Update Makefiles to default to FMS2; MOM6 update

The Makefiles for each model have been updated to include a variable to
the FMS source directory (FMS_CODEBASE) which is now passed to the FMS
Makefile.

FMS_CODEBASE defaults to the FMS2 source, in order to align with
autoconf changes in MOM6 which now default to FMS2 API.  The AM2-based
models default to FMS1, with separate FMS1-based build directories for
FMS, icebergs, and ice_param.

The FMS1 source and FMS symbolic link have been preserved, so no
exisiting mkmf-based builds should be affected by this change.

The MOM6 submodule has also been updated, which includes the commit
which updates the default autoconf FMS API (f9da67331).

Updated commits:

- NOAA-GFDL/MOM6@714d2da17 Minor refactoring in set_viscous_BBL
- NOAA-GFDL/MOM6@e1ea75847 Add the debugging routine test_L_open_concave
- NOAA-GFDL/MOM6@da02ffc60 +Add find_L_open_concave_iterative
- NOAA-GFDL/MOM6@2ae638504 Refactor set_viscous_BBL channel drag calculations
- NOAA-GFDL/MOM6@f9da67331 Create BUILD and WORK directory macros
- NOAA-GFDL/MOM6@fd5696ba0 Pinning package requirements for readthedocs
- NOAA-GFDL/MOM6@d0e9c25a0 *Corrected CFC diagnostics and non-Bous CFC fluxes
- NOAA-GFDL/MOM6@8f7df084d (*)non-Boussinesq Z unit update_OBC_segment_data
- NOAA-GFDL/MOM6@86c5ed989 (*)Fix bug in h_neglect used to remap diags to rho
- NOAA-GFDL/MOM6@f2e7abff8 MLE: Use default answer date outside of block (#570)
- NOAA-GFDL/MOM6@e69d77107 Merge branch 'main' into dev/gfdl
- NOAA-GFDL/MOM6@2ab885edd Merge pull request #1616 from NOAA-GFDL/dev-gfdl-main-candidate-2023-11-13
- NOAA-GFDL/MOM6@6d7c00a83 Restore bit repro using FMA in selected runs
- NOAA-GFDL/MOM6@f92e4ac31 Update MOM_mixed_layer_restrat.F90 (#568)
- NOAA-GFDL/MOM6@3f7465a57 +tracer_Z_init can rescale tracers
- NOAA-GFDL/MOM6@f14a68107 (*)Use thickness_to_dz with BRYAN_LEWIS_DIFFUSIVITY
- NOAA-GFDL/MOM6@0fb905fdc +(*)non-Boussinesq ALE_sponges work in Z units
- NOAA-GFDL/MOM6@c37a2f0d0 Document core and linear EOS variable units
- NOAA-GFDL/MOM6@de7e5b79f Document MOM_regridding and coord variable units
- NOAA-GFDL/MOM6@4757bcb52 Remove some unused calculations if non-Boussinesq
- NOAA-GFDL/MOM6@9282cd100 +(*)Bodner param with cuberoot and non-Boussinesq
- NOAA-GFDL/MOM6@ea12532d8 Fix issue with restart filenames when using ensembles.
- NOAA-GFDL/MOM6@9a6ddee47 *+non-Boussinesq revisions to MOM_generic_tracer
- NOAA-GFDL/MOM6@e7a7a82ab (*)MOM_temp_salt_init_from_Z Z-unit tracer remap
- NOAA-GFDL/MOM6@915cfe225 +ALE_remap_scalar with arbitrary thickness units
- NOAA-GFDL/MOM6@07bace68c *Fix two bugs in convert_temp_salt_for_TEOS10
- NOAA-GFDL/MOM6@671c85d32 (*)Use cuberoot in ePBL_column
- NOAA-GFDL/MOM6@736ef16a4 Cuberoot: Break **3 into explicit integer cubes
- NOAA-GFDL/MOM6@5edba9b4d Cuberoot: Refactor (re|de)scale functions
- NOAA-GFDL/MOM6@60cb551a3 Intrinsics: Faster cuberoot scaling functions
- NOAA-GFDL/MOM6@76f066814 (*)Avoid using RHO_0 in non-Boussinesq averaging
- NOAA-GFDL/MOM6@541c2f479 (*)Oil_tracer_column_physics unit conversion fix
- NOAA-GFDL/MOM6@0de5c1493 Merge pull request #1618 from jiandewang/DEV-EMC-candidate-20230122
- NOAA-GFDL/MOM6@5ca70bac6 Open parameter block before querying BODNER23
- NOAA-GFDL/MOM6@f1e0f01a8 Params: Add do_not_log to param block open/close
- NOAA-GFDL/MOM6@435ccaae4 Data table documentation (#551)
- NOAA-GFDL/MOM6@17f1c40df Cuberoot: Apply first iteration explicitly (#11)
- NOAA-GFDL/MOM6@4813b17c2 *Use Halley method iterations in cuberoot function
- NOAA-GFDL/MOM6@c8a7325c0 Merge pull request #126 from DeniseWorthen/feature/restartfh
- NOAA-GFDL/MOM6@d7d126a7f Update Gaea F5 datasets path
- NOAA-GFDL/MOM6@d9c7bd950 Merge branch 'NOAA-EMC:dev/emc' into feature/restartfh
- NOAA-GFDL/MOM6@a728ceaa5 allow restarts to be set on non-interval hours
- NOAA-GFDL/MOM6@60c397b91 Merge pull request #124 from jiandewang/feature/update-to-main-20231218
- NOAA-GFDL/MOM6@a03bb957c +Add cuberoot function
- NOAA-GFDL/MOM6@db62734a9 Merge remote-tracking branch 'MAIN/main' into feature/update-to-main-20231218
- NOAA-GFDL/MOM6@40134ed86 change target to pointer and check for association
- NOAA-GFDL/MOM6@7ef6a5725  Fix the saltFluxAdded diagnoistic, broken in #401
- NOAA-GFDL/MOM6@f4c95ec4b Revert post_data fix to CFC concentration
- NOAA-GFDL/MOM6@a36cb73d6 Merge pull request #122 from jiandewang/feature/update-NCAR-GMAO-20231031
- NOAA-GFDL/MOM6@80a93f633 Merge remote-tracking branch 'MAIN/main' into feature/update-NCAR-GMAO-20231031
- NOAA-GFDL/MOM6@e2c322eed Merge remote-tracking branch 'MAIN/main' into feature/update-NCAR-GMAO-20231031
- NOAA-GFDL/MOM6@02d4dc455 Merge pull request #120 from DeniseWorthen/feature/fldnames
- NOAA-GFDL/MOM6@abb0ad24f switch to cesm-style field names

