Merge pull request NCAR#113 from climbfuji/update_gsl_develop_from_de…

…velop_20211215 Update gsl/develop from develop 2021/12/15
SamuelTrahanNOAA · Dec 15, 2021 · dbdb629 · dbdb629
2 parents 0409aa0 + 9be19a3
commit dbdb629
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diff --git a/CDEPS-interface/CMakeLists.txt b/CDEPS-interface/CMakeLists.txt
@@ -7,7 +7,7 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
   set(CMAKE_Fortran_FLAGS "-g -traceback")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -O -assume realloc_lhs")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -fp-model precise")
-  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fpe0 -ftrapuv")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fpe0 -ftrapuv -init=snan,arrays")
 else()
   message(WARNING "Fortran compiler with ID ${CMAKE_Fortran_COMPILER_ID} will be used with CMake default options")
 endif()

diff --git a/CICE-interface/CICE b/CICE-interface/CICE
diff --git a/CICE-interface/CMakeLists.txt b/CICE-interface/CMakeLists.txt
@@ -9,7 +9,7 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
   set(CMAKE_Fortran_FLAGS "-g -traceback")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -FR -convert big_endian -assume byterecl -ftz -align array64byte -xHOST")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -fp-model precise")
-  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check uninit -check bounds -check pointers -fpe0 -check noarg_temp_created")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check uninit -check bounds -check pointers -fpe0 -check noarg_temp_created -init=snan,arrays")
   set(CMAKE_Fortran_LINK_FLAGS "")
 else()
   message(WARNING "Fortran compiler with ID ${CMAKE_Fortran_COMPILER_ID} will be used with CMake default options")

diff --git a/CMEPS-interface/CMakeLists.txt b/CMEPS-interface/CMakeLists.txt
@@ -12,7 +12,7 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
   set(CMAKE_Fortran_FLAGS "-g -traceback")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -O -assume realloc_lhs")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -fp-model precise")
-  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fpe0 -ftrapuv")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fpe0 -ftrapuv -init=snan,arrays")
   set(CMAKE_Fortran_LINK_FLAGS "")
 else()
   message(WARNING "Fortran compiler with ID ${CMAKE_Fortran_COMPILER_ID} will be used with CMake default options")

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -127,12 +127,9 @@ endif()
 find_package(bacio REQUIRED)
 find_package(sp REQUIRED)
 find_package(w3nco REQUIRED)
-if(INLINE_POST)
-  find_package(upp REQUIRED)
-endif()
 
 # Configure Python
-find_package(Python 3 REQUIRED COMPONENTS Interpreter)
+find_package(Python 3.6 REQUIRED COMPONENTS Interpreter)
 message("Found Python: ${Python_EXECUTABLE}")
 
 ###############################################################################

diff --git a/FV3 b/FV3
diff --git a/HYCOM-interface/CMakeLists.txt b/HYCOM-interface/CMakeLists.txt
@@ -11,7 +11,7 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
   set(CMAKE_Fortran_FLAGS "-g -traceback -xSSE4.2 -mcmodel=small -r8")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -fp-model source -warn nogeneral")
-  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fpe0 -ftrapuv -link_mpi=dbg")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fpe0 -ftrapuv -link_mpi=dbg -init=snan,arrays")
   set(CMAKE_Fortran_LINK_FLAGS "-V ${CMAKE_Fortran_FLAGS} -static-intel")
 else()
   message(WARNING "Fortran compiler with ID ${CMAKE_Fortran_COMPILER_ID} will be used with CMake default options")

diff --git a/MOM6-interface/CMakeLists.txt b/MOM6-interface/CMakeLists.txt
@@ -11,7 +11,7 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -i4 -r8")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fno-alias -auto -safe-cray-ptr -ftz -assume byterecl -sox")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -debug minimal -fp-model source")
-  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fpe0 -ftrapuv")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fpe0 -ftrapuv -init=snan,arrays")
   set(CMAKE_Fortran_LINK_FLAGS "")
 else()
   message(WARNING "Fortran compiler with ID ${CMAKE_Fortran_COMPILER_ID} will be used with CMake default options")

diff --git a/WW3 b/WW3
diff --git a/cmake/GNU.cmake b/cmake/GNU.cmake
@@ -27,7 +27,9 @@ else()
 endif()
 
