merge to cam6_3_135

brian-eaton · Nov 17, 2023 · 4578ae9 · 4578ae9
2 parents f1cfe38 + 408f014
commit 4578ae9
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Showing 27 changed files with 730 additions and 298 deletions.
diff --git a/Externals_CAM.cfg b/Externals_CAM.cfg
@@ -14,23 +14,18 @@ required = True
 
 [cosp2]
 local_path = src/physics/cosp2/src
-protocol = svn
-repo_url = https://github.com/CFMIP/COSPv2.0/tags/
-tag = v2.1.4cesm/src
+protocol = git
+repo_url = https://github.com/CFMIP/COSPv2.0
+sparse = ../.cosp_sparse_checkout
+tag = v2.1.4cesm
 required = True
 
 [clubb]
 local_path = src/physics/clubb
-protocol = svn
-repo_url = https://github.com/larson-group/clubb_release/tags/
-tag = clubb_4ncar_20221129_59cb19f_20230330_branchtag/src/CLUBB_core
-required = True
-
-[silhs]
-local_path = src/physics/silhs
-protocol = svn
-repo_url = https://github.com/larson-group/clubb_release/tags/
-tag = clubb_4ncar_20221129_59cb19f_20230330_branchtag/src/SILHS
+protocol = git
+repo_url = https://github.com/larson-group/clubb_release
+sparse = ../.clubb_sparse_checkout
+tag = clubb_4ncar_20221129_59cb19f_20230330_branchtag
 required = True
 
 [pumas]
@@ -55,9 +50,9 @@ tag = ALI_ARMS_v1.0.1
 required = True
 
 [atmos_phys]
-tag = atmos_phys0_00_011
+tag = atmos_phys0_01_000
 protocol = git
-repo_url = https://github.com/NCAR/atmospheric_physics
+repo_url = https://github.com/ESCOMP/atmospheric_physics
 required = True
 local_path = src/atmos_phys
 

diff --git a/bld/configure b/bld/configure
@@ -2225,11 +2225,11 @@ sub write_filepath
     }
 
     if ($clubb_sgs) {
-       print $fh "$camsrcdir/src/physics/clubb\n";
+       print $fh "$camsrcdir/src/physics/clubb/src/CLUBB_core\n";
     }
 
     if ($silhs) {
-       print $fh "$camsrcdir/src/physics/silhs\n";
+       print $fh "$camsrcdir/src/physics/clubb/src/SILHS\n";
     }
 
     if ($phys_pkg eq 'cam_dev') {
@@ -2290,6 +2290,7 @@ sub write_filepath
     print $fh "$camsrcdir/src/cpl/$cpl\n";
     print $fh "$camsrcdir/src/control\n";
     print $fh "$camsrcdir/src/utils\n";
+    print $fh "$camsrcdir/src/utils/cam_ccpp\n";
     print $fh "$camsrcdir/src/atmos_phys/utilities\n";
 
 
@@ -2325,13 +2326,13 @@ sub write_cosp_makefile
 
 CAM_BLD      := $cam_bld
 COSP_PATH    := $cam_dir/src/physics/cosp2
-ISCCP_PATH   := $cam_dir/src/physics/cosp2/src/simulator/icarus
-RS_PATH      := $cam_dir/src/physics/cosp2/src/simulator/quickbeam
-RT_PATH      := $cam_dir/src/physics/cosp2/src/simulator/rttov
-CS_PATH      := $cam_dir/src/physics/cosp2/src/simulator/actsim
-MISR_PATH    := $cam_dir/src/physics/cosp2/src/simulator/MISR_simulator
-MODIS_PATH   := $cam_dir/src/physics/cosp2/src/simulator/MODIS_simulator
-PARASOL_PATH := $cam_dir/src/physics/cosp2/src/simulator/parasol
+ISCCP_PATH   := $cam_dir/src/physics/cosp2/src/src/simulator/icarus
+RS_PATH      := $cam_dir/src/physics/cosp2/src/src/simulator/quickbeam
+RT_PATH      := $cam_dir/src/physics/cosp2/src/src/simulator/rttov
+CS_PATH      := $cam_dir/src/physics/cosp2/src/src/simulator/actsim
+MISR_PATH    := $cam_dir/src/physics/cosp2/src/src/simulator/MISR_simulator
+MODIS_PATH   := $cam_dir/src/physics/cosp2/src/src/simulator/MODIS_simulator
+PARASOL_PATH := $cam_dir/src/physics/cosp2/src/src/simulator/parasol
 
 EOF
 

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -161,6 +161,209 @@ Summarize any changes to answers: None.
 ===============================================================
 ===============================================================
 
