Merge branch 'release-v8.2.0'

MPAS Version 8.2.0

This release of MPAS introduces several significant changes to MPAS-Atmosphere.

New physics

 * The Noah-MP v5.0.1 land-surface model is now available by setting
   config_lsm_scheme = 'sf_noahmp' in the &physics namelist group.

   - New static files that include the 'soilcomp', 'soilcl1', 'soilcl2',
     'soilcl3', and 'soilcl4' fields are required when activating Noah-MP in
     the model.

 * The aerosol-aware Thompson microphysics (as in WRF v4.1.4) is available by
   setting config_microp_scheme = 'mp_thompson_aerosols' in the &physics
   namelist group.

   - An aerosol climatology file (QNWFA_QNIFA_SIGMA_MONTHLY.dat) is used when
     running the init_atmosphere_model program to produce initial and lateral
     boundary conditions for nifa and nwfa.

Physics changes

 * Physics schemes in the physics_mmm directory are now obtained from a
   separate, shared MMM-physics repository at compile time using the
   manage_externals tool.

 * The revised Monin-Obukhov scheme replaces the Monin-Obukhov scheme in the
   'mesoscale_reference' suite.

GPU capabilities

 * The scalar transport code has been ported to GPUs using OpenACC directives.

   - The atmosphere core must be compiled with OPENACC=true.
   - Additional timers in the log file capture host-device data transfer times.

Infrastructure

 * The build system no longer requires an intermediate clean step when compiling
   one core before another.

.gitignore

@@ -37,6 +37,7 @@ restart_timestamp
 
 # Text files (For statistical output from ocean model)
 *.txt
+!CMakeLists.txt
 
 # Directories with individual .gitignore files are:
 # src/external (Externals might have a different compilation method)
@@ -47,8 +48,8 @@ restart_timestamp
 *.TBL
 *DATA*
 
-# Ignore MPAS core build files.
-.mpas_core_*
+# Files for detecting whether builds of cores or shared framework can be reused
+.build_opts*
 
