Cherrypick ompoffload devturbo take2

.github/workflows/build_cmake_gnu.yml

@@ -10,7 +10,7 @@ jobs:
         omp-flags: [ -DOPENMP=on, -DOPENMP=off ]
         libyaml-flag: [ "", -DWITH_YAML=on ]
     container:
-      image: noaagfdl/hpc-me.ubuntu-minimal:cmake
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:15.1.0
       env:
         CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.libyaml-flag }} -D64BIT=on"
     steps:

.github/workflows/build_ubuntu_gnu.yml

@@ -5,32 +5,40 @@ on: [push, pull_request]
 jobs:
   build:
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash
     strategy:
       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]
+        conf-flag: [ --disable-openmp, --with-mpi=no, --disable-r8-default]
+        input-flag: [--with-yaml, --enable-test-input=/home/unit_tests_input]
+        exclude:
+          - conf-flag: --with-mpi=no
+            input-flag: --enable-test-input=/home/unit_tests_input
     container:
-      image: noaagfdl/hpc-me.ubuntu-minimal:gnu-input
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:15.1.0
       env:
-        TEST_VERBOSE: 1
-        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flags }} ${{ matrix.input-flag }}"
+        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }}"
+        DEBUG_FLAGS: "-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow" # debug compiler flags taken from the mkmf template
+        # diag manager openmp + logical mask tests fail with gcc, these are reproducible outside the CI
+        # test_mpp_clock_begin_end_id is an expected fail that is passing, only happens in the CI
+        # test_time_interp2 tests fail from file issues, only happens in the CI
+        SKIP_TESTS: "test_time_none.10 test_time_sum.10 test_time_avg.10 test_time_min.10 test_time_max.10 test_time_pow.10 test_time_rms.10 test_mpp_clock_begin_end_id.10 test_time_interp2.7 test_time_interp2.8"
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v6.0.1
     - 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} || cat config.log
-    - name: Configure the build with compiler 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/usr/include $FCFLAGS" || cat config.log
-    - name: Build the library
-      run: make distcheck
-      if: ${{ matrix.conf-flags != '--with-mpi=no' }}
+      run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} FCFLAGS="$FCFLAGS $DEBUG_FLAGS" || (cat config.log && exit 1)
+    - name: Run distcheck (compiles, tests, and packages)
+      run: make distcheck 2>&1 > distcheck.log
+      if: ${{ matrix.conf-flag != '--with-mpi=no' }}
+    - name: Output errors on failure
+      run: grep -E "^FAIL:|^XPASS:" distcheck.log
+      if: failure()
+    - name: Upload log on failure
+      uses: actions/upload-artifact@v7.0.0
+      if: failure()
+      with:
+        path: distcheck.log
     - 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' }}

