Merge remote-tracking branch 'upstream/main' into gc_2

NOAA-GFDL · Jul 13, 2023 · f20f849 · f20f849
2 parents 00b7ed8 + 7831d2e
commit f20f849
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diff --git a/.github/workflows/github_autotools_gnu.yml b/.github/workflows/github_autotools_gnu.yml
@@ -9,27 +9,27 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        conf-flags: [--disable-openmp, --enable-mixed-mode, --disable-setting-flags, --with-mpi=no]
-        input-flag:  [--with-yaml, --enable-test-input=/home/fms_test_input]
+        conf-flag: [--disable-openmp, --enable-mixed-mode, --with-mpi=no]
+        input-flag:  [--with-yaml, --enable-test-input=/home/unit_tests_input]
+        io-flag: [ --enable-deprecated-io, --disable-deprecated-io]
+        exclude:
+          - conf-flag: --with-mpi=no
+            input-flag: --enable-test-input=/home/unit_tests_input
     container:
       image: ryanmulhall/fms-ci-rocky-gnu:12.2.0
       env:
         TEST_VERBOSE: 1
-        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flags }} ${{ matrix.input-flag }}"
+        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }} ${{ matrix.io-flag }}"
     steps:
     - name: Checkout code
       uses: actions/checkout@v2
     - name: Prepare GNU autoconf for build
       run: autoreconf -if
     - name: Configure the build
-      if: ${{ matrix.conf-flags != '--disable-setting-flags' }}
       run: ./configure ${DISTCHECK_CONFIGURE_FLAGS}
-    - name: Configure the build with explicit required flags
-      if: ${{ matrix.conf-flags == '--disable-setting-flags' }}
-      run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} FCFLAGS="-fdefault-real-8 -fdefault-double-8 -fcray-pointer -ffree-line-length-none -I/opt/view/include $FCFLAGS"
     - name: Build the library
-      run: make -k distcheck
-      if: ${{ matrix.conf-flags != '--with-mpi=no' }}
+      run: make distcheck
+      if: ${{ matrix.conf-flag != '--with-mpi=no' }}
     - name: Build the library (without test suite for serial build)
       run: make
-      if: ${{ matrix.conf-flags == '--with-mpi=no' }}
+      if: ${{ matrix.conf-flag == '--with-mpi=no' }}
diff --git a/.github/workflows/github_autotools_intel.yml b/.github/workflows/github_autotools_intel.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
diff --git a/.github/workflows/github_cmake_gnu.yml b/.github/workflows/github_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

diff --git a/.github/workflows/github_doc_site.yml b/.github/workflows/github_doc_site.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
diff --git a/CHANGELOG.md b/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).

diff --git a/CMakeLists.txt b/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")
@@ -246,6 +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()
@@ -295,12 +300,16 @@ foreach(kind ${kinds})
 
   target_include_directories(${libTgt}_f PRIVATE include
                                                  fms
+                                                 fms/include
                                                  fms2_io/include
                                                  string_utils/include
                                                  mpp/include
+                                                 sat_vapor_pres/include
+                                                 horiz_interp/include
                                                  diag_manager/include
                                                  constants4
-                                                 constants)
+                                                 constants
+                                                 axis_utils/include)
   target_compile_definitions(${libTgt}_f PRIVATE "${fms_defs}")
   target_compile_definitions(${libTgt}_f PRIVATE "${${kind}_defs}")
 
@@ -334,7 +343,10 @@ foreach(kind ${kinds})
   target_include_directories(${libTgt} PUBLIC
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/fms>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/fms/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/fms2_io/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/sat_vapor_pres/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/horiz_interp/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/string_utils/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/mpp/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/diag_manager/include>)

diff --git a/amip_interp/amip_interp.F90 b/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 ----
 

diff --git a/axis_utils/Makefile.am b/axis_utils/Makefile.am
@@ -23,15 +23,23 @@
 # Ed Hartnett 2/22/19
 
 # Include .h and .mod files.
-AM_CPPFLAGS = -I$(top_srcdir)/include
+AM_CPPFLAGS = -I$(top_srcdir)/include -I$(top_srcdir)/axis_utils/include
 AM_FCFLAGS = $(FC_MODINC). $(FC_MODOUT)$(MODDIR)
 
 # Build this uninstalled convenience library.
 noinst_LTLIBRARIES = libaxis_utils.la
 
 libaxis_utils_la_SOURCES = \
   axis_utils.F90 \
-  axis_utils2.F90
+  axis_utils2.F90 \
+  include/axis_utils2_r4.fh \
+  include/axis_utils2_r8.fh \
+  include/axis_utils2.inc
+
+axis_utils2.$(FC_MODEXT) : \
+include/axis_utils2_r4.fh \
+include/axis_utils2_r8.fh \
+include/axis_utils2.inc
 
 # Mod file depends on its o file, is built and then installed.
 nodist_include_HEADERS = axis_utils_mod.$(FC_MODEXT) axis_utils2_mod.$(FC_MODEXT)

diff --git a/axis_utils/axis_utils.F90 b/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