Merge branch 'main' of github.com:noaa-gfdl/FMS into ci-fixes

.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

@@ -168,9 +168,7 @@ list(APPEND fms_fortran_src_files
   memutils/memutils.F90
   monin_obukhov/monin_obukhov_inter.F90
   monin_obukhov/monin_obukhov.F90
-  mosaic/gradient.F90
-  mosaic/grid.F90
-  mosaic/mosaic.F90
+  grid_utils/gradient.F90
   mosaic2/grid2.F90
   mosaic2/mosaic2.F90
   mpp/mpp.F90
@@ -205,11 +203,10 @@ list(APPEND fms_fortran_src_files
 list(APPEND fms_c_src_files
   affinity/affinity.c
   fms/fms_stacksize.c
-  mosaic/create_xgrid.c
-  mosaic/gradient_c2l.c
-  mosaic/interp.c
-  mosaic/mosaic_util.c
-  mosaic/read_mosaic.c
+  grid_utils/gradient_c2l.c
+  grid_utils/grid_utils.c
+  grid_utils/tree_utils.c
+  horiz_interp/include/horiz_interp_conserve_xgrid.c
   mpp/mpp_memuse.c
   parser/yaml_parser_binding.c
   parser/yaml_output_functions.c
@@ -257,6 +254,8 @@ 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()
 
@@ -298,7 +297,8 @@ foreach(kind ${kinds})
   # C
   add_library(${libTgt}_c OBJECT ${fms_c_src_files})
 
-  target_include_directories(${libTgt}_c PRIVATE include)
+  target_include_directories(${libTgt}_c PRIVATE include
+                                                 grid_utils)
   target_compile_definitions(${libTgt}_c PRIVATE "${fms_defs}")
 
   target_link_libraries(${libTgt}_c PRIVATE NetCDF::NetCDF_C
@@ -386,6 +386,7 @@ foreach(kind ${kinds})
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/monin_obukhov/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/sat_vapor_pres/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/field_manager/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/grid_utils>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/horiz_interp/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/mosaic2/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/string_utils/include>
@@ -429,13 +430,13 @@ 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::
@@ -458,3 +459,34 @@ install(EXPORT FMSExports
   NAMESPACE FMS::
   FILE fms-targets.cmake
   DESTINATION ${CONFIG_INSTALL_DESTINATION})
+
+# pkgconf
+set(prefix ${CMAKE_INSTALL_PREFIX})
+set(exec_prefix ${CMAKE_INSTALL_PREFIX})
+set(libdir ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
+set(includedir ${CMAKE_INSTALL_PREFIX}/${includeDir})
+
+set(CC ${CMAKE_C_COMPILER})
+set(FC ${CMAKE_Fortran_COMPILER})
+set(CFLAGS "${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE}}")
+set(CPPFLAGS "${CMAKE_CPP_FLAGS} ${CMAKE_CPP_FLAGS_${CMAKE_BUILD_TYPE}}")
+set(FCFLAGS "${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}}")
+set(LDFLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS_${CMAKE_BUILD_TYPE}}")
+
+set(VERSION ${PROJECT_VERSION})
+
+# TODO: If FMS depends on a library that is built as a static library, it
+#       should be listed here as an ldflag.
+set(LIBS "")
+
+if(NOT ${NetCDF_Fortran_LIBRARY_SHARED})
+  # autotools: Libs.private: -lnetcdff -lnetcdf
+  string(APPEND LIBS ${NetCDF_Fortran_LIBRARIES})
+endif()
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/FMS.pc.in
+               ${CMAKE_CURRENT_BINARY_DIR}/FMS.pc @ONLY)
+
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FMS.pc
+              DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig
+              COMPONENT utilities)

FMS.pc.in

@@ -35,7 +35,7 @@ Name: FMS
 Description: The Flexible Modeling System Infrastructure Library
 URL: https://www.gfdl.noaa.gov/fms
 Version: @VERSION@
-Libs: -L$(libdir) -lFMS
+Libs: -L${libdir} -lFMS
 Libs.private: @LIBS@
 Cflags: -I${includedir}
 Fflags: -I${includedir}

