Merge branch 'NOAA-GFDL:main' into am5-ci

.github/CODEOWNERS

@@ -25,7 +25,7 @@
 # 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.
-*          @thomas-robinson @bensonr @rem1776
+*          @uramirez8707 @bensonr @rem1776
 
 # GNU autotools files
 Makefile.am      @uramirez8707 @rem1776
@@ -41,7 +41,7 @@ cmake            @mlee03
 /.github/        @rem1776
 
 # Testing files
-/test_fms/       @uramirez8707 @mlee03 @bensonr @thomas-robinson @rem1776
+/test_fms/       @uramirez8707 @mlee03 @bensonr @rem1776
 
 # Specific component directories
 /affinity/          @bensonr
@@ -53,15 +53,15 @@ cmake            @mlee03
 #/data_override/ Currently no code owner
 /test_fms/data_override/ @rem1776
 
-/diag_manager            @thomas-robinson
-/test_fms/diag_manager/  @thomas-robinson
+/diag_manager            @uramirez8707
+/test_fms/diag_manager/  @uramirez8707
 
-/fms/             @thomas-robinson @rem1776
-/test_fms/fms/    @thomas-robinson @rem1776
+/fms/             @uramirez8707 @rem1776
+/test_fms/fms/    @uramirez8707 @rem1776
 /fms2/            @uramirez8707
 /test_fms/fms2/   @uramirez8707
 
-/libFMS/           @thomas-robinson @rem1776
+/libFMS/           @uramirez8707 @rem1776
 
-/mpp/              @thomas-robinson @bensonr
-/test_fms/mpp/     @thomas-robinson @bensonr @rem1776
+/mpp/              @uramirez8707 @bensonr
+/test_fms/mpp/     @uramirez8707 @bensonr @rem1776

CMakeLists.txt

@@ -257,6 +257,8 @@ if(WITH_YAML)
 endif()
 
 if(USE_DEPRECATED_IO)
+  message( WARNING "fms_io WILL BE DEPRECATED IN A FUTURE RELEASE. PLEASE UPDATE TO USE FMS2_IO AND REMOVE "
+                   "-DUSE_DEPRECATED_IO=on FROM YOUR OPTIONS")
   list(APPEND fms_defs use_deprecated_io)
 endif()
 
@@ -429,13 +431,13 @@ endforeach()
 install(
   TARGETS ${LIB_TARGETS}
   EXPORT FMSExports
-  RUNTIME DESTINATION bin
-  LIBRARY DESTINATION lib
-  ARCHIVE DESTINATION lib)
+  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
 
 ### Package config
 include(CMakePackageConfigHelpers)
-set(CONFIG_INSTALL_DESTINATION lib/cmake/fms)
+set(CONFIG_INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/fms)
 
 export(EXPORT FMSExports
   NAMESPACE FMS::

configure.ac

@@ -537,3 +537,7 @@ AC_CONFIG_FILES([
   ])
 
 AC_OUTPUT()
+
+if test $enable_deprecated_io = yes; then
+  AC_MSG_WARN(FMS_IO WILL BE DEPRECATED IN A FUTURE RLEASE. PLEASE UPDATE TO USE FMS2_IO AND REMOVE --enable-deprecated-io FROM YOUR CONFIGURE OPTIONS)
+fi

data_override/README.MD

@@ -8,6 +8,7 @@
 - [Converting legacy data_table to data_table.yaml](README.MD#3-converting-legacy-data_table-to-data_tableyaml)
 - [Examples](README.MD#4-examples)
 - [External Weight File Structure](README.MD#5-external-weight-file-structure)
+- [Ensemble and Nest Support](README.MD#6-ensemble-and-nest-support)
 