 # For ccpp
-set(CMAKE_Fortran_FLAGS_DEFAULT_PREC "-fdefault-real-8 -fdefault-double-8")
 set(CMAKE_C_FLAGS_RELEASE       "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELEASE     "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -fPIC" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_BITFORBIT       "-O2 -fPIC" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_BITFORBIT     "-O2 -fPIC" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_BITFORBIT "-O2 -fPIC" CACHE STRING "" FORCE)
diff --git a/cmake/Intel.cmake b/cmake/Intel.cmake
@@ -7,7 +7,7 @@ endif()
 
 if(DEBUG)
     add_definitions(-DDEBUG)
-    set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv")
+    set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv -init=snan,arrays")
     if(DEBUG_LINKMPI)
       if(OPENMP)
         set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -link_mpi=dbg_mt")
@@ -31,24 +31,19 @@ else()
     if(AVX2)
         set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -march=core-avx2")
         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=core-avx2")
-        set(CMAKE_Fortran_FLAGS_OPT "-no-prec-div -no-prec-sqrt -xCORE-AVX2")
     elseif(SIMDMULTIARCH)
         set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -axSSE4.2,CORE-AVX2")
         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -axSSE4.2,CORE-AVX2")
-        set(CMAKE_Fortran_FLAGS_OPT "-no-prec-div -no-prec-sqrt -axSSE4.2,CORE-AVX2")
      elseif(AVX)
         set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -march=core-avx-i")
         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=core-avx-i")
-        set(CMAKE_Fortran_FLAGS_OPT "-no-prec-div -no-prec-sqrt -xCORE-AVX-I")
     endif()
 endif()
 
 # For ccpp
-set(CMAKE_Fortran_FLAGS_DEFAULT_PREC "-real-size 64")
 set(CMAKE_C_FLAGS_RELEASE       "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELEASE     "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -fPIC" CACHE STRING "" FORCE)
-
 set(CMAKE_C_FLAGS_BITFORBIT       "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_BITFORBIT     "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_BITFORBIT "-O2 -fPIC" CACHE STRING "" FORCE)

diff --git a/cmake/configure_macosx.gnu.cmake b/cmake/configure_macosx.gnu.cmake
@@ -1,4 +1,5 @@
-set(INLINE_POST     ON  CACHE BOOL "Enable inline post" FORCE)
+set(INLINE_POST     ON CACHE BOOL "Enable inline post" FORCE)
+set(PARALLEL_NETCDF ON CACHE BOOL "Enable parallel NetCDF" FORCE)
 
 # OpenMP broken for clang compiler
 if(${CMAKE_C_COMPILER_ID} MATCHES "^(Clang|AppleClang)$")

diff --git a/cmake/configure_macosx.intel.cmake b/cmake/configure_macosx.intel.cmake
@@ -0,0 +1,3 @@
+set(INLINE_POST     ON CACHE BOOL "Enable inline post" FORCE)
+set(PARALLEL_NETCDF ON CACHE BOOL "Enable parallel NetCDF" FORCE)
+set(DEBUG_LINKMPI  OFF CACHE BOOL "Enable linkmpi option when DEBUG mode is on" FORCE)
diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst
@@ -497,68 +497,102 @@ The WW3 version number in mod_def.<grd> files must be consistent with version of
 .. _WW3_FixFiles:
 
 .. list-table:: *Input files containing grid information and conservative remapping for global configurations (GFSv16 Wave)*
-   :widths: 35 35 25
+   :widths: 35 35 25 10 10
    :header-rows: 1
 
