Merge pull request #2961 from E3SM-Project/jgfouca/upstream_merge_202…

…4_08_22 Jgfouca/upstream merge 2024 08 22
E3SM-Project · Aug 23, 2024 · edd1e20 · edd1e20
2 parents 3b9ff73 + b624485
commit edd1e20
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diff --git a/.github/workflows/e3sm-gh-ci-cime-tests.yml b/.github/workflows/e3sm-gh-ci-cime-tests.yml
@@ -27,16 +27,16 @@ jobs:
       fail-fast: false
       matrix:
         test: 
-          - SMS_D_P4.ne4pg2_oQU480.F2010.singularity_gnu
-          - SMS_P4.ne4pg2_oQU480.F2010.singularity_gnu
-          - REP_P4.ne4pg2_oQU480.F2010.singularity_gnu
-          - ERS_P4.ne4pg2_oQU480.F2010.singularity_gnu
-          - ERS_P4.ne4pg2_oQU480.F2010.singularity_gnu.eam-wcprod_F2010
-          - ERP_P4.ne4pg2_oQU480.F2010.singularity_gnu
-          - PET_P4.ne4pg2_oQU480.F2010.singularity_gnu
-          - PEM_P4.ne4pg2_oQU480.F2010.singularity_gnu
+          - SMS_D_P4.ne4pg2_oQU480.F2010.singularity2_gnu
+          - SMS_P4.ne4pg2_oQU480.F2010.singularity2_gnu
+          - REP_P4.ne4pg2_oQU480.F2010.singularity2_gnu
+          - ERS_P4.ne4pg2_oQU480.F2010.singularity2_gnu
+          - ERS_P4.ne4pg2_oQU480.F2010.singularity2_gnu.eam-wcprod_F2010
+          - ERP_P4.ne4pg2_oQU480.F2010.singularity2_gnu
+          - PET_P4.ne4pg2_oQU480.F2010.singularity2_gnu
+          - PEM_P4.ne4pg2_oQU480.F2010.singularity2_gnu
     container: 
-      image: ghcr.io/mahf708/e3sm-imgs:v0.0.6
+      image: ghcr.io/mahf708/e3sm-imgs:v0.0.9
 
     steps:
       - 

diff --git a/.github/workflows/e3sm-gh-ci-w-cime-tests.yml b/.github/workflows/e3sm-gh-ci-w-cime-tests.yml
@@ -20,16 +20,16 @@ jobs:
       fail-fast: false
       matrix:
         test: 
-          - SMS_D_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
-          - SMS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
-          - REP_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
-          - ERS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
-          - ERS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu.allactive-wcprod_1850
-          - ERP_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
-          - PET_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
-          - PEM_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
+          - SMS_D_P8.ne4pg2_oQU480.WCYCL2010NS.singularity2_gnu
+          - SMS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity2_gnu
+          - REP_P8.ne4pg2_oQU480.WCYCL2010NS.singularity2_gnu
+          - ERS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity2_gnu
+          - ERS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity2_gnu.allactive-wcprod_1850
+          - ERP_P8.ne4pg2_oQU480.WCYCL2010NS.singularity2_gnu
+          - PET_P8.ne4pg2_oQU480.WCYCL2010NS.singularity2_gnu
+          - PEM_P8.ne4pg2_oQU480.WCYCL2010NS.singularity2_gnu
     container: 
-      image: ghcr.io/mahf708/e3sm-imgs:v0.0.6
+      image: ghcr.io/mahf708/e3sm-imgs:v0.0.9
 
     steps:
       - 

diff --git a/.github/workflows/e3sm-gh-md-linter.yml b/.github/workflows/e3sm-gh-md-linter.yml
@@ -7,6 +7,8 @@ on:
     branches: ["master"]
     paths:
         - '**/*.md'
+        # for now let's not lint files in eamxx
+        - '!components/eamxx/**/*.md'
 
 jobs:
   linter:

diff --git a/cime b/cime
diff --git a/cime_config/allactive/config_compsets.xml b/cime_config/allactive/config_compsets.xml
@@ -421,6 +421,11 @@
   <lname>2000_DATM%JRA-1p5_SLND_MPASSI_MPASO%DATMFORCED_DROF%JRA-1p5_MALI%SIA_SWAV</lname>
 </compset>
 
