelevels: 1
   varlist:
   - module: ocn_mod
     var_name: var1

test_fms/diag_manager/test_diag_out_yaml.F90

@@ -41,7 +41,7 @@ subroutine check_output_yaml
   integer, parameter :: yaml_len = 402
   character(len=128) :: out_yaml_line, ref_yaml_line
   character(len=17), parameter :: ref_fname = 'diag_out_ref.yaml'
-  character(len=13), parameter :: out_fname = 'diag_out.yaml'
+  character(len=20), parameter :: out_fname = 'diag_manifest.yaml.0'
   if( mpp_root_pe() .ne. mpp_pe()) return
   open(newunit=un_out, file=out_fname, status="old", action="read")
   open(newunit=un_ref, file=ref_fname, status="old", action="read")
@@ -58,4 +58,4 @@ subroutine check_output_yaml
 end subroutine
 
 
-end program
+end program