ufs-community · DusanJovic-NOAA · Mar 21, 2021 · Nov 25, 2020 · Dec 2, 2020 · Dec 14, 2020
diff --git a/.gitmodules b/.gitmodules
@@ -1,7 +1,7 @@
 [submodule "FV3"]
   path = FV3
-  url = https://github.com/NOAA-EMC/fv3atm
-  branch = develop
+  url = https://github.com/pjpegion/fv3atm
+  branch = cld_perts
 [submodule "NEMS"]
   path = NEMS
   url = https://github.com/NOAA-EMC/NEMS
@@ -16,8 +16,8 @@
   branch = develop
 [submodule "stochastic_physics"]
   path = stochastic_physics
-  url = https://github.com/noaa-psd/stochastic_physics
-  branch = master
+  url = https://github.com/pjpegion/stochastic_physics
+  branch = ocn_stoch
 [submodule "CMakeModules"]
   path = CMakeModules
   url = https://github.com/NOAA-EMC/CMakeModules
@@ -28,8 +28,8 @@
   branch = emc/develop
 [submodule "MOM6"]
   path = MOM6-interface/MOM6
-  url = https://github.com/NOAA-EMC/MOM6
-  branch = dev/emc
+  url = https://github.com/pjpegion/MOM6
+  branch = ocn_stoch
 [submodule "CICE"]
   path = CICE-interface/CICE
   url = https://github.com/NOAA-EMC/CICE

diff --git a/CMEPS-interface/CMEPS b/CMEPS-interface/CMEPS
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -136,6 +136,7 @@ set_property(SOURCE FMS/fft/fft.F90 APPEND_STRING PROPERTY COMPILE_FLAGS "-DSGIC
 list(APPEND _fms_defs_public use_libMPI
                              use_netCDF
                              GFS_PHYS
+                             UFS
                              INTERNAL_FILE_NML)
 if(QUAD_PRECISION)
   list(APPEND _fms_defs_public ENABLE_QUAD_PRECISION)
@@ -169,9 +170,9 @@ set_target_properties(fms PROPERTIES PUBLIC_HEADER "${fms_headers}" )
 ###############################################################################
 ### stochastic_physics
 ###############################################################################
-if(NOT DATM)
+#if(NOT DATM)
   add_subdirectory(stochastic_physics)
-endif()
+#endif()
 
 ###############################################################################
 ### FV3 or Data Atmosphere
@@ -280,7 +281,7 @@ 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)
@@ -293,7 +294,7 @@ 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)
@@ -325,8 +326,7 @@ if(DATM)
 endif()
 target_link_libraries(ufs_model PRIVATE ufs
                                         esmf
-                                        NetCDF::NetCDF_Fortran
-                                        ${MKL_LIB})
+                                        NetCDF::NetCDF_Fortran)
 
 ###############################################################################
 ### Install
@@ -344,7 +344,8 @@ install(EXPORT fms-config
   DESTINATION lib/cmake
 )
 install(
-  TARGETS ufs
+  #TARGETS ufs
+  TARGETS ufs stochastic_physics
   EXPORT ufs-config
   LIBRARY DESTINATION lib
   ARCHIVE DESTINATION lib)

diff --git a/FV3 b/FV3
diff --git a/MOM6-interface/CMakeLists.txt b/MOM6-interface/CMakeLists.txt
@@ -22,11 +22,13 @@ set(MOM6SOLO OFF CACHE BOOL "Build MOM6 solo")
 