.github/workflows/intel_pr.yml

@@ -3,17 +3,17 @@ jobs:
   intel-autotools:
     runs-on: ubuntu-latest
     container:
-      image: intel/oneapi-hpckit:2022.2-devel-ubuntu20.04
+      image: intel/oneapi-hpckit:2025.2.2-0-devel-ubuntu24.04
       env:
-        CC: mpiicc
-        FC: mpiifort
+        CC: mpicc
+        FC: mpiifx
         CFLAGS:  "-I/libs/include"
         FCFLAGS: "-I/libs/include -g -traceback"
         LDFLAGS: "-L/libs/lib"
         TEST_VERBOSE: 1
         I_MPI_FABRICS: "shm" # needed for mpi in image
         # intel bug causes some failures with shm option(required in container)
-        SKIP_TESTS: "test_mpp_update_domains.1 test_update_domains_performance.1 test_diag_manager2.23"
+        SKIP_TESTS: "test_fms2_io.1 test_mpp_update_domains.1 test_update_domains_performance.1 test_diag_manager2.23"
     steps:
     - name: Cache dependencies
       id: cache
@@ -22,31 +22,33 @@ jobs:
         path: /libs
         key: ${{ runner.os }}-intel-libs
     - name: Install packages for building
-      run: apt update && apt install -y autoconf libtool automake zlibc zlib1g-dev
+      run: apt update && apt install -y autoconf libtool automake zlib1g-dev
     - if: steps.cache.outputs.cache-hit != 'true'
       name: Build netcdf
       run: |
         mkdir /libs
-        wget https://hdf-wordpress-1.s3.amazonaws.com/wp-content/uploads/manual/HDF5/HDF5_1_12_2/source/hdf5-1.12.2.tar.gz
-        tar xf hdf5-1.12.2.tar.gz && cd hdf5-1.12.2
+        # hdf5
+        wget https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/downloads/hdf5-1.14.6.tar.gz
+        tar xf hdf5-1.14.6.tar.gz && cd hdf5-1.14.6
         ./configure --prefix=/libs
         make -j install && cd ..
-        wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.8.1.tar.gz
-        tar xf v4.8.1.tar.gz && cd netcdf-c-4.8.1
-        ./configure --prefix=/libs --enable-remote-fortran-bootstrap
-        make -j install
-        # sets this here to pass embeded configure checks
-        export LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH"
-        make -j -k build-netcdf-fortran
-        make -j install-netcdf-fortran
-        wget https://github.com/yaml/libyaml/releases/download/0.2.5/yaml-0.2.5.tar.gz
-        tar xf yaml-0.2.5.tar.gz && cd yaml-0.2.5
+        # netcdf-c
+        wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.3.tar.gz
+        tar xf v4.9.3.tar.gz && cd netcdf-c-4.9.3
+        ./configure --prefix=/libs --disable-libxml2 --enable-netcdf-4 --enable-shared
+        make -j install && cd ..
+        # netcdf-fortran
+        wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.2.tar.gz
+        tar xf v4.6.2.tar.gz && cd netcdf-fortran-4.6.2
         ./configure --prefix=/libs
-        make -j install && cd
+        make -j install && cd ..
     - name: checkout
       uses: actions/checkout@v2
     - name: Configure
-      run: autoreconf -if ./configure.ac && ./configure --with-yaml
+      run: |
+        autoreconf -if ./configure.ac
+        export LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH"
+        ./configure
     - name: Compile
       run: make -j || make
     - name: Run test suite

CMakeLists.txt

@@ -159,9 +159,6 @@ 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
   mosaic2/grid2.F90
   mosaic2/mosaic2.F90
   mpp/mpp.F90
@@ -195,11 +192,6 @@ list(APPEND fms_fortran_src_files
 # Collect FMS C source files
 list(APPEND fms_c_src_files
   affinity/affinity.c
-  mosaic/create_xgrid.c
-  mosaic/gradient_c2l.c
-  mosaic/interp.c
-  mosaic/mosaic_util.c
-  mosaic/read_mosaic.c
   mpp/mpp_memuse.c
   parser/yaml_parser_binding.c
   parser/yaml_output_functions.c

Makefile.am

@@ -46,7 +46,6 @@ SUBDIRS = \
   fms \
   parser \
   affinity \
-  mosaic \
   time_manager \
   axis_utils \
   diag_manager \

configure.ac

@@ -54,12 +54,6 @@ AS_IF([test x${CRAYPE_VERSION:+yes} = "xyes"],[
 
 
 # Process user optons.
-AC_ARG_ENABLE([mixed-mode],
-  [AS_HELP_STRING([--enable-mixed-mode],
-    [Build using mixed mode.  Enables both 64-bit and 32-bit reals in Fortran. This option will be ignored if --disable-fortran-flag-setting is also given.])])
-AS_IF([test ${enable_mixed_mode:-no} = no],
-  [enable_mixed_mode=no],
-  [enable_mixed_mode=yes])
 AC_ARG_WITH([mpi],
   [AS_HELP_STRING([--with-mpi],
     [Build with MPI support.  This option will be ignored if --disable-fortran-flag-setting is also given. (Default yes)])])
@@ -110,6 +104,13 @@ AS_IF([test ${enable_8byte_int:-no} = yes],
   [enable_8byte_int=yes],
   [enable_8byte_int=no])
 
