chore: Update mixedmode (#1304)

.github/workflows/build_cmake_gnu.yml

@@ -9,10 +9,11 @@ jobs:
       matrix:
         omp-flags: [ -DOPENMP=on, -DOPENMP=off ]
         libyaml-flag: [ "", -DWITH_YAML=on ]
+        io-flag: [ "", -DUSE_DEPRECATED_IO=on ]
     container:
       image: noaagfdl/hpc-me.ubuntu-minimal:cmake
       env:
-        CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.libyaml-flag }} -D64BIT=on"
+        CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.io-flag  }} ${{ matrix.libyaml-flag }} -D64BIT=on"
     steps:
     - name: Checkout code
       uses: actions/checkout@v2

.github/workflows/build_ubuntu_gnu.yml

@@ -12,11 +12,12 @@ jobs:
       matrix:
         conf-flags: [--disable-openmp, --enable-mixed-mode, --disable-setting-flags, --with-mpi=no]
         input-flag:  [--with-yaml, --enable-test-input=/home/unit_tests_input]
+        io-flag: [ --enable-deprecated-io, --disable-deprecated-io]
     container:
       image: noaagfdl/hpc-me.ubuntu-minimal:gnu-input
       env:
         TEST_VERBOSE: 1
-        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flags }} ${{ matrix.input-flag }}"
+        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flags }} ${{ matrix.input-flag }} ${{ matrix.io-flag }}"
     steps:
     - name: Checkout code
       uses: actions/checkout@v2

.github/workflows/intel_pr.yml

@@ -3,7 +3,7 @@ jobs:
   intel-autotools:
     runs-on: ubuntu-latest
     container:
-      image: intel/oneapi-hpckit:2022.2-devel-ubuntu20.04
+      image: intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04
       env:
         CC: mpiicc
         FC: mpiifort
@@ -22,7 +22,7 @@ jobs:
         path: /libs
         key: ${{ runner.os }}-intel-libs
     - name: Install packages for building
-      run: apt update && apt install -y autoconf libtool automake zlibc zlib1g-dev
+      run: apt-get update && apt-get install -y autoconf libtool automake zlibc zlib1g-dev
     - if: steps.cache.outputs.cache-hit != 'true'
       name: Build netcdf
       run: |
@@ -50,4 +50,4 @@ jobs:
     - name: Compile
       run: make -j || make
     - name: Run test suite
-      run: make check LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH" SKIP_TESTS="$SKIP_TESTS" VERBOSE=1
+      run: make check LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH" TEST_VERBOSE=1

.github/workflows/update_docs.yml

@@ -6,7 +6,7 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  update_docs:
+  build:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
@@ -23,8 +23,26 @@ jobs:
         run: |
           sudo apt -y install doxygen graphviz
           doxygen gen_docs/Doxyfile
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
+      - name: Upload Pages Artifact
+        uses: actions/upload-pages-artifact@v1
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./gen_docs/html
+          path: 'gen_docs/html'
+  deploy:
+    needs: build
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    # Specify runner + deployment step
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1

CHANGELOG.md

@@ -6,6 +6,24 @@ 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`).
 
+<<<<<<< HEAD
+=======
+## [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)
+
+
+>>>>>>> origin/mixedmode_base
 ## [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).

CMakeLists.txt

@@ -66,6 +66,7 @@ option(ENABLE_QUAD_PRECISION "Enable compiler definition -DENABLE_QUAD_PRECISION
 option(GFS_PHYS              "Enable compiler definition -DGFS_PHYS"              OFF)
 option(LARGEFILE             "Enable compiler definition -Duse_LARGEFILE"         OFF)
 option(WITH_YAML             "Enable compiler definition -Duse_yaml"              OFF)
+option(USE_DEPRECATED_IO     "Enable compiler definition -Duse_deprecated_io (compile with fms_io/mpp_io)"   OFF)
 
 if(32BIT)
   list(APPEND kinds "r4")
@@ -109,6 +110,8 @@ list(APPEND fms_fortran_src_files
   column_diagnostics/column_diagnostics.F90
   constants/constants.F90
   constants/fmsconstants.F90
+  constants4/constantsr4.F90
+  constants4/fmsconstantsr4.F90
   coupler/atmos_ocean_fluxes.F90
   coupler/coupler_types.F90
   coupler/ensemble_manager.F90
@@ -244,6 +247,10 @@ if(WITH_YAML)
   list(APPEND fms_defs use_yaml)
 endif()
 
