Merge branch 'master' into develop

This merge introduces fixes from the release-v8.2.0 branch, and it connects the v8.2.0 tag to future commits on 'develop'. * master: Fix instances of incorrect quotes in init_atmosphere and atmosphere registries Add 'mp_thompson_aerosols' to list of possible_values for config_microp_scheme Add 'sf_noahmp' to list of possible_values for config_lsm_scheme Don't include FCINCLUDES in build options checked for build compatibility Ignore the entire physics_mmm subdirectory of src/core_atmosphere/physics Split physics source compilation from library updates for parallel builds Add missing dependency among physics in MPAS-A main physics Makefile Add 'sf_noahmp_in' package to Noah-MP static fields in atmosphere core registry Add module search paths to support compilation of Noah-MP code with nvfortran Update version number to 8.2.0 Improve check on deallocation of hash table in mpas_geotile_mgr_finalize Add ONLY clause to USE statements for the 'mpi_f08' module Add "-check all" to LDFLAGS_DEBUG for 'intel' build target
MPAS-Dev · Jun 28, 2024 · eb62cd1 · eb62cd1
2 parents 7070294 + 942d402
commit eb62cd1
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diff --git a/Makefile b/Makefile
@@ -670,7 +670,7 @@ intel:   # BUILDTARGET Intel oneAPI Fortran, C, and C++ compiler suite
 	"FFLAGS_DEBUG = -g -convert big_endian -free -check all -fpe0 -traceback" \
 	"CFLAGS_DEBUG = -g -traceback" \
 	"CXXFLAGS_DEBUG = -g -traceback" \
-	"LDFLAGS_DEBUG = -g -fpe0 -traceback" \
+	"LDFLAGS_DEBUG = -g -check all -fpe0 -traceback" \
 	"FFLAGS_OMP = -qopenmp" \
 	"CFLAGS_OMP = -qopenmp" \
 	"PICFLAG = -fpic" \
@@ -1042,7 +1042,6 @@ rebuild_check:
 	CPPFLAGS=$(CPPFLAGS)\n$\
 	LIBS=$(LIBS)\n$\
 	CPPINCLUDES=$(CPPINCLUDES)\n$\
-	FCINCLUDES=$(FCINCLUDES)\n$\
 	OPENMP=$(OPENMP)\n$\
 	OPENMP_OFFLOAD=$(OPENMP_OFFLOAD)\n$\
 	OPENACC=$(OPENACC)\n$\

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-MPAS-v8.1.0
+MPAS-v8.2.0
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for

diff --git a/src/core_atmosphere/Externals.cfg b/src/core_atmosphere/Externals.cfg
@@ -2,7 +2,7 @@
 local_path = ./physics_mmm
 protocol = git
 repo_url = https://github.com/NCAR/MMM-physics.git
-tag = 20240525-MPASv8.2
+tag = 20240626-MPASv8.2
 
 required = True
 

diff --git a/src/core_atmosphere/Registry.xml b/src/core_atmosphere/Registry.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="atmosphere" core_abbrev="atm" version="8.1.0">
+<registry model="mpas" core="atmosphere" core_abbrev="atm" version="8.2.0">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->
@@ -2161,7 +2161,7 @@
                 <nml_option name="config_microp_scheme" type="character" default_value="suite" in_defaults="false"
                      units="-"
                      description="configuration for cloud microphysics schemes"
-                     possible_values="`suite',`mp_wsm6',`mp_thompson',`mp_kessler',`off'"/>
+                     possible_values="`suite',`mp_wsm6',`mp_thompson',`mp_thompson_aerosols', `mp_kessler',`off'"/>
 
                 <nml_option name="config_convection_scheme" type="character" default_value="suite" in_defaults="false"
                      units="-"
@@ -2171,7 +2171,7 @@
                 <nml_option name="config_lsm_scheme" type="character" default_value="suite" in_defaults="false"
                      units="-"
                      description="configuration for land-surface schemes"
-                     possible_values="`suite',`noah',`off'"/>
+                     possible_values="`suite',`sf_noah',`sf_noahmp`, `off'"/>
 
                 <nml_option name="config_pbl_scheme" type="character" default_value="suite" in_defaults="false"
                      units="-"
@@ -3284,11 +3284,11 @@
                      packages="mp_thompson_aers_in"/>
 
                 <var name="rnifampten" type="real" dimensions="nVertLevels nCells Time" units="nb kg^{-1} s^{-1}"
-                     description="tendency of "ice-friendly" aerosol number concentration due to microphysics"
+                     description="tendency of ice-friendly aerosol number concentration due to microphysics"
                      packages="mp_thompson_aers_in"/>
 