+Tag name: cam6_3_135
+Originator(s): jedwards, nusbaume
+Date: 16 Nov 2023
+One-line Summary: removes svn sparse checkout
+Github PR URL: https://github.com/ESCOMP/CAM/pull/913
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+
+Use git sparse checkout for all repos, combine clubb and silhs into clubb.
+git sparse checkout has been available in manage_externals since version 1.2.1.
+
+Fixes #912 -> cosp2 svn access to github support is ending soon
+
+Describe any changes made to build system:
+
+Build path were modified in the "configure" Perl script, as well
+as in the COSP Makefile.in file, in order to account for the
+new source code paths.
+
+Describe any changes made to the namelist: N/A
+
+List any changes to the defaults for the boundary datasets: N/A
+
+Describe any substantial timing or memory changes: N/A
+
+Code reviewed by: nusbaume, cacraigucar, gold2718
+
+List all files eliminated: N/A
+
+List all files added and what they do:
+
+A       src/physics/.clubb_sparse_checkout
+ - Provides information on how to do the git sparse checkout of CLUBB and SILHS
+
+A       src/physics/cosp2/.cosp_sparse_checkout
+ - Provides information on how to do the git sparse checkout of COSP
+
+List all existing files that have been modified, and describe the changes:
+
+M       Externals_CAM.cfg
+ - Change the Github-SVN bridge method to git sparse checkout
+
+M       bld/configure
+ - Update source code paths for CLUBB, SILHS, and COSP
+
+M       src/physics/cosp2/Makefile.in
+ - Update source code paths for relevant COSP files.
+
+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: FAIL) details:
+    FAIL ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.cheyenne_intel.cam-outfrq9s_mg3 MODEL_BUILD time=3
+ 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
+ SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq3h (Overall: DIFF) details:
+    FAIL SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq3h BASELINE /glade/p/cesm/amwg/cesm_baselines/cam6_3_134: DIFF
+ - pre-existing failure
+
+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
+
+izumi/gnu/aux_cam: ALL PASS
+
+Summarize any changes to answers: bit-for-bit unchanged
+
+===============================================================
+
+Tag name: cam6_3_134
+Originator(s): nusbaume, jimmielin
+Date: 31 Oct 2023
+One-line Summary: Update atmospheric_physics external
+Github PR URL: https://github.com/ESCOMP/CAM/pull/891
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+
+This PR updates the atmospheric_physics external in CAM,
+which requires some source modifications on the CAM-side.
+There has also been some replacement of CAM code with CCPP
+physics routines in order to reduce duplication.
+
+This PR also fixes a bug found in Kessler where it was using
+the wrong pressure when converting to/from potential temperature
+via the exner function.
+
+Finally, this change also brings in a rename of the SE
+dycore's 'time_mod' module to 'se_dyn_time_mod' in order
+to avoid name collision with GEOS-Chem code.
+
+Fixes #752  -> Update atmospheric_physics external
+Fixes #802  -> Kessler physics using inconsistent reference pressures
+
+Closes #904 -> Rename SE dycore time_mod to dyn_time_mod (PR)
+
+Describe any changes made to build system:
+
+Added the "src/utils/cam_ccpp" and "src/atmos_phys/utilities" directory
+to the list of directories used during compilation.
+
+Describe any changes made to the namelist: N/A
+
+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, PeterHjortLauritzen, jtruesdal, peverwhee
+
+List all files eliminated:
+
+R       src/dynamics/se/dycore/time_mod.F90
+ - Renamed to 'se_dyn_time_mod'
+R       src/utils/ccpp_kinds.F90
+ - Moved to 'src/utils/cam_ccpp/ccpp_kinds.F90'
+
+List all files added and what they do:
+
+A       src/utils/cam_ccpp/ccpp_constituent_prop_mod.F90
+ - Creates a "CCPP Constituent Properties" object for CAM.
+
+List all existing files that have been modified, and describe the changes:
+
+M       Externals_CAM.cfg
+ - Update 'atmospheric_physics' external
+
+M       bld/configure
+ - Add 'src/utils/cam_ccpp' and 'src/atmos_phys/utilities' to build file paths
+
+M       src/dynamics/se/dp_coupling.F90
+ - Use CCPP-ized 'update_dry_static_energy_run' subroutine
+
+M       src/physics/cam/geopotential.F90
+ - Use CCPP-ized 'geopotential_temp_run' subroutine
+
+M       src/physics/cam/ref_pres.F90
+ - Update comment in order to avoid future confusion
+
+M       src/physics/cam/physpkg.F90
+M       src/physics/cam_dev/physpkg.F90
+M       src/physics/simple/held_suarez_cam.F90
+M       src/physics/simple/physpkg.F90
+ - Update physics calls and add new const. prop. DDT to work with new
+   atmospheric_physics external
+
+M       src/physics/simple/kessler_cam.F90
+- Update physics calls and add new const. prop. DDT to work with new
+  atmospheric_physics external.  Also replace use of "standard pressure"
+  with "reference pressure" in order to avoid unphysical mismatches.
+
+M       src/dynamics/se/dycore/fvm_consistent_se_cslam.F90
+M       src/dynamics/se/dycore/prim_advance_mod.F90
+M       src/dynamics/se/dycore/prim_advection_mod.F90
+M       src/dynamics/se/dycore/prim_driver_mod.F90
+M       src/dynamics/se/dycore/prim_init.F90
+M       src/dynamics/se/dycore/prim_state_mod.F90
+M       src/dynamics/se/stepon.F90
+ - Replace 'time_mod' with 'se_dyn_time_mod'
+
+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:
+
+ All tests have NLCOMP failures due to changes in input data paths on Cheyenne.
+
+ ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.cheyenne_intel.cam-outfrq9s_mg3 (Overall: FAIL) details:
+    FAIL ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.cheyenne_intel.cam-outfrq9s_mg3 NLCOMP
+    FAIL ERP_Ln9_Vnuopc.C96_C96_mg17.F2000climo.cheyenne_intel.cam-outfrq9s_mg3 MODEL_BUILD time=3
+ 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 NLCOMP
+    FAIL ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq9s COMPARE_base_rest
+ SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq3h (Overall: DIFF) details:
+    FAIL SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq3h NLCOMP
+    FAIL SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq3h BASELINE /glade/p/cesm/amwg/cesm_baselines/cam6_3_133: DIFF
+ - pre-existing failure
+
+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=9
+ - pre-existing failure
+
+ ERS_Ln27_Vnuopc.ne5pg3_ne5pg3_mg37.FKESSLER.izumi_nag.cam-outfrq9s (Overall: DIFF) details:
+    FAIL ERS_Ln27_Vnuopc.ne5pg3_ne5pg3_mg37.FKESSLER.izumi_nag.cam-outfrq9s BASELINE /fs/cgd/csm/models/atm/cam/pretag_bl/cam6_3_133_nag: DIFF
+ - expected failure
+
+izumi/gnu/aux_cam: All PASS
+
+Summarize any changes to answers:
+  All compsets which use Kessler idealized physics
+  will have larger-than-roundoff answer changes due
+  to reference pressure bug fix.
+
+===============================================================
+
 Tag name: cam6_3_133
 Originator(s): fvitt
 Date: 19 Oct 2023