+AC_ARG_ENABLE([r8-default],
+  [AS_HELP_STRING([--disable-r8-default],
+    [Disables the build from adding the 8 byte default real kind flag during compilation (default no)])])
+AS_IF([test ${enable_r8_default:-yes} = yes],
+  [enable_r8_default=yes],
+  [enable_r8_default=no])
+
 # user enabled testing with input files
 AC_MSG_CHECKING([whether to enable tests with input files])
 AC_ARG_ENABLE([test-input],
@@ -190,8 +191,10 @@ if test $with_yaml = yes; then
   AC_DEFINE([use_yaml], [1], [This is required to use yaml parser])
 
   AM_CONDITIONAL([SKIP_PARSER_TESTS], false )
+  AM_CONDITIONAL([USING_YAML], true)
 else
   AM_CONDITIONAL([SKIP_PARSER_TESTS], true )
+  AM_CONDITIONAL([USING_YAML], false)
 fi
 
 # Require netCDF
@@ -203,7 +206,6 @@ 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
@@ -258,6 +260,28 @@ GX_FC_CHECK_MOD([netcdf], [], [], [AC_MSG_ERROR([Can't find the netCDF Fortran m
 GX_FORTRAN_SEARCH_LIBS([nf90_create], [netcdff], [use netcdf], [iret = nf90_create('foo.nc', 1, ncid)], [],
   [AC_MSG_ERROR([Can't find the netCDF Fortran library.  Set LDFLAGS/LIBS])])
 
+# Check if we get a floating point exception with netcdf
+# this will only get triggered if you have FPE traps enabled via FCFLAGS
+AC_MSG_CHECKING([if HDF5 version causes floating point exceptions with set flags])
+AC_RUN_IFELSE([AC_LANG_PROGRAM([], [[
+      use netcdf
+      integer i, j
+      j = nf90_create("test.nc", NC_WRITE, i)
+]])], [hdf5_fpe_bug=no], [hdf5_fpe_bug=yes])
+AC_MSG_RESULT([$hdf5_fpe_bug])
+if test $hdf5_fpe_bug = yes; then
+  AC_MSG_ERROR([The HDF5 version used to build netcdf is incompatible with the set FCFLAGS. dnl
+NetCDF must be built with a HDF5 version other than 1.14.3 to support floating point exception traps.])
+fi
+
+rm -f test.nc
+
+# Check if we need a flag to not capitalize module output (needed with cray compiler)
+GX_FC_MOD_CASE_FLAG([FCFLAGS="$FCFLAGS $FC_MOD_CASE_FLAG"])
+
+# Check if new unit is supported
+GX_FC_08_OPEN_NEWUNIT([], [AC_MSG_ERROR([Compiler support for use of newunit argument is required to build FMS])])
+
 # Check if Fortran compiler has the Class, Character array assign bug
 GX_FC_CLASS_CHAR_ARRAY_BUG_CHECK()
 
@@ -276,7 +300,6 @@ AC_OPENMP()
 AC_LANG_POP(Fortran)
 
 # We passed all the tests.  Set the required defines.
-AC_DEFINE([use_netCDF], [1], [This is required for the library to build])
 if test $with_mpi = yes; then
   AC_DEFINE([use_libMPI], [1], [This is required for the library to build])
 fi
@@ -292,13 +315,8 @@ if test $enable_setting_flags = yes; then
   # necessary fortran flags.
   AC_FC_LINE_LENGTH([unlimited])
 