                 <var name="rnwfampten" type="real" dimensions="nVertLevels nCells Time" units="nb kg^{-1} s^{-1}"
-                     description="tendency of "water-friendly" aerosol number concentration due to microphysics"
+                     description="tendency of water-friendly aerosol number concentration due to microphysics"
                      packages="mp_thompson_aers_in"/>
 
                 <!-- ================================================================================================== -->
@@ -3573,7 +3573,7 @@
                           description="Ice mixing ratio increment"/>
 
                      <var name="qs_amb"  name_in_code="qs" array_group="moist" packages="mp_thompson_in;mp_thompson_aers_in;mp_wsm6_in"
-                          " units="kg kg^{-1}"
+                          units="kg kg^{-1}"
                           description="Snow mixing ratio increment"/>
 
                      <var name="qg_amb"  name_in_code="qg" array_group="moist" packages="mp_thompson_in;mp_thompson_aers_in;mp_wsm6_in"

diff --git a/src/core_atmosphere/build_options.mk b/src/core_atmosphere/build_options.mk
@@ -2,6 +2,9 @@ PWD=$(shell pwd)
 EXE_NAME=atmosphere_model
 NAMELIST_SUFFIX=atmosphere
 override CPPFLAGS += -DCORE_ATMOSPHERE
+FCINCLUDES += -I$(PWD)/src/core_atmosphere/physics/physics_noahmp/drivers/mpas \
+              -I$(PWD)/src/core_atmosphere/physics/physics_noahmp/utility \
+              -I$(PWD)/src/core_atmosphere/physics/physics_noahmp/src
 
 report_builds:
 	@echo "CORE=atmosphere"
diff --git a/src/core_atmosphere/physics/.gitignore b/src/core_atmosphere/physics/.gitignore
@@ -1,6 +1,4 @@
 *.f90
 physics_wrf/*.f90
 physics_wrf/files/
-physics_mmm/.gitignore
-physics_mmm/README.md
-physics_mmm/LICENSE
+physics_mmm
diff --git a/src/core_atmosphere/physics/Makefile b/src/core_atmosphere/physics/Makefile
@@ -68,11 +68,15 @@ core_physics_noahmp:
 	(cd physics_noahmp/drivers/mpas; $(MAKE) all COREDEF="$(COREDEF)")
 
 core_physics_init: $(OBJS_init)
-	ar -ru libphys.a $(OBJS_init)
 
-core_physics: core_physics_wrf
+core_physics: core_physics_wrf core_physics_noahmp
 	($(MAKE) phys_interface COREDEF="$(COREDEF)")
-	ar -ru libphys.a $(OBJS)
+	ar -ru libphys.a $(OBJS_init) $(OBJS)
+	($(MAKE) -C ./physics_mmm -f Makefile.mpas physics_mmm_lib)
+	($(MAKE) -C ./physics_wrf physics_wrf_lib)
+	($(MAKE) -C ./physics_noahmp/drivers/mpas driver_lib)
+	($(MAKE) -C ./physics_noahmp/src src_lib)
+	($(MAKE) -C ./physics_noahmp/utility utility_lib)
 
 phys_interface: $(OBJS)
 

diff --git a/src/core_atmosphere/physics/Registry_noahmp.xml b/src/core_atmosphere/physics/Registry_noahmp.xml
@@ -25,19 +25,24 @@
  <var_struct name="mesh" time_levs="1">
 
       <var name="soilcomp" type="real" dimensions="nSoilComps nCells" units="unitless"
-                description="soil composition needed as input in the NOAH-MP land surface model"/>
+                description="soil composition needed as input in the NOAH-MP land surface model"
+                packages="sf_noahmp_in"/>
 
       <var name="soilcl1" type="real" dimensions="nCells" units="unitless"
-                description="soil texture class level 1 needed as input for the NOAH-MP land surface model"/>
+                description="soil texture class level 1 needed as input for the NOAH-MP land surface model"
+                packages="sf_noahmp_in"/>
 
       <var name="soilcl2" type="real" dimensions="nCells" units="unitless"
-                description="soil texture class level 2 needed as input for the NOAH-MP land surface model"/>
+                description="soil texture class level 2 needed as input for the NOAH-MP land surface model"
+                packages="sf_noahmp_in"/>
 
       <var name="soilcl3" type="real" dimensions="nCells" units="unitless"
-                description="soil texture class level 3 needed as input for the NOAH-MP land surface model"/>
+                description="soil texture class level 3 needed as input for the NOAH-MP land surface model"
+                packages="sf_noahmp_in"/>
 
       <var name="soilcl4" type="real" dimensions="nCells" units="unitless"
-                description="soil texture class level 4 needed as input for the NOAH-MP land surface model"/>
+                description="soil texture class level 4 needed as input for the NOAH-MP land surface model"
+                packages="sf_noahmp_in"/>
 