 # Too many files to list, so include them via this file
 include("mom6_files.cmake")
-
+#SP LIB
+# sp::sp_d
 ### Use common object library for building target library
 add_library(mom6_obj OBJECT ${mom6_src_files})
 set_target_properties(mom6_obj PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(mom6_obj PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_include_directories(mom6_obj PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
+                                            $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/../stochastic_physics>)
 target_include_directories(mom6_obj PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/config_src/dynamic>
                                             $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/src/framework>)
 target_link_libraries(mom6_obj PRIVATE fms
@@ -38,9 +40,11 @@ target_link_libraries(mom6_obj PRIVATE fms
 
 add_library(mom6_nuopc_obj OBJECT ${mom6_nuopc_src_files})
 set_target_properties(mom6_nuopc_obj PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(mom6_nuopc_obj PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_include_directories(mom6_nuopc_obj PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
+                                                  $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/../stochastic_physics>)
 target_include_directories(mom6_nuopc_obj PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/config_src/dynamic>
                                                   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/src/framework>)
+#target_include_directories(mom6_nuopc_obj PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/../stochastic_physics)
 target_link_libraries(mom6_nuopc_obj PRIVATE mom6_obj
                                              fms
                                              esmf)
@@ -56,9 +60,13 @@ target_include_directories(mom6 PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_
                                        $<INSTALL_INTERFACE:mod>)
 target_include_directories(mom6 PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/config_src/dynamic>
                                        $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/src/framework>)
+#target_include_directories(mom6 PUBLIC  ${CMAKE_CURRENT_BINARY_DIR}/../stochastic_physics)
 target_link_libraries(mom6 PUBLIC fms
                                   esmf
                                   NetCDF::NetCDF_Fortran)
+target_link_libraries(mom6 PRIVATE fms
+                                   esmf
+                                   stochastic_physics )
 # OpenMP is disabled in MOM6
 #if(OpenMP_Fortran_FOUND)
 #  target_link_libraries(mom6 PRIVATE OpenMP::OpenMP_Fortran)
@@ -70,12 +78,15 @@ if(MOM6SOLO)
   add_executable(mom6solo ${mom6_solo_src_files})
   add_dependencies(mom6solo mom6_obj)
   set_target_properties(mom6solo PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod_solo)
-  target_include_directories(mom6solo PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
-  target_include_directories(mom6solo PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod_solo>)
+  target_include_directories(mom6solo PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
+                                              $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod_solo>
+                                              $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/../stochastic_physics>)
   target_include_directories(mom6solo PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/config_src/dynamic>
                                               $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/src/framework>)
   target_link_libraries(mom6solo PRIVATE mom6_obj
-                                         fms
+                                         fms  
+                                         stochastic_physics
+                                         esmf
                                          NetCDF::NetCDF_Fortran)
   # OpenMP is disabled in MOM6
   #if(OpenMP_Fortran_FOUND)
@@ -88,7 +99,8 @@ endif()
 ###############################################################################
 
 install(
-  TARGETS mom6
+  #TARGETS mom6 stochastic_physics
+  TARGETS mom6 
   EXPORT  mom6-config
   RUNTIME DESTINATION bin
   LIBRARY DESTINATION lib
@@ -101,5 +113,6 @@ install(EXPORT      mom6-config
         DESTINATION lib/cmake)
 