Makefile.am

@@ -47,7 +47,7 @@ SUBDIRS = \
   parser \
   string_utils \
   affinity \
-  mosaic \
+  grid_utils \
   time_manager \
   axis_utils \
   diag_manager \
@@ -147,4 +147,3 @@ install-data-hook:
 	@echo '| please see our page: https://www.github.com/NOAA-GFDL/FMS   |'
 	@echo '+-------------------------------------------------------------+'
 	@echo ''
-

block_control/block_control.F90

@@ -23,8 +23,9 @@
 
 module block_control_mod
 
-use mpp_mod,         only: mpp_error, NOTE, WARNING, FATAL
+use mpp_mod,         only: mpp_error, NOTE, WARNING, FATAL, mpp_sum, mpp_npes
 use mpp_domains_mod, only: mpp_compute_extent
+use fms_string_utils_mod, only: string
 implicit none
 
 public block_control_type
@@ -104,15 +105,19 @@ subroutine define_blocks (component, Block, isc, iec, jsc, jec, kpts, &
     integer, dimension(ny_block) :: j1, j2
     character(len=256) :: text
     integer :: i, j, nblks, ix, ii, jj
+    integer :: non_uniform_blocks !< Number of non uniform blocks
 
     if (message) then
+      non_uniform_blocks = 0
       if ((mod(iec-isc+1,nx_block) .ne. 0) .or. (mod(jec-jsc+1,ny_block) .ne. 0)) then
-        write( text,'(a,a,2i4,a,2i4,a)' ) trim(component),'define_blocks: domain (',&
-             (iec-isc+1), (jec-jsc+1),') is not an even divisor with definition (',&
-             nx_block, ny_block,') - blocks will not be uniform'
-        call mpp_error (WARNING, trim(text))
+        non_uniform_blocks = 1
+      endif
+      call mpp_sum(non_uniform_blocks)
+      if (non_uniform_blocks > 0 ) then
+        call mpp_error(NOTE, string(non_uniform_blocks)//" out of "//string(mpp_npes())//" total domains "//&
+                       "have non-uniform blocks for block size ("//string(nx_block)//","//string(ny_block)//")")
+        message = .false.
       endif
-      message = .false.
     endif
 
 !--- set up blocks

configure.ac

@@ -479,7 +479,7 @@ AC_CONFIG_FILES([
   tridiagonal/Makefile
   tracer_manager/Makefile
   topography/Makefile
-  mosaic/Makefile
+  grid_utils/Makefile
   mosaic2/Makefile
   monin_obukhov/Makefile
   memutils/Makefile
@@ -533,7 +533,12 @@ AC_CONFIG_FILES([
   test_fms/random_numbers/Makefile
   test_fms/topography/Makefile
   test_fms/column_diagnostics/Makefile
+  test_fms/block_control/Makefile
   FMS.pc
   ])
 
 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_integral/diag_integral.F90

@@ -40,7 +40,7 @@ module diag_integral_mod
                              fms_init, &
                              mpp_pe, mpp_root_pe,&
                              FATAL, write_version_number, &
-                             stdlog
+                             stdlog, string
 use fms2_io_mod,      only:  file_exists
 use constants_mod,    only:  radius, constants_init
 use mpp_mod,          only:  mpp_sum, mpp_init
@@ -195,7 +195,6 @@ module diag_integral_mod
 !-------------------------------------------------------------------------------
 character(len=160) :: format_text !< format statement for header
 character(len=160) :: format_data !< format statement for data output
-logical            :: do_format_data = .true. !< a data format needs to be generated ?
 integer            :: nd !< number of characters in data format statement
 integer            :: nt !< number of characters in text format statement
 
