Dm update main (#1422)

NOAA-GFDL · Nov 30, 2023 · 8d6373d · 8d6373d
1 parent 26aa42f
commit 8d6373d
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diff --git a/.github/workflows/github_autotools_gnu.yml b/.github/workflows/github_autotools_gnu.yml
@@ -4,12 +4,17 @@ name: Build libFMS test with autotools
 
 on: [push, pull_request]
 
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        conf-flag: [ --disable-openmp, --enable-mixed-mode, --disable-setting-flags, --with-mpi=no]
+        conf-flag: [ --disable-openmp, --disable-setting-flags, --with-mpi=no, --disable-r8-defaults]
         input-flag: [--with-yaml, --enable-test-input=/home/unit_tests_input]
         exclude:
           - conf-flag: --with-mpi=no
@@ -19,10 +24,10 @@ jobs:
       env:
         TEST_VERBOSE: 1
         DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }} ${{ matrix.io-flag }}"
-        SKIP_TESTS: "test_mpp_domains2.14 test_horiz_interp2.9 test_horiz_interp2.10 test_yaml_parser.5" # temporary till fixes are in
+        SKIP_TESTS: "test_yaml_parser.5" # temporary till fixes are in
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Prepare GNU autoconf for build
       run: autoreconf -if
     - name: Configure the build

diff --git a/.github/workflows/github_autotools_intel.yml b/.github/workflows/github_autotools_intel.yml
@@ -1,14 +1,23 @@
 on: pull_request
+
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   intel-autotools:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        io-flag: ["--disable-deprecated-io", "--enable-deprecated-io"]
     container:
       image: intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04
       env:
         CC: mpiicc
         FC: mpiifort
         CFLAGS:  "-I/libs/include"
-        FCFLAGS: "-I/libs/include -g -traceback"
+        FCFLAGS: "-I/libs/include -g -traceback ${{ matrix.io-flag }}"
         LDFLAGS: "-L/libs/lib"
         TEST_VERBOSE: 1
         I_MPI_FABRICS: "shm" # needed for mpi in image
@@ -44,7 +53,7 @@ jobs:
         ./configure --prefix=/libs
         make -j install && cd
     - name: checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Configure
       run: autoreconf -if ./configure.ac && ./configure --with-yaml
     - name: Compile

diff --git a/.github/workflows/github_cmake_gnu.yml b/.github/workflows/github_cmake_gnu.yml
@@ -2,6 +2,11 @@ name: Build libFMS with cmake
 
 on: [push, pull_request]
 
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -16,7 +21,7 @@ jobs:
         CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.io-flag  }} ${{ matrix.libyaml-flag }} -D64BIT=on"
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Generate makefiles with CMake
       run: cmake $CMAKE_FLAGS .
     - name: Build the library

diff --git a/.github/workflows/github_coupler_gnu.yml b/.github/workflows/github_coupler_gnu.yml
@@ -1,25 +1,32 @@
 name: Test coupler build
 on: [pull_request]
 
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   coupler-build:
     runs-on: ubuntu-latest
     container:
-      image: ryanmulhall/hpc-me.ubuntu-minimal:coupler
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:12.3.0
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.github_token }}
       env:
         CC: mpicc
         FC: mpif90
-        CPPFLAGS: '-I/usr/include -Duse_LARGEFILE -DMAXFIELDMETHODS_=500'
-        FCFLAGS: '-fcray-pointer -fdefault-double-8 -fdefault-real-8 -Waliasing -ffree-line-length-none -fno-range-check -I/usr/include'
-        LDFLAGS: '-L/usr/lib'
-        VERBOSE: 1
+        CPPFLAGS: '-I/opt/view/include'
+        FFLAGS: '-fallow-argument-mismatch' # mkmf uses FFLAGS instead of FC
+        LDFLAGS: '-L/opt/view/lib'
     steps:
     - name: Checkout FMS
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         path: FMS
     - name: Checkout FMScoupler
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: 'NOAA-GFDL/FMScoupler'
         path: FMScoupler

diff --git a/.github/workflows/github_doc_site.yml b/.github/workflows/github_doc_site.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Setup repo
         run: | # do autotool's job for substitutes since we don't need a full build environement
           mkdir gen_docs

diff --git a/.github/workflows/github_linter.yml b/.github/workflows/github_linter.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Run Lint
         uses: NOAA-GFDL/simple_lint@f5aa1fe976bd4c231db0536ba00cbfdc26708253
         with:

diff --git a/.github/workflows/version.yml b/.github/workflows/version.yml
@@ -7,7 +7,7 @@ jobs:
   add-dev-to-version:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Append version with dev
       run: sed -i '/20[0-9][0-9]\.[0-9][0-9]/ s/]/-dev]/' configure.ac
     - name: Create pull request

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,48 @@ 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`).
 
