Merge pull request ufs-community#96 from climbfuji/update_gsl_develop…

…_from_develop_20210721

Update gsl/develop from develop 20210721

.github/pull_request_template.md

@@ -37,6 +37,7 @@ How were these changes tested? What compilers / HPCs was it tested with? Are the
 - [ ] jet.intel
 - [ ] wcoss_cray
 - [ ] wcoss_dell_p3
+- [ ] CI
 
 ## Dependencies
 

.github/workflows/aux.yml

@@ -9,7 +9,7 @@ env:
  base_url: $GITHUB_API_URL/repos/$GITHUB_REPOSITORY/actions/runs
  AUTH: ${{ secrets.GITHUB_TOKEN }}
  aws_instance_id: ${{ secrets.AWS_INSTANCE_ID }}
- no_instances: 6
+ no_instances: 10
 
 
 jobs:

.gitmodules

@@ -38,3 +38,7 @@
  path = CDEPS-interface/CDEPS
  url = https://github.com/NOAA-EMC/CDEPS
  branch = develop
+[submodule "GOCART"]
+ path = GOCART
+ url = https://github.com/GEOS-ESM/GOCART
+ branch = develop

.readthedocs.yaml

@@ -0,0 +1,23 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+ configuration: doc/UsersGuide/source/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+# configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+ version: 3.7
+ install:
+ - requirements: doc/UsersGuide/requirements.txt

CDEPS-interface/CMakeLists.txt

@@ -16,103 +16,92 @@ endif()
 include("cdeps_files.cmake")
 
 # CDEPS/share
-add_library(share STATIC ${cdeps_share_files} ${ufs_cdeps_share_files})
-add_library(cdeps::share ALIAS share)
+add_library(share OBJECT ${cdeps_share_files} ${ufs_cdeps_share_files})
 set_target_properties(share PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
 target_include_directories(share PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ufs/cdeps_share)
-target_include_directories(share PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
- $<INSTALL_INTERFACE:mod>)
-target_link_libraries(share PUBLIC esmf)
-list(APPEND LIB_TARGETS share)
+target_include_directories(share PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_link_libraries(share PRIVATE esmf)
 
 # CDEPS/streams
-add_library(streams STATIC ${cdeps_streams_files})
-add_library(cdeps::streams ALIAS streams)
-add_dependencies(streams cdeps::share)
+add_library(streams OBJECT ${cdeps_streams_files})
+add_dependencies(streams share)
 set_target_properties(streams PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(streams PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
- $<INSTALL_INTERFACE:mod>)
+target_include_directories(streams PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
 target_compile_definitions(streams PUBLIC "DISABLE_FoX")
-target_link_libraries(streams PUBLIC cdeps::share)
-target_link_libraries(streams PUBLIC esmf PIO::PIO_Fortran)
-list(APPEND LIB_TARGETS streams)
+target_link_libraries(streams PRIVATE share)
+target_link_libraries(streams PRIVATE esmf PIO::PIO_Fortran)
 
 # CDEPS/dshr
-add_library(dshr STATIC ${cdeps_dshr_files})
-add_library(cdeps::dshr ALIAS dshr)
-add_dependencies(dshr cdeps::share cdeps::streams)
+add_library(dshr OBJECT ${cdeps_dshr_files})
+add_dependencies(dshr share streams)
 set_target_properties(dshr PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(dshr PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
- $<INSTALL_INTERFACE:mod>)
-target_link_libraries(dshr PUBLIC cdeps::share cdeps::streams)
-target_link_libraries(dshr PUBLIC esmf PIO::PIO_Fortran)
-list(APPEND LIB_TARGETS dshr)
+target_include_directories(dshr PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_link_libraries(dshr PRIVATE share streams)
+target_link_libraries(dshr PRIVATE esmf PIO::PIO_Fortran)
 
 # CDEPS/datm
-add_library(datm STATIC ${cdeps_datm_files})
-add_library(cdeps::datm ALIAS datm)
-add_dependencies(datm cdeps::share cdeps::streams cdeps::dshr)
+add_library(datm OBJECT ${cdeps_datm_files})
+add_dependencies(datm share streams dshr)
 set_target_properties(datm PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(datm PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
- $<INSTALL_INTERFACE:mod>)
-target_link_libraries(datm PUBLIC cdeps::dshr cdeps::share cdeps::streams)
-target_link_libraries(datm PUBLIC esmf PIO::PIO_Fortran)
-list(APPEND LIB_TARGETS datm)
+target_include_directories(datm PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_link_libraries(datm PRIVATE dshr share streams)
+target_link_libraries(datm PRIVATE esmf PIO::PIO_Fortran)
 
