Merge with the latest master, resolves conflict and redo non-cime sta…

…ndalone testing
E3SM-Project · Mar 22, 2024 · 5df69bd · 5df69bd
2 parents 9abfab4 + 815e4cd
commit 5df69bd
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,15 @@
+version: 2
+
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    assignees:
+      - "rljacob"
+    reviewers:
+      - "mahf708"
+      - "bartgol"
+    labels:
+      - "AT: Integrate Without Testing"
diff --git a/.github/workflows/e3sm-gh-ci-cime-tests.yml b/.github/workflows/e3sm-gh-ci-cime-tests.yml
@@ -0,0 +1,54 @@
+name: gh
+
+on:
+  pull_request:
+    branches: [ master ]
+
+  workflow_dispatch:
+
+jobs:
+
+  ci:
+    if: ${{ github.event.repository.name == 'e3sm' }}
+    runs-on: ubuntu-latest
+    strategy:
+      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
+          - ERP_P4.ne4pg2_oQU480.F2010.singularity_gnu
+          - PET_P4.ne4pg2_oQU480.F2010.singularity_gnu
+          - PEM_P4.ne4pg2_oQU480.F2010.singularity_gnu
+    container: 
+      image: ghcr.io/mahf708/e3sm-imgs:v0.0.6
+
+    steps:
+      - 
+        name: Checkout
+        uses: actions/checkout@v4
+        with:
+          show-progress: false
+          submodules: recursive
+      - 
+        name: CIME
+        working-directory: cime/scripts
+        run: |
+          mkdir -p $HOME/projects/e3sm/cesm-inputdata/atm/cam/physprops/
+          wget https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/p3_lookup_table_1.dat-v4.1.2
+          mv p3_lookup_table_1.dat-v4.1.2 $HOME/projects/e3sm/cesm-inputdata/atm/cam/physprops/
+          export USER=test
+          ./create_test ${{ matrix.test }} --wait --debug
+      - 
+        name: Artifacts
+        uses: actions/upload-artifact@v4
+        if: ${{ always() }}
+        with:
+          name: ${{ matrix.test }}
+          path: |
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/TestStatus.log
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/bld/*.bldlog.*
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/run/*.log.*
+            ~/projects/e3sm/scratch/${{ matrix.test }}*/run/*.cprnc.out
diff --git a/.github/workflows/e3sm-gh-pages.yml b/.github/workflows/e3sm-gh-pages.yml
@@ -15,23 +15,32 @@ concurrency:
 
 jobs:
   Build-and-Deploy-docs:
-    if: ${{ github.event.repository.name != 'scream' }}
+    if: ${{ github.event.repository.name == 'e3sm' }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
+          persist-credentials: false
           show-progress: false
           fetch-depth: 0 # Needed, or else gh-pages won't be fetched, and push rejected
-          submodules: false # speeds up clone and not building anything in submodules
+          # TODO: git rid of dependency on CIME
+          # TODO: another option to investigate is a sparse checkout. 
+          # In the scream repo, all other components do not need to be checked out. 
+          # And even in the upstream, we mainly need only components/xyz/docs (and a few more places).
+          submodules: true
       - name: Show action trigger
         run: echo "= The job was automatically triggered by a ${{github.event_name}} event on repo ${{github.event.repository.name}}."
       - name: Set up Python 3.10
-        uses: actions/setup-python@v4.7.0
+        uses: actions/setup-python@v5.0.0
         with:
           python-version: "3.10"
       - name: Install python deps
         run: python3 -m pip install mkdocs-material pymdown-extensions mkdocs-monorepo-plugin mdutils mkdocs-bibtex
       # build every time (PR or push to master)
+      - name: Generate EAMxx params docs
+        working-directory: components/eamxx/scripts
+        run: |
+          ./eamxx-params-docs-autogen
       - name: Build
         run: mkdocs build --strict --verbose
       # Only deploy to the main github page when there is a push to master

diff --git a/.github/workflows/gh-pages.yml → .github/workflows/eamxx-gh-pages.yml b/.github/workflows/gh-pages.yml → .github/workflows/eamxx-gh-pages.yml
@@ -21,6 +21,10 @@ on:
       - components/eamxx/docs/**
       - components/eamxx/cime_config/namelist_defaults_scream.xml
 
+  label:
+    types:
+      - created
+
   workflow_dispatch:
 
 concurrency:
@@ -30,12 +34,14 @@ concurrency:
 jobs:
 
   eamxx-docs:
+    if: ${{ github.event.repository.name == 'scream' }}
     runs-on: ubuntu-latest
 
     steps:
       - name: Check out the repository
         uses: actions/checkout@v4
         with:
+          persist-credentials: false
           show-progress: false
           # TODO: git rid of dependency on CIME
           # TODO: another option to investigate is a sparse checkout. 
@@ -48,7 +54,7 @@ jobs:
           echo "= The job was automatically triggered by a ${{github.event_name}} event."
 
