Merge pull request #908 from gdicker1/updateext_v8mpas

cam6_3_137: Update mpas external to use v8.0.1

Externals_CAM.cfg

@@ -68,7 +68,7 @@ local_path = src/dynamics/mpas/dycore
 protocol = git
 repo_url = https://github.com/MPAS-Dev/MPAS-Model.git
 sparse = ../.mpas_sparse_checkout
-hash = ff76a231
+hash = b8c33daa
 required = True
 
 [hemco]

bld/build-namelist

@@ -4056,6 +4056,7 @@ if ($dyn =~ /mpas/) {
  add_default($nl, 'mpas_zd');
  add_default($nl, 'mpas_xnutr');
  add_default($nl, 'mpas_cam_coef');
+ add_default($nl, 'mpas_cam_damping_levels');
  add_default($nl, 'mpas_print_detailed_minmax_vel');
  add_default($nl, 'mpas_rayleigh_damp_u');
  add_default($nl, 'mpas_rayleigh_damp_u_timescale_days');

bld/namelist_files/namelist_defaults_cam.xml

@@ -3176,6 +3176,7 @@
 <mpas_zd > 22000.0D0 </mpas_zd>
 <mpas_xnutr > 0.2D0 </mpas_xnutr>
 <mpas_cam_coef > 0.0D0 </mpas_cam_coef>
+<mpas_cam_damping_levels > 0 </mpas_cam_damping_levels>
 <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>

bld/namelist_files/namelist_definition.xml

@@ -8411,15 +8411,26 @@ Default: 0.2
 
 <entry id="mpas_cam_coef" type="real" category="mpas"
  group="damping" valid_values="">
-Coefficient for scaling the 2nd-order horizontal diffusion in the mpas_cam absorbing layer.
-A value of 1.0 will result in layered diffusion similar to CAM-SE and gives damping
-coefficients of 0.2216E7, 0.6482E6, 0.1927E6 in the top-most three layers on the dynamics
-variables u, w, and theta. The top 3 damping coefficients scale linearly with
-mpas_cam_coef. 0.0 disables SE like 2nd-order diffusion in the absorbing layer and is the
-current default. Sponge layer absorption can also be provided by Rayleigh damping.
+Coefficient for scaling the 2nd-order horizontal diffusion in the mpas_cam absorbing
+layer. The absorbing layer depth is controlled with mpas_cam_damping_levels. The damping
+coefficients scale linearly with mpas_cam_coef. A value of 0.0 (or
+mpas_cam_damping_levels=0) disables the 2nd-order diffusion in the absorbing layer. Sponge
+layer absorption can also be provided by Rayleigh damping.
+
+E.g. a value of 1.0 with mpas_cam_damping_levels=3 will result in damping coefficients of
+2E6 m^2/s, 6E5, 2E5 in the top-most three layers on the dynamics variables u, w, and
+theta.
 Default: 0.0
 </entry>
 
+<entry id="mpas_cam_damping_levels" type="integer" category="mpas"
+ group="damping" valid_values="">
+Number mpas_cam absorbing layers in which to apply 2nd-order horizontal diffusion.
+Viscocity linearly ramps to zero by layer number from the top. mpas_cam_damping_levels and
+mpas_cam_coef must both be greater than 0 for the diffusion to be enabled.
+Default: 0
+</entry>
+
 <entry id="mpas_rayleigh_damp_u" type="logical" category="mpas"
  group="damping" valid_values="">
 Whether to apply Rayleigh damping on horizontal velocity in the top-most model levels.

cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa480/user_nl_cam

@@ -2,3 +2,5 @@ mfilt=1,1,1,1,1,1
 ndens=1,1,1,1,1,1
 nhtfrq=9,9,9,9,9,9
 inithist='ENDOFRUN'
+mpas_cam_coef=1.0D0
+mpas_cam_damping_levels=3

