Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6 into rem…

…ap_v_extensive

.gitlab-ci.yml

@@ -63,6 +63,7 @@ gnu:ocean-only-nolibs:
     - 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} ../../../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)
 
@@ -75,6 +76,7 @@ gnu:ice-ocean-nolibs:
     - 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} ../../../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

@@ -9,17 +9,18 @@ DO_REPRO_TESTS ?= true
 
 #---
 # Dependencies
+DEPS = deps
 
 # mkmf, list_paths (GFDL build toolchain)
 MKMF_URL ?= https://github.com/NOAA-GFDL/mkmf.git
 MKMF_COMMIT ?= master
-LIST_PATHS := $(abspath build/mkmf/bin/list_paths)
-MKMF := $(abspath build/mkmf/bin/mkmf)
+LIST_PATHS := $(abspath $(DEPS)/mkmf/bin/list_paths)
+MKMF := $(abspath $(DEPS)/mkmf/bin/mkmf)
 
 # FMS framework
 FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
-FMS_COMMIT ?= f2e2c86f6c0eb6d389a20509a8a60fa22924e16b
-FMS := build/fms
+FMS_COMMIT ?= 2019.01.01
+FMS := $(DEPS)/fms
 
 #---
 # Build configuration
@@ -39,7 +40,7 @@ MKMF_TEMPLATE ?= build/mkmf/templates/ncrc-gnu.mk
 # Executables
 BUILDS = symmetric asymmetric repro openmp
 CONFIGS := $(wildcard tc*)
-TESTS = grids layouts restarts nans dims openmps
+TESTS = grids layouts restarts nans dims openmps rotations
 
 # REPRO tests enable reproducibility with optimization, and often do not match
 # the DEBUG results in older GCCs and vendor compilers, so we can optionally
@@ -85,7 +86,7 @@ SOURCE = \
 MOM_SOURCE = $(call SOURCE,../src) $(wildcard ../config_src/solo_driver/*.F90)
 TARGET_SOURCE = $(call SOURCE,build/target_codebase/src) \
   $(wildcard build/target_codebase/config_src/solo_driver/*.F90)
-FMS_SOURCE = $(call SOURCE,build/fms/src)
+FMS_SOURCE = $(call SOURCE,$(DEPS)/fms/src)
 
 #---
 # Rules
@@ -101,11 +102,11 @@ BUILD_TARGETS = MOM6 Makefile path_names
 # Conditionally build symmetric with coverage support
 COVFLAG=$(if $(REPORT_COVERAGE),COVERAGE=1,)
 
-build/target/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1
-build/symmetric/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1 $(COVFLAG)
-build/asymmetric/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1
+build/target/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1 INIT=1
+build/symmetric/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1 INIT=1 $(COVFLAG)
+build/asymmetric/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1 INIT=1
 build/repro/MOM6: MOMFLAGS=NETCDF=3 REPRO=1
-build/openmp/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1 OPENMP=1
+build/openmp/MOM6: MOMFLAGS=NETCDF=3 DEBUG=1 OPENMP=1 INIT=1
 
 build/asymmetric/path_names: GRID_SRC=config_src/dynamic
 build/%/path_names: GRID_SRC=config_src/dynamic_symmetric
@@ -117,9 +118,9 @@ build/%/Makefile: build/%/path_names
 	cp $(MKMF_TEMPLATE) $(@D)
 	cd $(@D) && $(MKMF) \
 		-t $(notdir $(MKMF_TEMPLATE)) \
-		-o '-I ../fms/build' \
+		-o '-I ../../$(DEPS)/fms/build' \
 		-p MOM6 \
-		-l '../fms/lib/libfms.a' \
+		-l '../../$(DEPS)/fms/lib/libfms.a' \
 		-c $(MKMF_CPP) \
 		path_names
 
@@ -173,8 +174,8 @@ $(FMS)/src:
 # Build Toolchain
 
 $(LIST_PATHS) $(MKMF):
-	git clone $(MKMF_URL) build/mkmf
-	cd build/mkmf; git checkout $(MKMF_COMMIT)
+	git clone $(MKMF_URL) $(DEPS)/mkmf
+	cd $(DEPS)/mkmf; git checkout $(MKMF_COMMIT)
 
 
 #----
@@ -185,9 +186,15 @@ test: $(foreach t,$(TESTS),test.$(t))
 
