Merge branch 'dev/gfdl' into patch-1

.github/actions/macos-setup/action.yml

@@ -16,3 +16,18 @@ runs:
         brew install netcdf-fortran
         brew install mpich
         echo "::endgroup::"
+
+    # NOTE: Floating point exceptions are currently disabled due to an error in
+    # HDF5 1.4.3.  They will be re-enabled when the default brew version has
+    # been updated to a working version.
+
+    - name: Set compiler flags
+      shell: bash
+      run: |
+        cd .testing
+        echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
+        cat config.mk
+        echo "::endgroup::"

.github/actions/testing-setup/action.yml

@@ -31,17 +31,6 @@ runs:
         REPORT_ERROR_LOGS=true make deps/lib/libFMS.a -s -j
         echo "::endgroup::"
 
-    - name: Store compiler flags used in Makefile
-      shell: bash
-      run: |
-        echo "::group::config.mk"
-        cd .testing
-        echo "FCFLAGS_DEBUG=-g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
-        echo "FCFLAGS_REPRO=-g -O2 -fbacktrace" >> config.mk
-        echo "FCFLAGS_INIT=-finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
-        cat config.mk
-        echo "::endgroup::"
-
     - name: Compile MOM6 in symmetric memory mode
       shell: bash
       run: |

.github/actions/ubuntu-setup/action.yml

@@ -17,3 +17,15 @@ runs:
         sudo apt-get install libopenmpi-dev
         sudo apt-get install linux-tools-common
         echo "::endgroup::"
+
+    - name: Store compiler flags used in Makefile
+      shell: bash
+      run: |
+        echo "::group::config.mk"
+        cd .testing
+        echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
+        cat config.mk
+        echo "::endgroup::"

ac/Makefile.in

@@ -19,7 +19,6 @@ SRC_DIRS = @SRC_DIRS@
 
 -include Makefile.dep
 
-
 # Generate Makefile from template
 Makefile: @srcdir@/ac/Makefile.in config.status
 	./config.status
@@ -33,7 +32,7 @@ rwildcard=$(foreach d,$(wildcard $(1:=/*)),$(call rwildcard,$d,$2) $(filter $(su
 .PHONY: depend
 depend: Makefile.dep
 Makefile.dep: $(MAKEDEP) $(call rwildcard,$(SRC_DIRS),*.h *.c *.inc *.F90)
-	$(PYTHON) $(MAKEDEP) -o Makefile.dep -e $(SRC_DIRS)
+	$(PYTHON) $(MAKEDEP) $(DEFS) -o Makefile.dep -e $(SRC_DIRS)
 
 
 # Delete any files associated with configuration (including the Makefile).

ac/makedep

@@ -13,9 +13,16 @@ import sys
 # Pre-compile re searches
 re_module = re.compile(r"^ *module +([a-z_0-9]+)")
 re_use = re.compile(r"^ *use +([a-z_0-9]+)")
+re_cpp_define = re.compile(r"^ *# *define +[_a-zA-Z][_a-zA-Z0-9]")
+re_cpp_undef = re.compile(r"^ *# *undef +[_a-zA-Z][_a-zA-Z0-9]")
+re_cpp_ifdef = re.compile(r"^ *# *ifdef +[_a-zA-Z][_a-zA-Z0-9]")
+re_cpp_ifndef = re.compile(r"^ *# *ifndef +[_a-zA-Z][_a-zA-Z0-9]")
+re_cpp_if = re.compile(r"^ *# *if +")
+re_cpp_else = re.compile(r"^ *# *else")
+re_cpp_endif = re.compile(r"^ *# *endif")
 re_cpp_include = re.compile(r"^ *# *include *[<\"']([a-zA-Z_0-9\.]+)[>\"']")
 re_f90_include = re.compile(r"^ *include +[\"']([a-zA-Z_0-9\.]+)[\"']")
-re_program = re.compile(r"^ *[pP][rR][oO][gG][rR][aA][mM] +([a-zA-Z_0-9]+)")
+re_program = re.compile(r"^ *program +([a-z_0-9]+)", re.IGNORECASE)
 re_end = re.compile(r"^ *end *(module|procedure) ", re.IGNORECASE)
 # NOTE: This excludes comments and tokens with substrings containing `function`
 # or `subroutine`, but will fail if the keywords appear in other contexts.
@@ -26,7 +33,7 @@ re_procedure = re.compile(
 