doc/ChangeLog

@@ -1,6 +1,125 @@
 
 ===============================================================
 
+Tag name: cam6_3_137
+Originator(s): gdicker
+Date: Nov 29, 2023
+One-line Summary: Update MPAS-A within CAM to v8.0
+Github PR URL: https://https://github.com/ESCOMP/CAM/pull/908
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+ - Update MPAS-A within CAM to v8.0.1: https://github.com/ESCOMP/CAM/issues/861
+
+Describe any changes made to build system: N/A
+
+Describe any changes made to the namelist:
+ - Added new namelist variable mpas_cam_damping_levels. Determines how many layers from
+ model top to apply CAM-SE-like horizontal diffusion in MPAS.
+
+
+List any changes to the defaults for the boundary datasets: N/A
+
+Describe any substantial timing or memory changes: N/A
+
+Code reviewed by: cacraigucar, jtruesdal, PeterHjortLauritzen
+
+List all files eliminated: N/A
+
+List all files added and what they do: N/A
+
+List all existing files that have been modified, and describe the changes:
+M Externals_CAM.cfg
+ - Update mpas hash to point a few commits after MPAS-Dev/MPAS-Model 'v8.0.1' tag
+
+M src/dynamics/mpas/Makefile
+ - Add MPAS_PIO_SUPPORT to CPPFLAGS to ensure PIO is used instead of the new SMIOL
+ - Rename diagnostics with "mpas_" prefix that was added
+ - Add mpas_string_utils, mpas_halo, mpas_atm_halos modules
+
+M bld/build-namelist
+M bld/namelist_files/namelist_defaults_cam.xml
+M bld/namelist_files/namelist_definition.xml
+ - Add mpas_cam_damping_levels namelist argument and update mpas_cam_coef
+ description
+
+M src/dynamics/mpas/driver/cam_mpas_subdriver.F90
+ - Update arguments for {postread,prewrite}_reindex subroutines
+ - Add calls to create/destroy mpas halo_groups during init and finalize
+ - Modify some halo exchange calls to use exchange_halo_group routine pointer
+
+M src/dynamics/mpas/dyn_comp.F90
+ - Add config_halo_exch_method to configs pool with default value 'mpas_halo'
+ - Add mpas_cam_damping_levels namelist argument
+
+M cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa480/user_nl_cam
+ - Modify F2000climo test using mpasa480_mpasa480 to test the mpas_cam damping
+
+M test/system/archive_baseline.sh
+ - Modify baselinedir path for derecho to point to /glade/campaign location
+
+If there were any failures reported from running test_driver.sh on any test
+platform, and checkin with these failures has been OK'd by the gatekeeper,
+then copy the lines from the td.*.status files for the failed tests to the
+appropriate machine below. All failed tests must be justified.
+
+cheyenne/intel/aux_cam:
+ ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.cheyenne_intel.cam-outfrq9s_mg3 (Overall: PEND) details:
+ PEND ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.cheyenne_intel.cam-outfrq9s_mg3 MODEL_BUILD RERUN
+ ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq9s (Overall: FAIL) details:
+ FAIL ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq9s COMPARE_base_rest
+ FAIL ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq9s BASELINE /glade/p/cesm/amwg/cesm_baselines/cam6_3_133: DIFF
+ - pre-existing failures
+
+ ERS_Ln9_P288x1_Vnuopc.mpasa120_mpasa120.F2000climo.cheyenne_intel.cam-outfrq9s_mpasa120 (Overall: NLFAIL) details:
+ FAIL ERS_Ln9_P288x1_Vnuopc.mpasa120_mpasa120.F2000climo.cheyenne_intel.cam-outfrq9s_mpasa120 NLCOMP