@@ -711,6 +710,8 @@ subroutine write_field_averages (Time)
       integer :: nn, ninc, nst, nend, fields_to_print
       integer :: i, kount
       integer(i8_kind) :: icount
+      character(len=128) :: xtime_str
+      logical :: use_exp_format
 
 !-------------------------------------------------------------------------------
 !    each header and data format may be different and must be generated
@@ -764,6 +765,12 @@ subroutine write_field_averages (Time)
 !-------------------------------------------------------------------------------
       xtime = get_axis_time (Time-Time_init_save, time_units)
 
+!-------------------------------------------------------------------------------
+!    check if the time value is too long for decimal output
+!-------------------------------------------------------------------------------
+      xtime_str = trim(string(xtime))
+      use_exp_format = len_trim(xtime_str(1:INDEX(xtime_str, "."))) .ge. 9
+
 !-------------------------------------------------------------------------------
 !    generate the new header and data formats.
 !-------------------------------------------------------------------------------
@@ -774,7 +781,7 @@ subroutine write_field_averages (Time)
         nst = 1 + (nn-1)*fields_per_print_line
         nend = MIN (nn*fields_per_print_line, num_field)
         if (print_header)  call format_text_init (nst, nend)
-        call format_data_init (nst, nend)
+        call format_data_init (nst, nend, use_exp_format)
         if (diag_unit /= 0) then
           write (diag_unit,format_data(1:nd)) &
                  xtime, (field_avg(i),i=nst,nend)
@@ -890,18 +897,22 @@ end subroutine format_text_init
 !! <b> Parameters: </b>
 !!
 !! @code{.f90}
-!! integer, intent(in), optional :: nst_in, nend_in
+!! integer, intent(in) :: nst_in, nend_in
 !! @endcode
 !!
 !! @param [in] <nst_in, nend_in> starting/ending integral index which will be
 !!        included in this format statement
+!! @param [in] <use_exp_format>  if true, uses exponent notation for the first format code
+!!        to avoid overflow with larger time values
 !!
-subroutine format_data_init (nst_in, nend_in)
+subroutine format_data_init (nst_in, nend_in, use_exp_format)
 
-integer, intent(in), optional :: nst_in !< starting/ending integral index which will be
+integer, intent(in) :: nst_in !< starting/ending integral index which will be
                                                  !! included in this format statement
-integer, intent(in), optional :: nend_in !< starting/ending integral index which will be
+integer, intent(in) :: nend_in !< starting/ending integral index which will be
                                                  !! included in this format statement
+logical, intent(in) :: use_exp_format !< if true, uses exponent notation for the first format code
+                                      !! to avoid overflow with larger time values
 
 !-------------------------------------------------------------------------------
 ! local variables:
@@ -917,28 +928,27 @@ subroutine format_data_init (nst_in, nend_in)
 !    integrals. this section is 9 characters long.
 !-------------------------------------------------------------------------------
       nd = 9
-      format_data(1:nd) = '(1x,f10.2'
+      if( use_exp_format ) then
+        format_data(1:nd) = '(1x,e10.2'
+      else
+        format_data(1:nd) = '(1x,f10.2'
+      endif
 
 !-------------------------------------------------------------------------------
 !    define the indices of the integrals that are to be written by this
 !    format statement.
 !-------------------------------------------------------------------------------
-      if ( present (nst_in) ) then
-        nst = nst_in
-        nend = nend_in
-      else
-        nst = 1
-        nend = num_field
-      endif
+      nst = nst_in
+      nend = nend_in
 
 !-------------------------------------------------------------------------------
 !    complete the data format. use the format defined for the
 !    particular integral in setting up the format statement.
 !-------------------------------------------------------------------------------
       do i=nst,nend
          nc = len_trim(field_format(i))
-         format_data(nd+1:nd+nc+5) =  ',1x,' // field_format(i)(1:nc)
-         nd = nd+nc+5
+         format_data(nd+1:nd+nc+4) =  ',1x,' // field_format(i)(1:nc)
+         nd = nd+nc+4
       end do
 
 !-------------------------------------------------------------------------------