Merge PR #420 'jgfouca/cvmix_bgc_as_subs' into ocean/develop

This is a significant change to the structure of the MPAS repository.
Instead of external code dependencies being downloaded by home-grown
scripts, we instead express the dependency as a git submodule. This will
impact the cvmix and BGC dependencies for core_ocean.

I tested building the E3SM case ERS_Ld5.T62_oQU120.CMPASO-NYF with both
the old (Makefile-based) and new (CMake-based) build systems.

For additional discussion, see #3377

.gitignore

@@ -1,8 +1,3 @@
-# Ignore all cvmix code.
-cvmix
-.cvmix_all
-BGC
-.BGC_all
 .*.zip
 
 # Ignore processed registry files.

Makefile

@@ -2,7 +2,7 @@
 
 
 OCEAN_SHARED_INCLUDES = -I$(PWD)/../framework -I$(PWD)/../external/esmf_time_f90 -I$(PWD)/../operators
-OCEAN_SHARED_INCLUDES += -I$(PWD)/BGC -I$(PWD)/shared -I$(PWD)/analysis_members -I$(PWD)/cvmix -I$(PWD)/mode_forward -I$(PWD)/mode_analysis -I$(PWD)/mode_init
+OCEAN_SHARED_INCLUDES += -I$(PWD)/BGC -I$(PWD)/shared -I$(PWD)/analysis_members -I$(PWD)/cvmix/src/shared -I$(PWD)/mode_forward -I$(PWD)/mode_analysis -I$(PWD)/mode_init
 
 all: shared libcvmix analysis_members libBGC
 	(cd mode_forward; $(MAKE) FCINCLUDES="$(FCINCLUDES) $(OCEAN_SHARED_INCLUDES)" all )
@@ -45,26 +45,18 @@ post_build:
 	( cp $(ROOT_DIR)/default_inputs/streams.ocean.analysis $(ROOT_DIR)/streams.ocean.analysis )
 	( cp $(ROOT_DIR)/default_inputs/streams.ocean.init $(ROOT_DIR)/streams.ocean.init )
 
-cvmix_source: get_cvmix.sh
-	(/bin/bash ./get_cvmix.sh)
-	(cd cvmix)
-
-BGC_source: get_BGC.sh
-	(/bin/bash ./get_BGC.sh)
-	(cd BGC)
-
-libcvmix: cvmix_source
-	if [ -d cvmix ]; then \
-		(cd cvmix; make all FC="$(FC)" FCFLAGS="$(FFLAGS)" FINCLUDES="$(FINCLUDES)") \
+libcvmix:
+	if [ -e cvmix/.git ]; then \
+		(cd cvmix/src/shared; make all FC="$(FC)" FCFLAGS="$(FFLAGS)" FINCLUDES="$(FINCLUDES)") \
 	else \
-		(exit 1) \
+		(pwd ; echo "Missing core_ocean/cvmix/.git, did you forget to 'git submodule update --init --recursive' ?"; exit 1) \
 	fi
 
-libBGC: BGC_source
-	if [ -d BGC ]; then \
+libBGC:
+	if [ -e BGC/.git ]; then \
 		(cd BGC; make all FC="$(FC)" FCFLAGS="$(FFLAGS)" FINCLUDES="$(FINCLUDES)") \
 	else \
-		(exit 1) \
+		(echo "Missing core_ocean/BGC/.git, did you forget to 'git submodule update --init --recursive' ?"; exit 1) \
 	fi
 
 shared: libcvmix libBGC
@@ -74,13 +66,13 @@ analysis_members: libcvmix shared
 	( cd analysis_members; $(MAKE) FCINCLUDES="$(FCINCLUDES) $(OCEAN_SHARED_INCLUDES)" CPPFLAGS="$(CPPFLAGS)" CPPINCLUDES="$(CPPINCLUDES)" all ) 
 
 clean:
-	if [ -d cvmix ]; then \
-		(cd cvmix; make clean) \
+	if [ -e cvmix/.git ]; then \
+		(cd cvmix/src/shared; make clean) \
 	fi
 	if [ -d inc ]; then \
 		($(RM) -r inc) \
 	fi
-	if [ -d BGC ]; then \
+	if [ -e BGC/.git ]; then \
 		(cd BGC; make clean) \
 	fi
 	(cd mode_forward; $(MAKE) clean)