-  # Will we build with default 64-bit reals in Fortran, or do mixed mode?
-  if test $enable_mixed_mode = yes; then
-    GX_FC_DEFAULT_REAL_KIND4_FLAG([dnl
-      FCFLAGS="$FCFLAGS $FC_DEFAULT_REAL_KIND8_FLAG"])
-    AC_DEFINE([OVERLOAD_R4], [1], [Set to overload the R4 Fortran routines])
-    AC_DEFINE([OVERLOAD_R8], [1], [Set to overload the R8 Fortran routines])
-  else
+  # Builds with r8 default unless disable flag is given
+  if test $enable_r8_default = yes; then
     GX_FC_DEFAULT_REAL_KIND8_FLAG([dnl
       FCFLAGS="$FCFLAGS $FC_DEFAULT_REAL_KIND8_FLAG"])
   fi
@@ -316,6 +334,11 @@ if test $enable_setting_flags = yes; then
     AC_DEFINE([no_8byte_integers], [1], [Set to disable 8 byte integer Fortran routines])
   fi
 
+  # Builds with C data types
+  if test $enable_portable_kinds = yes; then
+    AC_DEFINE([PORTABLE_KINDS], [1], [Set to define KIND parameters to iso_c_binding KIND parameters])
+  fi
+
   # Add Cray Pointer support flag
   if test ! -z "$FC_CRAY_POINTER_FLAG"; then
     FCFLAGS="$FCFLAGS $FC_CRAY_POINTER_FLAG"
@@ -434,7 +457,6 @@ AC_CONFIG_FILES([
   tridiagonal/Makefile
   tracer_manager/Makefile
   topography/Makefile
-  mosaic/Makefile
   mosaic2/Makefile
   monin_obukhov/Makefile
   memutils/Makefile
@@ -475,7 +497,6 @@ AC_CONFIG_FILES([
   test_fms/horiz_interp/Makefile
   test_fms/field_manager/Makefile
   test_fms/axis_utils/Makefile
-  test_fms/mosaic/Makefile
   test_fms/affinity/Makefile
   test_fms/coupler/Makefile
   test_fms/parser/Makefile

constants/cesm_constants.fh

@@ -27,12 +27,14 @@ character(len=18), public, parameter :: constants_version = 'FMSConstants: CESM'
 ! Constants below use CESM shr values
 
