Merge branch 'bishtgautam/lnd/emi-example' (PR #2823)

Updates EMI for ELM

Restructures the External Model Interface (EMI) directories and
adds a demo code showing the usage of EMI.

[BFB]

components/clm/bld/configure

@@ -659,12 +659,17 @@ sub write_filepath_cesmbld
 		     "external_models/mpp/src/mpp/util",
 		     "external_models/mpp/src/mpp/vsfm",
 		     "external_models/emi/src/",
-		     "external_models/emi/src/elm_types",
+		     "external_models/emi/src/constants",
+		     "external_models/emi/src/em/base",
 		     "external_models/emi/src/em/betr",
 		     "external_models/emi/src/em/fates",
 		     "external_models/emi/src/em/ptm",
+		     "external_models/emi/src/em/stub",
 		     "external_models/emi/src/em/vsfm",
-		     "external_models/emi/src/data_types",
+		     "external_models/emi/src/emi",
+		     "external_models/emi/src/emi_data_definition",
+		     "external_models/emi/src/emi_data_exchange",
+		     "external_models/emi/src/emi_data_types",
                      "external_models/sbetr/src/betr/betr_core",
                      "external_models/sbetr/src/betr/betr_dtype",
                      "external_models/sbetr/src/betr/betr_bgc",

