Autoconf-based builds for MOM6-examples models

This patch includes Makefiles for building each of the models and
supporting libraries in MOM6-examples.  Each build now uses autoconf to
configure its essential compiler flags, rather than relying on an
external mkmf template.

Each Makefile is usable on its own; for example the FMS Makefile will
build FMS, the ocean_only Makefile will build the ocean-only MOM6, etc.
When a Makefile requires a component from another part (such as
ocean_only requiring FMS), it now invokes the Makefile of the depedency,
rather than trying to orchestrate the entire build on its own.

There are still instances of "reaching" into other components.  For
example, many of the builds use autoconf files in the MOM6 repository.
Others use configure scripts from a common directory.  And any Makefile
dependencies are freely referenced from within the directory tree.  But
in principle, each of these "externals" can be indepdendently configured
and each Makefile can be used as a standalone build.

There is a top-level Makefile which builds both symmetric and
nonsymmetric versions of each model, as well as supporting libraries.
These are placed in a user-defined BUILD directory (default to `build`)
which is external to the individual default build directories within the
Makefiles of individual components.

This top-level Makefile does its best to emulate the output of the
existing MRS build system.  Assuming we are satisfied with this new
approach, we can start to change some of these conventions.

There are still many smaller issues which ought to be addressed:

- The default MRS build system creates libMOM and libSIS libraries for
the coupled builds (ice-ocean and AM2-based).  We do not create
equivalent libraries.

- There are perhaps too many local `configure.XXX.ac` configure script
templates floating around.  Many are nearly identical.

- Reaching into MOM6 for much of the content is not sustainable, and
this content should perhaps be moved into MOM6-examples itself.

- These Makefiles include some rules for running the models, but this is
not yet feature-complete and we are still quite far from replacing MRS
for running the tests.  (Regression testing would not happen at this
level, and would be handled by an even higher Makefile, such as from
Gaea-stats).