+ found extra variable: 'mpas_cam_damping_levels'
+ - expected failure, added mpas_cam_damping_levels to namelist
+
+ ERS_Ln9_P36x1_Vnuopc.mpasa480_mpasa480.F2000climo.cheyenne_intel.cam-outfrq9s_mpasa480 (Overall: DIFF) details:
+ FAIL ERS_Ln9_P36x1_Vnuopc.mpasa480_mpasa480.F2000climo.cheyenne_intel.cam-outfrq9s_mpasa480 NLCOMP
+ found extra variable: 'mpas_cam_damping_levels'
+ FAIL ERS_Ln9_P36x1_Vnuopc.mpasa480_mpasa480.F2000climo.cheyenne_intel.cam-outfrq9s_mpasa480 BASELINE /glade/ p/cesm/amwg/cesm_baselines/cam6_3_136: DIFF
+ - expected failure, added mpas_cam_damping_levels to namelist and modified test via outfrq9s_mpasa480/user_nl_cam
+
+derecho/intel/aux_cam:
+ ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.derecho_intel.cam-outfrq9s_mg3 (Overall: PEND) details:
+ PEND ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.derecho_intel.cam-outfrq9s_mg3 SHAREDLIB_BUILD RERUN
+ ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq9s (Overall: FAIL) details:
+ FAIL ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq9s BASELINE /glade/p/cesm/amwg/derecho_baselines/cam6_3_136: DIFF
+ ERP_Ln9_Vnuopc.ne30pg3_ne30pg3_mg17.FW2000climo.derecho_intel.cam-outfrq9s_wcm_ne30 (Overall: PEND) details:
+ PEND ERP_Ln9_Vnuopc.ne30pg3_ne30pg3_mg17.FW2000climo.derecho_intel.cam-outfrq9s_wcm_ne30 RUN
+ PEND ERP_Ln9_Vnuopc.ne30pg3_ne30pg3_mg17.FW2000climo.derecho_intel.cam-outfrq9s_wcm_ne30 COMPARE_base_rest
+ SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq3h (Overall: DIFF) details:
+ FAIL SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq3h BASELINE /glade/p/cesm/amwg/derecho_baselines/cam6_3_136: DIFF
+ - pre-existing failures
+
+ ERS_Ln9_P288x1_Vnuopc.mpasa120_mpasa120.F2000climo.derecho_intel.cam-outfrq9s_mpasa120 (Overall: NLFAIL) details:
+ FAIL ERS_Ln9_P288x1_Vnuopc.mpasa120_mpasa120.F2000climo.derecho_intel.cam-outfrq9s_mpasa120 NLCOMP
+ found extra variable: 'mpas_cam_damping_levels'
+ - expected failure, added mpas_cam_damping_levels to namelist
+
+ ERS_Ln9_P36x1_Vnuopc.mpasa480_mpasa480.F2000climo.derecho_intel.cam-outfrq9s_mpasa480 (Overall: DIFF) details:
+ FAIL ERS_Ln9_P36x1_Vnuopc.mpasa480_mpasa480.F2000climo.derecho_intel.cam-outfrq9s_mpasa480 NLCOMP
+ found extra variable: 'mpas_cam_damping_levels'
+ FAIL ERS_Ln9_P36x1_Vnuopc.mpasa480_mpasa480.F2000climo.derecho_intel.cam-outfrq9s_mpasa480 BASELINE /glade/p/cesm/amwg/derecho_baselines/cam6_3_136: DIFF
+ - expected failure, added mpas_cam_damping_levels to namelist and modified to use mpas_cam damping
+
+izumi/nag/aux_cam:
+ DAE_Vnuopc.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL) details:
+ FAIL DAE_Vnuopc.f45_f45_mg37.FHS94.izumi_nag.cam-dae RUN time=10
+ - pre-existing failure
+
+ ERC_D_Ln9_Vnuopc.mpasa480z32_mpasa480.FHS94.izumi_nag.cam-outfrq3s_usecase (Overall: NLFAIL) details:
+ FAIL ERC_D_Ln9_Vnuopc.mpasa480z32_mpasa480.FHS94.izumi_nag.cam-outfrq3s_usecase NLCOMP
+ found extra variable: 'mpas_cam_damping_levels'
+ - expected failure, added mpas_cam_damping_levels to namelist
+
+izumi/gnu/aux_cam: All PASS
+
+Summarize any changes to answers: bit-for-bit unchanged
+
+===============================================================
+
 Tag name: cam6_3_136
 Originator(s): cacraig, fischer
 Date: Nov 18, 2023