+## [2023.03] - 2023-10-27
+### Known Issues
+- GCC 9 and below as well as GCC 11.1.0 are unsupported due to compilation issues. See prior releases for more details.
+- `NO_QUAD_PRECISION` macro is no longer set by FMS, the `ENABLE_QUAD_PRECISION` macro has replaced prior usage of `NO_QUAD_PRECISION`. `-DENABLE_QUAD_PRECISION` should be set if quad precision is to be used, otherwise FMS will not use quad precision reals where applicable.
+
+### Added
+- UNIT_TESTS: New unit tests have been created or and existing ones expanded on for any modules utilizing mixed precision support.
+
+### Changed
+- MIXED PRECISION: Most subroutines and functions in FMS have been updated to simultaneously accept both 4 byte and 8 byte reals as arguments. This deprecates the `--enable-mixed-mode` option, which enabled similar functionality but was limited to certain directories and was not enabled by default. To facilitate easier testing of these code changes, the CMake precision options for default real size were left in (along with an equivalent `--disable-r8-default` flag for autotools). The resulting libraries will support mixed-precision real kinds regardless of default real size. It should also be noted that many routines that accept real arguments have been moved to include files along with headers in order to be compiled with both kinds. Most module level variables were explicitly declared as r8_kind for these updates.
+- Some type/module changes were made to facilitate mixed precision support. They are **intended** to have minimal impact to other codebases:
+  - COUPLER_TYPES: In coupler_types.F90,  `coupler_nd_field_type` and `coupler_nd_values_type` have been renamed to indicate real kind value: `coupler_nd_real4/8_field_type` and `coupler_nd_real4/8_values_type`. The `bc` field within `coupler_nd_bc_type` was modified to use r8_kind within the value and field types, and an additional field added `bc_r4` to use r4_kind values.
+  - TRIDIAGONAL: Module state between r4 and r8 calls are distinct (ie. subsequent calls will only be affected by calls of the same precision). This behaviour can be changed via the `save_both_kinds` optional argument to `tri_invert`.
+- CODE_STYLE: has been updated to reflect the formatting used for the mixed precision support updates.
+
+### Fixed
+- DIAG_MANAGER: Tile number (ie. tileX) will now be added to filenames for sub-regional diagnostics.
+- MPP: Bug affecting non-intel compilers coming from uninitialized pointer in the `nest_domain_type`
+- MPP: Bug fix for unallocated field causing seg faults in `mpp_check_field`
+- FMS2_IO: Fixed segfault occuring from use of cray pointer remapping along with mpp_scatter/gather
+- TEST_FMS: Added various fixes for different compilers within test programs for fms2_io, mpp, diag_manager, parser, and sat_vapor_pres.
+- INTERPOLATOR: Deallocates fields in the type that were previously left out in `interpolator_end`
+
+### Removed
+- CPP MACROS:
+  - `no_4byte_reals` was removed and will not set any additional macros if used. `no_8byte_integers` is still functional.
+  - `NO_QUAD_PRECISION` was removed. It was conditionally set if ENABLE_QUAD_PRECISION was undefined. ENABLE_QUAD_PRECISION should be used in model components instead (logic is flipped)
+  - `use_netCDF` was set by autotools previously but wasn't consistently used in the code. FMS should always be compiled with netcdf installed so this was removed with the exception of its use in deprecated IO modules.
+- DRIFTERS: The drifters subdirectory has been deprecated. It will only be compiled if using the `-Duse_drifters` CPP flag.
+
+### Tag Commit Hashes
+- 2023.03-beta1  06b94a7f574e7794684b8584391744ded68e2989
+- 2023.03-alpha3 b25a7c52a27dfd52edc10bc0ebe12776af0f03df
+- 2023.03-alpha2 9983ce308e62e9f7215b04c227cebd30fd75e784
+- 2023.03-alpha1 a46bd94fd8dd1f6f021501e29179003ff28180ec
+
+
+## [2023.02.01] - 2023-10-13
+### Fixed
+- DIAG_MANAGER: Fixes issue with incorrect start_time functionality
+
+
 ## [2023.02] - 2023-07-27
 ### Known Issues
 - GCC 11.1.0 is unsupported due to compilation issues with select type. The issue is resolved in later GCC releases.
@@ -20,7 +62,7 @@ sequential patch number (starting from `01`).
 - LIBFMS: The libFMS.F90 file (module name `fms`) meant to provide global access has been updated to include 'fms' and it's module/subdirectory name as prefixes for all names. This will only affect external codes that are already using the global module (via `use fms`) and not individual modules.
 - MIXED PRECISION: Updates the axis_utils2, horiz_interp, sat_vapor_pressure, and axis_utils subdirectories to support mixed precision real values.
 - FMS2_IO: Added in mpp_scatter and mpp_gather performance changes from the 2023.01.01 patch. See below for more details.
-- FMS2_IO: Improved error messages to give more debugging information 
+- FMS2_IO: Improved error messages to give more debugging information
 - FMS_MOD: Changed fms_init to include a system call to set the stack size to unlimited, removed previously added stack size fixes
 - MONIN_OBUKHOV: Restructures the subroutines in `stable_mix` interface so that 1d calls the underlying implementation, and 2 and 3d call it on 1d slices of the data as opposed to passing in mismatched arrays.
 - MPP: Updates from JEDI for ajoint version the mpp halo filling (mpp_do_update_ad.fh), adds checkpoint for forward buffer information.

