Merge branch 'cam_development' into hplin/hk_conv

ESCOMP · Feb 21, 2025 · eea5209 · eea5209
2 parents fab8493 + 25ede0a
commit eea5209
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Showing 340 changed files with 862 additions and 120,863 deletions.
diff --git a/.github/workflows/fleximod_test.yaml b/.github/workflows/fleximod_test.yaml
@@ -4,6 +4,7 @@ jobs:
   fleximod-test:
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         # oldest supported and latest supported
         python-version: ["3.7", "3.x"]
@@ -13,9 +14,16 @@ jobs:
       - id: run-fleximod
         run: |
           $GITHUB_WORKSPACE/bin/git-fleximod update
+          echo
+          echo "Update complete, checking status"
+          echo
           $GITHUB_WORKSPACE/bin/git-fleximod test
+      - id: check-cleanliness
+        run: |
+          echo
+          echo "Checking if git fleximod matches expected externals"
+          echo
+          git diff --exit-code
 #      - name: Setup tmate session
 #        if: ${{ failure() }}
 #        uses: mxschmitt/action-tmate@v3
-
-
diff --git a/.gitmodules b/.gitmodules
@@ -116,28 +116,28 @@
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_002
+fxtag = cismwrap_2_2_005
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
-fxtag = rtm1_0_80
+fxtag = rtm1_0_84
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.02
+fxtag = mosart1.1.07
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
 [submodule "mizuRoute"]
 path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
-fxtag = cesm-coupling.n02_v2.1.3
+fxtag = cesm-coupling.n03_v2.2.0
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 
@@ -151,14 +151,14 @@ fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.56
+fxtag = cime6.1.58
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.0.32
+fxtag = cmeps1.0.33
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
@@ -172,7 +172,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.1.6
+fxtag = share1.1.9
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
@@ -193,7 +193,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
 [submodule "clm"]
 path = components/clm
 url = https://github.com/ESCOMP/CTSM
-fxtag = ctsm5.3.016
+fxtag = ctsm5.3.017
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
 
@@ -203,3 +203,11 @@ url = https://github.com/ESCOMP/FMS_interface
 fxtag = fi_240828
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface
+
+[submodule "tools/CUPiD"]
+path = tools/CUPiD
+url = https://github.com/NCAR/CUPiD.git
+fxtag = v0.1.4
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git
+
diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py
@@ -2,7 +2,7 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.9.3"
+__version__ = "0.9.4"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree

diff --git a/.lib/git-fleximod/git_fleximod/git_fleximod.py b/.lib/git-fleximod/git_fleximod/git_fleximod.py
@@ -181,6 +181,8 @@ def init_submodule_from_gitmodules(gitmodules, name, root_dir, logger):
     url = gitmodules.get(name, "url")
     assert path and url, f"Malformed .gitmodules file {path} {url}"
     tag = gitmodules.get(name, "fxtag")
+    if not tag:
+        tag = gitmodules.get(name, "hash")
     fxurl = gitmodules.get(name, "fxDONOTUSEurl")
     fxsparse = gitmodules.get(name, "fxsparse")
     fxrequired = gitmodules.get(name, "fxrequired")
@@ -250,7 +252,6 @@ def submodules_update(gitmodules, root_dir, requiredlist, force):
                 newrequiredlist = ["AlwaysRequired"]
                 if optional:
                     newrequiredlist.append("AlwaysOptional")
-
                 submodules_update(gitsubmodules, repodir, newrequiredlist, force=force)
 
 def local_mods_output():

diff --git a/.lib/git-fleximod/pyproject.toml b/.lib/git-fleximod/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.9.3"
+version = "0.9.4"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <[email protected]>"]
 maintainers = ["Jim Edwards <[email protected]>"]

diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.9.3"
+current = "0.9.4"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

diff --git a/bld/build-namelist b/bld/build-namelist
@@ -3686,7 +3686,7 @@ if ($cfg->get('microphys') eq 'rk') {
 }
 
 # Eddy Diffusivity Adjustments
-if ($cfg->get('pbl') eq "uw" or $cfg->get('pbl') eq "spcam_m2005") {
+if ($cfg->get('pbl') eq "uw") {
     add_default($nl, 'kv_top_pressure');
     add_default($nl, 'kv_top_scale');
     add_default($nl, 'kv_freetrop_scale');
@@ -4079,27 +4079,6 @@ if ( $dyn eq 'fv3') {
 