ocean.cmake

@@ -1,7 +1,7 @@
 
 # build_options.mk stuff handled here
 list(APPEND CPPDEFS "-DCORE_OCEAN")
-list(APPEND INCLUDES "${CMAKE_BINARY_DIR}/core_ocean/BGC" "${CMAKE_BINARY_DIR}/core_ocean/shared" "${CMAKE_BINARY_DIR}/core_ocean/analysis_members" "${CMAKE_BINARY_DIR}/core_ocean/cvmix" "${CMAKE_BINARY_DIR}/core_ocean/mode_forward" "${CMAKE_BINARY_DIR}/core_ocean/mode_analysis" "${CMAKE_BINARY_DIR}/core_ocean/mode_init")
+list(APPEND INCLUDES "${CMAKE_BINARY_DIR}/core_ocean/shared") # Only need this for '#include "../inc/core_variables.inc"' to work
 
 # driver (files live in E3SM)
 list(APPEND RAW_SOURCES
@@ -118,37 +118,35 @@ set(OCEAN_DRIVER
 list(APPEND RAW_SOURCES ${OCEAN_DRIVER})
 list(APPEND DISABLE_QSMP ${OCEAN_DRIVER})
 
-# Get CVMix
-execute_process(COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/core_ocean/get_cvmix.sh
-  WORKING_DIRECTORY ${CORE_BLDDIR})
-
-# Get BGC
-execute_process(COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/core_ocean/get_BGC.sh
-  WORKING_DIRECTORY ${CORE_BLDDIR})
-
 # Add CVMix
+if (NOT EXISTS core_ocean/cvmix/.git)
+  message(FATAL "Missing core_ocean/cvmix/.git, did you forget to 'git submodule update --init --recursive' ?")
+endif()
 set(CVMIX_FILES
-  ${CORE_BLDDIR}/cvmix/cvmix_kinds_and_types.F90
-  ${CORE_BLDDIR}/cvmix/cvmix_background.F90
-  ${CORE_BLDDIR}/cvmix/cvmix_convection.F90
-  ${CORE_BLDDIR}/cvmix/cvmix_ddiff.F90
-  ${CORE_BLDDIR}/cvmix/cvmix_kpp.F90
-  ${CORE_BLDDIR}/cvmix/cvmix_math.F90
-  ${CORE_BLDDIR}/cvmix/cvmix_put_get.F90
-  ${CORE_BLDDIR}/cvmix/cvmix_shear.F90
-  ${CORE_BLDDIR}/cvmix/cvmix_tidal.F90
-  ${CORE_BLDDIR}/cvmix/cvmix_utils.F90
+  core_ocean/cvmix/src/shared/cvmix_kinds_and_types.F90
+  core_ocean/cvmix/src/shared/cvmix_background.F90
+  core_ocean/cvmix/src/shared/cvmix_convection.F90
+  core_ocean/cvmix/src/shared/cvmix_ddiff.F90
+  core_ocean/cvmix/src/shared/cvmix_kpp.F90
+  core_ocean/cvmix/src/shared/cvmix_math.F90
+  core_ocean/cvmix/src/shared/cvmix_put_get.F90
+  core_ocean/cvmix/src/shared/cvmix_shear.F90
+  core_ocean/cvmix/src/shared/cvmix_tidal.F90
+  core_ocean/cvmix/src/shared/cvmix_utils.F90
 )
 
 # Add BGC
+if (NOT EXISTS core_ocean/BGC/.git)
+  message(FATAL "Missing core_ocean/BGC/.git, did you forget to 'git submodule update --init --recursive' ?")
+endif()
 set(BGC_FILES
-  ${CORE_BLDDIR}/BGC/BGC_mod.F90
-  ${CORE_BLDDIR}/BGC/BGC_parms.F90
-  ${CORE_BLDDIR}/BGC/DMS_mod.F90
-  ${CORE_BLDDIR}/BGC/DMS_parms.F90
-  ${CORE_BLDDIR}/BGC/MACROS_mod.F90
-  ${CORE_BLDDIR}/BGC/MACROS_parms.F90
-  ${CORE_BLDDIR}/BGC/co2calc.F90
+  core_ocean/BGC/BGC_mod.F90
+  core_ocean/BGC/BGC_parms.F90
+  core_ocean/BGC/DMS_mod.F90
+  core_ocean/BGC/DMS_parms.F90
+  core_ocean/BGC/MACROS_mod.F90
+  core_ocean/BGC/MACROS_parms.F90
+  core_ocean/BGC/co2calc.F90
 )
 
 list(APPEND RAW_SOURCES ${CVMIX_FILES} ${BGC_FILES})