[codex] Embed CoLM2024 as MPAS land model

.gitignore

@@ -61,3 +61,4 @@ stream_list.*
 *.i90
 
 src/core_*/inc
+/build-cmake-colm-debug

CMakeLists.txt

@@ -22,13 +22,19 @@ option(MPAS_PROFILE "Enable GPTL profiling" OFF)
 option(MPAS_OPENMP "Enable OpenMP" OFF)
 option(BUILD_SHARED_LIBS "Build shared libraries" ON)
 option(MPAS_USE_PIO "Build with PIO I/O library" OFF)
+option(MPAS_COLM2024 "Build atmosphere core with embedded CoLM2024 land-surface physics" OFF)
+
+if(MPAS_COLM2024 AND NOT DO_PHYSICS)
+    message(FATAL_ERROR "MPAS_COLM2024 requires DO_PHYSICS=ON because CoLM2024 is built into the atmosphere physics driver.")
+endif()
 
 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}")
 message(STATUS "[OPTION] MPAS_USE_PIO: ${MPAS_USE_PIO}")
+message(STATUS "[OPTION] MPAS_COLM2024: ${MPAS_COLM2024}")
 
 # Build product output locations
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
@@ -43,8 +49,11 @@ if(NOT CMAKE_BUILD_TYPE)
 endif()
 
 # Detect MPAS git version
+if(DEFINED GIT_EXECUTABLE AND NOT EXISTS "${GIT_EXECUTABLE}")
+    unset(GIT_EXECUTABLE CACHE)
+endif()
+find_package(Git QUIET)
 if(NOT MPAS_GIT_VERSION)
-    find_package(Git QUIET)
     if(GIT_FOUND)
         execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty
                         WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
@@ -68,9 +77,11 @@ endif()
 find_package(MPI REQUIRED COMPONENTS Fortran)
 
 find_package(PnetCDF REQUIRED COMPONENTS Fortran)
+if(MPAS_USE_PIO OR MPAS_COLM2024)
+    find_package(NetCDF REQUIRED COMPONENTS Fortran C)
+endif()
 if(MPAS_USE_PIO)
     find_package(PIO REQUIRED COMPONENTS Fortran C)
-    find_package(NetCDF REQUIRED COMPONENTS Fortran C)
 endif()
 if(MPAS_PROFILE)
     find_package(GPTL REQUIRED)

Makefile

@@ -755,28 +755,85 @@ else # Not using PIO, using SMIOL
 endif
 
 ifneq "$(NETCDF)" ""
-ifneq ($(wildcard $(NETCDF)/lib/libnetcdf.*), )
+ifneq ($(filter-out %.settings,$(wildcard $(NETCDF)/lib/libnetcdf.*)), )
 	NETCDFLIBLOC = lib
 endif
-ifneq ($(wildcard $(NETCDF)/lib64/libnetcdf.*), )
+ifneq ($(filter-out %.settings,$(wildcard $(NETCDF)/lib64/libnetcdf.*)), )
 	NETCDFLIBLOC = lib64
 endif
 	CPPINCLUDES += -I$(NETCDF)/include
 	FCINCLUDES += -I$(NETCDF)/include
 	LIBS += -L$(NETCDF)/$(NETCDFLIBLOC)
 	NCLIB = -lnetcdf
 	NCLIBF = -lnetcdff
-	ifneq ($(wildcard $(NETCDF)/$(NETCDFLIBLOC)/libnetcdff.*), ) # CHECK FOR NETCDF4
+	ifneq ($(filter-out %.settings,$(wildcard $(NETCDF)/$(NETCDFLIBLOC)/libnetcdff.*)), ) # CHECK FOR NETCDF4
 		LIBS += $(NCLIBF)
 	endif # CHECK FOR NETCDF4
 	ifneq "$(NETCDFF)" ""
+		ifneq ($(filter-out %.settings,$(wildcard $(NETCDFF)/lib/libnetcdff.*)), )
+			NETCDFFLIBLOC = lib
+		endif
+		ifneq ($(filter-out %.settings,$(wildcard $(NETCDFF)/lib64/libnetcdff.*)), )
+			NETCDFFLIBLOC = lib64
+		endif
 		FCINCLUDES += -I$(NETCDFF)/include
-		LIBS += -L$(NETCDFF)/$(NETCDFLIBLOC)
+		LIBS += -L$(NETCDFF)/$(NETCDFFLIBLOC)
 		LIBS += $(NCLIBF)
 	endif
 	LIBS += $(NCLIB)
 endif
 
