Update gsd/develop from develop 2020/11/18

.gitignore

@@ -1,2 +1,70 @@
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+*.x
+
+# system files
+*.swp
+*~
+.DS_Store
+
+# python files
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# CMake files and directories
+build*/
+install*/
+CMakeLists.txt.user
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
+
+# repo-specific ignorables
 coupled*.mk
 rt.conf.single
+ufs_model
+tests/modules.fv3_*
+tests/ecflow_run/
+tests/log_*/
+tests/lock/
+tests/Compile_*.log
+tests/fail_test
+log*
+build*.log*

.gitmodules

@@ -1,20 +1,40 @@
 [submodule "FV3"]
-	path = FV3
-	url = https://github.com/NOAA-GSD/fv3atm
-	branch = gsd/develop
+  path = FV3
+  url = https://github.com/NOAA-GSD/fv3atm
+  branch = gsd/develop
 [submodule "NEMS"]
-	path = NEMS
-	url = https://github.com/NOAA-EMC/NEMS
-	branch = develop
+  path = NEMS
+  url = https://github.com/NOAA-EMC/NEMS
+  branch = develop
 [submodule "FMS"]
-	path = FMS
-	url = https://github.com/NOAA-GFDL/FMS
-	branch = master
+  path = FMS
+  url = https://github.com/NOAA-GFDL/FMS
+  branch = master
 [submodule "WW3"]
-	path = WW3
-	url = https://github.com/NOAA-EMC/WW3
-	branch = develop
+  path = WW3
+  url = https://github.com/NOAA-EMC/WW3
+  branch = develop
 [submodule "stochastic_physics"]
-	path = stochastic_physics
-	url = https://github.com/noaa-psd/stochastic_physics
-	branch = master
+  path = stochastic_physics
+  url = https://github.com/noaa-psd/stochastic_physics
+  branch = master
+[submodule "CMakeModules"]
+  path = CMakeModules
+  url = https://github.com/NOAA-EMC/CMakeModules
+  branch = develop
+[submodule "CMEPS"]
+  path = CMEPS-interface/CMEPS
+  url = https://github.com/NOAA-EMC/CMEPS.git
+  branch = emc/develop
+[submodule "MOM6"]
+  path = MOM6-interface/MOM6
+  url = https://github.com/NOAA-EMC/MOM6
+  branch = dev/emc
+[submodule "CICE"]
+  path = CICE-interface/CICE
+  url = https://github.com/NOAA-EMC/CICE
+  branch = emc/develop
+[submodule "DATM"]
+  path = DATM
+  url = https://github.com/NOAA-EMC/NEMSdatm
+  branch = develop

CICE-interface/CMakeLists.txt

@@ -0,0 +1,101 @@
+### CICE Fortran compiler flags
+if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
+  set(CMAKE_Fortran_FLAGS "-g -fbacktrace")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fconvert=big-endian -ffree-line-length-none ")
+  set(CMAKE_Fortran_FLAGS_RELEASE "-O2")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -Wall -Wextra -fcheck=bounds -ffpe-trap=invalid,zero,overflow,underflow" )
+  set(CMAKE_Fortran_LINK_FLAGS "" )
+elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
+  set(CMAKE_Fortran_FLAGS "-g -traceback")
+  set(CMAKE_Fortran_FLAGS "${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 -link_mpi=dbg")
+  set(CMAKE_Fortran_LINK_FLAGS "")
+else()
+  message(WARNING "Fortran compiler with ID ${CMAKE_Fortran_COMPILER_ID} will be used with CMake default options")
+endif()
+
+### CICE C compiler flags
+if(CMAKE_C_COMPILER_ID MATCHES "GNU")
+  set(CMAKE_C_FLAGS "-g")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+  set(CMAKE_C_FLAGS_RELEASE "-O3")
+  set(CMAKE_C_FLAGS_DEBUG "-O0")
+  set(CMAKE_C_LINK_FLAGS "")
+elseif(CMAKE_C_COMPILER_ID MATCHES "Intel")
+  set( CMAKE_C_FLAGS "-g -traceback")
+  set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -xHOST")
+  set( CMAKE_C_FLAGS_RELEASE "-O2 -fp-model precise")
+  set( CMAKE_C_FLAGS_DEBUG "-O0 -ftrapuv")
+  set( CMAKE_C_LINK_FLAGS "")
+elseif(CMAKE_C_COMPILER_ID MATCHES "Clang")
+  set(CMAKE_C_FLAGS "-g")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+  set( CMAKE_C_FLAGS_RELEASE "-O3" )
+  set( CMAKE_C_FLAGS_DEBUG "-O0" )
+  set( CMAKE_C_LINK_FLAGS "" )
+else()
+  message(WARNING "C compiler with ID ${CMAKE_C_COMPILER_ID} will be used with CMake default options")
+endif()
+
+# Configuration Options
+set(CICE_IO "NetCDF" CACHE STRING "CICE OPTIONS: Choose IO options.")
+set_property(CACHE CICE_IO PROPERTY STRINGS "NetCDF" "PIO" "Binary")
+
+# Too many files to list, so include them via this file
+include("cice_files.cmake")
+
+# Collect source files for library
+list(APPEND lib_src_files
+  ${cice_shared_files}
+  ${cice_shared_files_c}
+  ${icepack_files}
+  ${cice_mpi_comm_files}
+  ${cice_nuopc_cmeps_driver_files})
+
+list(APPEND _cice_defs FORTRANUNDERSCORE
+                       coupled)
+
+# Select IO source files based on CICE_IO
+if(CICE_IO MATCHES "NetCDF")
+  list(APPEND lib_src_files ${cice_netcdf_io_files})
+  list(APPEND _cice_defs USE_NETCDF)
+elseif(CICE_IO MATCHES "PIO")
+  list(APPEND lib_src_files ${cice_pio2_io_files})
+  list(APPEND _cice_defs USE_NETCDF)
+elseif(CICE_IO MATCHES "Binary")
+  list(APPEND lib_src_files ${cice_binary_io_files})
+endif()
+
+### Create target library and set PUBLIC interfaces on the library
+add_library(cice STATIC ${lib_src_files})
+set_target_properties(cice PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
+target_compile_definitions(cice PUBLIC "${_cice_defs}")
+target_include_directories(cice PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
+                                       $<INSTALL_INTERFACE:mod>)
+target_link_libraries(cice PUBLIC esmf)
+if(CICE_IO MATCHES "^(NetCDF|PIO)$")
+  target_link_libraries(cice PUBLIC NetCDF::NetCDF_Fortran)
+  if(CICE_IO MATCHES "PIO")
+    target_link_libraries(cice PUBLIC PIO::PIO_Fortran)
+  endif()
+endif()
+if(OpenMP_Fortran_FOUND)
+  target_link_libraries(cice PRIVATE OpenMP::OpenMP_Fortran)
+endif()
+
+###############################################################################
+### Install
+###############################################################################
+
+install(
+  TARGETS cice
+  EXPORT  cice-config
+  LIBRARY DESTINATION lib
+  ARCHIVE DESTINATION lib
+  COMPONENT Library)
+
+install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod DESTINATION ${CMAKE_INSTALL_PREFIX}/CICE)
+
+install(EXPORT      cice-config
+        DESTINATION lib/cmake)