    * - Filename
      - Description
-     - Resolution
+     - Spatial Resolution
+     - nFreq
+     - nDir
    * - mod_def.aoc_9km
      - Antarctic Ocean PolarStereo [50N 90N]
      - 9km
+     - 50
+     - 36
    * - mod_def.gnh_10m
      - Global mid core [15S 52N]
      - 10 min
+     - 50
+     - 36
    * - mod_def.gsh_15m
      - southern ocean [79.5S 10.5S]
      - 15 min
+     - 50
+     - 36
    * - mod_def.glo_15mxt
      - Global 1/4 extended grid [90S 90S]
      - 15 min
+     - 36
+     - 24
    * - mod_def.points
      - GFSv16-wave spectral grid point output
      - na
-   * - mod_def.points
-     - GFSv16-wave spectral grid point output
+     - na
      - na
    * - rmp_src_to_dst_conserv_002_001.nc
      - Conservative remapping gsh_15m to gnh_10m
      - na
+     - na
+     - na
    * - rmp_src_to_dst_conserv_003_001.nc
      - Conservative remapping aoc_9km to gnh_10m
      - na
+     - na
+     - na
 
 
 .. _WW3_FixFilesp:
 
 .. list-table:: *Input grid information for single global/regional configurations*
-   :widths: 30 50 20
+   :widths: 30 50 20 10 10
    :header-rows: 1
 
    * - Filename
      - Description
-     - Resolution
+     - Spatial Resolution
+     - nFreq
+     - nDir
    * - mod_def.ant_9km
      - Regional polar stereo antarctic grid [90S 50S]
      - 9km
+     - 36
+     - 24
    * - mod_def.glo_10m
      - Global grid [80S 80N]
      - 10 min
+     - 36
+     - 24
    * - mod_def.glo_30m
      - Global grid [80S 80N]
      - 30 min
+     - 36
+     - 36
    * - mod_def.glo_1deg
      - Global grid [85S 85N]
      - 1 degree
+     - 25
+     - 24
    * - mod_def.glo_2deg
      - Global grid [85S 85N]
      - 2 degree
+     - 20
+     - 18
+   * - mod_def.glo_5deg
+     - Global grid [85S 85N]
+     - 5 degree
+     - 18
+     - 12
    * - mod_def.glo_gwes_30m
      - Global NAWES 30 min wave grid [80S 80N]
      - 30 min
+     - 36
+     - 36
    * - mod_def.natl_6m
      - Regional North Atlantic Basin [1.5N 45.5N; 98W 8W]
      - 6 min
+     - 50
+     - 36
 
 Coupled regional configurations require forcing files to fill regions that cannot be interpolated from the atmospheric component. For a list of forcing files used to fill unmapped data points see :numref:`Table %s <WW3_ForcingFiles>`.
 

diff --git a/modulefiles/ufs_cheyenne.gnu b/modulefiles/ufs_cheyenne.gnu
@@ -7,6 +7,7 @@ proc ModulesHelp {} {
 module-whatis "loads UFS Model prerequisites for Cheyenne/GNU"
 
 module load cmake/3.18.2
+module load python/3.7.9
 
 # load programming environment
 module load ncarenv/1.3

diff --git a/modulefiles/ufs_cheyenne.gnu_debug b/modulefiles/ufs_cheyenne.gnu_debug
@@ -7,6 +7,7 @@ proc ModulesHelp {} {
 module-whatis "loads UFS Model prerequisites for Cheyenne/GNU"
 
 module load cmake/3.18.2
+module load python/3.7.9
 
 # load programming environment
 module load ncarenv/1.3

diff --git a/modulefiles/ufs_cheyenne.intel b/modulefiles/ufs_cheyenne.intel
@@ -7,6 +7,7 @@ proc ModulesHelp {} {
 module-whatis "loads UFS Model prerequisites for Cheyenne/Intel"
 
 module load cmake/3.18.2
+module load python/3.7.9
 
 # load programming environment
 module load ncarenv/1.3

diff --git a/modulefiles/ufs_cheyenne.intel_debug b/modulefiles/ufs_cheyenne.intel_debug
@@ -7,6 +7,7 @@ proc ModulesHelp {} {
 module-whatis "loads UFS Model prerequisites for Cheyenne/Intel"
 
 module load cmake/3.18.2
+module load python/3.7.9
 
 # load programming environment
 module load ncarenv/1.3

diff --git a/modulefiles/ufs_common b/modulefiles/ufs_common
@@ -17,7 +17,6 @@ module load g2tmpl/1.10.0
 module load ip/3.3.3
 module load sp/2.3.3
 module load w3nco/2.4.1
-module load upp/10.0.10
 
