Update MPAS dynamical core to version 8.4.0

.gitmodules

@@ -88,7 +88,7 @@
 	url = https://github.com/MPAS-Dev/MPAS-Model.git
         fxrequired = AlwaysRequired
         fxsparse = ../.mpas_sparse_checkout
-        fxtag = v8.2.1
+        fxtag = v8.4.0
 	fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
 
 [submodule "cosp2"]

bld/build-namelist

@@ -4398,7 +4398,6 @@ if ($dyn =~ /mpas/) {
     add_default($nl, 'mpas_coef_3rd_order');
     add_default($nl, 'mpas_smagorinsky_coef');
     add_default($nl, 'mpas_mix_full');
-    add_default($nl, 'mpas_epssm');
     add_default($nl, 'mpas_smdiv');
     add_default($nl, 'mpas_apvm_upwinding');
     add_default($nl, 'mpas_h_ScaleWithMesh');
@@ -4409,12 +4408,18 @@ if ($dyn =~ /mpas/) {
     add_default($nl, 'mpas_rayleigh_damp_u');
     add_default($nl, 'mpas_rayleigh_damp_u_timescale_days');
     add_default($nl, 'mpas_number_rayleigh_damp_u_levels');
+    add_default($nl, 'mpas_epssm_minimum');
+    add_default($nl, 'mpas_epssm_maximum');
+    add_default($nl, 'mpas_epssm_transition_bottom_z');
+    add_default($nl, 'mpas_epssm_transition_top_z');
     add_default($nl, 'mpas_apply_lbcs');
     add_default($nl, 'mpas_jedi_da');
     add_default($nl, 'mpas_do_restart');
     add_default($nl, 'mpas_print_global_minmax_vel');
     add_default($nl, 'mpas_print_detailed_minmax_vel');
     add_default($nl, 'mpas_print_global_minmax_sca');
+    add_default($nl, 'mpas_halo_exch_method');
+    add_default($nl, 'mpas_gpu_aware_mpi');
 
     # mpas_block_decomp_file_prefix should only be set when more than one task is used.
     # Otherwise the file is not used and should not be added to the input dataset file.

bld/namelist_files/namelist_defaults_cam.xml

@@ -3457,8 +3457,6 @@
 <mpas_coef_3rd_order          > 1.0D0 </mpas_coef_3rd_order>
 <mpas_smagorinsky_coef        > 0.125D0 </mpas_smagorinsky_coef>
 <mpas_mix_full                > .true. </mpas_mix_full>
-<mpas_epssm                   > 0.1D0 </mpas_epssm>
-<mpas_epssm hgrid="mpasa120" waccm_phys="1"> 0.5D0 </mpas_epssm>
 <mpas_smdiv                   > 0.1D0 </mpas_smdiv>
 <mpas_apvm_upwinding          > 0.5D0 </mpas_apvm_upwinding>
 <mpas_apvm_upwinding hgrid="mpasa120" waccm_phys="1"> 0.0D0 </mpas_apvm_upwinding>
@@ -3472,6 +3470,11 @@
 <mpas_rayleigh_damp_u         > .true. </mpas_rayleigh_damp_u>
 <mpas_rayleigh_damp_u_timescale_days> 5.0 </mpas_rayleigh_damp_u_timescale_days>
 <mpas_number_rayleigh_damp_u_levels> 5 </mpas_number_rayleigh_damp_u_levels>
+<mpas_epssm_minimum> 0.1D0 </mpas_epssm_minimum>
+<mpas_epssm_maximum> 0.1D0 </mpas_epssm_maximum>
+<mpas_epssm_maximum hgrid="mpasa120" waccm_phys="1"> 0.5D0 </mpas_epssm_maximum>
+<mpas_epssm_transition_bottom_z> 30000.0D0 </mpas_epssm_transition_bottom_z>
+<mpas_epssm_transition_top_z> 50000.0D0 </mpas_epssm_transition_top_z>
 <mpas_apply_lbcs> .false. </mpas_apply_lbcs>
 <mpas_jedi_da> .false. </mpas_jedi_da>
 <mpas_block_decomp_file_prefix hgrid="mpasa480">atm/cam/inic/mpas/mpasa480.graph.info.part.</mpas_block_decomp_file_prefix>
@@ -3487,6 +3490,9 @@
 <mpas_print_detailed_minmax_vel> .false. </mpas_print_detailed_minmax_vel>
 <mpas_print_global_minmax_sca  > .false. </mpas_print_global_minmax_sca>
 