 
 def create_deps(src_dirs, skip_dirs, makefile, debug, exec_target, fc_rule,
-                link_externals, script_path):
+                link_externals, defines):
     """Create "makefile" after scanning "src_dis"."""
 
     # Scan everything Fortran related
@@ -66,7 +73,7 @@ def create_deps(src_dirs, skip_dirs, makefile, debug, exec_target, fc_rule,
     o2mods, o2uses, o2h, o2inc, o2prg, prg2o, mod2o = {}, {}, {}, {}, {}, {}, {}
     externals, all_modules = [], []
     for f in F90_files:
-        mods, used, cpp, inc, prg, has_externals = scan_fortran_file(f)
+        mods, used, cpp, inc, prg, has_externals = scan_fortran_file(f, defines)
         # maps object file to modules produced
         o2mods[object_file(f)] = mods
         # maps module produced to object file
@@ -272,10 +279,16 @@ def nested_inc(inc_files, f2F):
     return inc_files + sorted(set(hlst)), used_mods
 
 
-def scan_fortran_file(src_file):
+def scan_fortran_file(src_file, defines=None):
     """Scan the Fortran file "src_file" and return lists of module defined,
     module used, and files included."""
     module_decl, used_modules, cpp_includes, f90_includes, programs = [], [], [], [], []
+
+    cpp_defines = defines if defines is not None else []
+
+    cpp_macros = [define.split('=')[0] for define in cpp_defines]
+    cpp_group_stack = []
+
     with io.open(src_file, 'r', errors='replace') as file:
         lines = file.readlines()
 
@@ -285,7 +298,72 @@ def scan_fortran_file(src_file):
         file_has_externals = False
             # True if the file contains any external objects
 
+        cpp_exclude = False
+            # True if the parser excludes the subsequent lines
+
+        cpp_group_stack = []
+            # Stack of condition group exclusion states
+
         for line in lines:
+            # Start of #ifdef condition group
+            match = re_cpp_ifdef.match(line)
+            if match:
+                cpp_group_stack.append(cpp_exclude)
+
+                # If outer group is excluding or macro is missing, then exclude
+                macro = line.lstrip()[1:].split()[1]
+                cpp_exclude = cpp_exclude or macro not in cpp_macros
+
+            # Start of #ifndef condition group
+            match = re_cpp_ifndef.match(line)
+            if match:
+                cpp_group_stack.append(cpp_exclude)
+
+                # If outer group is excluding or macro is present, then exclude
+                macro = line.lstrip()[1:].split()[1]
+                cpp_exclude = cpp_exclude or macro in cpp_macros
+
+            # Start of #if condition group
+            match = re_cpp_if.match(line)
+            if match:
+                cpp_group_stack.append(cpp_exclude)
+
+                # XXX: Don't attempt to parse #if statements, but store the state.
+                # if/endif stack.  For now, assume that these always fail.
+                cpp_exclude = False
+
+            # Complement #else condition group
+            match = re_cpp_else.match(line)
+            if match:
+                # Reverse the exclude state, if there is no outer exclude state
+                outer_grp_exclude = cpp_group_stack and cpp_group_stack[-1]
+                cpp_exclude = not cpp_exclude or outer_grp_exclude
+
+            # Restore exclude state when exiting conditional block
+            match = re_cpp_endif.match(line)
+            if match:
+                cpp_exclude = cpp_group_stack.pop()
+
+            # Skip lines inside of false condition blocks
+            if cpp_exclude:
+                continue
+
+            # Activate a new macro (ignoring the value)
+            match = re_cpp_define.match(line)
+            if match:
+                new_macro = line.lstrip()[1:].split()[1]
+                cpp_macros.append(new_macro)
+
+            # Deactivate a macro
+            match = re_cpp_undef.match(line)
+            if match:
+                new_macro = line.lstrip()[1:].split()[1]
+                try:
+                    cpp_macros.remove(new_macro)
+                except:
+                    # Ignore missing macros (for now?)
+                    continue
+
             match = re_module.match(line.lower())
             if match:
                 if match.group(1) not in 'procedure':   # avoid "module procedure" statements
@@ -404,8 +482,13 @@ parser.add_argument(
     action='append',
     help="Skip directory in source code search."
 )
+parser.add_argument(
+    '-D', '--define',
+    action='append',
+    help="Apply preprocessor define macros (of the form -DMACRO[=value])",
+)
 args = parser.parse_args()
 
