Stoch updates (#372)

Addition of stochastic physics restarts in netCDF format that will be written at the restart interval, and at end of run.
Addition of stochastic cloud perturbation and microphysics perturbations for SPPT.
Clean up of stochastic physics code.

Co-authored-by: mlee03 <Mikyung.Lee@noaa.gov>
Co-authored-by: MinsukJi-NOAA <minsuk.ji@noaa.gov>
Co-authored-by: Brian Curtis <brian.curtis@noaa.gov>

CMakeLists.txt

@@ -139,56 +139,27 @@ endif()
 ###############################################################################
 ### FMS
 ###############################################################################
-include(fms_files.cmake)
-add_library(fms ${fms_src_files} ${fms_headers})
-
-list(APPEND _fms_defs_public use_libMPI
-                             use_netCDF
-                             GFS_PHYS
-                             INTERNAL_FILE_NML)
-if(QUAD_PRECISION)
-  list(APPEND _fms_defs_public ENABLE_QUAD_PRECISION)
-endif()
+set(GFS_PHYS ON CACHE BOOL "Enable GFS Physics")
+if(NOT 32BIT)
+   set(64BIT ON CACHE BOOL "Enable 64-bit")
 
-# check gettid
-include(CheckFunctionExists)
-check_function_exists(gettid HAVE_GETTID)
-if(HAVE_GETTID)
-  list(APPEND _fms_defs_public HAVE_GETTID)
 endif()
-
-target_compile_definitions(fms PUBLIC "${_fms_defs_public}")
-
-if(32BIT)
-  list(APPEND _fms_defs_private OVERLOAD_R4
-                                OVERLOAD_R8)
+if(NOT QUAD_PRECISION)
+  set(ENABLE_QUAD_PRECISION OFF CACHE BOOL "Enable Quad-precision")
 endif()
 
-target_compile_definitions(fms PRIVATE "${_fms_defs_private}")
-
-target_include_directories(fms PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/FMS/include>
-                                      $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/FMS/fms>
-                                      $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/FMS/fms2_io/include>
-                                      $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/FMS/mod>
-                                      $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/FMS/mpp/include>)
-target_include_directories(fms INTERFACE
-                                      $<INSTALL_INTERFACE:${CMAKE_INSTALL_PREFIX}/include>
-                                      $<INSTALL_INTERFACE:${CMAKE_INSTALL_PREFIX}/mod>)
-target_link_libraries(fms PUBLIC MPI::MPI_Fortran
-                                 NetCDF::NetCDF_Fortran)
-if(OpenMP_Fortran_FOUND)
-  target_link_libraries(fms PRIVATE OpenMP::OpenMP_Fortran)
+add_subdirectory(FMS)
+
+if(32BIT) 
+   add_library(fms ALIAS fms_r4)
+else()
+   add_library(fms ALIAS fms_r8)
 endif()
-set_target_properties(fms PROPERTIES ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/FMS)
-set_target_properties(fms PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/FMS/mod)
-set_target_properties(fms PROPERTIES PUBLIC_HEADER "${fms_headers}" )
 
 ###############################################################################
 ### stochastic_physics
 ###############################################################################
-if(NOT DATM)
   add_subdirectory(stochastic_physics)
-endif()
 
 ###############################################################################
 ### FV3 or Data Atmosphere
@@ -291,7 +262,7 @@ endif()
 target_include_directories(ufs INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
                                          $<INSTALL_INTERFACE:mod>)
 
-target_link_libraries(ufs PUBLIC esmf)
+target_link_libraries(ufs PUBLIC esmf stochastic_physics)
 
 if(DATM)
   target_link_libraries(ufs PUBLIC datatm)
@@ -304,7 +275,7 @@ if(S2S)
                                 FRONT_CICE6=ice_comp_nuopc
                                 CMEPS
                                 FRONT_CMEPS=MED)
-  add_dependencies(ufs mom6 cice cmeps)
+  add_dependencies(ufs mom6 cice cmeps stochastic_physics)
   target_link_libraries(ufs PUBLIC mom6
                                    cice
                                    cmeps)
@@ -336,26 +307,14 @@ if(DATM)
 endif()
 target_link_libraries(ufs_model PRIVATE ufs
                                         esmf
-                                        NetCDF::NetCDF_Fortran
-                                        ${MKL_LIB})
+                                        NetCDF::NetCDF_Fortran)
 
 ###############################################################################
 ### Install
 ###############################################################################
-install(
-  TARGETS fms
-  EXPORT fms-config
-  LIBRARY DESTINATION lib
-  ARCHIVE DESTINATION lib
-  PUBLIC_HEADER DESTINATION include )
-
-install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/FMS/mod DESTINATION ${CMAKE_INSTALL_PREFIX})
-
-install(EXPORT fms-config
-  DESTINATION lib/cmake
-)
 install(
   TARGETS ufs
+
   EXPORT ufs-config
   LIBRARY DESTINATION lib
   ARCHIVE DESTINATION lib)

modulefiles/macosx.gnu/fv3

@@ -39,6 +39,6 @@ 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"
+#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"

modulefiles/macosx.gnu/fv3_debug

@@ -39,6 +39,6 @@ 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"
+#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"