 # Ignore all runtime config files
 namelist.*

CMakeLists.txt

@@ -0,0 +1,160 @@
+## MPAS-Model
+cmake_minimum_required(VERSION 3.12)
+
+include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/Functions/MPAS_Functions.cmake)
+get_mpas_version(MPAS_VERSION)
+project(MPAS LANGUAGES C Fortran VERSION ${MPAS_VERSION} DESCRIPTION "MPAS - Model for Prediction Across Scales")
+
+list(INSERT CMAKE_MODULE_PATH 0 ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
+set(CMAKE_DIRECTORY_LABELS ${PROJECT_NAME})
+include(GNUInstallDirs)
+
+# Options
+set(MPAS_ALL_CORES atmosphere init_atmosphere)
+set(MPAS_CORES atmosphere CACHE STRING "MPAS cores to build. Options: ${MPAS_ALL_CORES}")
+if(MPAS_CORES MATCHES " ") #Convert strings separated with spaces to CMake list separated with ';'
+    string(REPLACE " " ";" MPAS_CORES ${MPAS_CORES})
+    set(MPAS_CORES ${MPAS_CORES} CACHE STRING "MPAS cores to build. Options: ${MPAS_ALL_CORES}" FORCE)
+endif()
+option(DO_PHYSICS "Use built-in physics schemes." TRUE)
+option(MPAS_DOUBLE_PRECISION "Use double precision 64-bit Floating point." TRUE)
+option(MPAS_PROFILE "Enable GPTL profiling" OFF)
+option(MPAS_OPENMP "Enable OpenMP" OFF)
+option(BUILD_SHARED_LIBS "Build shared libraries" ON)
+
+message(STATUS "[OPTION] MPAS_CORES: ${MPAS_CORES}")
+message(STATUS "[OPTION] MPAS_DOUBLE_PRECISION: ${MPAS_DOUBLE_PRECISION}")
+message(STATUS "[OPTION] MPAS_PROFILE: ${MPAS_PROFILE}")
+message(STATUS "[OPTION] MPAS_OPENMP: ${MPAS_OPENMP}")
+message(STATUS "[OPTION] BUILD_SHARED_LIBS: ${BUILD_SHARED_LIBS}")
+
+# Build product output locations
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+
+# Set default build type to RelWithDebInfo
+if(NOT CMAKE_BUILD_TYPE)
+  message(STATUS "Setting default build type to Release.  Specify CMAKE_BUILD_TYPE to override.")
+  set(CMAKE_BUILD_TYPE "Release" CACHE STRING "CMake Build type" FORCE)
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
+
+# Detect MPAS git version
+if(NOT MPAS_GIT_VERSION)
+    find_package(Git QUIET)
+    if(GIT_FOUND)
+        execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty
+                        WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+                        OUTPUT_VARIABLE _mpas_git_version
+                        ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+    else()
+        set(_mpas_git_version "Unknown")
+    endif()
+    set(MPAS_GIT_VERSION ${_mpas_git_version} CACHE STRING "MPAS-Model git version")
+endif()
+
+### Dependencies
+find_package(OpenMP COMPONENTS Fortran)
+find_package(MPI REQUIRED COMPONENTS Fortran)
+find_package(NetCDF REQUIRED COMPONENTS Fortran C)
+find_package(PnetCDF REQUIRED COMPONENTS Fortran)
+find_package(PIO REQUIRED COMPONENTS Fortran C)
+if(MPAS_PROFILE)
+    find_package(GPTL REQUIRED)
+endif()
+
+# Find C pre-processor
+if(CMAKE_C_COMPILER_ID MATCHES GNU)
+    find_program(CPP_EXECUTABLE NAMES cpp REQUIRED)
+    set(CPP_EXTRA_FLAGS -traditional)
+elseif(CMAKE_C_COMPILER_ID MATCHES "(Apple)?Clang" )
+    find_program(CPP_EXECUTABLE NAMES cpp REQUIRED)
+else()
+    message(STATUS "Unknown compiler: ${CMAKE_C_COMPILER_ID}")
+    set(CPP_EXECUTABLE ${CMAKE_C_COMPILER})
+endif()
+
+## Common Variables
+
+# Fortran module output directory for build interface
+set(MPAS_MODULE_DIR ${PROJECT_NAME}/module/${CMAKE_Fortran_COMPILER_ID}/${CMAKE_Fortran_COMPILER_VERSION})
+# Install Fortran module directory
+install(DIRECTORY ${CMAKE_BINARY_DIR}/${MPAS_MODULE_DIR}/ DESTINATION ${CMAKE_INSTALL_LIBDIR}/${MPAS_MODULE_DIR}/)
+
+# Location of common subdriver module compiled by each cores
+set(MPAS_MAIN_SRC  ${CMAKE_CURRENT_SOURCE_DIR}/src/driver/mpas.F)
+set(MPAS_SUBDRIVER_SRC  ${CMAKE_CURRENT_SOURCE_DIR}/src/driver/mpas_subdriver.F)
+
+## Create targets