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -26,7 +26,7 @@ set(CMAKE_Fortran_FLAGS_DEBUG)
 
 # Define the CMake project
 project(FMS
-  VERSION 2023.02.0
+  VERSION 2023.03.0
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)
@@ -316,12 +316,28 @@ foreach(kind ${kinds})
                                                  fms2_io/include
                                                  string_utils/include
                                                  mpp/include
+                                                 column_diagnostics/include
+                                                 monin_obukhov/include
                                                  sat_vapor_pres/include
                                                  horiz_interp/include
+                                                 diag_integral/include
+                                                 random_numbers/include
                                                  diag_manager/include
                                                  constants4
+                                                 topography/include
+                                                 axis_utils/include
+                                                 mosaic2/include
                                                  constants
-                                                 axis_utils/include)
+                                                 astronomy/include
+                                                 field_manager/include
+                                                 time_interp/include
+                                                 tracer_manager/include
+                                                 tridiagonal/include
+                                                 interpolator/include
+                                                 coupler/include
+                                                 data_override/include
+                                                 amip_interp/include)
+
   target_compile_definitions(${libTgt}_f PRIVATE "${fms_defs}")
   target_compile_definitions(${libTgt}_f PRIVATE "${${kind}_defs}")
 
@@ -344,7 +360,7 @@ foreach(kind ${kinds})
   if ( CMAKE_Fortran_COMPILER_VERSION MATCHES "1[0-9]\.[0-9]*\.[0-9]*" AND CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
     if(MPI_C_COMPILER MATCHES ".*mpich.*" )
       message(STATUS "Adding -fallow-argument-mismatch flag to compile with GCC >=10 and MPICH")
-      set_target_properties(${libTgt}_f PROPERTIES COMPILE_FLAGS "-fallow-argument-mismatch -w")
+      target_compile_options(${libTgt}_f PRIVATE "-fallow-argument-mismatch;-w")
     endif()
   endif()
 
@@ -357,11 +373,27 @@ foreach(kind ${kinds})
     $<BUILD_INTERFACE:${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}/column_diagnostics/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/astronomy/include>
+    $<BUILD_INTERFACE:${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}/horiz_interp/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/mosaic2/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>)
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/diag_manager/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/topography/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/random_numbers/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/diag_integral/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/diag_manager/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/tracer_manager/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/interpolator/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/coupler/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/mosaic2/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/data_override/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/tridiagonal/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/amip_interp/include>)
 
   target_include_directories(${libTgt} INTERFACE
     $<BUILD_INTERFACE:${moduleDir}>