diff --git a/src/dynamics/se/dp_coupling.F90 b/src/dynamics/se/dp_coupling.F90
@@ -54,7 +54,7 @@ subroutine d_p_coupling(phys_state, phys_tend,  pbuf2d, dyn_out)
    use phys_control,           only: use_gw_front, use_gw_front_igw
    use hycoef,                 only: hyai, ps0
    use fvm_mapping,            only: dyn2phys_vector, dyn2phys_all_vars
-   use time_mod,               only: timelevel_qdp
+   use se_dyn_time_mod,        only: timelevel_qdp
    use control_mod,            only: qsplit
    use test_fvm_mapping,       only: test_mapping_overwrite_dyn_state, test_mapping_output_phys_state
    use prim_advance_mod,       only: tot_energy_dyn
@@ -546,15 +546,17 @@ subroutine derived_phys_dry(phys_state, phys_tend, pbuf2d)
    use shr_const_mod,   only: shr_const_rwv
    use phys_control,    only: waccmx_is
    use geopotential,    only: geopotential_t
+   use static_energy,   only: update_dry_static_energy_run
    use check_energy,    only: check_energy_timestep_init
    use hycoef,          only: hyai, ps0
    use shr_vmath_mod,   only: shr_vmath_log
    use qneg_module,     only: qneg3
    use dyn_tests_utils, only: vc_dry_pressure
+   use shr_kind_mod,    only: shr_kind_cx
    ! arguments
    type(physics_state), intent(inout), dimension(begchunk:endchunk) :: phys_state
    type(physics_tend ), intent(inout), dimension(begchunk:endchunk) :: phys_tend
-   type(physics_buffer_desc),      pointer     :: pbuf2d(:,:)
+   type(physics_buffer_desc), pointer :: pbuf2d(:,:)
 
    ! local variables
    integer :: lchnk
@@ -564,6 +566,10 @@ subroutine derived_phys_dry(phys_state, phys_tend, pbuf2d)
 
    integer :: m, i, k, ncol, m_cnst
    type(physics_buffer_desc), pointer :: pbuf_chnk(:)
+
+   !Needed for "update_dry_static_energy" CCPP scheme
+   integer :: errflg
+   character(len=shr_kind_cx) :: errmsg
    !----------------------------------------------------------------------------
 