 # NOTE: We remove tc3 (OBC) from grid test since it cannot run asymmetric grids
 
+# NOTE: rotation diag chksum disabled since we cannot yet compare rotationally
+#       equivalent diagnostics
+
+# TODO: restart checksum comparison is not yet implemented
+
 .PHONY: $(foreach t,$(TESTS),test.$(t))
 test.grids: $(foreach c,$(filter-out tc3,$(CONFIGS)),$(c).grid $(c).grid.diag)
 test.layouts: $(foreach c,$(CONFIGS),$(c).layout $(c).layout.diag)
+test.rotations: $(foreach c,$(CONFIGS),$(c).rotate)
 test.restarts: $(foreach c,$(CONFIGS),$(c).restart)
 test.repros: $(foreach c,$(CONFIGS),$(c).repro $(c).repro.diag)
 test.openmps: $(foreach c,$(CONFIGS),$(c).openmp $(c).openmp.diag)
@@ -209,6 +216,7 @@ endef
 
 $(eval $(call CMP_RULE,grid,symmetric asymmetric))
 $(eval $(call CMP_RULE,layout,symmetric layout))
+$(eval $(call CMP_RULE,rotate,symmetric rotate))
 $(eval $(call CMP_RULE,repro,symmetric repro))
 $(eval $(call CMP_RULE,openmp,symmetric openmp))
 $(eval $(call CMP_RULE,nan,symmetric nan))
@@ -259,7 +267,7 @@ results/%/ocean.stats.$(1): build/$(2)/MOM6
 	cp -rL $$*/* work/$$*/$(1)
 	cd work/$$*/$(1) && if [ -f Makefile ]; then make; fi
 	mkdir -p work/$$*/$(1)/RESTART
-	echo $(4) > work/$$*/$(1)/MOM_override
+	echo -e "$(4)" > work/$$*/$(1)/MOM_override
 	cd work/$$*/$(1) && $$(call MPIRUN_CMD,$(5)) -n $(6) ../../../$$< 2> debug.out > std.out \
 		|| ! sed 's/^/$$*.$(1): /' std.out debug.out \
 		&& sed 's/^/$$*.$(1): /' std.out
@@ -281,6 +289,7 @@ $(eval $(call STAT_RULE,target,target,,,,1))
 $(eval $(call STAT_RULE,repro,repro,,,,1))
 $(eval $(call STAT_RULE,openmp,openmp,,,,1))
 $(eval $(call STAT_RULE,layout,symmetric,,LAYOUT=2$(,)1,,2))
+$(eval $(call STAT_RULE,rotate,symmetric,,ROTATE_INDEX=True\nINDEX_TURNS=1,,1))
 $(eval $(call STAT_RULE,nan,symmetric,,,MALLOC_PERTURB_=256,1))
 $(eval $(call STAT_RULE,dim.t,symmetric,,T_RESCALE_POWER=11,,1))
 $(eval $(call STAT_RULE,dim.l,symmetric,,L_RESCALE_POWER=11,,1))

.testing/linux-ubuntu-xenial-gnu.mk

@@ -24,7 +24,7 @@ LD = mpif90 $(MAIN_PROGRAM)
 DEBUG =              # If non-blank, perform a debug build (Cannot be
                      # mixed with REPRO or TEST)
 
-REPRO =              # If non-blank, erform a build that guarentees
+REPRO =              # If non-blank, perform a build that guarentees
                      # reprodicuibilty from run to run.  Cannot be used
                      # with DEBUG or TEST
 
@@ -54,6 +54,8 @@ SSE =                # The SSE options to be used to compile.  If blank,
 
 COVERAGE =           # Add the code coverage compile options.
 
+INIT =               # Enable aggressive initialization
+
 # Need to use at least GNU Make version 3.81
 need := 3.81
 ok := $(filter $(need),$(firstword $(sort $(MAKE_VERSION) $(need))))
@@ -89,6 +91,10 @@ FFLAGS := -fcray-pointer -fdefault-double-8 -fdefault-real-8 -Waliasing -ffree-l
 FFLAGS_OPT = -O3
 FFLAGS_REPRO = -O2 -fbounds-check
 FFLAGS_DEBUG = -O0 -g -W -Wno-compare-reals -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow
+# Enable aggressive initialization
+ifdef INIT
+FFLAGS_DEBUG += -finit-real=snan -finit-integer=2147483647 -finit-derived
+endif
 
 # Flags to add additional build options
 FFLAGS_OPENMP = -fopenmp

.testing/tc2/MOM_input

@@ -600,3 +600,4 @@ ENERGYSAVEDAYS = 0.5            !   [days] default = 3600.0
                                 ! energies of the run and other globally summed diagnostics.
 DIAG_AS_CHKSUM = True
 DEBUG = True
+USE_GM_WORK_BUG = False