 module load gftl-shared/v1.3.3
 module load yafyaml/v0.5.1

diff --git a/modulefiles/ufs_common_debug b/modulefiles/ufs_common_debug
@@ -17,7 +17,6 @@ module load g2tmpl/1.10.0
 module load ip/3.3.3
 module load sp/2.3.3
 module load w3nco/2.4.1
-module load upp/10.0.10
 
 module load gftl-shared/v1.3.3
 module load yafyaml/v0.5.1

diff --git a/modulefiles/ufs_macosx.gnu b/modulefiles/ufs_macosx.gnu
@@ -22,20 +22,3 @@ export MPIF90=${MPIF90:-mpif90}
 ## load cmake
 ##
 export CMAKE_Platform=macosx.gnu
-
-##
-## use SIONlib library if installed and environment variable is set
-##
-SIONLIB=${SIONLIB:-}
-if [ ! "x$SIONLIB" == "x" ]; then
-  echo "Use SIONlib installation in ${SIONLIB}"
-  export SIONLIB_INC="-I${SIONLIB}/include -I${SIONLIB}/include/mod_64"
-  export SIONLIB_LIB="-L${SIONLIB}/lib -lsionmpi_f90_64 -lsionser_f90_64 -lsionmpi_64 -lsiongen_64 -lsionser_64 -lsioncom_64 -lsioncom_64_lock_none"
-fi
-
-##
-## Intel MKL library
-##
-#export MKL_DIR=${MKL_DIR:-/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl}
-#export MKL_INC="-m64 -I${MKL_DIR}/include"
-#export MKL_LIB="-L${MKL_DIR}/lib -Wl,-rpath,${MKL_DIR}/lib -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl"
diff --git a/modulefiles/ufs_macosx.gnu_debug b/modulefiles/ufs_macosx.gnu_debug
@@ -22,20 +22,3 @@ export MPIF90=${MPIF90:-mpif90}
 ## load cmake
 ##
 export CMAKE_Platform=macosx.gnu
-
-##
-## use SIONlib library if installed and environment variable is set
-##
-SIONLIB=${SIONLIB:-}
-if [ ! "x$SIONLIB" == "x" ]; then
-  echo "Use SIONlib installation in ${SIONLIB}"
-  export SIONLIB_INC="-I${SIONLIB}/include -I${SIONLIB}/include/mod_64"
-  export SIONLIB_LIB="-L${SIONLIB}/lib -lsionmpi_f90_64 -lsionser_f90_64 -lsionmpi_64 -lsiongen_64 -lsionser_64 -lsioncom_64 -lsioncom_64_lock_none"
-fi
-
-##
-## Intel MKL library
-##
-#export MKL_DIR=${MKL_DIR:-/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl}
-#export MKL_INC="-m64 -I${MKL_DIR}/include"
-#export MKL_LIB="-L${MKL_DIR}/lib -Wl,-rpath,${MKL_DIR}/lib -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl"
diff --git a/modulefiles/ufs_macosx.intel b/modulefiles/ufs_macosx.intel
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+#%Module######################################################################
+##
+##    UFS prerequisites: MACOSX with clang/gfortran compilers
+
+echo "Setting environment variables for NEMSfv3gfs on MACOSX with icc/ifort"
+
+##
+## load programming environment: compiler, flags, paths
+##
+export CC=${MPICC:-mpicc}
+export CXX=${MPICXX:-mpicxx}
+export F77=${MPIF77:-mpif77}
+export F90=${MPIF90:-mpif90}
+export FC=${MPIFORT:-mpifort}
+export CPP=${CPP:-"${F90} -E -x f95-cpp-input"}
+export MPICC=${MPICC:-mpicc}
+export MPIF90=${MPIF90:-mpif90}
+
+##
+## load cmake
+##
+export CMAKE_Platform=macosx.intel
diff --git a/modulefiles/ufs_macosx.intel_debug b/modulefiles/ufs_macosx.intel_debug
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+#%Module######################################################################
+##
+##    UFS prerequisites: MACOSX with clang/gfortran compilers
+
+echo "Setting environment variables for NEMSfv3gfs on MACOSX with icc/ifort"
+
+##
+## load programming environment: compiler, flags, paths
+##
+export CC=${MPICC:-mpicc}
+export CXX=${MPICXX:-mpicxx}
+export F77=${MPIF77:-mpif77}
+export F90=${MPIF90:-mpif90}
+export FC=${MPIFORT:-mpifort}
+export CPP=${CPP:-"${F90} -E -x f95-cpp-input"}
+export MPICC=${MPICC:-mpicc}
+export MPIF90=${MPIF90:-mpif90}
+
+##
+## load cmake
+##
+export CMAKE_Platform=macosx.intel
diff --git a/modulefiles/ufs_wcoss_cray b/modulefiles/ufs_wcoss_cray
@@ -49,12 +49,6 @@ module load sp/2.3.3
 module load w3emc/2.7.3
 module load w3nco/2.4.1
 