 }
 
-# EUL dycore
-if ($dyn eq 'eul') {
-    add_default($nl, 'eul_dif2_coef');
-    add_default($nl, 'eul_hdif_order');
-    add_default($nl, 'eul_hdif_kmnhdn');
-    add_default($nl, 'eul_hdif_coef');
-    add_default($nl, 'eul_divdampn');
-    add_default($nl, 'eul_tfilt_eps');
-    add_default($nl, 'eul_kmxhdc');
-    add_default($nl, 'eul_nsplit');
-}
-
-# SLD dycore
-if ($dyn eq 'sld') {
-    add_default($nl, 'sld_dif2_coef');
-    add_default($nl, 'sld_dif4_coef');
-    add_default($nl, 'sld_divdampn');
-    add_default($nl, 'sld_tfilt_eps');
-    add_default($nl, 'sld_kmxhdc');
-}
-
 # Single column model
 if ($cfg->get('scam')) {
     add_default($nl, 'iopfile');
@@ -4369,11 +4348,6 @@ if ($offline_drv ne 'stub') {
     }
 }
 
-if ($phys eq 'spcam_sam1mom' or $phys eq 'spcam_m2005') {
-    add_default($nl, 'iradsw', 'val'=>'1');
-    add_default($nl, 'iradlw', 'val'=>'1');
-}
-
 #-----------------------------------------------------------------------------------------------
 # Rename component logfiles.
 #

diff --git a/bld/config_files/definition.xml b/bld/config_files/definition.xml
@@ -26,8 +26,8 @@ Switch specifies whether CAM is being built by the CCSM sequential scripts.  0 =
 <entry id="cpl" valid_values="mct,nuopc" value="mct" >
 Coupling framework: mct or nuopc.  Default: mct.
 </entry>
-<entry id="dyn" valid_values="eul,fv,fv3,se,mpas" value="">
-Dynamics package: eul, fv, fv3, se, or mpas.
+<entry id="dyn" valid_values="fv,fv3,se,mpas" value="">
+Dynamics package: fv, fv3, se, or mpas.
 </entry>
 <entry id="waccm_phys" valid_values="0,1" value="0">
 Switch to turn on waccm physics: 0 => no, 1 => yes.
@@ -57,19 +57,19 @@ Option to turn on waccmx thermosphere/ionosphere extension: 0 => no, 1 => yes
 <entry id="ionosphere" valid_values="none,wxie" value="none">
 Ionosphere model used in WACCMX.
 </entry>
-<entry id="phys" valid_values="cam4,cam5,cam6,cam7,held_suarez,adiabatic,kessler,tj2016,grayrad,spcam_sam1mom,spcam_m2005" value="">
-Physics package: cam4, cam5, cam6, cam7, held_suarez, adiabatic, kessler, tj2016, grayrad, spcam_sam1mom, spcam_m2005.
+<entry id="phys" valid_values="cam4,cam5,cam6,cam7,held_suarez,adiabatic,kessler,tj2016,grayrad" value="">
+Physics package: cam4, cam5, cam6, cam7, held_suarez, adiabatic, kessler, tj2016, grayrad.
 </entry>
 <entry id="hemco" valid_values="0,1" value="0">
 Switch to turn on Harmonized Emissions Component (HEMCO) for chemistry: 0 => no, 1 => yes.
 </entry>
-<entry id="microphys" valid_values="rk,mg1,mg2,mg3,pumas,spcam_m2005,spcam_sam1mom,none" value="">
+<entry id="microphys" valid_values="rk,mg1,mg2,mg3,pumas,none" value="">
 Microphysics package: rk (Rasch and Kristjansson), mg1 (Morrison and
 Gettelman two moment scheme CAM5.1), mg2 (Morrison and Gettelman second
-version CAM6), mg3 (MG scheme 3rd version, graupel), PUMAS, SPCAM_m2005, SPCAM_sam1mom.
+version CAM6), mg3 (MG scheme 3rd version, graupel), PUMAS.
 </entry>
-<entry id="macrophys" valid_values="rk,park,clubb_sgs,spcam_sam1mom,spcam_m2005,none" value="">
-Macrophysics package: RK, Park, CLUBB_SGS, SPCAM_sam1mom, SPCAM_m2005.
+<entry id="macrophys" valid_values="rk,park,clubb_sgs,none" value="">
+Macrophysics package: RK, Park, CLUBB_SGS.
 </entry>
 <entry id="clubb_sgs" valid_values="0,1" value="0">
 Switch to turn on CLUBB_SGS package: 0 => no, 1 => yes
@@ -83,9 +83,9 @@ Switch to turn on UNICON package: 0 => off, 1 => on
 <entry id="clubb_do_adv" valid_values="0,1" value="0">
 Switch to turn on/off advecting CLUBB moments: 0 => no, 1 => yes
 </entry>
-<entry id="pbl" valid_values="uw,hb,hbr,clubb_sgs,spcam_sam1mom,spcam_m2005,none" value="">
+<entry id="pbl" valid_values="uw,hb,hbr,clubb_sgs,none" value="">
 PBL package: uw (University of Washington), hb (Holtslag and Boville), hbr
- (Holtslag, Boville, and Rasch), clubb_sgs, spcam_sam1om, spcam_m2005, none.
+ (Holtslag, Boville, and Rasch), clubb_sgs, none.
 </entry>
 <entry id="rad" valid_values="rrtmgp,rrtmg,camrt,none" value="">
 Radiative transfer calculation:
@@ -144,15 +144,15 @@ Modifications that allow perturbation growth testing: 0=off, 1=on.
 </entry>
 <entry id="scam" valid_values="0,1" value="0">
 Configure CAM for single column mode and specify an IOP: 0=no, 1=yes.
-This option only supported for the Eulerian and SE dycores.
+This option only supported for the SE dycore.
 </entry>
 <entry id="scam_iop" valid_values="arm95,arm97,atex,bomex,cgilss11,cgilss12,cgilss6,dycomsrf01,dycomsrf02,gateiii,mpace,rico,sas,sparticus,togaii,twp06,camfrc,none" value="none">
 Single column IOP
-Supported for Eulerian and SE dycores.
+Only supported for SE dycore.
 </entry>
 <entry id="camiop" valid_values="0,1" value="0">
 Configure CAM to generate an IOP file that can be used to drive SCAM: 0=no, 1=yes.
-Supported for Eulerian and SE dycores.
+Only supported for SE dycore.
 </entry>
 <entry id="hgrid" value="">
 Horizontal grid specifier.  The recognized values depend on
@@ -191,15 +191,6 @@ Switch on (off) age of air tracers: 0=off, 1=on.
 Maximum number of constituents that are radiatively active or in any one
 diagnostic list.
 </entry>
-<entry id="trm" value="1">
-Maximum Fourier wavenumber.
-</entry>
-<entry id="trn" value="1">
-Highest degree of the Legendre polynomials for m=0.
-</entry>
-<entry id="trk" value="1">
-Highest degree of the associated Legendre polynomials.
-</entry>
 <entry id="pcols" value="16">
 Maximum number of columns in a chunk (physics data structure).
 </entry>
@@ -310,23 +301,5 @@ that setting to allow for cross-compilation, and for instances where the
 $OSNAME value is too generic.  For example, currently on both cray-xt and
 bluegene systems $OSNAME has the value "linux".
 </entry>
-<entry id="spcam_clubb_sgs" valid_values="0,1" value="0">
-Switch to turn on SPCAM version of CLUBB_SGS package: 0 => no, 1 => yes
-</entry>
-<entry id="spcam_nx" value="4">
-SPCAM number of grid points in x
-</entry>
-<entry id="spcam_ny" value="1">
-SPCAM number of grid points in y
-</entry>
-<entry id="spcam_nz" value="1">
-SPCAM number of grid points in z
-</entry>
-<entry id="spcam_dx" value="1">
-SPCAM horizontal grid spacing, m
-</entry>
-<entry id="spcam_dt" value="1">
-SPCAM time step, s
-</entry>
 