 real(R8),   public, parameter :: KAPPA  = RDGAS/CP_AIR             !< RDGAS / CP_AIR [dimensionless]
-real(R8),   public, parameter :: RHO0R   = 1.0_r8/RHO0        	   !< Reciprocal of average density of sea water [m^3/kg]
+real(R8),   public, parameter :: RHO0R   = 1.0_r8/RHO0             !< Reciprocal of average density of sea water
+                                                                   !!  [m^3/kg]
 real(R8),   public, parameter :: RHO_CP  = RHO0*CP_OCEAN           !< (kg/m^3)*(cal/kg/deg C)(joules/cal) =
                                                                    !<(joules/m^3/deg C) [J/m^3/deg]
-real(R8),   public, parameter :: ES0 = 1.0_r8                      !< Humidity factor. Controls the humidity content of the
-                                                                   !< atmosphere through the Saturation Vapour Pressure
-                                                                   !< expression when using DO_SIMPLE. [dimensionless]
+real(R8),   public, parameter :: ES0 = 1.0_r8                      !< Humidity factor. Controls the humidity content of
+                                                                   !! the atmosphere through the Saturation Vapour
+                                                                   !! Pressure expression when using DO_SIMPLE.
+                                                                   !! [dimensionless]
 real(R8),   public, parameter :: HLS = HLV + HLF                   !< Latent heat of sublimation [J/kg]
 real(R8),   public, parameter :: WTMOZONE =  47.99820_r8           !< Molecular weight of ozone [AMU]
 real(R8),   public, parameter :: WTMC     =  12.00000_r8           !< Molecular weight of carbon [AMU]
@@ -49,15 +51,22 @@ real(R8),   public, parameter :: SECONDS_PER_HOUR   = 3600._r8     !< Seconds in
 real(R8),   public, parameter :: SECONDS_PER_MINUTE = 60._r8       !< Seconds in a minute [s]
 real(R8),   public, parameter :: RAD_TO_DEG         = 180._r8/PI   !< Degrees per radian [deg/rad]
 real(R8),   public, parameter :: DEG_TO_RAD         = PI/180._r8   !< Radians per degree [rad/deg]
-real(R8),   public, parameter :: RADIAN             = RAD_TO_DEG   !< Equal to RAD_TO_DEG for backward compatability. [rad/deg]
-real(R8),   public, parameter :: ALOGMIN            = -50.0_r8     !< Minimum value allowed as argument to log function [N/A]
-real(R8),   public, parameter :: EPSLN              = 1.0e-40_r8   !< A small number to prevent divide by zero exceptions [N/A]
-real(R8),   public, parameter :: RADCON = ((1.0E+02_r8*GRAV)/(1.0E+04_r8*CP_AIR))*SECONDS_PER_DAY !< convert flux divergence
-                                                                   !to heating rate in degrees per day [deg sec/(cm day)]
-real(R8),   public, parameter :: RADCON_MKS  = (GRAV/CP_AIR)*SECONDS_PER_DAY !< Factor used to convert flux divergence to
-                                                                   !< heating rate in degrees per day [deg sec/(m day)]
-real(R8),   public, parameter :: O2MIXRAT    = 2.0953E-01_r8       !< Mixing ratio of molecular oxygen in air [dimensionless]
-real(R8),   public, parameter :: C2DBARS     = 1.e-4_r8            !< rho*g*z(mks) to dbars: 1dbar = 10^4 (kg/m^3)(m/s^2)m [dbars]
+real(R8),   public, parameter :: RADIAN             = RAD_TO_DEG   !< Equal to RAD_TO_DEG for backward compatability.
+                                                                   !! [rad/deg]
+real(R8),   public, parameter :: ALOGMIN            = -50.0_r8     !< Minimum value allowed as argument to log function
+                                                                   !! [N/A]
+real(R8),   public, parameter :: EPSLN              = 1.0e-40_r8   !< A small number to prevent divide by zero
+                                                                   !! exceptions [N/A]
+real(R8),   public, parameter :: RADCON = ((1.0E+02_r8*GRAV)/(1.0E+04_r8*CP_AIR))*SECONDS_PER_DAY !< convert flux
+                                                                   !! divergence to heating rate in degrees per day
+                                                                   !! [deg sec/(cm day)]
+real(R8),   public, parameter :: RADCON_MKS  = (GRAV/CP_AIR)*SECONDS_PER_DAY !< Factor used to convert flux divergence
+                                                                   !! to heating rate in degrees per day
+                                                                   !! [deg sec/(m day)]
+real(R8),   public, parameter :: O2MIXRAT    = 2.0953E-01_r8       !< Mixing ratio of molecular oxygen in air
+                                                                   !! [dimensionless]
+real(R8),   public, parameter :: C2DBARS     = 1.e-4_r8            !< rho*g*z(mks) to dbars: 1dbar = 10^4
+                                                                   !! (kg/m^3)(m/s^2)m [dbars]
 real(R8),   public, parameter :: KELVIN      = 273.15_r8           !< Degrees Kelvin at zero Celsius [K]
 
 #ifdef SMALL_EARTH
@@ -70,4 +79,4 @@ real(R8),   public, parameter :: KELVIN      = 273.15_r8           !< Degrees Ke
 #endif
 #else
  real, public, parameter :: small_fac = 1._r8
-#endif
+#endif

constants/fmsconstants.F90

@@ -55,7 +55,6 @@ module FMSconstants
 
   use platform_mod, only: r4_kind, r8_kind
 
-#define CESM_CONSTANTS
 #if defined(CESM_CONSTANTS)
 use shr_kind_mod,   only : R8 => shr_kind_r8
 use shr_const_mod,  only : &

diag_manager/Makefile.am

@@ -33,6 +33,7 @@ noinst_LTLIBRARIES = libdiag_manager.la
 libdiag_manager_la_SOURCES = \
   diag_axis.F90 \
   diag_data.F90 \
+  mppnccombine.c \
   diag_grid.F90 \
   diag_manager.F90 \
   diag_output.F90 \