       - name: Set up Python 3.10
-        uses: actions/setup-python@v4.7.0
+        uses: actions/setup-python@v5.0.0
         with:
           python-version: "3.10"
 

diff --git a/.github/workflows/eamxx_default_files.yml b/.github/workflows/eamxx_default_files.yml
@@ -21,7 +21,7 @@ jobs:
           show-progress: false
           submodules: false
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4.7.0
+        uses: actions/setup-python@v5.0.0
         with:
           python-version: "3.11"
       - name: Run unit tests

diff --git a/cime b/cime
diff --git a/cime_config/allactive/config_compsets.xml b/cime_config/allactive/config_compsets.xml
@@ -41,33 +41,33 @@
 
 <compset>
   <alias>WCYCL1850</alias>
-  <lname>1850SOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>WCYCL1850_chemUCI-Linozv3</alias>
-  <lname>1850SOI_EAM%CHEMUCI-LINOZV3_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CHEMUCI-LINOZV3_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>WCYCL1850_chemUCI-Linozv3-mam5</alias>
-  <lname>1850SOI_EAM%CHEMUCI-LINOZV3-MAM5_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CHEMUCI-LINOZV3-MAM5_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>WCYCL1850-1pctCO2</alias>
-  <lname>1850SOI_EAM%CMIP6-1pctCO2_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6-1pctCO2_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>WCYCL1850-4xCO2</alias>
-  <lname>1850SOI_EAM%CMIP6-4xCO2_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6-4xCO2_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <!-- WCYCL1850NS uses no spun-up ICs for mpaso and mpassi. It is only being used for nigthly tests on small grids such as ne11_oQU480-->
 <compset>
   <alias>WCYCL1850NS</alias>
-  <lname>1850_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>1850_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
@@ -77,7 +77,7 @@
 
 <compset>
   <alias>WCYCL20TR</alias>
-  <lname>20TRSOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>20TRSOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <!-- ************************************************ -->
@@ -108,7 +108,7 @@
 
 <compset>
   <alias>WCYCL20TR_chemUCI-Linozv3-mam5</alias>
-  <lname>20TRSOI_EAM%CHEMUCI-LINOZV3-MAM5_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>20TRSOI_EAM%CHEMUCI-LINOZV3-MAM5_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>

