Merge pull request #61 from jiandewang/feature/update-to-GFDL-20210308

Feature/update to gfdl 20210308

.gitlab-ci.yml

@@ -31,7 +31,7 @@ setup:
     # Clone regressions directory
     - git clone --recursive http://gitlab.gfdl.noaa.gov/ogrp/Gaea-stats-MOM6-examples.git tests && cd tests
     # Install / update testing scripts
-    - git clone https://github.com/adcroft/MRS.git MRS
+    - git clone -b new-code-struct https://github.com/adcroft/MRS.git MRS
     # Update MOM6-examples and submodules
     - (cd MOM6-examples && git checkout . && git checkout dev/gfdl && git pull && git submodule init && git submodule update)
     - (cd MOM6-examples/src/MOM6 && git submodule update)
@@ -60,7 +60,7 @@ gnu:ocean-only-nolibs:
     - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
     - make -f MRS/Makefile.build build/gnu/env && cd build/gnu
     # mkdir -p build/gnu/repro/symmetric_dynamic/ocean_only && cd build/gnu/repro/symmetric_dynamic/ocean_only
-    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{solo_driver,dynamic_symmetric,ext*} ../../../src ../../MOM6-examples/src/FMS
+    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{drivers/solo_driver,memory/dynamic_symmetric,infra/FMS1,ext*} ../../../src ../../MOM6-examples/src/FMS
     - sed -i '/FMS\/.*\/test_/d' path_names
     - ../../MOM6-examples/src/mkmf/bin/mkmf -t ../../MOM6-examples/src/mkmf/templates/ncrc-gnu.mk -p MOM6 -c"-Duse_libMPI -Duse_netCDF" path_names
     - time (source ./env ; make NETCDF=3 REPRO=1 MOM6 -s -j)
@@ -73,7 +73,7 @@ gnu:ice-ocean-nolibs:
     - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
     - make -f MRS/Makefile.build build/gnu/env && cd build/gnu
     # mkdir -p build/gnu/repro/symmetric_dynamic/ocean_only && cd build/gnu/repro/symmetric_dynamic/ocean_only
-    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{coupled_driver,dynamic,ext*} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_param,land_null,atmos_null}
+    - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{drivers/FMS_cap,memory/dynamic_nonsymmetric,infra/FMS1,ext*} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_param,land_null,atmos_null}
     - sed -i '/FMS\/.*\/test_/d' path_names
     - ../../MOM6-examples/src/mkmf/bin/mkmf -t ../../MOM6-examples/src/mkmf/templates/ncrc-gnu.mk -p MOM6 -c"-Duse_libMPI -Duse_netCDF -D_USE_LEGACY_LAND_ -Duse_AM3_physics" path_names
     - time (source ./env ; make NETCDF=3 REPRO=1 MOM6 -s -j)

.testing/Makefile

@@ -32,7 +32,6 @@
 #   MPIFC   MPI Fortran compiler
 #
 # Build configuration:
-#
 #   FCFLAGS_DEBUG       Testing ("debug") compiler flags
 #   FCFLAGS_REPRO       Production ("repro") compiler flags
 #   FCFLAGS_INIT        Variable initialization flags
@@ -76,7 +75,6 @@ FCFLAGS_REPRO ?= -g -O2
 FCFLAGS_INIT ?=
 FCFLAGS_COVERAGE ?=
 # Additional notes:
-#
 # - The default values are simple, minimalist flags, supported by nearly all
 #   compilers which are comparable to GFDL's canonical DEBUG and REPRO builds.
 #
@@ -87,13 +85,14 @@ FCFLAGS_COVERAGE ?=
 #   so FCFLAGS_INIT is used to provide additional MOM6 configuration.
 