Makefile

@@ -0,0 +1,194 @@
+# Test build
+BUILD ?= build
+
+# Models
+MODELS=ocean_only ice_ocean_SIS2 coupled_AM2_LM3_SIS2
+LIBS=AM2 atmos_null LM3 land_null icebergs ice_param fms
+
+.PHONY: all
+all: $(MODELS)
+
+# ocean_only
+
+.PHONY: ocean_only
+ocean_only: ocean_only.symmetric ocean_only.asymmetric
+
+.PHONY: ocean_only.symmetric
+ocean_only.symmetric: fms
+	$(MAKE) -C ocean_only \
+	  BUILD=../$(BUILD)/dynamic_symmetric/ocean_only \
+	  FMS_BUILD=../$(BUILD)/fms
+
+.PHONY: ocean_only.asymmetric
+ocean_only.asymmetric: fms
+	$(MAKE) -C ocean_only \
+	  BUILD=../$(BUILD)/dynamic_nonsymmetric/ocean_only \
+	  FMS_BUILD=../$(BUILD)/fms \
+	  MOM_MEMORY=../src/MOM6/config_src/memory/dynamic_nonsymmetric/MOM_memory.h
+
+
+# ice_ocean_SIS2
+
+.PHONY: ice_ocean_SIS2
+ice_ocean_SIS2: ice_ocean_SIS2.symmetric ice_ocean_SIS2.asymmetric
+
+.PHONY: ice_ocean_SIS2.symmetric
+ice_ocean_SIS2.symmetric: fms atmos_null land_null ice_param icebergs
+	$(MAKE) -C ice_ocean_SIS2 \
+	  BUILD=../$(BUILD)/dynamic_symmetric/ice_ocean_SIS2 \
+	  FMS_BUILD=../$(BUILD)/fms \
+	  ATMOS_BUILD=../$(BUILD)/atmos_null \
+	  ICEBERGS_BUILD=../$(BUILD)/icebergs \
+	  ICE_PARAM_BUILD=../$(BUILD)/ice_param \
+	  LAND_BUILD=../$(BUILD)/land_null
+
+.PHONY: ice_ocean_SIS2.asymmetric
+ice_ocean_SIS2.asymmetric: fms atmos_null land_null ice_param icebergs
+	$(MAKE) -C ice_ocean_SIS2 \
+	  BUILD=../$(BUILD)/dynamic_nonsymmetric/ice_ocean_SIS2 \
+	  FMS_BUILD=../$(BUILD)/fms \
+	  ATMOS_BUILD=../$(BUILD)/atmos_null \
+	  ICEBERGS_BUILD=../$(BUILD)/icebergs \
+	  ICE_PARAM_BUILD=../$(BUILD)/ice_param \
+	  LAND_BUILD=../$(BUILD)/land_null \
+	  MOM_MEMORY=../src/MOM6/config_src/memory/dynamic_nonsymmetric/MOM_memory.h \
+	  SIS_MEMORY=../src/SIS2/config_src/dynamic/SIS2_memory.h
+
+
+# Full coupled model
+
+.PHONY: coupled_AM2_LM3_SIS2
+coupled_AM2_LM3_SIS2: coupled_AM2_LM3_SIS2.symmetric coupled_AM2_LM3_SIS2.asymmetric
+
+.PHONY: coupled_AM2_LM3_SIS2.symmetric
+coupled_AM2_LM3_SIS2.symmetric: fms AM2 LM3 ice_param icebergs
+	$(MAKE) -C coupled_AM2_LM3_SIS2 \
+	  BUILD=../$(BUILD)/dynamic_symmetric/coupled_AM2_LM3_SIS2 \
+	  FMS_BUILD=../$(BUILD)/fms \
+	  AM2_BUILD=../$(BUILD)/AM2 \
+	  ICEBERGS_BUILD=../$(BUILD)/icebergs \
+	  ICE_PARAM_BUILD=../$(BUILD)/ice_param \
+	  LM3_BUILD=../$(BUILD)/LM3
+
+.PHONY: coupled_AM2_LM3_SIS2.asymmetric
+coupled_AM2_LM3_SIS2.asymmetric: fms AM2 LM3 ice_param icebergs
+	$(MAKE) -C coupled_AM2_LM3_SIS2 \
+	  BUILD=../$(BUILD)/dynamic_nonsymmetric/coupled_AM2_LM3_SIS2 \
+	  FMS_BUILD=../$(BUILD)/fms \
+	  AM2_BUILD=../$(BUILD)/AM2 \
+	  ICEBERGS_BUILD=../$(BUILD)/icebergs \
+	  ICE_PARAM_BUILD=../$(BUILD)/ice_param \
+	  LM3_BUILD=../$(BUILD)/LM3 \
+	  MOM_MEMORY=../src/MOM6/config_src/memory/dynamic_nonsymmetric/MOM_memory.h \
+	  SIS_MEMORY=../src/SIS2/config_src/dynamic/SIS2_memory.h
+
+# TODO: Coupled asymmetric?
+
+# Libraries
+
+.PHONY: fms
+fms:
+	$(MAKE) -C shared/fms \
+	  BUILD=../../$(BUILD)/fms
+
+.PHONY: atmos_null
+atmos_null: fms
+	$(MAKE) -C shared/atmos_null \
+	  BUILD=../../$(BUILD)/atmos_null \
+	  FMS_BUILD=../../$(BUILD)/fms
+
+.PHONY: AM2
+AM2: fms
+	$(MAKE) -C shared/AM2 \
+	  BUILD=../../$(BUILD)/AM2 \
+	  FMS_BUILD=../../$(BUILD)/fms
+
+.PHONY: land_null
+land_null: fms
+	$(MAKE) -C shared/land_null \
+	  BUILD=../../$(BUILD)/land_null \
+	  FMS_BUILD=../../$(BUILD)/fms
+
+.PHONY: LM3
+LM3: fms
+	$(MAKE) -C shared/LM3 \
+	  BUILD=../../$(BUILD)/LM3 \
+	  FMS_BUILD=../../$(BUILD)/fms
+
+.PHONY: ice_param
+ice_param: fms
+	$(MAKE) -C shared/ice_param \
+	  BUILD=../../$(BUILD)/ice_param \
+	  FMS_BUILD=../../$(BUILD)/fms
+
+.PHONY: icebergs
+icebergs: fms
+	$(MAKE) -C shared/icebergs \
+	  BUILD=../../$(BUILD)/icebergs \
+	  FMS_BUILD=../../$(BUILD)/fms
+
+
+# Runs
+# NOTE: This is not yet implemented, and is only an example of how this could
+# look in a future version.
+
+RUNDIR ?= runs
+
+# unused
+rwildcard=$(foreach d,$(wildcard $(1:=/*)),\
+  $(call rwildcard,$d,$2) $(filter $(subst *,%,$2),$d))
+
+# Build manifest
+# TODO: recursive wildcard
+PARAM_LIST=$(shell find $1 -name MOM_parameter_doc.all)
+EXPT_DIRS=$(patsubst $1/%/MOM_parameter_doc.all,%,$(call PARAM_LIST,$1))
+
+# 1: rundir
+# 2: build dir
+# 3: expt dir
+define EXPT_RULE
+$(1)/ocean.stats: ocean_only ;
+	$(MAKE) -C ocean_only ../$(1)/ocean.stats \
+	  BUILD=../$(2) \
+	  OUTPUT=../$(1) \
+	  EXPT=$(3)
+endef
+$(foreach e,$(call EXPT_DIRS,ocean_only),\
+  $(eval $(call EXPT_RULE,$(RUNDIR)/ocean_only/symmetric/$e,$(BUILD)/ocean_only/symmetric,$e)))
+
+
+run.ocean_only: $(foreach e,$(call EXPT_DIRS,ocean_only),\
+  $(RUNDIR)/ocean_only/symmetric/$(e)/ocean.stats)
+
+
+# Cleanup
+
+clean: $(foreach model,$(MODELS),$(model).clean)
+	rm -rf build
+
+define MODEL_CLEAN_RULE
+.PHONY: $(1).clean
+$(1).clean: $(1).symmetric.clean $(1).asymmetric.clean
+
+.PHONY: $(1).symmetric.clean
+$(1).symmetric.clean:
+	$(MAKE) -C $(1) \
+	  BUILD=../$(BUILD)/dynamic_symmetric/$(1) \
+	  clean
+
+.PHONY: $(1).asymmetric.clean
+$(1).asymmetric.clean:
+	$(MAKE) -C $(1) \
+	  BUILD=../$(BUILD)/dynamic_nonsymmetric/$(1) \
+	  clean
+endef
+$(foreach model,$(MODELS),$(eval $(call MODEL_CLEAN_RULE,$(model))))
+
+define CLEAN_RULE
+.PHONY: $(1).clean
+$(1).clean:
+	$(MAKE) -C shared/$(1) \
+	  BUILD=../../$(BUILD)/$(1) \
+	  clean
+endef
+$(foreach lib,$(LIBS),$(eval $(call CLEAN_RULE,$(lib))))