-module load gfsio/1.4.1
-module load sfcio/1.4.1
-module load sigio/2.3.2
-
-module load upp/10.0.10
-
 ## WCOSS Cray execution prereqs:
 module load rca
 module load alps

diff --git a/modulefiles/ufs_wcoss_cray_debug b/modulefiles/ufs_wcoss_cray_debug
@@ -49,12 +49,6 @@ module load sp/2.3.3
 module load w3emc/2.7.3
 module load w3nco/2.4.1
 
-module load gfsio/1.4.1
-module load sfcio/1.4.1
-module load sigio/2.3.2
-
-module load upp/10.0.10
-
 ## WCOSS Cray execution prereqs:
 module load rca
 module load alps
+2 −3		.gitmodules
+2 −2		README.md
+68 −12		cice.setup
+40 −18		cicecore/cicedynB/analysis/ice_history.F90
+29 −29		cicecore/cicedynB/analysis/ice_history_bgc.F90
+3 −0		cicecore/cicedynB/analysis/ice_history_drag.F90
+49 −60		cicecore/cicedynB/dynamics/ice_dyn_eap.F90
+59 −45		cicecore/cicedynB/dynamics/ice_dyn_evp.F90
+95 −12		cicecore/cicedynB/dynamics/ice_dyn_shared.F90
+137 −110		cicecore/cicedynB/dynamics/ice_dyn_vp.F90
+11 −4		cicecore/cicedynB/general/ice_forcing.F90
+40 −22		cicecore/cicedynB/general/ice_init.F90
+40 −9		cicecore/drivers/nuopc/cmeps/CICE_InitMod.F90
+73 −7		cicecore/drivers/nuopc/cmeps/CICE_RunMod.F90
+0 −4		cicecore/drivers/nuopc/cmeps/ice_comp_nuopc.F90
+44 −11		cicecore/drivers/nuopc/dmi/CICE_InitMod.F90
+88 −9		cicecore/drivers/nuopc/dmi/CICE_RunMod.F90
+3 −4		configuration/scripts/Makefile
+3 −2		configuration/scripts/ice_in
+3 −2		configuration/scripts/machines/Macros.daley_intel
+7 −0		configuration/scripts/machines/env.cheyenne_gnu
+7 −0		configuration/scripts/machines/env.cheyenne_intel
+7 −0		configuration/scripts/machines/env.cheyenne_pgi
+0 −1		configuration/scripts/options/set_env.box2001
+1 −1		configuration/scripts/options/set_nml.alt03
+1 −0		configuration/scripts/options/set_nml.atmbndyconstant
+1 −0		configuration/scripts/options/set_nml.atmbndymixed
+0 −10		configuration/scripts/options/set_nml.gx1coreii
+0 −8		configuration/scripts/options/set_nml.qc_nonbfb
+16 −0		configuration/scripts/options/set_nml.qcnonbfb
+0 −0		configuration/scripts/options/set_nml.snwitdrdg
+8 −10		configuration/scripts/parse_namelist.sh
+2 −1		configuration/scripts/parse_namelist_from_env.sh
+21 −13		configuration/scripts/parse_settings.sh
+8 −2		configuration/scripts/tests/QC/cice.t-test.py
+2 −2		configuration/scripts/tests/QC/gen_qc_cases.csh
+4 −3		configuration/scripts/tests/base_suite.ts
+48 −0		configuration/scripts/tests/baseline.script
+24 −0		configuration/scripts/tests/create_fails.csh