 # CDEPS/dice
-add_library(dice STATIC ${cdeps_dice_files})
-add_library(cdeps::dice ALIAS dice)
-add_dependencies(dice cdeps::share cdeps::streams cdeps::dshr)
+add_library(dice OBJECT ${cdeps_dice_files})
+add_dependencies(dice share streams dshr)
 set_target_properties(dice PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(dice PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
- $<INSTALL_INTERFACE:mod>)
-target_link_libraries(dice PUBLIC cdeps::dshr cdeps::share cdeps::streams)
-target_link_libraries(dice PUBLIC esmf)
-list(APPEND LIB_TARGETS dice)
+target_include_directories(dice PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_link_libraries(dice PRIVATE dshr share streams)
+target_link_libraries(dice PRIVATE esmf)
 
 # CDEPS/dlnd
-add_library(dlnd STATIC ${cdeps_dlnd_files})
-add_library(cdeps::dlnd ALIAS dlnd)
-add_dependencies(dlnd cdeps::share cdeps::streams cdeps::dshr)
+add_library(dlnd OBJECT ${cdeps_dlnd_files})
+add_dependencies(dlnd share streams dshr)
 set_target_properties(dlnd PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(dlnd PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
- $<INSTALL_INTERFACE:mod>)
-target_link_libraries(dlnd PUBLIC cdeps::dshr cdeps::share cdeps::streams)
-target_link_libraries(dlnd PUBLIC esmf)
-list(APPEND LIB_TARGETS dlnd)
+target_include_directories(dlnd PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_link_libraries(dlnd PRIVATE dshr share streams)
+target_link_libraries(dlnd PRIVATE esmf)
 
 # CDEPS/docn
-add_library(docn STATIC ${cdeps_docn_files})
-add_library(cdeps::docn ALIAS docn)
-add_dependencies(docn cdeps::share cdeps::streams cdeps::dshr)
+add_library(docn OBJECT ${cdeps_docn_files})
+add_dependencies(docn share streams dshr)
 set_target_properties(docn PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(docn PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
- $<INSTALL_INTERFACE:mod>)
-target_link_libraries(docn PUBLIC cdeps::dshr cdeps::share cdeps::streams)
-target_link_libraries(docn PUBLIC esmf)
-list(APPEND LIB_TARGETS docn)
+target_include_directories(docn PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_link_libraries(docn PRIVATE dshr share streams)
+target_link_libraries(docn PRIVATE esmf)
 
 # CDEPS/drof
-add_library(drof STATIC ${cdeps_drof_files})
-add_library(cdeps::drof ALIAS drof)
-add_dependencies(drof cdeps::share cdeps::streams cdeps::dshr)
+add_library(drof OBJECT ${cdeps_drof_files})
+add_dependencies(drof share streams dshr)
 set_target_properties(drof PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(drof PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
- $<INSTALL_INTERFACE:mod>)
-target_link_libraries(drof PUBLIC cdeps::dshr cdeps::share cdeps::streams)
-target_link_libraries(drof PUBLIC esmf)
-list(APPEND LIB_TARGETS drof)
+target_include_directories(drof PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_link_libraries(drof PRIVATE dshr share streams)
+target_link_libraries(drof PRIVATE esmf)
 
 # CDEPS/dwav
-add_library(dwav STATIC ${cdeps_dwav_files})
-add_library(cdeps::dwav ALIAS dwav)
-add_dependencies(dwav cdeps::share cdeps::streams cdeps::dshr)
+add_library(dwav OBJECT ${cdeps_dwav_files})
+add_dependencies(dwav share streams dshr)
 set_target_properties(dwav PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(dwav PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
- $<INSTALL_INTERFACE:mod>)
-target_link_libraries(dwav PUBLIC cdeps::dshr cdeps::share cdeps::streams)
-target_link_libraries(dwav PUBLIC esmf)
-list(APPEND LIB_TARGETS dwav)
+target_include_directories(dwav PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_link_libraries(dwav PRIVATE dshr share streams)
+target_link_libraries(dwav PRIVATE esmf)
+
+# CDEPS
+add_library(cdeps STATIC $<TARGET_OBJECTS:share>
+ $<TARGET_OBJECTS:streams>
+ $<TARGET_OBJECTS:dshr>
+ $<TARGET_OBJECTS:datm>
+ $<TARGET_OBJECTS:dice>
+ $<TARGET_OBJECTS:dlnd>
+ $<TARGET_OBJECTS:docn>
+ $<TARGET_OBJECTS:drof>
+ $<TARGET_OBJECTS:dwav>)
+add_library(cdeps::cdeps ALIAS cdeps)
+target_include_directories(cdeps PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
+ $<INSTALL_INTERFACE:mod>)
+target_link_libraries(cdeps PUBLIC esmf PIO::PIO_Fortran)
+list(APPEND LIB_TARGETS cdeps)
 