components/clm/src/external_models/emi/.gitignore

@@ -0,0 +1 @@
+local

components/clm/src/external_models/emi/src/.gitignore

@@ -0,0 +1 @@
+build

components/clm/src/external_models/emi/src/CMakeLists.txt

@@ -0,0 +1,181 @@
+
+cmake_minimum_required (VERSION 2.8.12)
+
+# Adjust CMake's module path.
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+
+option(CMAKE_INSTALL_PREFIX "Sets installation prefix [/usr/local].")
+option(BUILD_SHARED_LIBS "Builds shared libraries [ON]." ON)
+#option(WITH_NETCDF "Enables support for netcdf [OFF]." ON)
+#option(TPL_NETCDF_LIBRARIES "List of absolute paths to netcdf link libraries [].")
+#option(TPL_NETCDF_INCLUDE_DIRS "List of absolute paths to netcdf include directories [].")
+
+# For now, we disable shared libs on Macs.
+if (APPLE)
+  set(BUILD_SHARED_LIBS OFF)
+endif()
+
+if (NOT CMAKE_INSTALL_PREFIX)
+  set(CMAKE_INSTALL_PREFIX /usr/local)
+endif()
+
+#set(PETSC_ARCH $ENV{PETSC_ARCH})
+#set(PETSC_DIR $ENV{PETSC_DIR})
+#include($ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/initial_cache_file.cmake)
+
+# Make sure compilers are set. This must be done before enabling languages.
+#if (NOT CMAKE_C_COMPILER)
+#  if (NOT $ENV{CC} STREQUAL "")
+#    set(CMAKE_C_COMPILER $ENV{CC})
+#  else()
+#    set(CMAKE_C_COMPILER cc)
+#  endif()
+#endif()
+#if (NOT CMAKE_C_FLAGS)
+#  set(CMAKE_C_FLAGS $ENV{CFLAGS})
+#endif()
+#if (NOT CMAKE_CXX_COMPILER)
+#  if (NOT $ENV{CXX} STREQUAL "")
+#    set(CMAKE_CXX_COMPILER $ENV{CXX})
+#  else()
+#    set(CMAKE_CXX_COMPILER c++)
+#  endif()
+#endif()
+#if (NOT CMAKE_CXX_FLAGS)
+#  set(CMAKE_CXX_FLAGS $ENV{CXX_FLAGS})
+#endif()
+if (NOT CMAKE_Fortran_COMPILER)
+  if (NOT $ENV{FC} STREQUAL "")
+    set(CMAKE_Fortran_COMPILER $ENV{FC})
+  else()
+    set(CMAKE_Fortran_COMPILER gfortran)
+  endif()
+endif()
+if (NOT CMAKE_Fortran_FLAGS)
+  set(CMAKE_Fortran_FLAGS $ENV{FCFLAGS})
+endif()
+#enable_language(C)
+#enable_language(CXX)
+enable_language(Fortran)
+
+# We declare the project here.
+project (EMI)
+
+#message("-- C compiler is ${CMAKE_C_COMPILER} (${CMAKE_C_COMPILER_ID})")
+#message("-- CXX compiler is ${CMAKE_CXX_COMPILER} (${CMAKE_CXX_COMPILER_ID})")
+message("-- Fortran compiler is ${CMAKE_Fortran_COMPILER} (${CMAKE_Fortran_COMPILER_ID})")
+
+if (BUILD_SHARED_LIBS)
+  message("-- EMI will be built as a shared library.")
+else()
+  message("-- EMI will be built as a static library.")
+endif()
+
+set (EMI_VERSION_MAJOR 0)
+set (EMI_VERSION_MINOR 1)
+set (EMI_VERSION_PATCH 0)
+set (EMI_VERSION "${EMI_MAJOR_VERSION}.${EMI_MINOR_VERSION}.${EMI_PATCH_VERSION}")
+
+# General C compiler flags.
+#if (CMAKE_C_COMPILER_ID STREQUAL "GNU")
+#  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99 -Wall -pedantic-errors -Wextra -Werror-implicit-function-declaration")
+#  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-sign-compare -Wno-unused-parameter -Wno-unused-but-set-variable -Wno-int-to-pointer-cast -Wno-pointer-to-int-cast")
+#
+#  if (BUILD_SHARED_LIBS)
+#    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
+#    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fPIC")
+#  endif()
+#
+#  if (LINUX EQUAL 1)
+#    # Counter some of GCC's more recent stinginess on Linux.
+#    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D_POSIX_C_SOURCE=200809L")# -D_BSD_SOURCE")
+#  endif()
+#
+#elseif (CMAKE_C_COMPILER_ID STREQUAL "Clang")
+#  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99 -Wall -pedantic-errors -Wextra -Werror-implicit-function-declaration -fno-builtin")
+#  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-sign-compare -Wno-unused-parameter -Wno-int-to-pointer-cast -Wno-pointer-to-int-cast -Wno-unused-function")
+#elseif (CMAKE_C_COMPILER_ID STREQUAL "Intel")
+#  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99 -Wall")
+#endif()
+#set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${SYS_FLAGS}")
+
+# Fortran compiler flags.
+if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -W -Wall -std=gnu -pedantic -ffree-line-length-0 -Wno-unused-variable -Wno-unused-parameter -DCPRGNU -fprofile-arcs -ftest-coverage")
+elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -DCPRINTEL")
+endif()
+
+
+# Figure out the system type.
+set(BETR_HAVE_BOOL 1) # All reasonable C99 compilers have this now.
+if (APPLE EQUAL 1)
+  set(SYS_FLAGS "-DAPPLE=1")
+  set(DYLIB_SUFFIX "dylib")
+  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -framework Accelerate")
+else ()
+  if (LINUX EQUAL 1)
+    set(SYS_FLAGS "-DLINUX=1")
+    set(DYLIB_SUFFIX "so")
+  else()
+    if (WIN32 EQUAL 1)
+      set(BETR_HAVE_BOOL 0) # MS doesn't have reasonable C compilers.
+      set(SYS_FLAGS "-DWINDOWS=1")
+      set(DYLIB_SUFFIX "dll")
+    endif()
+  endif ()
+endif ()
+
+# Here we make sure CMake-installed binaries use the correct runpath, and
+# that the path is not stripped during installation.
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+
+#find_package(PETSc)
+#if (NOT PETSC_FOUND)
+#  message(FATAL_ERROR "PETSc was not found.")
+#endif()
+#include_directories(${PETSC_INCLUDES})
+# Include PETSc in the rpath.
+#set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_RPATH}:${PETSC_DIR}/${PETSC_ARCH}/lib")
+
+#find_package(NetCDF COMPONENTS F90 REQUIRED)
+#if (NOT NETCDF_FOUND)
+#  message(FATAL_ERROR "NetCDF was not found.")
+#endif()
+#include_directories(${NETCDF_INCLUDE_DIR})
+#include_directories(${NETCDF_F90_INCLUDE_DIR})
+
+
+# Other third-party libraries.
+#add_subdirectory(3rd-party)
+
+# Include the binary directory in the header file search path,
+# since it's where we place the third-party libraries.
+include_directories("${PROJECT_BINARY_DIR}")
+include_directories("${PROJECT_BINARY_DIR}/include")
+link_directories("${PROJECT_BINARY_DIR}/lib")
+
+# Unit testing.
+enable_testing()
+
+# Source code itself.
+include_directories("${PROJECT_SOURCE_DIR}")
+add_subdirectory(elm_stub)
+add_subdirectory(constants)
+add_subdirectory(emi_data_types)
+add_subdirectory(emi_data_definition)
+add_subdirectory(emi_data_exchange)
+add_subdirectory(em)
+add_subdirectory(emi)
+add_subdirectory(demo)
+
+add_test(
+NAME regression_tests
+COMMAND regression_tests.py --backtrace --executable local/bin/standalone_EMI
+WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/regression_tests
+)
+
+
+