+<compset>
+  <alias>MPAS_FOLISIO_JRA1p5</alias>
+  <lname>2000_DATM%JRA-1p5_SLND_MPASSI_MPASO%DATMFORCED_DROF%JRA-1p5_MALI_SWAV</lname>
+</compset>
+
 <!-- Slab ocean cases -->
 <compset>
   <alias>E1850C5ELM</alias>

diff --git a/cime_config/allactive/config_pesall.xml b/cime_config/allactive/config_pesall.xml
@@ -1253,7 +1253,7 @@
   </grid>
   <grid name="a%ne30np4.pg2_l%r05_oi%IcoswISC30E3r5_r%r05_.+">
     <mach name="chrysalis">
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="T">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="T">
         <comment> --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 4 nodes pure-MPI, ~1.5 sypd </comment>
         <ntasks>
           <ntasks_atm>-4</ntasks_atm>
@@ -1264,7 +1264,7 @@
           <ntasks_lnd>-4</ntasks_lnd>
         </ntasks>
       </pes>
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="S">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="S">
         <comment> --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 20 nodes pure-MPI, ~7.25 sypd </comment>
         <ntasks>
           <ntasks_atm>1024</ntasks_atm>
@@ -1283,7 +1283,7 @@
           <rootpe_lnd>640</rootpe_lnd>
         </rootpe>
       </pes>
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="M">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="M">
         <comment> --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 54 nodes pure-MPI, ~17.5 sypd </comment>
         <ntasks>
           <ntasks_atm>2752</ntasks_atm>
@@ -1302,7 +1302,7 @@
           <rootpe_lnd>2048</rootpe_lnd>
         </rootpe>
       </pes>
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="L">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="L">
         <comment> --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 105 nodes pure-MPI, ~27.7 sypd </comment>
         <ntasks>
           <ntasks_atm>5440</ntasks_atm>
@@ -1322,8 +1322,67 @@
         </rootpe>
       </pes>
     </mach>
+    <mach name="anvil">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+_SESP$" pesize="S">
+        <comment> --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 25 nodes pure-MPI, ~2.9 sypd </comment>
+        <ntasks>
+          <ntasks_atm>675</ntasks_atm>
+          <ntasks_lnd>324</ntasks_lnd>
+          <ntasks_rof>324</ntasks_rof>
+          <ntasks_ice>360</ntasks_ice>
+          <ntasks_ocn>216</ntasks_ocn>
+          <ntasks_cpl>684</ntasks_cpl>
+        </ntasks>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_lnd>360</rootpe_lnd>
+          <rootpe_rof>360</rootpe_rof>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_ocn>684</rootpe_ocn>
+          <rootpe_cpl>0</rootpe_cpl>
+        </rootpe>
+      </pes>
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+_SESP$" pesize="M">
+        <comment> --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 50 nodes pure-MPI, ~5.6 sypd </comment>
+        <ntasks>
+          <ntasks_atm>1350</ntasks_atm>
+          <ntasks_lnd>648</ntasks_lnd>
+          <ntasks_rof>648</ntasks_rof>
+          <ntasks_ice>720</ntasks_ice>
+          <ntasks_ocn>432</ntasks_ocn>
+          <ntasks_cpl>1368</ntasks_cpl>
+        </ntasks>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_lnd>720</rootpe_lnd>
+          <rootpe_rof>720</rootpe_rof>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_ocn>1368</rootpe_ocn>
+          <rootpe_cpl>0</rootpe_cpl>
+        </rootpe>
+      </pes>
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+_SESP$" pesize="L">
+        <comment> --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 100 nodes pure-MPI, ~8.8 sypd </comment>
+        <ntasks>
+          <ntasks_atm>2700</ntasks_atm>
+          <ntasks_lnd>1260</ntasks_lnd>
+          <ntasks_rof>1260</ntasks_rof>
+          <ntasks_ice>1440</ntasks_ice>
+          <ntasks_ocn>900</ntasks_ocn>
+          <ntasks_cpl>2700</ntasks_cpl>
+        </ntasks>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_lnd>1440</rootpe_lnd>
+          <rootpe_rof>1440</rootpe_rof>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_ocn>2700</rootpe_ocn>
+          <rootpe_cpl>0</rootpe_cpl>
+        </rootpe>
+      </pes>
+    </mach>
     <mach name="gcp12">
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="any">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="any">
