Makefile now invokes submakefiles

The top-level Makefile no longer attempts to emulate the MRS build
structure, and now simply invokes the Makefiles of each submodel.
It is no longer the point of reference for testing the suite, which
should now be handled by a parent repository (e.g. Gaea-stats).

The top Makefile is now the starting point for public usage.  As part of
this, the CM2-based models were removed from the default `all` rule.

Many changes were added to reliably track changes in the source code.

* A "FORCE" rule has been introduced to ensure that changes tracked by
  the submakes are also tracked by the top Makefile.  Similar changes
  have been applied to the relevant submakes.

* Library dependency is explicitly tracked inside of the rules, with
  `test .. -nt ...` conditionals.

  This was done because the top Makefile cannot reliably track the state
  of products from the submakes, but there may be a better way to do
  this.

* The MOM6 source was updated to use the latest version of makedep,
  which was required by AM2 to fix some errors in tracking source code
  dependencies.

Several minor fixes are outlined below.

* Many explicit CPPDEFS were removed, and the macros are set by
  autoconf's AC_DEFINE macro, and assigned to DEFS.

* LIBS ordering should now be correct on all systems.  FMS linking is
  once again tested.  GFDL dependencies are explicitly prepended to LIBS
  during autoconf setup.  (Someday, these should be replaced with
  proper tests for each library.)

  As part of this, the CM2-based and ice-ocean configure.ac files have
  been split.

* Minor issues around propagation of environment variables (FCFLAGS,
  etc) have been fixed.

Makefile

@@ -1,131 +1,64 @@
-# Test build
-BUILD ?= build
+MODELS = ocean_only ice_ocean_SIS2 coupled_AM2_LM3_SIS2
+DEPS = AM2 atmos_null LM3 land_null ice_param icebergs
+
+# Variable `export` replaces the default autoconf values with empty strings.
+# This restores the default values.
+CFLAGS ?= -g -O2
+FCFLAGS ?= -g -O2
+
+# Pass autoconf environment variables to submakes
+export CPPFLAGS
+export CC
+export MPICC
+export CFLAGS
+export FC
+export MPIFC
+export FCFLAGS
+export LDFLAGS
+export LIBS
+export PYTHON
+
+# Disable builtin rules and variables
+MAKEFLAGS += -rR
+
+#---
+
+# Public models
+.PHONY: all
+all: ocean_only ice_ocean_SIS2
 
-# Models
-MODELS=ocean_only ice_ocean_SIS2 coupled_AM2_LM3_SIS2
-LIBS=AM2 atmos_null LM3 land_null icebergs ice_param fms
+# GFDL-specific coupled models (requires access to GFDL intranet)
+.PHONY: gfdl
+gfdl: ocean_only ice_ocean_SIS2 coupled_AM2_LM3_SIS2
 
-.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=../../$(BUILD)/fms
+# Dependencies
+$(MODELS): fms
+ice_ocean_SIS2 coupled_AM2_LM3_SIS2: ice_param icebergs
+ice_ocean_SIS2: atmos_null land_null
+coupled_AM2_LM3_SIS2: AM2 LM3
+$(DEPS): fms
+
+.PHONY: $(MODELS)
+$(MODELS):
+	$(MAKE) -C $@
+
+
+.PHONY: $(DEPS) fms
+$(DEPS) fms:
+	$(MAKE) -C shared/$@
+
+
+# Cleanup
+.PHONY: clean
+clean: $(foreach m,$(MODELS),$(m).clean) $(foreach d,$(DEPS),$(d).clean) fms.clean
+
+.PHONY: $(foreach m,$(MODELS) $(DEPS) fms,$(m).clean)
+
+$(foreach model,$(MODELS),$(model).clean):
+	$(MAKE) -C $(subst .clean,,$@) clean
+
+$(foreach dep,$(DEPS) fms,$(dep).clean):
+	$(MAKE) -C shared/$(subst .clean,,$@) clean
 
 
 # Runs
@@ -159,36 +92,3 @@ $(foreach e,$(call EXPT_DIRS,ocean_only),\
 
 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))))

ac/configure.mom6sis2.ac → ac/configure.coupled.ac

@@ -214,30 +214,18 @@ AX_FC_CHECK_MODULE([fms_mod], [], [
     [-I${srcdir}/ac/deps/include])
 ])
 
-# TODO: We cannot currently use this test, since it prepends -lFMS to LIBS.
-#   However, we need to append -lFMS, not prepend, since we are putting
-#   libraries in LIBS which depend on FMS, and some linkers can fail if in the
-#   wrong order (per POSIX convention).
-#
-#   This could be resolved in a few different ways:
-#   * AX_FC_CHECK_LIB macros for each library
-#   * AX_FC_SEARCH_LIBS for FMS
-#   but there are issues with each of these options.
-#
-#   For now, we remove the test and rely on LIBS, but should revisit this.
-#
-## Test for fms_init to verify FMS library linking
-#AX_FC_CHECK_LIB([FMS], [fms_init], [fms_mod],
-#  [], [
-#    AS_UNSET([ax_fc_cv_lib_FMS_fms_init])
-#    AX_FC_CHECK_LIB([FMS], [fms_init], [fms_mod], [
-#      AC_SUBST([LDFLAGS], ["-L${srcdir}/ac/deps/lib $LDFLAGS"])
-#      AC_SUBST([LIBS], ["-lFMS $LIBS"])
-#    ],
-#    [AC_MSG_ERROR([Could not find FMS library.])],
-#    [-L${srcdir}/ac/deps/lib])
-#  ]
-#)
+# Test for fms_init to verify FMS library linking
+AX_FC_CHECK_LIB([FMS], [fms_init], [fms_mod],
+  [], [
+    AS_UNSET([ax_fc_cv_lib_FMS_fms_init])
+    AX_FC_CHECK_LIB([FMS], [fms_init], [fms_mod], [
+      AC_SUBST([LDFLAGS], ["-L${srcdir}/ac/deps/lib $LDFLAGS"])
+      AC_SUBST([LIBS], ["-lFMS $LIBS"])
+    ],
+    [AC_MSG_ERROR([Could not find FMS library.])],
+    [-L${srcdir}/ac/deps/lib])
+  ]
+)
 
 
 # Verify that FMS is at least 2019.01.02
@@ -323,6 +311,18 @@ AC_CHECK_SIZEOF([sigjmp_buf], [], [#include <setjmp.h>])
 AC_LANG_POP([C])
 
 
+# Coupler macros
+AC_DEFINE([use_AM3_physics])
+AC_DEFINE([_USE_LEGACY_LAND_])
+
+
+# TODO: We cannot currently provide tests for these libraries, and explicitly
+#   setting LIBS in the Makefile will append, rather than prepend, the flags,
+#   which would break the ordering.
+# For now, we explicitly prepend these libraries, but this needs to be fixed.
+LIBS="-licebergs -lice_param -lAM2 -lLM3 ${LIBS}"
+
+
 # Prepare output
 AC_SUBST([CPPFLAGS])
 AC_CONFIG_FILES([Makefile:Makefile.in])