+if(USE_DEPRECATED_IO)
+  list(APPEND fms_defs use_deprecated_io)
+endif()
+
 if(INTERNAL_FILE_NML)
   list(APPEND fms_defs INTERNAL_FILE_NML)
 endif()

Makefile.am

@@ -38,6 +38,7 @@ SUBDIRS = \
   tridiagonal \
   mpp \
   constants \
+  constants4 \
   memutils \
   string_utils \
   fms2_io \

amip_interp/amip_interp.F90

@@ -1353,7 +1353,10 @@ subroutine read_record (type, Date, Adate, dat)
      else
           call fms2_io_read_data(fileobj, ncfieldname, dat, unlim_dim_level=k)
      endif
-     idat =  nint(dat, I2_KIND) ! reconstruct packed data for reproducibility
+     !TODO This assumes that the data is "packed" (has the scale_factor and add_offset attributes)
+     ! in fms2_io_read_data the data is unpacked (data_in_file*scale_factor + add_offset)
+     ! the line below "packs" the data again. This is needed for reproducibility
+     idat =  nint(dat*100., I2_KIND)
 
    !---- unpacking of data ----
 

amip_interp/include/amip_interp.inc

@@ -1353,7 +1353,10 @@ endif
      else
           call fms2_io_read_data(fileobj, ncfieldname, dat, unlim_dim_level=k)
      endif
-     idat =  nint(dat, I2_KIND) ! reconstruct packed data for reproducibility
+     !TODO This assumes that the data is "packed" (has the scale_factor and add_offset attributes)
+     ! in fms2_io_read_data the data is unpacked (data_in_file*scale_factor + add_offset)
+     ! the line below "packs" the data again. This is needed for reproducibility
+     idat =  nint(dat*100., I2_KIND)
 
    !---- unpacking of data ----
 

axis_utils/axis_utils.F90

@@ -27,6 +27,7 @@
 !> @addtogroup axis_utils_mod
 !> @{
 module axis_utils_mod
+#ifdef use_deprecated_io
   use netcdf
   use mpp_io_mod, only: axistype, atttype, default_axis, default_att,         &
                         mpp_get_atts, mpp_get_axis_data, mpp_modify_meta,     &
@@ -787,7 +788,7 @@ subroutine find_index(grid1, xs, xe, ks, ke)
     if(ke == 0 ) call mpp_error(FATAL,' xe locate outside of grid1')
 
   end subroutine find_index
-
+#endif
 end module axis_utils_mod
 !> @}
 ! close documentation grouping

axis_utils/include/axis_utils2.inc

@@ -1,4 +1,3 @@
-
 !***********************************************************************
 !*                   GNU Lesser General Public License
 !*
@@ -165,28 +164,27 @@
 
   end function LON_IN_RANGE_
 
-  !> @brief Returns monotonic array of longitudes s.t., lon_strt <= lon(:) <= lon_strt+360.
+  !> @brief Returns monotonic array of longitudes s.t., lon_strt <= lon(:) < lon_strt+360.
+  !!
+  !! This may require that entries be moved from the beginning of the array to
+  !! the end. If no entries are moved (i.e., if lon(:) is already monotonic in
+  !! the range from lon_start to lon_start + 360), then istrt is set to 0. If
+  !! any entries are moved, then istrt is set to the original index of the entry
+  !! which becomes lon(1).
+  !!
+  !! e.g.,
   !!
-  !> <br>The first istrt-1 entries are moved to the end of the array:
+  !!        lon = 0 1 2 3 4 5  ...  358 359; lon_strt = 3
+  !!    ==> lon = 3 4 5 6 7 8  ...  359 360 361 362; istrt = 4
   !!
-  !! e.g.
-  !!        lon =      0 1 2 3 4 5  ...  358 359; lon_strt = 3 ==>
-  !!        tranlon =  3 4 5 6 7 8  ...  359 360 361 362; istrt = 4
+  !!        lon = 0 1 2 3 4 5  ...  358 359; lon_strt = 0
+  !!    ==> lon = 0 1 2 3 4 5  ...  358 359; istrt = 0
 