 if(MOM6SOLO)
-  install(TARGETS mom6solo RUNTIME DESTINATION bin)
+  #install(TARGETS mom6solo RUNTIME DESTINATION bin)
+  install(TARGETS mom6solo stochastic_physics RUNTIME DESTINATION bin)
 endif()
diff --git a/MOM6-interface/MOM6 b/MOM6-interface/MOM6
diff --git a/modulefiles/macosx.gnu/fv3 b/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"
diff --git a/modulefiles/macosx.gnu/fv3_debug b/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"
diff --git a/stochastic_physics b/stochastic_physics
diff --git a/tests/RegressionTests_hera.gnu.log b/tests/RegressionTests_hera.gnu.log
@@ -1,4 +1,4 @@
-Thu Jan 28 20:21:09 UTC 2021
+Tue Jan 12 21:53:42 UTC 2021
 Start Regression test
+3 −3		.github/pull_request_template.md
+16 −6		.github/workflows/extbuild.yml
+0 −4		.gitmodules
+2 −2		CMakeLists.txt
+16 −7		Makefile
+10 −5		cime_config/buildnml
+16 −8		cime_config/config_component.xml
+3 −1		cime_config/config_component_cesm.xml
+9 −100		cime_config/namelist_definition_drv.xml
+3 −23		cime_config/testdefs/testlist_drv.xml
+0 −1		doc/source/field_naming_convention.rst
+1 −1		mediator/CMakeLists.txt
+5 −5		mediator/Makefile
+17 −2		mediator/esmFlds.F90
+440 −49		mediator/esmFldsExchange_hafs_mod.F90
+0 −485		mediator/fd_hafs.yaml
+40 −0		mediator/fd_nems.yaml
+26 −10		mediator/med.F90
+140 −94		mediator/med_fraction_mod.F90
+60 −10		mediator/med_map_mod.F90
+15 −6		mediator/med_methods_mod.F90
+0 −1		mediator/med_phases_prep_ice_mod.F90
+15 −31		mediator/med_phases_prep_lnd_mod.F90
+22 −8		mediator/med_phases_prep_rof_mod.F90
+0 −2		mediator/med_utils_mod.F90
+0 −1		nems/lib/genf90
+0 −0		util/CMakeLists.txt
+6 −3		util/Makefile
+0 −0		util/dtypes.h
+0 −0		util/genf90.pl
+0 −0		util/glc_elevclass_mod.F90
+0 −0		util/perf_mod.F90
+0 −0		util/shr_abort_mod.F90
+0 −0		util/shr_const_mod.F90
+0 −0		util/shr_flux_mod.F90
+0 −0		util/shr_kind_mod.F90
+0 −0		util/shr_log_mod.F90
+0 −0		util/shr_mem_mod.F90
+0 −0		util/shr_mpi_mod.F90
+0 −0		util/shr_pio_mod.F90
+0 −0		util/shr_sys_mod.F90
+2 −2		.gitmodules
+2 −1		CMakeLists.txt
+3 −2		atmos_model.F90
+0 −12		ccpp/CMakeLists.txt
+24 −7		ccpp/data/GFS_typedefs.F90
+36 −11		ccpp/data/GFS_typedefs.meta
+22 −0		ccpp/driver/GFS_diagnostics.F90
+1 −1		ccpp/physics
+0 −506		coupler_main.F90
+2 −0		module_fcst_grid_comp.F90
+13 −13		stochastic_physics/stochastic_physics_wrapper.F90
+15 −0		config_src/nuopc_driver/mom_cap.F90
+53 −1		config_src/nuopc_driver/mom_ocean_model_nuopc.F90
+4 −0		src/core/MOM_forcing_type.F90
+62 −4		src/parameterizations/vertical/MOM_diabatic_driver.F90
+39 −10		src/parameterizations/vertical/MOM_energetic_PBL.F90
+2 −7		CMakeLists.txt
+158 −6		compns_stochy.F90
+0 −1		dezouv_stochy.f
+0 −1		dozeuv_stochy.f
+0 −1		epslon_stochy.f
+536 −0		fftpack_stochy.f
+10 −236		four_to_grid_stochy.F
+0 −1		get_lats_node_a_stochy.f
+3 −3		get_ls_node_stochy.f
+311 −203		get_stochy_pattern.F90
+3 −6		getcon_lag_stochy.f
+10 −19		getcon_spectral.F90
+1 −4		gozrineo_stochy.f
+13 −30		initialize_spectral_mod.F90
+0 −1		makefile
+2 −4		pln2eo_stochy.f
+1 −2		setlats_a_stochy.f
+15 −12		setlats_lag_stochy.f
+32 −54		spectral_layout.F90
+2 −2		standalone_stochy.F90
+205 −101		stochastic_physics.F90
+510 −172		stochy_data_mod.F90
+0 −10		stochy_gg_def.f
+28 −45		stochy_internal_state_mod.F90
+0 −14		stochy_layout_lag.f
+6 −4		stochy_namelist_def.F90
+0 −46		stochy_resol_def.f
+17 −40		sumfln_stochy.f