+add_subdirectory(src/external/ezxml) # Target: MPAS::external::ezxml
+if(ESMF_FOUND)
+  message(STATUS "Configure MPAS for external ESMF")
+  add_definitions(-DMPAS_EXTERNAL_ESMF_LIB -DMPAS_NO_ESMF_INIT)
+  add_library(${PROJECT_NAME}::external::esmf ALIAS esmf)
+else()
+  message(STATUS "Configure MPAS for internal ESMF")
+  add_subdirectory(src/external/esmf_time_f90) # Target: MPAS::external::esmf_time
+endif()
+add_subdirectory(src/tools/input_gen) # Targets: namelist_gen, streams_gen
+add_subdirectory(src/tools/registry) # Targets: mpas_parse_<core_name>
+add_subdirectory(src/framework) # Target: MPAS::framework
+add_subdirectory(src/operators) # Target: MPAS::operators
+
+foreach(_core IN LISTS MPAS_CORES)
+    add_subdirectory(src/core_${_core}) # Target: MPAS::core::<core_name>
+endforeach()
+
+### Package config
+include(CMakePackageConfigHelpers)
+
+# Build-tree target exports
+export(EXPORT ${PROJECT_NAME}ExportsExternal NAMESPACE ${PROJECT_NAME}::external:: FILE ${PROJECT_NAME}-targets-external.cmake)
+export(EXPORT ${PROJECT_NAME}Exports NAMESPACE ${PROJECT_NAME}:: FILE ${PROJECT_NAME}-targets.cmake)
+export(EXPORT ${PROJECT_NAME}ExportsCore NAMESPACE ${PROJECT_NAME}::core:: FILE ${PROJECT_NAME}-targets-core.cmake)
+
+# CMake Config file install location
+set(CONFIG_INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
+# Install MPAS-supplied Find<Pkg>.cmake modules for use by downstream CMake dependencies
+install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules DESTINATION ${CONFIG_INSTALL_DESTINATION})
+
+## <pkgname>-config.cmake: build-tree
+# Variables to export for use from build-tree
+set(BINDIR ${CMAKE_BINARY_DIR}/bin)
+set(CORE_DATADIR_ROOT ${CMAKE_BINARY_DIR}/${PROJECT_NAME})
+set(CMAKE_MODULE_INSTALL_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
+string(TOLOWER ${PROJECT_NAME} PROJECT_NAME_LOWER)
+configure_package_config_file(cmake/PackageConfig.cmake.in ${PROJECT_NAME_LOWER}-config.cmake
+                              INSTALL_DESTINATION .
+                              INSTALL_PREFIX ${CMAKE_CURRENT_BINARY_DIR}
+                              PATH_VARS BINDIR CORE_DATADIR_ROOT CMAKE_MODULE_INSTALL_PATH)
+
+## <pkgname>-config.cmake: install-tree
+# Variables to export for use from install-tree
+set(BINDIR ${CMAKE_INSTALL_BINDIR})
+set(CORE_DATADIR_ROOT ${CMAKE_INSTALL_DATADIR}/${PROJECT_NAME})
+set(CMAKE_MODULE_INSTALL_PATH ${CONFIG_INSTALL_DESTINATION}/Modules)
+configure_package_config_file(cmake/PackageConfig.cmake.in install/${PROJECT_NAME_LOWER}-config.cmake
+                              INSTALL_DESTINATION ${CONFIG_INSTALL_DESTINATION}
+                              PATH_VARS BINDIR CORE_DATADIR_ROOT CMAKE_MODULE_INSTALL_PATH)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/install/${PROJECT_NAME_LOWER}-config.cmake
+        DESTINATION ${CONFIG_INSTALL_DESTINATION})
+
+## <pkgname>-config-version.cmake
+write_basic_package_version_file(
+    ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config-version.cmake
+    VERSION ${PROJECT_VERSION}
+    COMPATIBILITY AnyNewerVersion)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config-version.cmake
+        DESTINATION ${CONFIG_INSTALL_DESTINATION})
+
+## package-targets.cmake and package-targets-<build-type>.cmake
+install(EXPORT ${PROJECT_NAME}ExportsExternal NAMESPACE ${PROJECT_NAME}::external::
+        FILE ${PROJECT_NAME_LOWER}-targets-external.cmake
+        DESTINATION ${CONFIG_INSTALL_DESTINATION})
+install(EXPORT ${PROJECT_NAME}Exports NAMESPACE ${PROJECT_NAME}::
+        FILE ${PROJECT_NAME_LOWER}-targets.cmake
+        DESTINATION ${CONFIG_INSTALL_DESTINATION})
+install(EXPORT ${PROJECT_NAME}ExportsCore NAMESPACE ${PROJECT_NAME}::core::
+        FILE ${PROJECT_NAME_LOWER}-targets-core.cmake
+        DESTINATION ${CONFIG_INSTALL_DESTINATION})