+ifeq "$(COLM2024)" "true"
+NF_CONFIG ?= nf-config
+COLM2024_NETCDF_C_LIB := $(if $(strip $(NETCDFLIBLOC)),$(firstword $(filter-out %.settings,$(wildcard $(NETCDF)/$(NETCDFLIBLOC)/libnetcdf.*))))
+COLM2024_NETCDF_F_ROOT := $(if $(strip $(NETCDFF)),$(NETCDFF),$(NETCDF))
+COLM2024_NETCDF_F_LIBLOC := $(if $(strip $(NETCDFF)),$(NETCDFFLIBLOC),$(NETCDFLIBLOC))
+COLM2024_NETCDF_F_LIB := $(if $(strip $(COLM2024_NETCDF_F_LIBLOC)),$(firstword $(filter-out %.settings,$(wildcard $(COLM2024_NETCDF_F_ROOT)/$(COLM2024_NETCDF_F_LIBLOC)/libnetcdff.*))))
+COLM2024_NETCDF_F_MOD := $(if $(strip $(COLM2024_NETCDF_F_ROOT)),$(firstword $(wildcard $(COLM2024_NETCDF_F_ROOT)/include/netcdf.mod $(COLM2024_NETCDF_F_ROOT)/include/NETCDF.mod)))
+COLM2024_NETCDF_ROOTS_READY := $(and $(COLM2024_NETCDF_C_LIB),$(COLM2024_NETCDF_F_LIB),$(COLM2024_NETCDF_F_MOD))
+
+ifneq ($(strip $(NETCDF)),)
+ifeq ($(strip $(COLM2024_NETCDF_C_LIB)),)
+$(error COLM2024=true but NETCDF=$(NETCDF) does not contain libnetcdf under lib or lib64)
+endif
+endif
+ifneq ($(strip $(NETCDFF)),)
+ifeq ($(strip $(COLM2024_NETCDF_F_LIB)),)
+$(error COLM2024=true but NETCDFF=$(NETCDFF) does not contain libnetcdff under lib or lib64)
+endif
+ifeq ($(strip $(COLM2024_NETCDF_F_MOD)),)
+$(error COLM2024=true but NETCDFF=$(NETCDFF) does not contain include/netcdf.mod)
+endif
+endif
+
+ifeq ($(strip $(COLM2024_NETCDF_ROOTS_READY)),)
+ifneq ($(strip $(NETCDF)$(NETCDFF)),)
+COLM2024_NF_CONFIG := $(firstword \
+	$(if $(strip $(NETCDFF)),$(wildcard $(NETCDFF)/bin/nf-config)) \
+	$(if $(strip $(NETCDF)),$(wildcard $(NETCDF)/bin/nf-config)))
+else
+COLM2024_NF_CONFIG := $(shell command -v $(NF_CONFIG) 2>/dev/null)
+endif
+ifeq ($(strip $(COLM2024_NF_CONFIG)),)
+ifneq ($(strip $(NETCDF)$(NETCDFF)),)
+$(error COLM2024=true received incomplete NETCDF/NETCDFF roots; provide matching NetCDF-C and NetCDF-Fortran libraries plus netcdf.mod, or a root-local bin/nf-config)
+else
+$(error COLM2024=true requires NetCDF-C and NetCDF-Fortran; set NETCDF/NETCDFF or provide nf-config in PATH)
+endif
+endif
+COLM2024_NETCDF_FFLAGS := $(strip $(shell "$(COLM2024_NF_CONFIG)" --fflags 2>/dev/null))
+COLM2024_NETCDF_FLIBS := $(strip $(shell "$(COLM2024_NF_CONFIG)" --flibs 2>/dev/null))
+ifeq ($(strip $(COLM2024_NETCDF_FFLAGS)),)
+$(error $(COLM2024_NF_CONFIG) did not return NetCDF-Fortran compile flags from --fflags)
+endif
+ifeq ($(strip $(COLM2024_NETCDF_FLIBS)),)
+$(error $(COLM2024_NF_CONFIG) did not return NetCDF-C/Fortran link flags from --flibs)
+endif
+override FCINCLUDES += $(COLM2024_NETCDF_FFLAGS)
+override LIBS += $(COLM2024_NETCDF_FLIBS)
+endif
+endif
+
 ifneq "$(SCOTCH)" ""
 	SCOTCH_INCLUDES += -I$(SCOTCH)/include
 	SCOTCH_LIBS += -L$(SCOTCH)/lib64 -lptscotch -lscotch  -lptscotcherr -lm
@@ -1029,6 +1086,12 @@ endif # END OF GIT DESCRIBE VERSION
 ####################################################
 # Section for adding external libraries and includes
 ####################################################
+ifeq "$(COLM2024)" "true"
+override CPPFLAGS += -DMPAS_COLM2024
+COLM2024_MESSAGE = "MPAS was built with the bundled CoLM2024 physics package."
+else
+COLM2024_MESSAGE = "MPAS was not built with CoLM2024."
+endif
 ifdef MPAS_EXTERNAL_LIBS
 	override LIBS += $(MPAS_EXTERNAL_LIBS)
 endif
@@ -1573,6 +1636,7 @@ mpas_main: $(MAIN_DEPS)
 	@echo $(OPENMP_OFFLOAD_MESSAGE)
 	@echo $(OPENACC_MESSAGE)
 	@echo $(MUSICA_MESSAGE)
+	@echo $(COLM2024_MESSAGE)
 	@echo $(SCOTCH_MESSAGE)
 	@echo $(SHAREDLIB_MESSAGE)
 ifeq "$(AUTOCLEAN)" "true"
@@ -1648,4 +1712,3 @@ errmsg:
 ifdef CORE
 	exit 1
 endif
-

cmake/Functions/MPAS_Functions.cmake

@@ -148,7 +148,8 @@ function(mpas_fortran_target target)
 endfunction()
 