+<mpas_halo_exch_method> mpas_halo </mpas_halo_exch_method>
+<mpas_gpu_aware_mpi> .false. </mpas_gpu_aware_mpi>
+
 <!-- ================================================================== -->
 <!-- Chemistry Rates Diagnostics                                        -->
 <!-- ================================================================== -->

bld/namelist_files/namelist_definition.xml

@@ -8810,8 +8810,8 @@ Default: 120000.0
 
 <entry id="mpas_visc4_2dsmag" type="real" category="mpas"
        group="nhyd_model" valid_values="">
-Scaling coefficient of delta_x^3 to obtain Del^4 diffusion coefficient in
-MPAS dycore.
+Coefficient multiplied by delta x^3 to obtain Del^4 physical hyperviscosity
+in MPAS dycore.
 Default: 0.05
 </entry>
 
@@ -8902,13 +8902,6 @@ MPAS dycore.
 Default: TRUE
 </entry>
 
-<entry id="mpas_epssm" type="real" category="mpas"
-       group="nhyd_model" valid_values="">
-Off-centering parameter for the vertically implicit acoustic integration in
-MPAS dycore
-Default: 0.1
-</entry>
-
 <entry id="mpas_smdiv" type="real" category="mpas"
        group="nhyd_model" valid_values="">
 3-d divergence damping coefficient in MPAS dycore.
@@ -8984,6 +8977,32 @@ damping linearly ramps to zero by layer number from the top
 Default: 3
 </entry>
 
+<entry id="mpas_epssm_minimum" type="real" category="mpas"
+       group="damping" valid_values="real values between 0 and 1">
+Value of epssm, the off-centering parameter for the vertically implicit acoustic integration,
+below transition zone.
+Default: 0.1
+</entry>
+
+<entry id="mpas_epssm_maximum" type="real" category="mpas"
+       group="damping" valid_values="real values between 0 and 1">
+Value of epssm, the off-centering parameter for the vertically implicit acoustic integration,
+above transition zone.
+Default: 0.5
+</entry>
+
+<entry id="mpas_epssm_transition_bottom_z" type="real" category="mpas"
+       group="damping" valid_values="positive real values">
+Height above MSL for the bottom of transition zone for epssm.
+Default: 30000.0
+</entry>
+
+<entry id="mpas_epssm_transition_top_z" type="real" category="mpas"
+       group="damping" valid_values="positive real values">
+Height above MSL for the top of transition zone for epssm.
+Default: 50000.0
+</entry>
+
 <entry id="mpas_apply_lbcs" type="logical" category="mpas"
        group="limited_area" valid_values="">
 Whether to apply lateral boundary conditions
@@ -9034,6 +9053,18 @@ dycore.
 Default: FALSE
 </entry>
 
+<entry id="mpas_halo_exch_method" type="char*512" category="mpas"
+       group="development" valid_values="mpas_dmpar,mpas_halo">
+Method to use for exchanging halos in MPAS dycore.
+Default: mpas_halo
+</entry>
+
+<entry id="mpas_gpu_aware_mpi" type="logical" category="mpas"
+       group="development" valid_values=".false.,.true.">
+Whether to use GPU-aware MPI for halo exchanges in MPAS dycore. GPU-aware MPI
+is only implemented for mpas_halo_exch_method = mpas_halo.
+Default: FALSE
+</entry>
 
 <!-- Dycore testing  -->
 

src/dynamics/mpas/Makefile

@@ -1,4 +1,4 @@
-GIT_VERSION=$(shell git -C "$(MPAS_SRC_ROOT)/dycore" describe --always --dirty --tags || echo "N/A" )
+GIT_VERSION=$(shell git -C "$(MPAS_SRC_ROOT)/dycore" describe --always --dirty --tags || echo "N/A")
 CPPFLAGS := -D_MPI -DMPAS_NATIVE_TIMERS -DMPAS_CAM_DYCORE -DMPAS_PIO_SUPPORT -DMPAS_NO_ESMF_INIT -DMPAS_GIT_VERSION="$(GIT_VERSION)" -DMPAS_BUILD_TARGET="N/A" -DMPAS_NAMELIST_SUFFIX="atmosphere"
 ifdef PIODEF
   CPPFLAGS += $(PIODEF)
@@ -27,7 +27,8 @@ INTERFACE_OBJS = \
 DYN_OBJS = \
 	mpas_atm_time_integration.o \
 	mpas_atm_boundaries.o \
-	mpas_atm_iau.o
+	mpas_atm_iau.o \
+	mpas_atm_dissipation_models.o
 