  </var_struct>
 

diff --git a/src/core_atmosphere/physics/physics_noahmp/drivers/mpas/Makefile b/src/core_atmosphere/physics/physics_noahmp/drivers/mpas/Makefile
@@ -1,5 +1,7 @@
 .SUFFIXES: .o .F90
 
+.PHONY: driver driver_lib
+
 all: dummy driver
 
 dummy:
@@ -26,6 +28,8 @@ OBJS =  NoahmpSnowInitMod.o \
 	PedoTransferSR2006Mod.o
 
 driver: $(OBJS)
+
+driver_lib:
 	ar -ru ./../../../libphys.a $(OBJS)
 
 # DEPENDENCIES:
@@ -66,5 +70,5 @@ clean:
 	$(RM) *.i
 
 .F90.o:
-	$(FC) $(CPPFLAGS) $(COREDEF) $(FFLAGS) -c $*.F90 $(CPPINCLUDES) $(FCINCLUDES) -I. -I../../utility -I../../src -I../../../../../framework
+	$(FC) $(CPPFLAGS) $(COREDEF) $(FFLAGS) -c $*.F90 $(CPPINCLUDES) $(FCINCLUDES) -I. -I../../utility -I../../src -I../../../../../framework -I../../../../../external/esmf_time_f90
 
diff --git a/src/core_atmosphere/physics/physics_noahmp/src/Makefile b/src/core_atmosphere/physics/physics_noahmp/src/Makefile
@@ -1,5 +1,7 @@
 .SUFFIXES: .F90 .o
 
+.PHONY: src src_lib
+
 #
 # The Noah-MP code fails to build with the GNU compilers with -std=f2008,
 # so remove that flag here if it is present in FFLAGS
@@ -138,6 +140,8 @@ OBJS =  ConstantDefineMod.o \
 	WaterMainGlacierMod.o
 
 src: $(OBJS)
+
+src_lib:
 	ar -ru ./../../libphys.a $(OBJS)
 
 # DEPENDENCIES:

diff --git a/src/core_atmosphere/physics/physics_noahmp/utility/Makefile b/src/core_atmosphere/physics/physics_noahmp/utility/Makefile
@@ -1,5 +1,7 @@
 .SUFFIXES: .F90 .o
 
+.PHONY: utility utility_lib
+
 all: dummy utility
 
 dummy:
@@ -9,6 +11,8 @@ OBJS =  Machine.o \
 	CheckNanMod.o
 
 utility: $(OBJS)
+
+utility_lib:
 	ar -ru ./../../libphys.a $(OBJS)
 
 # DEPENDENCIES:

diff --git a/src/core_atmosphere/physics/physics_wrf/Makefile b/src/core_atmosphere/physics/physics_wrf/Makefile
@@ -1,5 +1,7 @@
 .SUFFIXES: .F .o
 
+.PHONY: physics_wrf physics_wrf_lib
+
 all: dummy physics_wrf
 
 dummy:
@@ -52,6 +54,8 @@ OBJS = \
 
 
 physics_wrf: $(OBJS)
+
+physics_wrf_lib:
 	ar -ru ./../libphys.a $(OBJS)
 
 # DEPENDENCIES:

diff --git a/src/core_init_atmosphere/Registry.xml b/src/core_init_atmosphere/Registry.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="8.1.0">
+<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="8.2.0">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->
@@ -570,7 +570,7 @@
                         <var name="v_init" packages="met_stage_out"/>
                         <var name="t_init" packages="met_stage_out"/>
                         <var name="qv_init" packages="met_stage_out"/>
-                        <var_array name="scalars" packages="met_stage_out";mp_thompson_aers_in"/>
+                        <var_array name="scalars" packages="met_stage_out;mp_thompson_aers_in"/>
                         <var name="u" packages="met_stage_out"/>
                         <var name="w" packages="met_stage_out"/>
                         <var name="dz" packages="met_stage_out"/>

diff --git a/src/core_init_atmosphere/mpas_geotile_manager.F b/src/core_init_atmosphere/mpas_geotile_manager.F
@@ -345,9 +345,9 @@ function mpas_geotile_mgr_finalize(mgr) result(ierr)
                 endif
             enddo
         enddo
-        deallocate(mgr % hash)
+        deallocate(mgr % hash, stat=ierr)
 
-        if (associated(mgr % hash)) then
+        if (associated(mgr % hash) .or. (ierr /= 0)) then
             call mpas_log_write("Problem deallocating the geotile hash table", messageType=MPAS_LOG_ERR)
             ierr = -1
             return

diff --git a/src/core_landice/Registry.xml b/src/core_landice/Registry.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="landice" core_abbrev="li" version="8.1.0">
+<registry model="mpas" core="landice" core_abbrev="li" version="8.2.0">
 