    ! Evaluate derived quantities
@@ -686,18 +692,17 @@ subroutine derived_phys_dry(phys_state, phys_tend, pbuf2d)
       end do
 
       ! Compute initial geopotential heights - based on full pressure
-      call geopotential_t (phys_state(lchnk)%lnpint, phys_state(lchnk)%lnpmid  , phys_state(lchnk)%pint  , &
-         phys_state(lchnk)%pmid  , phys_state(lchnk)%pdel    , phys_state(lchnk)%rpdel , &
-         phys_state(lchnk)%t     , phys_state(lchnk)%q(:,:,:), rairv(:,:,lchnk),  gravit,  zvirv       , &
-         phys_state(lchnk)%zi    , phys_state(lchnk)%zm      , ncol                )
+      call geopotential_t(phys_state(lchnk)%lnpint, phys_state(lchnk)%lnpmid  , phys_state(lchnk)%pint, &
+         phys_state(lchnk)%pmid  , phys_state(lchnk)%pdel    , phys_state(lchnk)%rpdel                , &
+         phys_state(lchnk)%t     , phys_state(lchnk)%q(:,:,:), rairv(:,:,lchnk), gravit, zvirv        , &
+         phys_state(lchnk)%zi    , phys_state(lchnk)%zm      , ncol)
 
       ! Compute initial dry static energy, include surface geopotential
-      do k = 1, pver
-         do i = 1, ncol
-            phys_state(lchnk)%s(i,k) = cpairv(i,k,lchnk)*phys_state(lchnk)%t(i,k) &
-                                     + gravit*phys_state(lchnk)%zm(i,k) + phys_state(lchnk)%phis(i)
-         end do
-      end do
+      call update_dry_static_energy_run(pver, gravit, phys_state(lchnk)%t(1:ncol,:),  &
+                                        phys_state(lchnk)%zm(1:ncol,:),               &
+                                        phys_state(lchnk)%phis(1:ncol),               &
+                                        phys_state(lchnk)%s(1:ncol,:),                &
+                                        cpairv(1:ncol,:,lchnk), errflg, errmsg)
 
       ! Ensure tracers are all positive
       call qneg3('D_P_COUPLING',lchnk  ,ncol    ,pcols   ,pver    , &

diff --git a/src/dynamics/se/dycore/fvm_consistent_se_cslam.F90 b/src/dynamics/se/dycore/fvm_consistent_se_cslam.F90
@@ -6,7 +6,7 @@ module fvm_consistent_se_cslam
   use cam_abortutils,         only: endrun
   use cam_logfile,            only: iulog
 
-  use time_mod,               only: timelevel_t
+  use se_dyn_time_mod,        only: timelevel_t
   use element_mod,            only: element_t
   use fvm_control_volume_mod, only: fvm_struct
   use hybrid_mod,             only: hybrid_t, config_thread_region, get_loop_ranges, threadOwnsVertLevel

diff --git a/src/dynamics/se/dycore/prim_advance_mod.F90 b/src/dynamics/se/dycore/prim_advance_mod.F90
@@ -53,7 +53,7 @@ subroutine prim_advance_exp(elem, fvm, deriv, hvcoord, hybrid,dt, tl,  nets, net
     use element_mod,       only: element_t
     use hybvcoord_mod,     only: hvcoord_t
     use hybrid_mod,        only: hybrid_t
-    use time_mod,          only: TimeLevel_t,  timelevel_qdp, tevolve
+    use se_dyn_time_mod,   only: TimeLevel_t,  timelevel_qdp, tevolve
     use fvm_control_volume_mod, only: fvm_struct
     use cam_thermo,        only: get_kappa_dry
     use air_composition,   only: thermodynamic_active_species_num

diff --git a/src/dynamics/se/dycore/prim_advection_mod.F90 b/src/dynamics/se/dycore/prim_advection_mod.F90
@@ -23,7 +23,7 @@ module prim_advection_mod
   use element_mod,            only: element_t
   use fvm_control_volume_mod, only: fvm_struct
   use hybvcoord_mod,          only: hvcoord_t
-  use time_mod,               only: TimeLevel_t, TimeLevel_Qdp
+  use se_dyn_time_mod,        only: TimeLevel_t, TimeLevel_Qdp
   use control_mod,            only: nu_q, nu_p, limiter_option, hypervis_subcycle_q, rsplit
   use edge_mod,               only: edgevpack, edgevunpack, initedgebuffer, initedgesbuffer