+0 −2		configuration/scripts/tests/decomp_suite.ts
+1 −0		configuration/scripts/tests/first_suite.ts
+2 −2		configuration/scripts/tests/nothread_suite.ts
+5 −3		configuration/scripts/tests/prod_suite.ts
+0 −1		configuration/scripts/tests/reprosum_suite.ts
+36 −0		configuration/scripts/tests/test_qcchk.script
+36 −0		configuration/scripts/tests/test_qcchkf.script
+7 −3		doc/source/cice_index.rst
+0 −15		doc/source/developer_guide/dg_forcing.rst
+6 −5		doc/source/developer_guide/dg_scripts.rst
+12 −1		doc/source/master_list.bib
+109 −105		doc/source/science_guide/sg_dynamics.rst
+4 −3		doc/source/user_guide/ug_case_settings.rst
+13 −3		doc/source/user_guide/ug_testing.rst
+2 −2		doc/source/user_guide/ug_troubleshooting.rst
+1 −1		icepack
+4 −0		.gitmodules
+2 −0		CMakeLists.txt
+1 −1		atmos_cubed_sphere
+7 −6		ccpp/CMakeLists.txt
+1 −1		ccpp/data/CCPP_typedefs.meta
+111 −47		ccpp/data/GFS_typedefs.F90
+236 −123		ccpp/data/GFS_typedefs.meta
+195 −1		ccpp/driver/GFS_diagnostics.F90
+1 −1		ccpp/framework
+1 −1		ccpp/physics
+105 −0		ccpp/suites/suite_FV3_GFS_v16_coupled_p7_rrtmgp.xml
+35 −27		ccpp/suites/suite_FV3_GFS_v16_p7_rrtmgp.xml
+34 −26		ccpp/suites/suite_FV3_GFS_v16_p8.xml
+0 −86		ccpp/suites/suite_FV3_GSD_SAR.xml
+0 −4		ccpp/suites/suite_FV3_HRRR.xml
+0 −1		ccpp/suites/suite_FV3_RAP.xml
+3 −4		ccpp/suites/suite_FV3_RAP_RRTMGP.xml
+1 −1		ccpp/suites/suite_FV3_RAP_cires_ugwp.xml
+91 −0		ccpp/suites/suite_FV3_RAP_flake.xml
+3 −4		ccpp/suites/suite_FV3_RAP_noah.xml
+2 −2		ccpp/suites/suite_FV3_RAP_noah_sfcdiff_cires_ugwp.xml
+1 −1		ccpp/suites/suite_FV3_RAP_sfcdiff.xml
+2 −2		ccpp/suites/suite_FV3_RAP_unified_ugwp.xml
+0 −84		ccpp/suites/suite_FV3_RRFS_v1alpha.xml
+0 −1		ccpp/suites/suite_FV3_RRFS_v1beta.xml
+2 −2		io/FV3GFS_io.F90
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+82 −3		io/post_gfs.F90
+1 −0		upp
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+3 −0		manual/intro/about.tex
+3 −0		model/bin/cmplr.env
+1 −1		model/src/gx_outp.F90
+1 −1		model/src/w3fldsmd.F90
+3 −3		model/src/w3flx5md.F90
+1 −1		model/src/w3gridmd.F90
+6 −6		model/src/w3initmd.F90
+1 −1		model/src/w3iogrmd.F90
+2 −2		model/src/w3iopomd.F90
+1 −1		model/src/w3odatmd.F90
+3 −3		model/src/w3ounfmetamd.F90
+11 −5		model/src/w3src4md.F90
+3 −3		model/src/w3srcemd.F90
+1 −1		model/src/w3updtmd.F90
+6 −6		model/src/w3wavemd.F90
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+2 −2		model/src/ww3_outp.F90
+1 −1		model/src/ww3_uprstr.F90