         <comment> gcp12 --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 4 nodes </comment>
         <ntasks>
           <ntasks_atm>-4</ntasks_atm>
@@ -1336,7 +1395,7 @@
       </pes>
     </mach>
     <mach name="pm-cpu|muller-cpu|alvarez">
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="any">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="any">
         <comment> pm-cpu --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 8 nodes, stacked layout, 128x1 4-5 sypd</comment>
         <MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
         <ntasks>
@@ -1356,7 +1415,7 @@
           <nthrds_cpl>1</nthrds_cpl>
         </nthrds>
       </pes>
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="L">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="L">
         <comment> pm-cpu --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 30 nodes, 128x1 ~15 sypd</comment>
         <MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
         <ntasks>
@@ -1384,7 +1443,7 @@
           <rootpe_cpl>0</rootpe_cpl>
         </rootpe>
       </pes>
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="XL">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="XL">
         <comment> pm-cpu: -compset WCYCL* -res ne30pg2_r05_IcoswISC30E3r5 on 61 nodes, 120x1, ~23 sypd</comment>
         <MAX_MPITASKS_PER_NODE>120</MAX_MPITASKS_PER_NODE>
         <ntasks>
@@ -1416,7 +1475,7 @@
   </grid>
   <grid name="a%ne30np4.pg2_l%r05_oi%IcosXISC30E3r7_r%r05_.+">
     <mach name="chrysalis">
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="S">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="S">
         <comment> --compset WCYCL* --res ne30pg2_r05_IcosXISC30E3r7 on 20 nodes pure-MPI, ~7.25 sypd </comment>
         <ntasks>
           <ntasks_atm>1024</ntasks_atm>
@@ -1435,7 +1494,7 @@
           <rootpe_lnd>640</rootpe_lnd>
         </rootpe>
       </pes>
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="M">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="M">
         <comment> --compset WCYCL* --res ne30pg2_r05_IcosXISC30E3r7 on 54 nodes pure-MPI, ~17.5 sypd </comment>
         <ntasks>
           <ntasks_atm>2752</ntasks_atm>
@@ -1454,7 +1513,7 @@
           <rootpe_lnd>2048</rootpe_lnd>
         </rootpe>
       </pes>
-      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="L">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="L">
         <comment> --compset WCYCL* --res ne30pg2_r05_IcosXISC30E3r7 on 105 nodes pure-MPI, ~27.7 sypd </comment>
         <ntasks>
           <ntasks_atm>5440</ntasks_atm>
@@ -2442,4 +2501,42 @@
       </pes>
     </mach>
   </grid>
+  <grid name="a%ne30np4.pg2_l%r05_oi%IcoswISC30E3r5_r%r05_g%mpas.gis20km_w%null_z%null_m%IcoswISC30E3r5">
+    <mach name="chrysalis|pm-cpu|alvarez">
+      <pes compset="1850_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_MALI_SWAV" pesize="any">
+        <comment>GIS 20km (low-res) testing config</comment>
+        <MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
+        <MAX_TASKS_PER_NODE>128</MAX_TASKS_PER_NODE>
+        <ntasks>
+          <ntasks_atm>512</ntasks_atm>
+          <ntasks_lnd>512</ntasks_lnd>
+          <ntasks_rof>512</ntasks_rof>
+          <ntasks_ice>512</ntasks_ice>
+          <ntasks_ocn>512</ntasks_ocn>
+          <ntasks_glc>256</ntasks_glc>
+          <ntasks_wav>512</ntasks_wav>
+          <ntasks_cpl>512</ntasks_cpl>
+        </ntasks>
+        <nthrds>
+          <nthrds_atm>1</nthrds_atm>
+          <nthrds_lnd>1</nthrds_lnd>
+          <nthrds_rof>1</nthrds_rof>
+          <nthrds_ice>1</nthrds_ice>
+          <nthrds_ocn>1</nthrds_ocn>
+          <nthrds_glc>1</nthrds_glc>
+          <nthrds_wav>1</nthrds_wav>
+          <nthrds_cpl>1</nthrds_cpl>
+        </nthrds>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_lnd>0</rootpe_lnd>
+          <rootpe_rof>0</rootpe_rof>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_ocn>0</rootpe_ocn>
+          <rootpe_glc>0</rootpe_glc>
+          <rootpe_cpl>0</rootpe_cpl>
+        </rootpe>
+      </pes>
+    </mach>
+  </grid>
 </config_pes>
diff --git a/cime_config/config_archive.xml b/cime_config/config_archive.xml
@@ -117,7 +117,7 @@
     </test_file_names>
   </comp_archive_spec>
 