.travis.yml

@@ -3,7 +3,7 @@
 
 # This is a not a c-language project but we use the same environment.
 language: c
-dist: xenial
+dist: bionic
 
 # --depth flag is breaking our merge, try disabling it
 # NOTE: We may be able to go back to depth=50 in production

config_src/coupled_driver/MOM_surface_forcing_gfdl.F90

@@ -1361,7 +1361,7 @@ subroutine surface_forcing_init(Time, G, US, param_file, diag, CS)
   call get_param(param_file, mdl, "WIND_STRESS_MULTIPLIER", CS%wind_stress_multiplier, &
                  "A factor multiplying the wind-stress given to the ocean by the "//&
                  "coupler. This is used for testing and should be =1.0 for any "//&
-                 "production runs.", default=1.0)
+                 "production runs.", units="nondim", default=1.0)
 
   if (CS%restore_salt) then
     call get_param(param_file, mdl, "FLUXCONST", CS%Flux_const, &

config_src/ice_solo_driver/ice_shelf_driver.F90

@@ -50,7 +50,7 @@ program SHELF_main
   use MOM_write_cputime, only : write_cputime_start_clock, write_cputime_CS
 
   use MOM_ice_shelf, only : initialize_ice_shelf, ice_shelf_end, ice_shelf_CS
-  use MOM_ice_shelf, only : ice_shelf_save_restart, solo_time_step
+  use MOM_ice_shelf, only : ice_shelf_save_restart, solo_step_ice_shelf
 ! , add_shelf_flux_forcing, add_shelf_flux_IOB
   implicit none
 
@@ -330,7 +330,7 @@ program SHELF_main
 
     ! This call steps the model over a time time_step.
     Time1 = Master_Time ; Time = Master_Time
-    call solo_time_step (ice_shelf_CSp, time_step, m, Time)
+    call solo_step_ice_shelf(ice_shelf_CSp, Time_step_shelf, m, Time)
 
 !    Time = Time + Time_step_ocean
 !  This is here to enable fractional-second time steps.

config_src/mct_driver/mom_ocean_model_mct.F90

@@ -80,16 +80,8 @@ module MOM_ocean_model_mct
 public ocean_model_restart
 public ice_ocn_bnd_type_chksum
 public ocean_public_type_chksum
-public ocean_model_data_get
 public get_ocean_grid
 
-!> This interface extracts a named scalar field or array from the ocean surface or public type
-interface ocean_model_data_get
-  module procedure ocean_model_data1D_get
-  module procedure ocean_model_data2D_get
-end interface
-
-
 !> This type is used for communication with other components via the FMS coupler.
 !! The element names and types can be changed only with great deliberation, hence
 !! the persistnce of things like the cutsy element name "avg_kount".
@@ -1051,98 +1043,6 @@ subroutine Ocean_stock_pe(OS, index, value, time_index)
 