 </config_definition>
diff --git a/bld/config_files/horiz_grid.xml b/bld/config_files/horiz_grid.xml
@@ -2,15 +2,6 @@
 
 <config_horiz_grid>
 
-<horiz_grid dyn="eul"   hgrid="512x1024"  nlat="512" nlon="1024" m="341" n="341" k="341" />
-<horiz_grid dyn="eul"   hgrid="256x512"   nlat="256" nlon="512"  m="170" n="170" k="170" />
-<horiz_grid dyn="eul"   hgrid="128x256"   nlat="128" nlon="256"  m="85"  n="85"  k="85"  />
-<horiz_grid dyn="eul"   hgrid="64x128"    nlat="64"  nlon="128"  m="42"  n="42"  k="42"  />
-<horiz_grid dyn="eul"   hgrid="48x96"     nlat="48"  nlon="96"   m="31"  n="31"  k="31"  />
-<horiz_grid dyn="eul"   hgrid="32x64"     nlat="32"  nlon="64"   m="21"  n="21"  k="21"  />
-<horiz_grid dyn="eul"   hgrid="8x16"      nlat="8"   nlon="16"   m="5"   n="5"   k="5"   />
-<horiz_grid dyn="eul"   hgrid="1x1"       nlat="1"   nlon="1"    m="1"   n="1"   k="1"   />
-
 <horiz_grid dyn="fv"    hgrid="0.23x0.31"  nlat="768"  nlon="1152" />
 <horiz_grid dyn="fv"    hgrid="0.47x0.63"  nlat="384"  nlon="576"  />
 <horiz_grid dyn="fv"    hgrid="0.5x0.625"  nlat="361"  nlon="576"  />