 DIAG_OBJS = \
 	mpas_atm_diagnostics_manager.o \
@@ -48,10 +49,6 @@ REG_OBJS = \
 	fortprintf.o \
 	utility.o
 
-STREAMS_GEN_OBJS = \
-	streams_gen.o \
-	test_functions.o
-
 OPERATOR_OBJS = \
 	mpas_vector_operations.o \
 	mpas_matrix_operations.o \
@@ -83,8 +80,6 @@ FRAME_OBJS = \
 	mpas_io_streams.o \
 	mpas_bootstrapping.o \
 	mpas_io_units.o \
-	mpas_stream_inquiry.o \
-	stream_inquiry.o \
 	mpas_stream_manager.o \
 	mpas_stream_list.o \
 	mpas_forcing.o \
@@ -99,23 +94,33 @@ FRAME_OBJS = \
 	regex_matching.o \
 	mpas_log.o \
 	mpas_halo.o \
-	mpas_string_utils.o
-
+	mpas_string_utils.o \
+	mpas_ptscotch_interface.o \
+	ptscotch_interface.o \
+	mpas_stream_inquiry.o \
+	stream_inquiry.o
 
 UTIL_OBJS = \
 	ezxml.o
 
 
 all:
+	( $(MAKE) apply-patch )
 	( $(MAKE) xml )
 	( $(MAKE) framework )
 	( $(MAKE) operators )
 	( $(MAKE) registry )
-	( $(MAKE) streams_gen )
 	( $(MAKE) incs )
 	( $(MAKE) dycore )
 	( ar -ru libmpas.a $(INTERFACE_OBJS) $(DYN_OBJS) $(DIAG_OBJS) $(DIAGNOSTICS) $(OPERATOR_OBJS) $(FRAME_OBJS) $(UTIL_OBJS) )
 
+apply-patch:
+	@for file in "$(MPAS_SRC_ROOT)"/driver/*.patch; do \
+		if [ -f "$${file}" ] && git -C "$(MPAS_SRC_ROOT)"/dycore apply --check -p1 "$${file}" 1>/dev/null 2>&1; then \
+			echo "Applying $${file}"; \
+			git -C "$(MPAS_SRC_ROOT)"/dycore apply -p1 "$${file}"; \
+		fi; \
+	done
 
 #
 # EZXML
@@ -139,8 +144,7 @@ mpas_framework.o: mpas_dmpar.o \
                   mpas_io_units.o \
                   mpas_block_decomp.o \
                   mpas_stream_manager.o \
-                  mpas_c_interfacing.o \
-                  mpas_halo.o
+                  mpas_c_interfacing.o
 
 mpas_abort.o: mpas_kind_types.o mpas_io_units.o mpas_threading.o
 
@@ -160,7 +164,7 @@ mpas_pool_routines.o: mpas_derived_types.o mpas_field_routines.o mpas_threading.
 
 mpas_decomp.o: mpas_derived_types.o mpas_stream_manager.o mpas_log.o
 
-mpas_hash.o : mpas_derived_types.o
+mpas_hash.o: mpas_derived_types.o
 
 mpas_dmpar.o: mpas_sort.o mpas_kind_types.o mpas_derived_types.o mpas_hash.o mpas_threading.o mpas_pool_routines.o mpas_log.o
 
@@ -170,7 +174,7 @@ mpas_timekeeping.o: mpas_string_utils.o mpas_kind_types.o mpas_derived_types.o m
 
 mpas_timer.o: mpas_kind_types.o mpas_dmpar.o mpas_threading.o mpas_log.o
 
-mpas_block_decomp.o: mpas_derived_types.o mpas_hash.o mpas_io_units.o mpas_dmpar.o
+mpas_block_decomp.o: mpas_derived_types.o mpas_hash.o mpas_io_units.o mpas_dmpar.o mpas_timer.o mpas_ptscotch_interface.o
 
 mpas_block_creator.o: mpas_dmpar.o mpas_hash.o mpas_sort.o mpas_io_units.o mpas_block_decomp.o mpas_stream_manager.o mpas_decomp.o mpas_abort.o $(DEPS)
 