 #### 1. YAML Data Table format:
 Each entry in the data_table has the following key values:
@@ -200,3 +201,7 @@ variables:
   - weight(:,:,2) -> (i,j+1)
   - weight(:,:,3) -> (i+1,j)
   - weight(:,:,4) -> (i+1,j+1)
+
+#### 6. Ensemble and Nest Support
+
+It may be desired to have each member of an ensemble use a different forcing file. In other to support this, FMS allows for each ensemble member to have its own data_table.yaml. For example, for a run with 2 ensemble members, fms will search for data_table_ens_01.yaml and data_table_ens_02.yaml. However, if both the data_table.yaml and the data_table_ens_* files are present, the code will crash as only 1 option is allowed. Similary, each nest can have its own data_table (data_table_nest_01.yaml), but in this case FMS will not crash if both data_table_nest_01.yaml and data_table.yaml are present. The main grid will use the data_table.yaml and the first nest will use the data_table_nest_01.yaml file.

data_override/include/data_override.inc

@@ -21,7 +21,7 @@
 ! modules. These modules are not intended to be used directly - they should be
 ! used through the data_override_mod API. See data_override.F90 for details.
 
-use platform_mod, only: r4_kind, r8_kind, FMS_PATH_LEN
+use platform_mod, only: r4_kind, r8_kind, FMS_PATH_LEN, FMS_FILE_LEN
 use yaml_parser_mod
 use constants_mod, only: DEG_TO_RAD
 use mpp_mod, only : mpp_error, FATAL, WARNING, NOTE, stdout, stdlog, mpp_max
@@ -45,7 +45,7 @@ use mpp_domains_mod, only : domainUG, mpp_pass_SG_to_UG, mpp_get_UG_SG_domain, N
 use time_manager_mod, only: time_type, OPERATOR(>), OPERATOR(<)
 use fms2_io_mod,     only : FmsNetcdfFile_t, open_file, close_file, &
                             read_data, fms2_io_init, variable_exists, &
-                            get_mosaic_tile_file, file_exists
+                            get_mosaic_tile_file, file_exists, get_instance_filename
 use get_grid_version_mod, only: get_grid_version_1, get_grid_version_2
 use fms_string_utils_mod, only: string
 
@@ -591,9 +591,18 @@ subroutine read_table_yaml(data_table)
     integer :: nentries, mentries
     integer :: i
     character(len=50) :: buffer
+    character(len=FMS_FILE_LEN) :: filename !< Name of the expected data_table.yaml
     integer :: file_id
 
-    file_id = open_and_parse_file("data_table.yaml")
+    ! If doing and ensemble or nest run add the filename appendix (ens_XX or nest_XX) to the filename
+    call get_instance_filename("data_table.yaml", filename)
+    if (index(trim(filename), "ens_") .ne. 0) then
+      if (file_exists(filename) .and. file_exists("data_table.yaml")) &
+        call mpp_error(FATAL, "Both data_table.yaml and "//trim(filename)//" exists, pick one!")
+    endif
+
+    file_id = open_and_parse_file(trim(filename))
+
     if (file_id==999) then
       nentries = 0
     else

diag_manager/diag_yaml_format.md

@@ -15,6 +15,7 @@ The purpose of this document is to explain the diag_table yaml format.
 - [2.6 Sub_region Section](diag_yaml_format.md#26-sub_region-section)
 - [3. More examples](diag_yaml_format.md#3-more-examples)
 - [4. Schema](diag_yaml_format.md#4-schema)
+- [5. Ensemble and Nest Support](diag_yaml_format.md#5-ensemble-and-nest-support)
 
 ### 1. Converting from legacy ascii diag_table format
 
@@ -349,3 +350,6 @@ diag_files:
 A formal specification of the file format, in the form of a JSON schema, can be
 found in the [gfdl_msd_schemas](https://github.com/NOAA-GFDL/gfdl_msd_schemas)
 repository on Github.
+
+### 5. Ensemble and Nest Support
+When using nests, it may be desired for a nest to have a different file frequency or number of variables from the parent grid. This may allow users to save disk space and reduce simulations time. In order to supports, FMS allows each nest to have a different diag_table.yaml from the parent grid. For example, if running with 1 test FMS will use diag_table.yaml for the parent grid and diag_table.nest_01.yaml for the first nest Similary, each ensemble member can have its own diag_table (diag_table_ens_XX.yaml, where XX is the ensemble number). However, for the ensemble case if both the diag_table.yaml and the diag_table_ens_* files are present, the code will crash as only 1 option is allowed.