   subroutine TRANLON_(lon, lon_start, istrt)
-
-    ! returns array of longitudes s.t.  lon_strt <= lon < lon_strt+360.
-    ! also, the first istrt-1 entries are moved to the end of the array
-    !
-    ! e.g.
-    !        lon =      0 1 2 3 4 5  ...  358 359; lon_strt = 3 ==>
-    !        tranlon =  3 4 5 6 7 8  ...  359 360 361 362; istrt = 4
-
     real(kind=FMS_AU_KIND_), intent(inout), dimension(:) :: lon
     real(kind=FMS_AU_KIND_), intent(in)                  :: lon_start
     integer, intent(out)                                 :: istrt
 
-
     integer                 :: len, i
     real(kind=FMS_AU_KIND_) :: lon_strt, tmp(size(lon(:))-1)
 
@@ -214,7 +212,7 @@
        endif
 
        lon_strt = lon(1)
-       do i=2,len+1
+       do i=2,len
           lon(i)   = lon_in_range(lon(i),lon_strt)
           lon_strt = lon(i)
        enddo

configure.ac

@@ -110,6 +110,13 @@ AS_IF([test ${enable_8byte_int:-no} = yes],
   [enable_8byte_int=yes],
   [enable_8byte_int=no])
 
+AC_ARG_ENABLE([deprecated-io],
+  [AS_HELP_STRING([--enable-deprecated-io],
+    [Enables compilation of deprecated mpp_io and fms_io modules in addition to the updated fms2_io modules (default no)])])
+AS_IF([test ${enable_deprecated_io:-no} = yes],
+  [enable_deprecated_io=yes],
+  [enable_deprecated_io=no])
+
 # user enabled testing with input files
 AC_MSG_CHECKING([whether to enable tests with input files])
 AC_ARG_ENABLE([test-input],
@@ -203,7 +210,6 @@ AC_MSG_CHECKING([if netCDF was built with HDF5])
 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[
 #include <netcdf_meta.h>
 #if !(NC_HAS_NC4)
-      choke me
 #endif]])], [nc_has_nc4=yes], [nc_has_nc4=no])
 AC_MSG_RESULT([$nc_has_nc4])
 if test $nc_has_nc4 = no; then
@@ -281,6 +287,15 @@ if test $with_mpi = yes; then
   AC_DEFINE([use_libMPI], [1], [This is required for the library to build])
 fi
 
+# check if compiling old io
+if test $enable_deprecated_io = yes; then
+  #If the test pass, define use_deprecated_io macro and skip it's unit tests
+  AC_DEFINE([use_deprecated_io], [1], [This is required to use mpp_io and fms_io modules])
+  AM_CONDITIONAL([SKIP_DEPRECATED_IO_TESTS], true)
+else
+  AM_CONDITIONAL([SKIP_DEPRECATED_IO_TESTS], false)
+fi
+
 # Set any required compile flags.  This will not be done if the user wants to
 # define all their own flags.
 if test $enable_setting_flags = yes; then
@@ -426,6 +441,7 @@ AC_CONFIG_FILES([
   time_interp/Makefile
   time_manager/Makefile
   constants/Makefile
+  constants4/Makefile
   platform/Makefile
   fms/Makefile
   fms2_io/Makefile