 ###############################################################################
 ### Install

CICE-interface/cice_files.cmake

@@ -154,6 +154,7 @@ list(APPEND cice_nuopc_cmeps_driver_files
  CICE/cicecore/drivers/nuopc/cmeps/ice_prescribed_mod.F90
  CICE/cicecore/drivers/nuopc/cmeps/ice_scam.F90
  CICE/cicecore/drivers/nuopc/cmeps/ice_shr_methods.F90
+ CICE/cicecore/drivers/nuopc/cmeps/ice_mesh_mod.F90
 )
 
 #-- Using NUOPC DMI driver

CMEPS-interface/CMakeLists.txt

@@ -64,13 +64,9 @@ list(APPEND _mediator_files
  CMEPS/mediator/med_phases_post_rof_mod.F90
  CMEPS/mediator/med_phases_post_wav_mod.F90)
 
-list(APPEND _mediator_defs ESMF_VERSION_MAJOR=${ESMF_VERSION_MAJOR}
- ESMF_VERSION_MINOR=${ESMF_VERSION_MINOR})
-
 ### Create target library and set PUBLIC interfaces on the library
 add_library(cmeps STATIC ${_nems_util_files} ${_mediator_files})
 set_target_properties(cmeps PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_compile_definitions(cmeps PUBLIC "${_mediator_defs}")
 target_include_directories(cmeps PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
  $<INSTALL_INTERFACE:mod>)
 target_link_libraries(cmeps PUBLIC esmf

CMakeLists.txt

@@ -16,14 +16,15 @@ list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMakeModules/Modules)
 ###############################################################################
 
 # Valid applications and choices
-list(APPEND VALID_APPS ATM ATMW S2S S2SW NG-GODAS NG-GODAS-NEMSDATM)
+list(APPEND VALID_APPS ATM ATMAERO ATMW S2S S2SW NG-GODAS NG-GODAS-NEMSDATM)
 set(APP NONE CACHE BOOL "Application Name")
 if(NOT (APP IN_LIST VALID_APPS))
  message(FATAL_ERROR "${APP} is not a valid application.\nValid Applications are: ${VALID_APPS}")
 endif()
 
 set(FMS OFF CACHE BOOL "Enable FMS")
 set(FV3 OFF CACHE BOOL "Enable FV3")
+set(UFS_GOCART OFF CACHE BOOL "Enable GOCART")
 set(MOM6 OFF CACHE BOOL "Enable MOM6")
 set(CICE6 OFF CACHE BOOL "Enable CICE6")
 set(WW3 OFF CACHE BOOL "Enable WW3")
@@ -39,6 +40,7 @@ include(cmake/configure_apps.cmake)
 message("")
 message("FMS .............. ${FMS}")
 message("FV3 .............. ${FV3}")
+message("GOCART ........... ${UFS_GOCART}")
 message("MOM6 ............. ${MOM6}")
 message("CICE6 ............ ${CICE6}")
 message("WW3 .............. ${WW3}")
@@ -129,7 +131,7 @@ if(INLINE_POST)
 endif()
 
 # See https://github.com/NOAA-EMC/NCEPLIBS-nemsio/pull/22
-target_link_libraries(nemsio::nemsio INTERFACE w3emc::w3emc_d bacio::bacio_4)
+target_link_libraries(nemsio::nemsio INTERFACE w3nco::w3nco_d bacio::bacio_4)
 
 # Configure Python
 find_package(Python 3 REQUIRED COMPONENTS Interpreter)
@@ -149,14 +151,19 @@ if(FV3)
  add_subdirectory(FV3)
 endif()
 