diag_manager/fms_diag_object.F90

@@ -224,6 +224,7 @@ integer function fms_register_diag_field_obj &
  integer, allocatable :: file_ids(:) !< The file IDs for this variable
  integer :: i !< For do loops
  integer, allocatable :: diag_field_indices(:) !< indices where the field was found in the yaml
+ class(diagDomain_t), pointer :: null_diag_domain => NULL() !< Workaround for a Cray bug which will be fixed in CCE 19
 #endif
 #ifndef use_yaml
 fms_register_diag_field_obj = DIAG_FIELD_NOT_FOUND
@@ -267,7 +268,7 @@ integer function fms_register_diag_field_obj &
      call fileptr%add_field_and_yaml_id(fieldptr%get_id(), diag_field_indices(i))
      call fileptr%add_buffer_id(fieldptr%buffer_ids(i))
      if(fieldptr%get_type_of_domain() .eq. NO_DOMAIN) then
-       call fileptr%set_file_domain(NULL(), fieldptr%get_type_of_domain())
+       call fileptr%set_file_domain(null_diag_domain, fieldptr%get_type_of_domain())
      else
        call fileptr%set_file_domain(fieldptr%get_domain(), fieldptr%get_type_of_domain())
      endif
@@ -284,7 +285,7 @@ integer function fms_register_diag_field_obj &
      call fileptr%add_buffer_id(fieldptr%buffer_ids(i))
      call fileptr%init_diurnal_axis(this%diag_axis, this%registered_axis, diag_field_indices(i))
      if(fieldptr%get_type_of_domain() .eq. NO_DOMAIN) then
-       call fileptr%set_file_domain(NULL(), fieldptr%get_type_of_domain())
+       call fileptr%set_file_domain(null_diag_domain, fieldptr%get_type_of_domain())
      else
        call fileptr%set_file_domain(fieldptr%get_domain(), fieldptr%get_type_of_domain())
      endif

diag_manager/fms_diag_yaml.F90

@@ -45,6 +45,7 @@ module fms_diag_yaml_mod
                                 fms_f2c_string
 use platform_mod, only: r4_kind, i4_kind, r8_kind, i8_kind, FMS_FILE_LEN
 use fms_mod, only: lowercase
+use fms2_io_mod, only: file_exists, get_instance_filename
 
 implicit none
 
@@ -381,10 +382,17 @@ subroutine diag_yaml_object_init(diag_subset_output)
                                            !! outputing data at every frequency)
   character(len=:), allocatable :: filename!< Diag file name (for error messages)
   logical              :: is_instantaneous !< .True. if the file is instantaneous (i.e no averaging)
+  character(len=FMS_FILE_LEN)   :: yamlfilename     !< Name of the expected diag_table.yaml
 
   if (diag_yaml_module_initialized) return
 
-  diag_yaml_id = open_and_parse_file("diag_table.yaml")
+  ! If doing and ensemble or nest run add the filename appendix (ens_XX or nest_XX) to the filename
+  call get_instance_filename("diag_table.yaml", yamlfilename)
+  if (index(trim(yamlfilename), "ens_") .ne. 0) then
+    if (file_exists(yamlfilename) .and. file_exists("diag_table.yaml")) &
+      call mpp_error(FATAL, "Both diag_table.yaml and "//trim(yamlfilename)//" exists, pick one!")
+  endif
+  diag_yaml_id = open_and_parse_file(trim(yamlfilename))
 
   call diag_get_value_from_key(diag_yaml_id, 0, "title", diag_yaml%diag_title)
   call get_value_from_key(diag_yaml_id, 0, "base_date", diag_yaml%diag_basedate)