components/clm/src/external_models/emi/src/Makefile

@@ -0,0 +1,127 @@
+# Makefile -- Use this to build on *NIX systems.
+
+# Options set on command line.
+debug      = not-set
+mpi        = not-set
+shared     = not-set
+precision  = not-set
+verbose    = not-set
+prefix     = not-set
+sanitize   = not-set
+FC         = not-set
+travis = not-set
+# This proxies everything to the builddir cmake.
+
+cputype = $(shell uname -m | sed "s/\\ /_/g")
+systype = $(shell uname -s)
+
+BUILDDIR := build/$(systype)-$(cputype)
+CONFIG_FLAGS = -DUNIX=1 -Wno-dev
+
+# Process configuration options.
+
+# Verbose builds?
+ifeq ($(verbose), 1)
+  CONFIG_FLAGS += -DCMAKE_VERBOSE_MAKEFILE=1
+endif
+
+# MPI
+ifeq ($(mpi), 1)
+  BUILDDIR := ${BUILDDIR}-mpi
+  FC = mpif90
+else
+  ifeq ($(FC), not-set)
+    FC = gfortran
+  endif
+endif
+
+# Shared libs?
+ifeq ($(shared), 1)
+  BUILDDIR := ${BUILDDIR}-shared
+  CONFIG_FLAGS += -DBUILD_SHARED_LIBS=ON
+else
+  BUILDDIR := ${BUILDDIR}-static
+  CONFIG_FLAGS += -DBUILD_SHARED_LIBS=OFF
+endif
+
+# Precision.
+ifneq ($(precision), not-set)
+  BUILDDIR := ${BUILDDIR}-$(precision)
+else
+  BUILDDIR := ${BUILDDIR}-double
+endif
+
+BUILDDIR := ${BUILDDIR}#-`basename ${CC}`
+#CONFIG_FLAGS += -DCC=${CC} -DCXX=${CXX}
+#ifneq ($(FC), )
+#  CONFIG_FLAGS += -DFC=${FC}
+#endif
+
+# Debugging symbols
+ifeq ($(debug), not-set)
+  BUILDDIR := ${BUILDDIR}-Debug
+  CONFIG_FLAGS += -DCMAKE_BUILD_TYPE=Debug
+else
+  ifeq ($(debug), 0)
+    BUILDDIR := ${BUILDDIR}-Release
+    CONFIG_FLAGS += -DCMAKE_BUILD_TYPE=Release
+  else
+    BUILDDIR := ${BUILDDIR}-Debug
+    CONFIG_FLAGS += -DCMAKE_BUILD_TYPE=Debug
+  endif
+endif
+
+# Installation prefix.
+ifeq ($(prefix), not-set)
+  prefix = $(CURDIR)/local
+endif
+CONFIG_FLAGS += -DCMAKE_INSTALL_PREFIX:PATH=$(prefix)
+
+# Special considerations for specific systems.
+ifeq ($(systype), Darwin)
+  CONFIG_FLAGS += -DAPPLE=1
+else
+  ifeq ($(systype), Linux)
+    CONFIG_FLAGS += -DLINUX=1
+  endif
+endif
+
+# Address sanitizer.
+ifeq ($(sanitize), 1)
+  BUILDDIR := ${BUILDDIR}-AddressSanitizer
+  CONFIG_FLAGS += -DADDRESS_SANITIZER=1
+endif
+
+define run-config
+@mkdir -p $(BUILDDIR)
+@cd $(BUILDDIR) && cmake $(CURDIR) $(CONFIG_FLAGS)
+endef
+
+all test clean install:
+	@if [ ! -f $(BUILDDIR)/Makefile ]; then \
+		more INSTALL; \
+	else \
+		$(MAKE) -C $(BUILDDIR) $@ --no-print-directory $(MAKEFLAGS); \
+	fi
+
+config: distclean
+	$(run-config)
+
+distclean:
+	@rm -rf $(BUILDDIR)
+	@rm -rf ./local
+
+stats:
+	@python tools/gather_stats.py
+
+prepend-license:
+	@python tools/prepend_license.py
+
+ctags-emacs :
+	@ctags -e -f ETAGS -R --exclude=.git --exclude=build
+
+#dist:
+#	utils/mkdist.sh $(PKGNAME)
+
+.PHONY: config distclean all clean install uninstall
+

components/clm/src/external_models/emi/src/README.md

@@ -0,0 +1,24 @@
+### Instructions to run the demo code
+
+#### 
+
+1. Specify the Fortran compiler 
+```
+export FC=<fortran-compiler>
+```
+
+2. Run configure command that will create a new directory  `./build/`
+```
+make FC=$FC config
+```
+
+3. Install the demo code that will create a new directory `./local`.
+```
+make FC=$FC install
+```
+
+4. Run the demo code
+```
+cd local/bin
+./demo
+```

components/clm/src/external_models/emi/src/cmake/Modules/CorrectWindowsPaths.cmake

@@ -0,0 +1,14 @@
+# CorrectWindowsPaths - this module defines one macro
+#
+# CONVERT_CYGWIN_PATH( PATH )
+#  This uses the command cygpath (provided by cygwin) to convert
+#  unix-style paths into paths useable by cmake on windows
+
+macro (CONVERT_CYGWIN_PATH _path)
+  if (WIN32)
+    EXECUTE_PROCESS(COMMAND cygpath.exe -m ${${_path}}
+      OUTPUT_VARIABLE ${_path})
+    string (STRIP ${${_path}} ${_path})
+  endif (WIN32)
+endmacro (CONVERT_CYGWIN_PATH)
+