+###############################################################################
+### GOCART
+###############################################################################
+if(UFS_GOCART)
+ add_subdirectory(GOCART)
+endif()
+
 ###############################################################################
 ### Wave components [WW3]
 ###############################################################################
 if(WW3)
  if(CMAKE_Platform)
- if(${CMAKE_Platform} STREQUAL "wcoss2")
- set(WW3_COMP "wcoss_cray")
- elseif(${CMAKE_Platform} MATCHES "linux*" OR ${CMAKE_Platform} MATCHES "macosx*")
+ if(${CMAKE_Platform} MATCHES "linux*" OR ${CMAKE_Platform} MATCHES "macosx*")
  if (CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
  set(WW3_COMP "gnu")
  elseif (CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
@@ -210,25 +217,26 @@ endif()
 ###############################################################################
 ### UFS Library [NEMS]
 ###############################################################################
-list(APPEND _nems_srcs NEMS/src/module_NEMS_UTILS.F90
- NEMS/src/module_EARTH_GRID_COMP.F90
- NEMS/src/module_NEMS_GRID_COMP.F90
+list(APPEND _nems_srcs NEMS/src/module_EARTH_GRID_COMP.F90
  NEMS/src/module_NEMS_Rusage.F90
  NEMS/src/nems_c_rusage.c)
 
 add_library(ufs ${_nems_srcs})
 set_target_properties(ufs PROPERTIES Fortran_MODULE_DIRECTORY
  ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(ufs PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/NEMS/src)
 target_include_directories(ufs INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
  $<INSTALL_INTERFACE:mod>)
 
-list(APPEND _ufs_defs_private ESMF_VERSION_MAJOR=${ESMF_VERSION_MAJOR})
-
 if(JEDI_DRIVER)
  list(APPEND _ufs_defs_private JEDI_DRIVER=ON)
 endif()
 
+if(UFS_GOCART)
+ add_dependencies(ufs UFS_Aerosols)
+ list(APPEND _ufs_defs_private FRONT_GOCART=Aerosol_Cap)
+ list(APPEND _ufs_libs_public UFS_Aerosols)
+endif()
+
 if(WW3)
  add_dependencies(ufs ww3_nems)
  list(APPEND _ufs_defs_private FRONT_WW3=WMESMFMD)
@@ -242,11 +250,6 @@ if(STOCH_PHYS)
  list(APPEND _ufs_libs_public stochastic_physics)
 endif()
 
-if(FMS)
- add_dependencies(ufs fms)
- list(APPEND _ufs_defs_private FRONT_FMS)
-endif()
-
 if(NEMSdatm)
  add_dependencies(ufs datatm)
  list(APPEND _ufs_defs_private FRONT_NEMS_DATM=datm)
@@ -278,11 +281,9 @@ if(CMEPS)
 endif()
 
 if(CDEPS)
- add_dependencies(ufs cdeps::datm)
- list(APPEND _ufs_defs_private CDEPS-interface/CDEPS
- FRONT_CDEPS_DATM=atm_comp_nuopc)
- include_directories(${CMAKE_CURRENT_BINARY_DIR}/CDEPS-interface/CDEPS/datm)
- target_link_libraries(ufs PUBLIC cdeps::datm)
+ add_dependencies(ufs cdeps::cdeps)
+ list(APPEND _ufs_defs_private FRONT_CDEPS_DATM=cdeps_datm_comp)
+ target_link_libraries(ufs PUBLIC cdeps::cdeps)
 endif()
 
 target_compile_definitions(ufs PRIVATE "${_ufs_defs_private}")
@@ -293,28 +294,7 @@ target_link_libraries(ufs PUBLIC "${_ufs_libs_public}")
 ###############################################################################
 add_executable(ufs_model NEMS/src/MAIN_NEMS.F90)
 add_dependencies(ufs_model ufs)
-
-list(APPEND _ufs_model_defs_private ESMF_VERSION_MAJOR=${ESMF_VERSION_MAJOR})
-
-set_target_properties(ufs_model PROPERTIES Fortran_MODULE_DIRECTORY
- ${CMAKE_CURRENT_BINARY_DIR}/mod)
-
-target_include_directories(ufs_model PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/NEMS/src)
-
-if(WW3)
- list(APPEND _ufs_model_defs_private FRONT_WW3=WMESMFMD)
- target_include_directories(ufs_model PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/WW3/model/mod)
-endif()
-
-target_compile_definitions(ufs_model PRIVATE "${_ufs_model_defs_private}")
-
-if(NEMSdatm OR CDEPS)
- target_link_libraries(ufs_model PUBLIC ufs w3nco::w3nco_d)
-endif()
-
-target_link_libraries(ufs_model PRIVATE ufs
- esmf
- NetCDF::NetCDF_Fortran)
+target_link_libraries(ufs_model ufs esmf w3nco::w3nco_d)
 
 ###############################################################################
 ### Install