@@ -184,8 +188,6 @@ mpas_io_units.o: mpas_kind_types.o
 
 mpas_threading.o: mpas_kind_types.o
 
-mpas_stream_inquiry.o: mpas_derived_types.o mpas_log.o mpas_c_interfacing.o stream_inquiry.o
-
 mpas_stream_list.o: mpas_derived_types.o mpas_kind_types.o mpas_io_streams.o mpas_timekeeping.o regex_matching.o mpas_log.o
 
 mpas_stream_manager.o: mpas_io_streams.o mpas_timekeeping.o mpas_derived_types.o mpas_kind_types.o mpas_c_interfacing.o mpas_stream_list.o mpas_dmpar.o mpas_io.o mpas_threading.o mpas_log.o
@@ -194,6 +196,10 @@ mpas_forcing.o: mpas_derived_types.o mpas_timekeeping.o mpas_stream_manager.o mp
 
 mpas_halo.o: mpas_derived_types.o mpas_pool_routines.o mpas_log.o
 
+mpas_ptscotch_interface.o: mpas_derived_types.o mpas_log.o
+
+mpas_stream_inquiry.o: mpas_derived_types.o mpas_log.o mpas_c_interfacing.o
+
 #
 # Operator dependencies
 #
@@ -220,14 +226,6 @@ mpas_geometry_utils.o: mpas_vector_operations.o mpas_matrix_operations.o
 registry: $(REG_OBJS) ezxml.o
 	$(CC) $(CPPFLAGS) $(CFLAGS) -o $@ $(REG_OBJS) ezxml.o
 
-
-#
-# Default stream file generator
-#
-streams_gen: $(STREAMS_GEN_OBJS) ezxml.o
-	$(CC) $(CPPFLAGS) $(CFLAGS) -o $@ $(STREAMS_GEN_OBJS) ezxml.o
-
-
 #
 # Include files manufactured by the registry code generator
 #
@@ -240,8 +238,9 @@ incs: $(REGISTRY_FILE)
 #
 dycore: $(DYN_OBJS) $(DIAGNOSTICS) $(DIAG_OBJS) $(INTERFACE_OBJS)
 
-mpas_atm_time_integration.o: mpas_atm_iau.o mpas_atm_dimensions.o mpas_atm_boundaries.o
+mpas_atm_dissipation_models.o: mpas_atm_dimensions.o
 
+mpas_atm_time_integration.o: mpas_atm_iau.o mpas_atm_dimensions.o mpas_atm_boundaries.o mpas_atm_dissipation_models.o
 
 #
 # Diagnostics
@@ -261,8 +260,7 @@ mpas_atm_core_interface.o: mpas_atm_core.o incs
 
 mpas_atm_core.o: mpas_atm_threading.o mpas_atm_time_integration.o mpas_atm_diagnostics_manager.o mpas_atm_halos.o
 
-cam_mpas_subdriver.o: mpas_atm_core_interface.o mpas_derived_types.o mpas_framework.o mpas_domain_routines.o mpas_pool_routines.o
-
+cam_mpas_subdriver.o: mpas_atm_core.o mpas_atm_core_interface.o mpas_atm_time_integration.o mpas_atm_dimensions.o mpas_atm_halos.o mpas_atm_threading.o
 
 clean:
 	rm registry Registry_processed.xml *.inc *.o *.mod lib*.a
@@ -275,7 +273,7 @@ clean:
 	$(CC) -c $(CFLAGS) -DUNDERSCORE $(CPPFLAGS) $(CPPINCLUDES) -I$(MPAS_SRC_ROOT)/dycore/src/external/ezxml $<
 
 %.o : %.F
-	$(FC) -c $(CPPFLAGS) $(FFLAGS) $(CPPINCLUDES) $(FCINCLUDES) $<
+	$(FC) -c $(CPPFLAGS) $(FFLAGS) $(CPPINCLUDES) $(FCINCLUDES) -I$(MPAS_SRC_ROOT)/dycore/src/framework $<
 