coupler/coupler_types.F90

@@ -31,8 +31,10 @@ module coupler_types_mod
   use fms2_io_mod,       only: get_variable_attribute, get_dimension_size, get_dimension_names
   use fms2_io_mod,       only: register_variable_attribute, get_variable_dimension_names
   use fms2_io_mod,       only: get_variable_num_dimensions
+#ifdef use_deprecated_io
   use fms_io_mod,        only: restart_file_type, fms_io_register_restart_field=>register_restart_field
   use fms_io_mod,        only: query_initialized, restore_state
+#endif
   use time_manager_mod,  only: time_type
   use diag_manager_mod,  only: register_diag_field, send_data
   use data_override_mod, only: data_override
@@ -96,8 +98,10 @@ module coupler_types_mod
     integer                           :: atm_tr_index = 0 !< atm_tr_index
     character(len=128)                :: ice_restart_file = ' ' !< ice_restart_file
     character(len=128)                :: ocean_restart_file = ' ' !< ocean_restart_file
+#ifdef use_deprecated_io
     type(restart_file_type), pointer  :: rest_type => NULL() !< A pointer to the restart_file_type
                                                              !! that is used for this field.
+#endif
     type(FmsNetcdfDomainFile_t), pointer :: fms2_io_rest_type => NULL() !< A pointer to the restart_file_type
                                                                         !! That is used for this field
     logical                           :: use_atm_pressure !< use_atm_pressure
@@ -150,8 +154,10 @@ module coupler_types_mod
     integer                           :: atm_tr_index = 0 !< atm_tr_index
     character(len=128)                :: ice_restart_file = ' ' !< ice_restart_file
     character(len=128)                :: ocean_restart_file = ' ' !< ocean_restart_file
+#ifdef use_deprecated_io
     type(restart_file_type), pointer  :: rest_type => NULL() !< A pointer to the restart_file_type
                                                              !! that is used for this field.
+#endif
     type(FmsNetcdfDomainFile_t), pointer :: fms2_io_rest_type => NULL() !< A pointer to the restart_file_type
                                                                         !! That is used for this field
     logical                           :: use_atm_pressure !< use_atm_pressure
@@ -327,17 +333,20 @@ module coupler_types_mod
   !! in restart files.
   !> @ingroup coupler_types_mod
   interface coupler_type_register_restarts
+#ifdef use_deprecated_io
     module procedure mpp_io_CT_register_restarts_2d, mpp_io_CT_register_restarts_3d
     module procedure mpp_io_CT_register_restarts_to_file_2d, mpp_io_CT_register_restarts_to_file_3d
-
+#endif
     module procedure CT_register_restarts_2d, CT_register_restarts_3d
   end interface coupler_type_register_restarts
 
   !> This is the interface to read in the fields in a coupler_bc_type that have
   !! been saved in restart files.
   !> @ingroup coupler_types_mod
   interface coupler_type_restore_state
+#ifdef use_deprecated_io
     module procedure mpp_io_CT_restore_state_2d, mpp_io_CT_restore_state_3d
+#endif
     module procedure CT_restore_state_2d, CT_restore_state_3d
   end interface coupler_type_restore_state
 
@@ -3751,6 +3760,7 @@ end subroutine CT_destructor_3d
   !!
   !! This subroutine registers the fields in a coupler_2d_bc_type to be saved in restart files
   !! specified in the field table.
+#ifdef use_deprecated_io
   subroutine mpp_io_CT_register_restarts_2d(var, bc_rest_files, num_rest_files, mpp_domain, ocean_restart)
     type(coupler_2d_bc_type), intent(inout) :: var  !< BC_type structure to be registered for restarts
     type(restart_file_type),  dimension(:), pointer :: bc_rest_files !< Structures describing the restart files
@@ -4064,7 +4074,7 @@ subroutine mpp_io_CT_restore_state_3d(var, directory, all_or_nothing, all_requir
       endif
     endif
   end subroutine mpp_io_CT_restore_state_3d
-
+#endif
 end module coupler_types_mod
 !> @}
 ! close documentation grouping

coupler/ensemble_manager.F90

@@ -30,7 +30,9 @@ module ensemble_manager_mod
   use mpp_mod, only : mpp_pe, mpp_declare_pelist
   use mpp_mod, only : input_nml_file
   use fms2_io_mod, only : fms2_io_set_filename_appendix=>set_filename_appendix
+#ifdef use_deprecated_io
   use fms_io_mod, only  : fms_io_set_filename_appendix=>set_filename_appendix
+#endif
 
   IMPLICIT NONE
 
@@ -408,7 +410,9 @@ subroutine ensemble_pelist_setup(concurrent, atmos_npes, ocean_npes, land_npes,
 
        !< Both calls are needed for cases where both fms2io/fmsio are used
        call fms2_io_set_filename_appendix(trim(text))
+#ifdef use_deprecated_io
        call fms_io_set_filename_appendix(trim(text))
+#endif
     endif
 
   end subroutine ensemble_pelist_setup