 
 <!-- ======================================================================= -->

diff --git a/src/core_ocean/Registry.xml b/src/core_ocean/Registry.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="ocean" core_abbrev="ocn" version="8.1.0">
+<registry model="mpas" core="ocean" core_abbrev="ocn" version="8.2.0">
 
 	<dims>
 		<dim name="nCells" units="unitless"

diff --git a/src/core_seaice/Registry.xml b/src/core_seaice/Registry.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="seaice" core_abbrev="seaice" version="8.1.0">
+<registry model="mpas" core="seaice" core_abbrev="seaice" version="8.2.0">
 
 	<dims>
 		<dim name="nCells"

diff --git a/src/core_sw/Registry.xml b/src/core_sw/Registry.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="sw" core_abbrev="sw" version="8.1.0">
+<registry model="mpas" core="sw" core_abbrev="sw" version="8.2.0">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

diff --git a/src/core_test/Registry.xml b/src/core_test/Registry.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="test" core_abbrev="test" version="8.1.0">
+<registry model="mpas" core="test" core_abbrev="test" version="8.2.0">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

diff --git a/src/framework/mpas_abort.F b/src/framework/mpas_abort.F
@@ -33,7 +33,7 @@ subroutine mpas_dmpar_global_abort(mesg, deferredAbort)!{{{
 #ifdef _MPI
 #ifndef NOMPIMOD
 #ifdef MPAS_USE_MPI_F08
-      use mpi_f08
+      use mpi_f08, only : MPI_COMM_WORLD, MPI_Comm_rank, MPI_Comm_size, MPI_Abort
 #else
       use mpi
 #endif

diff --git a/src/framework/mpas_dmpar.F b/src/framework/mpas_dmpar.F
@@ -32,7 +32,16 @@ module mpas_dmpar
 #ifdef _MPI
 #ifndef NOMPIMOD
 #ifdef MPAS_USE_MPI_F08
-   use mpi_f08
+   use mpi_f08, only : MPI_Comm, MPI_Datatype
+   use mpi_f08, only : MPI_INTEGER, MPI_2INTEGER, MPI_REAL, MPI_2REAL, MPI_DOUBLE_PRECISION, &
+                       MPI_2DOUBLE_PRECISION, MPI_CHARACTER, MPI_INTEGER8
+   use mpi_f08, only : MPI_COMM_SELF, MPI_COMM_WORLD, MPI_INFO_NULL, MPI_THREAD_SINGLE, &
+                       MPI_THREAD_SERIALIZED, MPI_THREAD_FUNNELED, MPI_THREAD_MULTIPLE, MPI_STATUS_IGNORE
+   use mpi_f08, only : MPI_Query_thread, MPI_Comm_dup
+   use mpi_f08, only : MPI_Init_thread , MPI_Init, MPI_Comm_rank, MPI_Comm_size, MPI_Finalize, &
+                       MPI_Comm_free, MPI_Abort, MPI_Bcast, MPI_Allreduce, MPI_Scatterv, MPI_Recv, &
+                       MPI_Send, MPI_Request, MPI_Irecv, MPI_Isend, MPI_Wait, MPI_Wtime, MPI_Test
+   use mpi_f08, only : MPI_SUM, MPI_MIN, MPI_MAX, MPI_MINLOC, MPI_MAXLOC
 #else
    use mpi
 #endif

diff --git a/src/framework/mpas_halo.F b/src/framework/mpas_halo.F
@@ -486,7 +486,10 @@ end subroutine mpas_halo_exch_group_add_field
     subroutine mpas_halo_exch_group_full_halo_exch(domain, groupName, iErr)
 
 #ifdef MPAS_USE_MPI_F08
-        use mpi_f08
+        use mpi_f08, only : MPI_Datatype, MPI_Comm
+        use mpi_f08, only : MPI_REAL, MPI_DOUBLE_PRECISION, MPI_REQUEST_NULL, &
+                            MPI_STATUS_IGNORE, MPI_STATUSES_IGNORE
+        use mpi_f08, only : MPI_Irecv, MPI_Isend, MPI_Waitany, MPI_Waitall
 #else
         use mpi
 #endif

diff --git a/src/framework/mpas_log.F b/src/framework/mpas_log.F
@@ -809,7 +809,7 @@ subroutine log_abort()
 #ifdef _MPI
 #ifndef NOMPIMOD
 #ifdef MPAS_USE_MPI_F08
-      use mpi_f08
+      use mpi_f08, only : MPI_COMM_WORLD, MPI_Abort
 #else
       use mpi
 #endif