diff --git a/cime_config/allactive/config_pesall.xml b/cime_config/allactive/config_pesall.xml
@@ -107,7 +107,7 @@
         </nthrds>
       </pes>
     </mach>
-    <mach name="theta|pm-cpu|alvarez|pm-gpu|muller|jlse">
+    <mach name="theta|pm-cpu|muller-cpu|alvarez|pm-gpu|muller-gpu|jlse">
       <pes compset="any" pesize="any">
         <comment>allactive: default, 1 node x MAX_MPITASKS_PER_NODE mpi x 1 omp @ root 0</comment>
         <ntasks>
@@ -263,7 +263,7 @@
   <!-- 2000_DATM%JRA_ELM%SPBC_MPASSI_MPASO%DATMFORCED_MOSART_SGLC_SWAV_SIAC_SESP -->
   <!-- ATM_GRID is ne30np4.pg2  ICE_GRID is EC30to60E2r2 -->
   <grid name="a%ne30np4">
-    <mach name="pm-cpu|alvarez">
+    <mach name="pm-cpu|muller-cpu|alvarez">
       <pes compset="JRA_ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV" pesize="any">
         <comment>"pm-cpu 4 nodes, 256 partition, 128x1"</comment>
         <ntasks>
@@ -547,7 +547,7 @@
     </mach>
   </grid>
   <grid name="a%ne120np4">
-    <mach name="pm-cpu|alvarez">
+    <mach name="pm-cpu|muller-cpu|alvarez">
       <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.*" pesize="any">
         <comment>ne120-wcycl on 42 nodes 128x1 ~0.7 sypd</comment>
         <MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
@@ -1244,7 +1244,7 @@
         </rootpe>
       </pes>
     </mach>
-    <mach name="pm-cpu|alvarez">
+    <mach name="pm-cpu|muller-cpu|alvarez">
       <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+" pesize="any">
         <comment> -compset A_WCYCL* -res ne30pg2_oECv3 with MPASO on 7 nodes, 128x1 </comment>
         <MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
@@ -1460,6 +1460,78 @@
       </pes>
     </mach>
   </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">
+        <comment> --compset WCYCL* --res ne30pg2_r05_IcoswISC30E3r5 on 4 nodes pure-MPI, ~1.5 sypd </comment>
+        <ntasks>
+          <ntasks_atm>-4</ntasks_atm>
+          <ntasks_cpl>-4</ntasks_cpl>
+          <ntasks_ocn>-4</ntasks_ocn>
+          <ntasks_ice>-4</ntasks_ice>
+          <ntasks_rof>-4</ntasks_rof>
+          <ntasks_lnd>-4</ntasks_lnd>
+        </ntasks>
+      </pes>
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+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>
+          <ntasks_cpl>1024</ntasks_cpl>
+          <ntasks_ocn>256</ntasks_ocn>
+          <ntasks_ice>640</ntasks_ice>
+          <ntasks_rof>384</ntasks_rof>
+          <ntasks_lnd>385</ntasks_lnd>
+        </ntasks>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_cpl>0</rootpe_cpl>
+          <rootpe_ocn>1024</rootpe_ocn>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_rof>640</rootpe_rof>
+          <rootpe_lnd>640</rootpe_lnd>
+        </rootpe>
+      </pes>
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+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>
+          <ntasks_cpl>2752</ntasks_cpl>
+          <ntasks_ocn>704</ntasks_ocn>
+          <ntasks_ice>2048</ntasks_ice>
+          <ntasks_rof>704</ntasks_rof>
+          <ntasks_lnd>704</ntasks_lnd>
+        </ntasks>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_cpl>0</rootpe_cpl>
+          <rootpe_ocn>2752</rootpe_ocn>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_rof>2048</rootpe_rof>
+          <rootpe_lnd>2048</rootpe_lnd>
+        </rootpe>
+      </pes>
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+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>
+          <ntasks_cpl>5440</ntasks_cpl>
+          <ntasks_ocn>1280</ntasks_ocn>
+          <ntasks_ice>4352</ntasks_ice>
+          <ntasks_rof>1088</ntasks_rof>
+          <ntasks_lnd>1088</ntasks_lnd>
+        </ntasks>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_cpl>0</rootpe_cpl>
+          <rootpe_ocn>5440</rootpe_ocn>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_rof>4352</rootpe_rof>
+          <rootpe_lnd>4352</rootpe_lnd>
+        </rootpe>
+      </pes>
+    </mach>
+  </grid>
   <grid name="a%ne30np4.pg.+_oi%EC30to60E2r2">
     <mach name="chrysalis">
       <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="XS">
@@ -1720,7 +1792,7 @@
     </mach>
   </grid>
   <grid name="a%ne30np4">
-    <mach name="pm-gpu|muller">
+    <mach name="pm-gpu|muller-gpu">
       <pes compset="any" pesize="any">
         <comment>"pm-gpu ne30np4 and ne30np4.pg2  2 nodes, 4x16"</comment>
         <ntasks>
@@ -1743,7 +1815,7 @@
         </nthrds>
       </pes>
     </mach>
-    <mach name="pm-cpu|alvarez">
+    <mach name="pm-cpu|muller-cpu|alvarez">
       <pes compset="any" pesize="any">
         <comment>"pm-cpu ne30np4 and ne30np4.pg2 2 nodes 1 thread, 128x1"</comment>
         <ntasks>
@@ -2078,7 +2150,7 @@
         </rootpe>
       </pes>
     </mach>
-    <mach name="pm-cpu|alvarez">
+    <mach name="pm-cpu|muller-cpu|alvarez">
       <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+" pesize="any">
         <comment> 8 nodes, 128x1</comment>
         <ntasks>
@@ -2311,19 +2383,18 @@
         </nthrds>
       </pes>
     </mach>
-    <mach name="pm-gpu|muller">
+    <mach name="pm-gpu|muller-gpu">
       <pes compset="any" pesize="any">
+        <comment>pm-gpu conus 2 nodes, 4x1 except 16 threads in LND</comment>
         <MAX_MPITASKS_PER_NODE>4</MAX_MPITASKS_PER_NODE>
         <MAX_TASKS_PER_NODE>16</MAX_TASKS_PER_NODE>
         <ntasks>
-          <ntasks_atm>-4</ntasks_atm>
-          <ntasks_lnd>-4</ntasks_lnd>
-          <ntasks_rof>-4</ntasks_rof>
-          <ntasks_ice>-4</ntasks_ice>
-          <ntasks_ocn>-4</ntasks_ocn>
-          <ntasks_glc>-4</ntasks_glc>
-          <ntasks_wav>-4</ntasks_wav>
-          <ntasks_cpl>-4</ntasks_cpl>
+          <ntasks_atm>-2</ntasks_atm>
+          <ntasks_lnd>-2</ntasks_lnd>
+          <ntasks_rof>-2</ntasks_rof>
+          <ntasks_ice>-2</ntasks_ice>
+          <ntasks_ocn>-2</ntasks_ocn>
+          <ntasks_cpl>-2</ntasks_cpl>
         </ntasks>
         <nthrds>
           <nthrds_atm>1</nthrds_atm>