coupled_AM2_LM3_SIS2/Makefile

@@ -4,10 +4,11 @@ MOM_MEMORY ?=
 SIS_MEMORY ?=
 
 # Dependencies
-FMS_BUILD ?= ../shared/fms/build
+FMS_CODEBASE ?= ../src/FMS1
+FMS_BUILD ?= ../shared/fms/build_fms1
 AM2_BUILD ?= ../shared/AM2/build
-ICEBERGS_BUILD ?= ../shared/icebergs/build
-ICE_PARAM_BUILD ?= ../shared/ice_param/build
+ICEBERGS_BUILD ?= ../shared/icebergs/build_fms1
+ICE_PARAM_BUILD ?= ../shared/ice_param/build_fms1
 LM3_BUILD ?= ../shared/LM3/build
 
 # Autoconf configuration
@@ -32,6 +33,7 @@ EXTRA_SRC_DIRS = \
 CONFIG_FLAGS := --config-cache
 CONFIG_FLAGS += --srcdir=$(abspath $(MOM_CODEBASE))
 CONFIG_FLAGS += --with-driver=FMS_cap
+CONFIG_FLAGS += --with-framework=fms1
 ifdef MOM_MEMORY
  CONFIG_FLAGS += MOM_MEMORY=$(abspath $(MOM_MEMORY))
 endif
@@ -46,7 +48,7 @@ FCFLAGS ?= -g -O2
 # Path to fms_platform.h
 # NOTE: Most libraries need an explicit path to this file. Someday, this could
 # be handled by library-specific autoconf tests.
-FCFLAGS += -I$(abspath ../src/FMS/include)
+FCFLAGS += -I$(abspath $(FMS_CODEBASE)/include)
 
 MOM_FCFLAGS = $(FCFLAGS) \
  -I$(abspath $(FMS_BUILD)) \
@@ -170,7 +172,8 @@ $(ICEBERGS_BUILD)/libicebergs.a: FORCE $(FMS_BUILD)/libFMS.a
 
 $(FMS_BUILD)/libFMS.a: FORCE
  $(MAKE) -C ../shared/fms \
- BUILD=$(abspath $(FMS_BUILD))
+ BUILD=$(abspath $(FMS_BUILD)) \
+ CODEBASE=$(abspath $(FMS_CODEBASE))
 
 FORCE:
 