 
-# mpas_core_target(CORE <core-name> TARGET <cmake-target-name> INCLUDE <file1.inc, ...> )
+# mpas_core_target(CORE <core-name> TARGET <cmake-target-name>
+#                  INCLUDES <file1.inc, ...> REGISTRY_DEPENDS <file1.xml, ...> )
 #
 # Common configuration and properties for `MPAS::core::<core_name>` targets.
 # * Calls mpas_fortran_target() for common Fortran target configuration.
@@ -164,9 +165,10 @@ endfunction()
 #   CORE - Name of core
 #   TARGET - Name of core_target (without namespace)
 #   INCLUDES - List of generated include files
+#   REGISTRY_DEPENDS - Files included by the core Registry.xml preprocessor input
 #
 function(mpas_core_target)
-    cmake_parse_arguments(ARG "" "CORE;TARGET" "INCLUDES" ${ARGN})
+    cmake_parse_arguments(ARG "" "CORE;TARGET" "INCLUDES;REGISTRY_DEPENDS" ${ARGN})
 
     mpas_fortran_target(${ARG_TARGET})
 
@@ -214,25 +216,26 @@ function(mpas_core_target)
     if (${DO_PHYSICS})
         set(CPP_EXTRA_FLAGS ${CPP_EXTRA_FLAGS} -DDO_PHYSICS)
     endif()
+    set(REGISTRY_PROCESSED_XML ${CMAKE_CURRENT_BINARY_DIR}/Registry_processed.xml)
 
-add_custom_command(OUTPUT Registry_processed.xml
-            COMMAND ${CPP_EXECUTABLE} -E -P ${CPP_EXTRA_FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Registry.xml > Registry_processed.xml
+add_custom_command(OUTPUT ${REGISTRY_PROCESSED_XML}
+            COMMAND ${CPP_EXECUTABLE} -E -P ${CPP_EXTRA_FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Registry.xml > ${REGISTRY_PROCESSED_XML}
             COMMENT "CORE ${ARG_CORE}: Pre-Process Registry"
-            DEPENDS Registry.xml)
+            DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/Registry.xml ${ARG_REGISTRY_DEPENDS})
     add_custom_command(OUTPUT ${ARG_INCLUDES}
-            COMMAND mpas_parse_${ARG_CORE} Registry_processed.xml ${CPP_EXTRA_FLAGS}
+            COMMAND mpas_parse_${ARG_CORE} ${REGISTRY_PROCESSED_XML} ${CPP_EXTRA_FLAGS}
             COMMENT "CORE ${ARG_CORE}: Parse Registry"
-            DEPENDS mpas_parse_${ARG_CORE} Registry_processed.xml)
+            DEPENDS mpas_parse_${ARG_CORE} ${REGISTRY_PROCESSED_XML})
     add_custom_command(OUTPUT namelist.${ARG_CORE}
             WORKING_DIRECTORY ${CORE_DATADIR}
-            COMMAND mpas_namelist_gen ${CMAKE_CURRENT_BINARY_DIR}/Registry_processed.xml namelist.${ARG_CORE} in_defaults=true
+            COMMAND mpas_namelist_gen ${REGISTRY_PROCESSED_XML} namelist.${ARG_CORE} in_defaults=true
             COMMENT "CORE ${ARG_CORE}: Generate Namelist"
-            DEPENDS mpas_namelist_gen Registry_processed.xml)
+            DEPENDS mpas_namelist_gen ${REGISTRY_PROCESSED_XML})
     add_custom_command(OUTPUT streams.${ARG_CORE}
             WORKING_DIRECTORY ${CORE_DATADIR}
-            COMMAND mpas_streams_gen ${CMAKE_CURRENT_BINARY_DIR}/Registry_processed.xml streams.${ARG_CORE} stream_list.${ARG_CORE}. listed
+            COMMAND mpas_streams_gen ${REGISTRY_PROCESSED_XML} streams.${ARG_CORE} stream_list.${ARG_CORE}. listed
             COMMENT "CORE ${ARG_CORE}: Generate Streams"
-            DEPENDS mpas_streams_gen Registry_processed.xml)
+            DEPENDS mpas_streams_gen ${REGISTRY_PROCESSED_XML})
     add_custom_target(gen_${ARG_CORE} DEPENDS ${ARG_INCLUDES} namelist.${ARG_CORE} streams.${ARG_CORE})
     add_dependencies(${ARG_TARGET} gen_${ARG_CORE})