 %.o : %.F90
 	$(FC) -c $(CPPFLAGS) $(FFLAGS) $(CPPINCLUDES) $(FCINCLUDES) $<

src/dynamics/mpas/dp_coupling.F90

@@ -76,10 +76,8 @@ subroutine d_p_coupling(phys_state, phys_tend, pbuf2d, dyn_out)
    ! mesh information and coefficients needed for
    ! frontogenesis function calculation
    !
-   real(r8), pointer :: defc_a(:,:)
-   real(r8), pointer :: defc_b(:,:)
-   real(r8), pointer :: cell_gradient_coef_x(:,:)
-   real(r8), pointer :: cell_gradient_coef_y(:,:)
+   real(r8), pointer :: deformation_coef_c(:, :) ! Introduced in MPAS 8.4.0, replacing cell_gradient_coef_x.
+   real(r8), pointer :: deformation_coef_s(:, :) ! Introduced in MPAS 8.4.0, replacing cell_gradient_coef_y.
    real(r8), pointer :: edgesOnCell_sign(:,:)
    real(r8), pointer :: dvEdge(:)
    real(r8), pointer :: areaCell(:)
@@ -169,10 +167,8 @@ subroutine d_p_coupling(phys_state, phys_tend, pbuf2d, dyn_out)
       !
       ! compute frontogenesis function and angle for gravity wave scheme
       !
-      defc_a => dyn_out % defc_a
-      defc_b => dyn_out % defc_b
-      cell_gradient_coef_x => dyn_out % cell_gradient_coef_x
-      cell_gradient_coef_y => dyn_out % cell_gradient_coef_y
+      deformation_coef_c => dyn_out % deformation_coef_c
+      deformation_coef_s => dyn_out % deformation_coef_s
       edgesOnCell_sign => dyn_out % edgesOnCell_sign
       dvEdge => dyn_out % dvEdge
       areaCell => dyn_out % areaCell
@@ -192,15 +188,13 @@ subroutine d_p_coupling(phys_state, phys_tend, pbuf2d, dyn_out)
       allocate(frontga_phys(pcols, pver, begchunk:endchunk), stat=ierr)
       if( ierr /= 0 ) call endrun(subname//':failed to allocate frontga_phys array')
 
-
       call calc_frontogenesis( frontogenesisFunction, frontogenesisAngle,  &
                                theta_m, tracers(index_qv,:,:),             &
-                               uperp, utangential, defc_a, defc_b,         &
-                               cell_gradient_coef_x, cell_gradient_coef_y, &
+                               uperp, utangential, dyn_out % defc_a, dyn_out % defc_b, &
+                               deformation_coef_c, deformation_coef_s, &
                                areaCell, dvEdge, cellsOnEdge, edgesOnCell, &
                                nEdgesOnCell, edgesOnCell_sign,             &
                                plev, nCellsSolve )
-
    end if
 
    if (use_gw_movmtn_pbl) then

src/dynamics/mpas/driver/0001-Fix-Fortran-standard-violation.patch

@@ -0,0 +1,45 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Kuan-Chih Wang <kuanchihw@ucar.edu>
+Date: Tue, 21 Apr 2026 13:50:09 -0600
+Subject: [PATCH] Fix Fortran standard violation due to pointer argument not
+ being associated
+
+At line 1970, if the `DO_PHYSICS` macro is undefined, the `diag_physics` pointer
+will not be initialized by the call to `mpas_pool_get_subpool`, and therefore
+its pointer association status will remain undefined.
+
+However, at line 2250, this pointer is used as an argument to call `atm_compute_dyn_tend`,
+which constitutes a Fortran standard violation.
+
+Quoted from Fortran 2023,
+
+> 15.5.2.4 Argument association
+> Except in references to intrinsic inquiry functions, a pointer actual argument that
+> corresponds to a nonoptional nonpointer dummy argument shall be pointer associated with
+> a target.
+
+This bug can lead to a runtime crash for models that use MPAS as a dynamical core
+(e.g., CAM, CAM-SIMA).
+
+Fix this issue by adding the `pointer` attribute to the `diag_physics` dummy argument
+for the `atm_compute_dyn_tend` subroutine.
+---
+ src/core_atmosphere/dynamics/mpas_atm_time_integration.F | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/core_atmosphere/dynamics/mpas_atm_time_integration.F b/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
+index 238ca7235..c16072976 100644
+--- a/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
++++ b/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
+@@ -5813,7 +5813,7 @@ module atm_time_integration
+       type (mpas_pool_type), intent(in) :: state
+       type (mpas_pool_type), intent(in) :: diag
+       type (mpas_pool_type), intent(in) :: mesh
+-      type (mpas_pool_type), intent(in) :: diag_physics
++      type (mpas_pool_type), pointer, intent(in) :: diag_physics
+       type (mpas_pool_type), intent(in) :: configs
+       integer, intent(in) :: nVertLevels              ! for allocating stack variables
+       integer, intent(in) :: rk_step, dynamics_substep
+-- 
+2.48.1
+