 # Set to `true` to require identical results from DEBUG and REPRO builds
+# NOTE: Many compilers (Intel, GCC on ARM64) do not yet produce identical
+#   results across DEBUG and REPRO builds (as defined below), so we disable on
+#   default.
 DO_REPRO_TESTS ?=
 
+# Time measurement (configurable by the CI)
 TIME ?= time
 
-# Many compilers (Intel, GCC on ARM64) do not yet produce identical results
-# across DEBUG and REPRO builds (as defined below), so we disable on default.
-
 #---
 # Dependencies
 DEPS = deps
@@ -154,10 +153,12 @@ SOURCE = \
   $(foreach ext,F90 inc c h,$(wildcard $(1)/*/*.$(ext) $(1)/*/*/*.$(ext)))
 
 MOM_SOURCE = $(call SOURCE,../src) \
-  $(wildcard ../config_src/solo_driver/*.F90) \
+  $(wildcard ../config_src/infra/FMS1/*.F90) \
+  $(wildcard ../config_src/drivers/solo_driver/*.F90) \
   $(wildcard ../config_src/ext*/*/*.F90)
 TARGET_SOURCE = $(call SOURCE,build/target_codebase/src) \
-  $(wildcard build/target_codebase/config_src/solo_driver/*.F90) \
+  $(wildcard build/target_codebase/config_src/infra/FMS1/*.F90) \
+  $(wildcard build/target_codebase/config_src/drivers/solo_driver/*.F90) \
   $(wildcard build/target_codebase/config_src/ext*/*.F90)
 FMS_SOURCE = $(call SOURCE,$(DEPS)/fms/src)
 
@@ -249,7 +250,7 @@ build/target/Makefile: | $(TARGET_CODEBASE)
 #   Ideally we would want to re-run both Makefile and mkmf, but our mkmf call
 #   is inside ./configure, so we must re-run ./configure as well.
 $(foreach b,$(filter-out target,$(BUILDS)),build/$(b)/Makefile): $(MOM_SOURCE)
-build/target/configure: $(TARGET_SOURCE)
+build/target_codebase/configure: $(TARGET_SOURCE)
 
 
 # Build MOM6
@@ -286,9 +287,6 @@ $(TARGET_CODEBASE)/ac/configure: $(TARGET_CODEBASE)
 $(TARGET_CODEBASE):
 	git clone --recursive $(MOM_TARGET_URL) $@
 	cd $@ && git checkout $(MOM_TARGET_BRANCH)
-	# Copy modern autoconf files to target?
-	mkdir -p $(TARGET_CODEBASE)/ac
-	cp -r ../ac/{configure.ac,Makefile.in,m4} $(TARGET_CODEBASE)/ac
 
 
 #---

ac/configure.ac

@@ -42,18 +42,18 @@ srcdir=$srcdir/..
 # Default to symmetric grid
 # NOTE: --enable is more properly used to add a feature, rather than to select
 #   a compile-time mode, so this is not exactly being used as intended.
-MEM_LAYOUT=${srcdir}/config_src/dynamic_symmetric
+MEM_LAYOUT=${srcdir}/config_src/memory/dynamic_symmetric
 AC_ARG_ENABLE([asymmetric],
   AS_HELP_STRING([--enable-asymmetric], [Use the asymmetric grid]))
 AS_IF([test "$enable_asymmetric" = yes],
-  [MEM_LAYOUT=${srcdir}/config_src/dynamic])
+  [MEM_LAYOUT=${srcdir}/config_src/memory/dynamic_nonsymmetric])
 
 # Default to solo_driver
-DRIVER_DIR=${srcdir}/config_src/solo_driver
+DRIVER_DIR=${srcdir}/config_src/drivers/solo_driver
 AC_ARG_WITH([driver],
   AS_HELP_STRING([--with-driver=coupled_driver|solo_driver], [Select directory for driver source code]))
 AS_IF([test "x$with_driver" != "x"],
-  [DRIVER_DIR=${srcdir}/config_src/${with_driver}])
+  [DRIVER_DIR=${srcdir}/config_src/drivers/${with_driver}])
 