-  <comp_archive_spec compname="mali" compclass="glc" exclude_testing="true">
+  <comp_archive_spec compname="mali" compclass="glc">
     <rest_file_extension>rst</rest_file_extension>
     <hist_file_extension>hist</hist_file_extension>
     <rest_history_varname>unset</rest_history_varname>

diff --git a/cime_config/config_files.xml b/cime_config/config_files.xml
@@ -351,6 +351,7 @@
       <value component="mpaso"    >$COMP_ROOT_DIR_OCN/cime_config/testdefs/testmods_dirs</value>
       <value component="mpassi"   >$COMP_ROOT_DIR_ICE/cime_config/testdefs/testmods_dirs</value>
       <value component="ww3"      >$COMP_ROOT_DIR_WAV/cime_config/testdefs/testmods_dirs</value>
+      <value component="mali"      >$COMP_ROOT_DIR_GLC/cime_config/testdefs/testmods_dirs</value>
     </values>
     <group>case_last</group>
     <file>env_case.xml</file>
+86 −22		.github/scripts/ghcr-prune.py
+20 −12		.github/workflows/docs.yml
+3 −7		.github/workflows/ghcr-prune.yml
+2 −1		.github/workflows/testing.yml
+1 −0		.gitignore
+2 −0		.pre-commit-config.yaml
+1 −1		CIME/ParamGen/xml_schema/entry_id_pg.xsd
+6 −2		CIME/SystemTests/eri.py
+2 −2		CIME/SystemTests/system_tests_common.py
+4 −1		CIME/Tools/check_case
+2 −1		CIME/Tools/check_lockedfiles
+28 −26		CIME/Tools/xmlchange
+1 −8		CIME/XML/archive_base.py
+8 −3		CIME/XML/env_batch.py
+30 −15		CIME/XML/grids.py
+1 −1		CIME/XML/test_reporter.py
+8 −6		CIME/build.py
+0 −5		CIME/case/case.py
+12 −2		CIME/case/case_run.py
+18 −9		CIME/case/case_setup.py
+0 −4		CIME/case/case_st_archive.py
+19 −10		CIME/case/case_submit.py
+0 −151		CIME/case/check_lockedfiles.py
+4 −1		CIME/config.py
+56 −77		CIME/data/config/cesm/config_files.xml
+0 −6		CIME/hist_utils.py
+185 −8		CIME/locked_files.py
+1 −1		CIME/non_py/cprnc
+1 −1		CIME/tests/base.py
+6 −4		CIME/tests/test_sys_cime_case.py
+4 −1		CIME/tests/test_sys_create_newcase.py
+3 −1		CIME/tests/test_sys_full_system.py
+1 −1		CIME/tests/test_unit_case.py
+55 −0		CIME/tests/test_unit_config.py
+344 −0		CIME/tests/test_unit_locked_files.py
+3 −1		CIME/utils.py
+4 −2		CIME/wait_for_tests.py
+0 −1		doc/requirements.txt
+0 −15		doc/source/_static/custom.css
+0 −23		doc/source/_static/pop_ver.js
+0 −3		doc/source/_templates/layout.html
+64 −0		doc/source/_templates/versions.html
+27 −13		doc/source/conf.py
+10 −13		doc/source/users_guide/cime-dir.rst
+62 −0		doc/source/users_guide/components.rst
+31 −25		doc/source/users_guide/create-a-case.rst
+4 −4		doc/source/users_guide/index.rst
+53 −21		doc/source/users_guide/introduction-and-overview.rst
+29 −7		doc/source/users_guide/setting-up-a-case.rst
+245 −170		doc/source/users_guide/testing.rst
+7 −4		doc/source/what_cime/index.rst
+3 −0		docker/Dockerfile