@@ -230,11 +233,16 @@ $(foreach expt,$(EXPTS),$(eval $(call EXPT_RULE,$(expt))))
 .PHONY: clean
 clean:
  rm -rf $(BUILD)
- $(MAKE) -C ../shared/AM2 clean
+ $(MAKE) -C ../shared/AM2 clean \
+ BUILD=$(abspath $(AM2_BUILD))
  $(MAKE) -C ../shared/LM3 clean
- $(MAKE) -C ../shared/ice_param clean
- $(MAKE) -C ../shared/icebergs clean
- $(MAKE) -C ../shared/fms clean
+ BUILD=$(abspath $(LM3_BUILD))
+ $(MAKE) -C ../shared/ice_param clean \
+ BUILD=$(abspath $(ICE_PARAM_BUILD))
+ $(MAKE) -C ../shared/icebergs clean \
+ BUILD=$(abspath $(ICEBERGS_BUILD))
+ $(MAKE) -C ../shared/fms clean \
+ BUILD=$(abspath $(FMS_BUILD))
 
 .PHONY: clean.runs
 clean.runs: $(foreach e,$(EXPTS),clean.$(e))

ice_ocean_SIS2/Makefile

@@ -4,6 +4,7 @@ MOM_MEMORY ?=
 SIS_MEMORY ?=
 
 # Dependencies
+FMS_CODEBASE ?= ../src/FMS2
 FMS_BUILD ?= ../shared/fms/build
 ICEBERGS_BUILD ?= ../shared/icebergs/build
 ICE_PARAM_BUILD ?= ../shared/ice_param/build
@@ -172,7 +173,8 @@ $(ICEBERGS_BUILD)/libicebergs.a: FORCE $(FMS_BUILD)/libFMS.a
 
 $(FMS_BUILD)/libFMS.a: FORCE
  $(MAKE) -C ../shared/fms \
- BUILD=$(abspath $(FMS_BUILD))
+ BUILD=$(abspath $(FMS_BUILD)) \
+ CODEBASE=$(abspath $(FMS_CODEBASE))
 
 FORCE:
 

ocean_only/Makefile

@@ -3,6 +3,7 @@ BUILD ?= build
 MOM_MEMORY ?=
 
 # Dependencies
+FMS_CODEBASE ?= ../src/FMS2
 FMS_BUILD ?= ../shared/fms/build
 
 # Autoconf configuration
@@ -104,7 +105,9 @@ $(BUILD):
 # Dependencies
 
 $(FMS_BUILD)/libFMS.a: FORCE
- $(MAKE) -C ../shared/fms BUILD=$(abspath $(FMS_BUILD))
+ $(MAKE) -C ../shared/fms \
+ BUILD=$(abspath $(FMS_BUILD)) \
+ CODEBASE=$(abspath $(FMS_CODEBASE))
 
 FORCE:
 

shared/AM2/Makefile

@@ -1,6 +1,7 @@
 # Configuration
 BUILD ?= build
 FMS_BUILD ?= ../fms/build
+FMS_CODEBASE ?= ../../src/FMS1
 
 TARGET = libAM2.a
 CODEBASE = ../../src/AM2
@@ -13,7 +14,7 @@ SRCDIRS = $(addprefix $(abspath $(CODEBASE))/, \
  atmos_param_am3)
 
 FCFLAGS += -I$(abspath $(FMS_BUILD))
-FCFLAGS += -I$(abspath ../../src/FMS/include)
+FCFLAGS += -I$(abspath $(FMS_CODEBASE)/include)
 
 LDFLAGS += -L$(abspath $(FMS_BUILD))
 

shared/config/Libs.mk

@@ -10,6 +10,10 @@ MAKEPATH = $(realpath $(dir $(abspath $(lastword $(MAKEFILE_LIST)))))
 M4DIR ?= $(MAKEPATH)/../../src/MOM6/ac/m4
 MAKEDEP = $(MAKEPATH)/../../src/MOM6/ac/makedep
 
+# `export` disables autoconf defaults; this restores them
+CFLAGS ?= -g -O2
+FCFLAGS ?= -g -O2
+
 # Autoconf configuration
 export CPPFLAGS
 export CC

shared/fms/Makefile

@@ -1,7 +1,7 @@
 # Configuration
 BUILD ?= build
+CODEBASE ?= ../../src/FMS2
 
-CODEBASE = ../../src/FMS
 TARGET = libFMS.a
 MAKEFILE_IN = ../../src/MOM6/ac/deps/Makefile.fms.in
 CONFIGURE_AC = ../../src/MOM6/ac/deps/configure.fms.ac