 # TODO: Rather than point to a pre-configured header file, autoconf could be
 # used to configure a header based on a template.
@@ -216,6 +216,7 @@ AS_IF([test -z "$MKMF"], [
 AC_CONFIG_COMMANDS([path_names],
   [list_paths -l \
     ${srcdir}/src \
+    ${srcdir}/config_src/infra/FMS1 \
     ${srcdir}/config_src/ext* \
     ${DRIVER_DIR} \
     ${MEM_LAYOUT}

docs/Doxyfile_nortd

@@ -860,10 +860,10 @@ WARN_LOGFILE           = _build/doxygen_warn_nortd_log.txt
 
 INPUT                  = ../src \
                          front_page.md \
-                         ../config_src/solo_driver \
-                         ../config_src/dynamic_symmetric \
+                         ../config_src/drivers/solo_driver \
+                         ../config_src/memory/dynamic_symmetric \
                          ../config_src/external \
-                         ../config_src/coupled_driver
+                         ../config_src/drivers/FMS_cap
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -2212,7 +2212,7 @@ SEARCH_INCLUDES        = YES
 # This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
 INCLUDE_PATH           = ../src/framework \
-                         ../config_src/dynamic_symmetric
+                         ../config_src/memory/dynamic_symmetric
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the

docs/Doxyfile_nortd_latex

@@ -860,10 +860,10 @@ WARN_LOGFILE           = _build/doxygen_warn_nortd_latex_log.txt
 
 INPUT                  = ../src \
                          front_page.md \
-                         ../config_src/solo_driver \
-                         ../config_src/dynamic_symmetric \
+                         ../config_src/drivers/solo_driver \
+                         ../config_src/memory/dynamic_symmetric \
                          ../config_src/external \
-                         ../config_src/coupled_driver
+                         ../config_src/drivers/FMS_cap
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -2212,7 +2212,7 @@ SEARCH_INCLUDES        = YES
 # This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
 INCLUDE_PATH           = ../src/framework \
-                         ../config_src/dynamic_symmetric
+                         ../config_src/memory/dynamic_symmetric
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the

docs/Doxyfile_rtd

@@ -810,10 +810,10 @@ WARN_LOGFILE           = _build/doxygen_warn_rtd_log.txt
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = ../src \
-                         ../config_src/solo_driver \
-                         ../config_src/dynamic_symmetric \
+                         ../config_src/drivers/solo_driver \
+                         ../config_src/memory/dynamic_symmetric \
                          ../config_src/external \
-                         ../config_src/coupled_driver
+                         ../config_src/drivers/FMS_cap
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -2072,7 +2072,7 @@ SEARCH_INCLUDES        = YES
 # preprocessor.
 # This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
-INCLUDE_PATH           = ../src/framework ../config_src/dynamic_symmetric
+INCLUDE_PATH           = ../src/framework ../config_src/memory/dynamic_symmetric
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the

docs/Doxyfile_rtd_dox

@@ -810,10 +810,10 @@ WARN_LOGFILE           = _build/doxygen_rtd_dox_debug.txt
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = ../src \
-                         ../config_src/solo_driver \
-                         ../config_src/dynamic_symmetric \
+                         ../config_src/drivers/solo_driver \
+                         ../config_src/memory/dynamic_symmetric \
                          ../config_src/external \
-                         ../config_src/coupled_driver \
+                         ../config_src/drivers/FMS_cap \
                          ../src/ALE/MOM_ALE.F90 \
                          ../src/ALE/PCM_functions.F90 \
                          ../src/core/MOM.F90 \
@@ -838,10 +838,10 @@ INPUT                  = ../src \
 #INPUT                  = ../src/equation_of_state
 
 #INPUT                  = ../src/ALE \
-#                         ../config_src/solo_driver \
-#                         ../config_src/dynamic_symmetric \
+#                         ../config_src/drivers/solo_driver \
+#                         ../config_src/memory/dynamic_symmetric \
 #                         ../config_src/external \
-#                         ../config_src/coupled_driver
+#                         ../config_src/drivers/FMS_cap
 