field_manager/field_manager.F90

@@ -190,7 +190,7 @@ module field_manager_mod
 use    fms_mod, only : lowercase,   &
                        write_version_number, &
                        check_nml_error
-use fms2_io_mod, only: file_exists
+use fms2_io_mod, only: file_exists, get_instance_filename
 use platform_mod, only: r4_kind, r8_kind, FMS_PATH_LEN, FMS_FILE_LEN
 #ifdef use_yaml
 use fm_yaml_mod
@@ -606,18 +606,27 @@ subroutine read_field_table_yaml(nfields, table_name)
 logical                         :: fm_success !< logical for whether fm_change_list was a success
 logical                         :: subparams !< logical whether subparams exist in this iteration
 
+character(len=FMS_FILE_LEN) :: filename !< Name of the expected field_table.yaml
+
 if (.not.PRESENT(table_name)) then
    tbl_name = 'field_table.yaml'
 else
    tbl_name = trim(table_name)
 endif
-if (.not. file_exists(trim(tbl_name))) then
+
+call get_instance_filename(tbl_name, filename)
+if (index(trim(filename), "ens_") .ne. 0) then
+  if (file_exists(filename) .and. file_exists(tbl_name)) &
+    call mpp_error(FATAL, "Both "//trim(tbl_name)//" and "//trim(filename)//" exists, pick one!")
+endif
+
+if (.not. file_exists(trim(filename))) then
   if(present(nfields)) nfields = 0
   return
 endif
 
 ! Construct my_table object
-call build_fmTable(my_table, trim(tbl_name))
+call build_fmTable(my_table, trim(filename))
 
 do h=1,size(my_table%types)
   do i=1,size(my_table%types(h)%models)

fms/fms_io.F90

@@ -693,6 +693,11 @@ subroutine fms_io_init()
      call mpp_error(FATAL,'=>fms_io_init: Error reading input nml file')
   endif
 
+  call mpp_error(NOTE, "fms_io_init: fms_io WILL BE DEPRECATED IN A FUTURE RELEASE! "//&
+                       "PLEASE REMOVE -Duse_deprecated_io FROM YOUR COMPILE FLAGS "// &
+                       "AND MOVE TO FMS2_IO. CONTACT YOUR MODEL LIASISON IF YOU NEED "// &
+                       "ASSISTANCE")
+
 ! take namelist options if present
 ! read_data_bug is no longer supported.
   if (read_data_bug) then
@@ -802,6 +807,11 @@ subroutine fms_io_exit()
 
     if( .NOT.module_is_initialized )return !make sure it's only called once per PE
 
+    call mpp_error(NOTE, "fms_io_exit: fms_io WILL BE DEPRECATED IN A FUTURE RELEASE! "//&
+                         "PLEASE REMOVE -Duse_deprecated_io FROM YOUR COMPILE FLAGS "// &
+                         "AND MOVE TO FMS2_IO. CONTACT YOUR MODEL LIASISON IF YOU NEED "// &
+                         "ASSISTANCE")
+
     do i=1,max_axis_size
        axisdata(i) = i
     enddo

fms2_io/fms_io_utils.F90

@@ -824,8 +824,14 @@ subroutine get_instance_filename(name_in,name_out)
      if ( i .ne. 0 ) then
         name_out = name_in(1:i-1)//'.'//trim(filename_appendix)//name_in(i:length)
      else
-     !< If .nc is not in the name, add the appendix at the end of the file
-        name_out = name_in(1:length)  //'.'//trim(filename_appendix)
+        i = index(trim(name_in), ".yaml", back=.true.)
+        if (i .ne. 0) then
+          !< If .yaml is in the filename add the appendix before it
+          name_out = name_in(1:i-1)//'.'//trim(filename_appendix)//name_in(i:length)
+        else
+          !< If .nc  and .yaml are not in the name, add the appendix at the end of the file
+          name_out = name_in(1:length)  //'.'//trim(filename_appendix)
+        endif
      end if
   end if