 # Do the thing
 create_deps(args.path, args.skip, args.makefile, args.debug, args.exec_target,
-            args.fc_rule, args.link_externals, sys.argv[0])
+            args.fc_rule, args.link_externals, args.define)

config_src/drivers/FMS_cap/MOM_surface_forcing_gfdl.F90

@@ -1522,7 +1522,7 @@ subroutine surface_forcing_init(Time, G, US, param_file, diag, CS, wind_stagger)
   endif
   call get_param(param_file, mdl, "SPEAR_DTFREEZE_DS", CS%SPEAR_dTf_dS, &
                  "The derivative of the freezing temperature with salinity.", &
-                 units="deg C PSU-1", default=-0.054, scale=US%degC_to_C*US%S_to_ppt, &
+                 units="degC ppt-1", default=-0.054, scale=US%degC_to_C*US%S_to_ppt, &
                  do_not_log=.not.CS%trestore_SPEAR_ECDA)
   call get_param(param_file, mdl, "RESTORE_FLUX_RHO", CS%rho_restore, &
                  "The density that is used to convert piston velocities into salt or heat "//&

config_src/drivers/solo_driver/MOM_surface_forcing.F90

@@ -1907,19 +1907,19 @@ subroutine surface_forcing_init(Time, G, US, param_file, diag, CS, tracer_flow_C
       call get_param(param_file, mdl, "SST_NORTH", CS%T_north, &
                  "With buoy_config linear, the sea surface temperature "//&
                  "at the northern end of the domain toward which to "//&
-                 "to restore.", units="deg C", default=0.0, scale=US%degC_to_C)
+                 "to restore.", units="degC", default=0.0, scale=US%degC_to_C)
       call get_param(param_file, mdl, "SST_SOUTH", CS%T_south, &
                  "With buoy_config linear, the sea surface temperature "//&
                  "at the southern end of the domain toward which to "//&
-                 "to restore.", units="deg C", default=0.0, scale=US%degC_to_C)
+                 "to restore.", units="degC", default=0.0, scale=US%degC_to_C)
       call get_param(param_file, mdl, "SSS_NORTH", CS%S_north, &
                  "With buoy_config linear, the sea surface salinity "//&
                  "at the northern end of the domain toward which to "//&
-                 "to restore.", units="PSU", default=35.0, scale=US%ppt_to_S)
+                 "to restore.", units="ppt", default=35.0, scale=US%ppt_to_S)
       call get_param(param_file, mdl, "SSS_SOUTH", CS%S_south, &
                  "With buoy_config linear, the sea surface salinity "//&
                  "at the southern end of the domain toward which to "//&
-                 "to restore.", units="PSU", default=35.0, scale=US%ppt_to_S)
+                 "to restore.", units="ppt", default=35.0, scale=US%ppt_to_S)
     endif
     call get_param(param_file, mdl, "RESTORE_FLUX_RHO", CS%rho_restore, &
                  "The density that is used to convert piston velocities into salt or heat "//&