 #INPUT                  = \
 #        ../src/ALE/_ALE.dox \
@@ -2112,7 +2112,7 @@ SEARCH_INCLUDES        = YES
 # preprocessor.
 # This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
-INCLUDE_PATH           = ../src/framework ../config_src/dynamic_symmetric
+INCLUDE_PATH           = ../src/framework ../config_src/memory/dynamic_symmetric
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the

docs/README.md

@@ -53,15 +53,19 @@ The starting state of directories and files:
 ```
 SRC/
   config_src/
-    coupled_driver
-    dynamic
-    dynamic_symmetric
+    drivers/
+      FMS_cap
+      ice_solo_driver
+      mct_cap
+      nuopc_cap
+      solo_driver
+      unit_drivers
     external
-    ice_solo_driver
-    mct_driver
-    nuopc_driver
-    solo_driver
-    unit_drivers
+    infra/
+      FMS1
+    memory/
+      dynamic
+      dynamic_symmetric
   pkg/
     CVMix-src
     GSW-Fortran

docs/code_organization.rst

@@ -34,17 +34,19 @@ The directory tree is::
 
   MOM6
   ├── config_src
-  │   ├── coupled_driver
-  │   ├── dynamic
-  │   ├── dynamic_symmetric
+  │   ├── drivers
+  │   │   ├── FMS_cap
+  │   │   ├── ice_solo_driver
+  │   │   ├── mct_cap
+  │   │   ├── nuopc_cap
+  │   │   ├── solo_driver
+  │   │   └── unit_drivers
   │   ├── external
   │   │   ├── GFDL_ocean_BGC
   │   │   └── ODA_hooks
-  │   ├── ice_solo_driver
-  │   ├── mct_driver
-  │   ├── nuopc_driver
-  │   ├── solo_driver
-  │   └── unit_drivers
+  │   ├── memory
+  │   │   ├── dynamic_nonsymmetric
+  │   │   ├── dynamic_symmetric
   ├── docs
   │   └── images
   ├── pkg
@@ -84,11 +86,11 @@ The directory tree is::
 `config_src/`
 -------------
 
-`dynamic/`, `dynamic_symmetric/`
-  One or none of `config_src/dynamic/` or `config_src/dynamic_symmetric/` can
-  be included at compile time. If neither is used then a `MOM_memory.h` file
-  specific to the model configuration must be present - this is known as a
-  "static" compile with fixed layout and domain shape.
+`memory/dynamic_nonsymmetric/`, `memory/dynamic_symmetric/`
+  One or none of `config_src/memory/dynamic_nonsymmetric/` or
+  `config_src/dynamic_symmetric/` can be included at compile time. If neither
+  is used then a `MOM_memory.h` file specific to the model configuration must be
+  present - this is known as a"static" compile with fixed layout and domain shape.
 
 `external/`
   Contains "null" modules providing the API to optional components to use
@@ -98,12 +100,17 @@ The directory tree is::
   To use the actual ODA or BGC, add the appropriate source to the search
   paths .
 
-`solo_driver/`
+`infra/FMS1`
+  Contains MOM6-specific thin wrappers to all of the FMS types and routines that
+  are used by MOM6.  The code in this directory should only be called by the
+  infrastructure-agnostic code in src/framework.
+
+`drivers/solo_driver/`
   This driver produces an ocean-only executable with no other coupled
   components (no sea-ice, no atmosphere, etc.). It is the simplest
   configuration and fastest to compile and thus used for a lot of testing.
 
-`coupled_driver/`
+`drivers/FMS_cap/`
   This driver provides an interface for the GFDL coupler to call. It requires
   compiling MOM6 along with at least a sea-ice model and possibly all other
   components in a coupled model.