mixed precision to interpolator

.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 +6,58 @@ 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`).
 
+## [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)
+
+
+## [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).
+- GCC 11.1.0 is unsupported due to compilation issues with select type. The issue is resolved in later GCC releases.
+- When outputting sub-region diagnostics, the current diag_manager does not add "tileX" to the filename when using a cube sphere. This leads to trouble when trying to combine the files and regrid them (if the region is in two different tiles)
+
+### Added
+- DIAG_MANAGER: Added code refactored as part of larger diag_manager rewrite for the send_data routines. The refactored code is disabled by default and enabled by setting  `use_refactored_send` to true in the diag_manager_nml, and should mirror current behaviour.
+- FMS2_IO: Added the ability to set deflate_level and shuffle netcdf options in `fms2_io_nml`. Also added functionality for registering dimensions as unlimited compressed.
+- YAML_PARSER: Added support for emitting multiple tabbed section keys to allow diag manager yaml output
+
+### Changed
+- STRING_UTILS: Extended the `string` interface in fms_string_utils_mod to accept reals of 4 or 8 kind, as well as 1, 2, and 3 dimensional real arrays
+- DIAG_MANAGER: Changed the `log_diag_field_info` routine to allow for specifying seperator
+- INTERPOLATOR(s): In horiz_interp, amip_interp and interpolator, changed pointers arrays into allocatables
+
+### Fixed
+- TRIDIAGONAL: Added OMP directives to prevent race conditions
+- DIAG_MANAGER: Added `diag_send_data` routine to fix class(\*) related compiler issues from the refactor update
+- SAT_VAPOR_PRES_K: Removed implied saves causing issues with class(\*) type checking
+- TIME_INTERP: Fixed naming conflicts between module level and local variables
+- YAML_PARSER: Fixed typo in variable name, rename variables to avoid fortran keywords
+- DOCS: Fixed incorrect serial build instructions
+- COMPILER SUPPORT: Fixed compilation errors with Intel's llvm-based compiler and added support for the CMake build. Also fixed mpp_checksum unit test failures with openmpi and nvhpc compilation issues.
+- TIME_MANAGER: Fixed an bug from PR #1169 that was causing answer changes in land models
+
+### Tag Commit Hashes
+- 2023.01-beta4		(63626578cb8ed4bed1ce670b88acd6a1ec438e32)
+- 2023.01-beta3		(0ff254e409b74d7d17ab234abe5ecd985967256c)
+- 2023.01-beta2		(74d8e734bd43b0ce043003da74896e5d747afc2f)
+- 2023.01-beta1		(6255971af28381fad22547bdc2c538fc3ea2e8bf)
+- 2023.01-alpha4	(4526cc94a3e19fe8fa151f54b0db432e1fb2f7d0)
+- 2023.01-alpha3	(f0e8cab3d8e58195f7c2663b84fd0bed12fa8b64)
+- 2023.01-alpha2	(91e732473f7cffce070f9ce239f8ffa22c081261)
+- 2023.01-alpha1	(203c8bf464ff26fe0fe39b1451caedd026bbce55)
+
+
 ## [2022.04] - 2022-10-13
 ### 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

@@ -26,7 +26,7 @@ set(CMAKE_Fortran_FLAGS_DEBUG)
 
 # Define the CMake project
 project(FMS
-  VERSION 2022.04.0
+  VERSION 2023.01.0
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)
@@ -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()

FMS.pc

@@ -24,17 +24,17 @@ includedir=${prefix}/include
 
 # Including the following, as they may be useful when building other components
 # and as a way to better record how the library was built.
-ccompiler=mpiicc
-fccompiler=mpiifort
+ccompiler=mpicc
+fccompiler=mpif90
 cppflagss.compiled= -fopenmp
-cflags.compiled=-I/opt/netcdf/4.9.2/ONEAPI/2023.1/include -I/opt/hdf5/1.14.1-2/ONEAPI/2023.1/include -fopenmp
-fcflags.compiled=-O0 -g -traceback -I/opt/netcdf/4.9.2/ONEAPI/2023.1/include -I/opt/netcdf/4.9.2/ONEAPI/2023.1/include  -FR -real-size 64 -fopenmp
-ldflags.compiled=-L/opt/netcdf/4.9.2/ONEAPI/2023.1/lib64 -lnetcdf
+cflags.compiled=-I/opt/netcdf/4.9.2/GCC/13.1.0/include -I/opt/libyaml/0.2.5/GNU/13.1.0/include -fopenmp
+fcflags.compiled=-I/opt/netcdf/4.9.2/GCC/13.1.0/include -I/opt/netcdf/4.9.2/GCC/13.1.0/include -g -fbacktrace -fopenmp -Wall -Wconversion-extra -I/opt/libyaml/0.2.5/GNU/13.1.0/include  -ffree-form -ffree-line-length-none -fdefault-real-8 -fcray-pointer
+ldflags.compiled= -L/opt/netcdf/4.9.2/GCC/13.1.0/lib64 -lnetcdf -L/opt/mpich/4.0.3/GNU/12.2.0/lib -L/opt/libyaml/0.2.5/GNU/13.1.0/lib
 
 Name: FMS
 Description: The Flexible Modeling System Infrastructure Library
 URL: https://www.gfdl.noaa.gov/fms
-Version: 2022.04.00-dev
+Version: 2023.01.00-dev
 Libs: -L$(libdir) -lFMS
 Libs.private: -lnetcdff 
 Cflags: -I${includedir}

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

@@ -25,7 +25,7 @@ AC_PREREQ([2.69])
 
 # Initialize with name, version, and support email address.
 AC_INIT([GFDL FMS Library],
-  [2022.04.00-dev],
+  [2023.01.00-dev],
   [[email protected]],
   [FMS],
   [https://www.github.com/NOAA-GFDL/FMS])
@@ -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