 end subroutine Ocean_stock_pe
 
-!> This subroutine extracts a named 2-D field from the ocean surface or public type
-subroutine ocean_model_data2D_get(OS,Ocean, name, array2D,isc,jsc)
-  use MOM_constants, only : CELSIUS_KELVIN_OFFSET
-  type(ocean_state_type),     pointer    :: OS    !< A pointer to the structure containing the
-                                                  !! internal ocean state (intent in).
-  type(ocean_public_type),    intent(in) :: Ocean !< A structure containing various publicly
-                                                  !! visible ocean surface fields.
-  character(len=*)          , intent(in) :: name  !< The name of the field to extract
-  real, dimension(isc:,jsc:), intent(out):: array2D !< The values of the named field, it must
-                                                  !! cover only the computational domain
-  integer                   , intent(in) :: isc   !< The starting i-index of array2D
-  integer                   , intent(in) :: jsc   !< The starting j-index of array2D
-
-  integer :: g_isc, g_iec, g_jsc, g_jec,g_isd, g_ied, g_jsd, g_jed, i, j
-
-  if (.not.associated(OS)) return
-  if (.not.OS%is_ocean_pe) return
-
-! The problem is %areaT is on MOM domain but Ice_Ocean_Boundary%... is on mpp domain.
-! We want to return the MOM data on the mpp (compute) domain
-! Get MOM domain extents
-  call mpp_get_compute_domain(OS%grid%Domain%mpp_domain, g_isc, g_iec, g_jsc, g_jec)
-  call mpp_get_data_domain   (OS%grid%Domain%mpp_domain, g_isd, g_ied, g_jsd, g_jed)
-
-  g_isc = g_isc-g_isd+1 ; g_iec = g_iec-g_isd+1 ; g_jsc = g_jsc-g_jsd+1 ; g_jec = g_jec-g_jsd+1
-
-
-  select case(name)
-  case('area')
-    array2D(isc:,jsc:) = OS%US%L_to_m**2*OS%grid%areaT(g_isc:g_iec,g_jsc:g_jec)
-  case('mask')
-    array2D(isc:,jsc:) = OS%grid%mask2dT(g_isc:g_iec,g_jsc:g_jec)
-!OR same result
-!     do j=g_jsc,g_jec ; do i=g_isc,g_iec
-!        array2D(isc+i-g_isc,jsc+j-g_jsc) = OS%grid%mask2dT(i,j)
-!     enddo ; enddo
-  case('t_surf')
-    array2D(isc:,jsc:) = Ocean%t_surf(isc:,jsc:)-CELSIUS_KELVIN_OFFSET
-  case('t_pme')
-    array2D(isc:,jsc:) = Ocean%t_surf(isc:,jsc:)-CELSIUS_KELVIN_OFFSET
-  case('t_runoff')
-    array2D(isc:,jsc:) = Ocean%t_surf(isc:,jsc:)-CELSIUS_KELVIN_OFFSET
-  case('t_calving')
-    array2D(isc:,jsc:) = Ocean%t_surf(isc:,jsc:)-CELSIUS_KELVIN_OFFSET
-  case('btfHeat')
-    array2D(isc:,jsc:) = 0
-  case('tlat')
-    array2D(isc:,jsc:) = OS%grid%geoLatT(g_isc:g_iec,g_jsc:g_jec)
-  case('tlon')
-    array2D(isc:,jsc:) = OS%grid%geoLonT(g_isc:g_iec,g_jsc:g_jec)
-  case('ulat')
-    array2D(isc:,jsc:) = OS%grid%geoLatCu(g_isc:g_iec,g_jsc:g_jec)
-  case('ulon')
-    array2D(isc:,jsc:) = OS%grid%geoLonCu(g_isc:g_iec,g_jsc:g_jec)
-  case('vlat')
-    array2D(isc:,jsc:) = OS%grid%geoLatCv(g_isc:g_iec,g_jsc:g_jec)
-  case('vlon')
-    array2D(isc:,jsc:) = OS%grid%geoLonCv(g_isc:g_iec,g_jsc:g_jec)
-  case('geoLatBu')
-    array2D(isc:,jsc:) = OS%grid%geoLatBu(g_isc:g_iec,g_jsc:g_jec)
-  case('geoLonBu')
-    array2D(isc:,jsc:) = OS%grid%geoLonBu(g_isc:g_iec,g_jsc:g_jec)
-  case('cos_rot')
-    array2D(isc:,jsc:) = OS%grid%cos_rot(g_isc:g_iec,g_jsc:g_jec) ! =1
-  case('sin_rot')
-    array2D(isc:,jsc:) = OS%grid%sin_rot(g_isc:g_iec,g_jsc:g_jec) ! =0
-  case default
-    call MOM_error(FATAL,'get_ocean_grid_data2D: unknown argument name='//name)
-  end select
-end subroutine ocean_model_data2D_get
-
-!> This subroutine extracts a named scalar field from the ocean surface or public type
-subroutine ocean_model_data1D_get(OS, Ocean, name, value)
-  type(ocean_state_type),     pointer    :: OS    !< A pointer to the structure containing the
-                                                  !! internal ocean state (intent in).
-  type(ocean_public_type),    intent(in) :: Ocean !< A structure containing various publicly
-                                                  !! visible ocean surface fields.
-  character(len=*)          , intent(in) :: name  !< The name of the field to extract
-  real                      , intent(out):: value !< The value of the named field
-
-  if (.not.associated(OS)) return
-  if (.not.OS%is_ocean_pe) return
-
-  select case(name)
-  case('c_p')
-     value = OS%C_p
-  case default
-     call MOM_error(FATAL,'get_ocean_grid_data1D: unknown argument name='//name)
-  end select
-
-end subroutine ocean_model_data1D_get
-
 !> Write out FMS-format checsums on fields from the ocean surface state
 subroutine ocean_public_type_chksum(id, timestep, ocn)
 

config_src/mct_driver/ocn_comp_mct.F90

@@ -36,7 +36,7 @@ module ocn_comp_mct
 use MOM_time_manager,     only: time_type, set_date, set_time, set_calendar_type, NOLEAP
 use MOM_time_manager,     only: operator(+), operator(-), operator(*), operator(/)
 use MOM_time_manager,     only: operator(==), operator(/=), operator(>), get_time
-use MOM_file_parser,      only: get_param, log_version, param_file_type
+use MOM_file_parser,      only: get_param, log_version, param_file_type, close_param_file
 use MOM_get_input,        only: Get_MOM_Input, directories
 use MOM_EOS,              only: gsw_sp_from_sr, gsw_pt_from_ct
 use MOM_constants,        only: CELSIUS_KELVIN_OFFSET
@@ -281,6 +281,9 @@ subroutine ocn_init_mct( EClock, cdata_o, x2o_o, o2x_o, NLFilename )
     glb%c1 = 0.0; glb%c2 = 0.0; glb%c3 = 0.0; glb%c4 = 0.0
   endif
 
+  ! Close param file before it gets opened by ocean_model_init again.
+  call close_param_file(param_file)
+
   ! Initialize the MOM6 model
   runtype = get_runtype()
   if (runtype == "initial") then