src/dynamics/mpas/Makefile

@@ -1,4 +1,4 @@
-CPPFLAGS := -D_MPI -DMPAS_NATIVE_TIMERS -DMPAS_GIT_VERSION=unknown -DMPAS_NAMELIST_SUFFIX=atmosphere -DMPAS_CAM_DYCORE -DMPAS_NO_ESMF_INIT
+CPPFLAGS := -D_MPI -DMPAS_NATIVE_TIMERS -DMPAS_GIT_VERSION=unknown -DMPAS_NAMELIST_SUFFIX=atmosphere -DMPAS_CAM_DYCORE -DMPAS_PIO_SUPPORT -DMPAS_NO_ESMF_INIT
 ifdef PIODEF
  CPPFLAGS += $(PIODEF)
 endif
@@ -18,6 +18,7 @@ INTERFACE_OBJS = \
  mpas_atm_core_interface.o \
  mpas_atm_dimensions.o \
  mpas_atm_threading.o \
+ mpas_atm_halos.o \
  cam_mpas_subdriver.o
 
 DYN_OBJS = \
@@ -31,10 +32,11 @@ DIAG_OBJS = \
 
 DIAGNOSTICS = \
  mpas_atm_diagnostic_template.o \
- isobaric_diagnostics.o \
- convective_diagnostics.o \
- pv_diagnostics.o \
- soundings.o
+ mpas_isobaric_diagnostics.o \
+ mpas_cloud_diagnostics.o \
+ mpas_convective_diagnostics.o \
+ mpas_pv_diagnostics.o \
+ mpas_soundings.o
 
 REG_OBJS = \
  parse.o \
@@ -90,7 +92,10 @@ FRAME_OBJS = \
  mpas_pool_routines.o \
  xml_stream_parser.o \
  regex_matching.o \
- mpas_log.o
+ mpas_log.o \
+ mpas_halo.o \
+ mpas_string_utils.o
+
 
 UTIL_OBJS = \
  ezxml.o
@@ -129,7 +134,8 @@ mpas_framework.o: mpas_dmpar.o \
  mpas_io_units.o \
  mpas_block_decomp.o \
  mpas_stream_manager.o \
- mpas_c_interfacing.o
+ mpas_c_interfacing.o \
+ mpas_halo.o
 
 mpas_abort.o: mpas_kind_types.o mpas_io_units.o mpas_threading.o
 
@@ -155,7 +161,7 @@ mpas_dmpar.o: mpas_sort.o mpas_kind_types.o mpas_derived_types.o mpas_hash.o mpa
 
 mpas_sort.o: mpas_kind_types.o mpas_log.o
 
-mpas_timekeeping.o: mpas_kind_types.o mpas_derived_types.o mpas_dmpar.o mpas_threading.o mpas_log.o
+mpas_timekeeping.o: mpas_string_utils.o mpas_kind_types.o mpas_derived_types.o mpas_dmpar.o mpas_threading.o mpas_log.o
 
 mpas_timer.o: mpas_kind_types.o mpas_dmpar.o mpas_threading.o mpas_log.o
 
@@ -179,6 +185,7 @@ mpas_stream_manager.o: mpas_io_streams.o mpas_timekeeping.o mpas_derived_types.o
 
 mpas_forcing.o: mpas_derived_types.o mpas_timekeeping.o mpas_stream_manager.o mpas_log.o mpas_io_units.o
 
+mpas_halo.o: mpas_derived_types.o mpas_pool_routines.o mpas_log.o
 
 #
 # Operator dependencies
@@ -234,17 +241,18 @@ mpas_atm_time_integration.o: mpas_atm_iau.o mpas_atm_dimensions.o mpas_atm_bound
 #
 mpas_atm_diagnostics_manager.o: mpas_atm_diagnostics_utils.o $(DIAGNOSTICS)
 
-convective_diagnostics.o: mpas_atm_diagnostics_utils.o
-isobaric_diagnostics.o: mpas_atm_diagnostics_utils.o
-pv_diagnostics.o: mpas_atm_diagnostics_utils.o
+mpas_cloud_diagnostics.o: mpas_atm_diagnostics_utils.o
+mpas_convective_diagnostics.o: mpas_atm_diagnostics_utils.o
+mpas_isobaric_diagnostics.o: mpas_atm_diagnostics_utils.o
+mpas_pv_diagnostics.o: mpas_atm_diagnostics_utils.o
 
 
 #
 # Core interface objects
 #
 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_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