Jgfouca/upstream merge 2024 11 14

.github/workflows/e3sm-gh-ci-cime-tests.yml

@@ -22,10 +22,14 @@ on:
 
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
+  cancel-in-progress: true
+
 jobs:
 
   ci:
-    if: false
+    if: ${{ github.repository == 'E3SM-Project/E3SM' }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -36,7 +40,7 @@ jobs:
           - SMS_D_Ln5_P4.ne4pg2_oQU480.F2010-SCREAMv1-MPASSI.ghci-oci_gnu
           - ERS_Ld5_P4.ne4pg2_oQU480.F2010-SCREAMv1-MPASSI.ghci-oci_gnu.eamxx-prod
     container: 
-      image: ghcr.io/e3sm-project/containers-ghci:ghci-0.1.0
+      image: ghcr.io/e3sm-project/containers-ghci:ghci-0.2.0
 
     steps:
       - 

.github/workflows/e3sm-gh-ci-w-cime-tests.yml

@@ -1,4 +1,4 @@
-name: gh
+name: gh-w
 
 on:
   pull_request:
@@ -11,10 +11,14 @@ on:
 
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
+  cancel-in-progress: true
+
 jobs:
 
-  ci-w:
-    if: ${{ github.event.repository.name == 'e3sm' }}
+  ci:
+    if: ${{ github.repository == 'E3SM-Project/E3SM' }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -23,7 +27,7 @@ jobs:
           - SMS_D_Ld1_P8.ne4pg2_oQU480.WCYCL2010NS.ghci-oci_gnu
           - ERS_Ld3_P8.ne4pg2_oQU480.WCYCL2010NS.ghci-oci_gnu.allactive-wcprod_1850
     container: 
-      image: ghcr.io/e3sm-project/containers-ghci:ghci-0.1.0
+      image: ghcr.io/e3sm-project/containers-ghci:ghci-0.2.0
 
     steps:
       - 

.github/workflows/e3sm-gh-md-linter.yml

@@ -10,8 +10,13 @@ on:
         # for now let's not lint files in eamxx
         - '!components/eamxx/**/*.md'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
+  cancel-in-progress: true
+
 jobs:
   linter:
+    if: ${{ github.repository == 'E3SM-Project/E3SM' }}
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4

.github/workflows/e3sm-gh-pages.yml

@@ -15,7 +15,7 @@ concurrency:
 
 jobs:
   Build-and-Deploy-docs:
-    if: ${{ github.event.repository.name == 'e3sm' }}
+    if: ${{ github.repository == 'E3SM-Project/E3SM' }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

.github/workflows/e3sm-gh-tools-mkatmsrffile-test.yml

@@ -11,8 +11,13 @@ on:
     - cron: '00 15 * * 2'
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
+  cancel-in-progress: true
+
 jobs:
   mkatmsrffile-test:
+    if: ${{ github.repository == 'E3SM-Project/E3SM' }}
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -31,18 +36,15 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: "envmkatmsrffile"
-          miniforge-variant: Mambaforge
           miniforge-version: latest
-          use-mamba: true
-          mamba-version: "*"
           channel-priority: strict
           auto-update-conda: true
           python-version: 3.11
       - 
         name: Install dependencies
         run: |
           echo $CONDA_PREFIX
-          mamba install -y nco xarray numba numpy netcdf4
+          conda install -y nco xarray numba numpy netcdf4 -c conda-forge
       - 
         name: Run tests
         working-directory: components/eam/tools/mkatmsrffile

.github/workflows/eamxx-gh-ci-standalone.yml

@@ -0,0 +1,60 @@
+name: gh-standalone
+
+on:
+  pull_request:
+    branches: [ master ]
+    paths:
+      # first, yes to these
+      - '.github/workflows/eamxx-gh-ci-standalone.yml'
+      - 'cime_config/machine/config_machines.xml'
+      - 'components/eamxx/**'
+      - 'components/homme/**'
+      # second, no to these
+      - '!components/eamxx/docs/**'
+      - '!components/eamxx/mkdocs.yml'
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+
+  ci:
+    if: ${{ github.repository == 'E3SM-Project/E3SM' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        test:
+          - sp
+          - opt
+          - dbg
+          - fpe
+    container: 
+      image: ghcr.io/e3sm-project/containers-standalone-ghci:standalone-ghci-0.1.0
+
+    steps:
+      - 
+        name: Checkout
+        uses: actions/checkout@v4
+        with:
+          show-progress: false
+          submodules: recursive
+      - 
+        name: standalone
+        env:
+          SHELL: sh
+        run: |
+          # TODO: get rid of this extra line if we can?
+          git config --global safe.directory '*'
+          ./components/eamxx/scripts/test-all-scream -m ghci-oci -t ${{ matrix.test }} -c BUILD_SHARED_LIBS=ON
+      - 
+        name: Artifacts
+        uses: actions/upload-artifact@v4
+        if: ${{ always() }}
+        with:
+          name: ${{ matrix.test }}
+          path: |
+            components/eamxx/ctest-build/*/Testing/Temporary/Last*.log

.github/workflows/eamxx-gh-pages.yml

@@ -34,7 +34,7 @@ concurrency:
 jobs:
 
   eamxx-docs:
-    if: ${{ github.event.repository.name == 'scream' }}
+    if: ${{ github.repository == 'E3SM-Project/scream' }}
     runs-on: ubuntu-latest
 
     steps:

.github/workflows/eamxx_default_files.yml

@@ -11,9 +11,13 @@ on:
     - cron: '00 00 * * *'
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
+  cancel-in-progress: true
+
 jobs:
   scream-defaults:
-    if: false
+    if: ${{ github.repository == 'E3SM-Project/E3SM' }}
     runs-on: ubuntu-latest
     outputs:
       event_name: ${{ github.event_name }}

CITATION.cff

@@ -9,7 +9,7 @@ authors:
   - given-names: E3SM
     family-names: Project
 version: 3.0.0
-doi: 10.11578/E3SM/dc.20240301.3
+doi: 10.11578/E3SM/dc.20240930.1
 repository-code: 'https://github.com/E3SM-Project/E3SM'
 url: 'https://e3sm.org'
 license: BSD-3-Clause

LICENSE

@@ -2,7 +2,7 @@ Except for the separable pieces descibed below, E3SM is released
 under the following 3-Clause BSD Open Source license.
 
 *******************************************************************************
-Copyright ©2023, UChicago Argonne, LLC All Rights Reserved
+Copyright 2024, UChicago Argonne, LLC All Rights Reserved
 
 Software Name: Energy Exascale Earth System Model (E3SM)
 
@@ -55,15 +55,29 @@ GPTL            share/timing                    author              non-commeric
 MCT             externals/mct                   ANL                 BSD
 YAKL		externals/YAKL			author              BSD
 cub		externals/cub                   author, NVIDIA      BSD
-kokkos          externals/kokkos                SNL                 BSD
+kokkos          externals/ekat                  SNL                 BSD
+haero           externals/haero                 SNL/Battelle        BSD
+mam4xx          externals/mam4xx                SNL/Battelle        BSD
 
 Ocean/Ice       under components/
 -----------     -----------------
 CICE            cice                            LANL                BSD
 MPAS Framework  mpas-framework                  LANL                BSD
-MPAS Ocean      mpas-ocean                      LANL                BSD
-MPAS SeaIce     mpas-seaice                     LANL                BSD
-MPAS-Albany LandIce   mpas-albany-landice       LANL, SNL           BSD
+FFTW            mpas-ocean/src/FFTW             author/MIT          GPL
+MARBL           mpas-ocean/src/MARBL            NCAR                BSD
+SHTNS           mpas-ocean/src/SHTNS            CeCILL              GPL
+cvmix           mpas-ocean/src/cvmix            NCAR                LGPL
+gotm            mpas-ocean/src/gotm             authors             GPL
+ppr             mpas-ocean/src/ppr              author              custom
+Icepack         mpas-seaice/src/icepack         LANL                BSD
+
+Waves           under components/ww3
+-----------     --------------------
+WW3             src/WW3                         NWS/NOAA            custom
+
+Land-ice        under components/mpas-albany-landice
+-----------     ------------------------------------
+SeaLevelModel   src/SeaLevelModel               author              MIT
 
 Land            under components/elm/src
 -----------     ------------------------
@@ -91,7 +105,7 @@ HOMMEXX         components/homme/src/share/cxx  SNL                 BSD
 
 Actual copyright holder for above Institutions:
 NCAR =  University Corporation for Atmospheric Research
-LANL =  Los Alamos National Security, LLC
+LANL =  Los Alamos National Security, LLC, Triad National Security, LLC
 SNL  =  National Technology & Engineering Solutions of Sandia, LLC 
 LBNL =  The Regents of the University of California, 
         through Lawrence Berkeley National Laboratory

README.md

@@ -1,3 +1,5 @@
+<!-- markdownlint-disable -->
+
 [![E3SM Logo](https://e3sm.org/wp-content/themes/e3sm/assets/images/e3sm-logo.png)](https://e3sm.org)
 
 Energy Exascale Earth System Model (E3SM)
@@ -9,14 +11,14 @@ the most challenging and demanding climate-change research problems and
 Department of Energy mission needs while efficiently using DOE Leadership
 Computing Facilities.  
 
-DOI: [10.11578/E3SM/dc.20240301.3](http://dx.doi.org/10.11578/E3SM/dc.20240301.3)
+DOI: [10.11578/E3SM/dc.20240930.1](http://dx.doi.org/10.11578/E3SM/dc.20240930.1)
 
 Please visit the [project website](https://e3sm.org) or our [Confluence site](https://acme-climate.atlassian.net/wiki/spaces/DOC/overview)
 for further details.
 
 For questions about the model, use [Github Discussions](https://github.com/E3SM-Project/E3SM/discussions).
 
-See our Github-hosted documentation at [https://e3sm-project.github.io/E3SM/](https://e3sm-project.github.io/E3SM/).
+See our Github-hosted documentation at [https://docs.e3sm.org/E3SM](https://docs.e3sm.org/E3SM/).
 
 Table of Contents 
 --------------------------------------------------------------------------------

cime_config/allactive/config_compsets.xml

@@ -383,42 +383,52 @@
 
 <compset>
   <alias>CRYO1850</alias>
-  <lname>1850SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYO1850-4xCO2</alias>
-  <lname>1850SOI_EAM%CMIP6-4xCO2_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6-4xCO2_ELM%CNPRDCTCBCTOP_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>CRYO1850-1pctCO2</alias>
+  <lname>1850SOI_EAM%CMIP6-1pctCO2_ELM%CNPRDCTCBCTOP_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYO1950</alias>
-  <lname>1950SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
+  <lname>1950SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYO1850-DISMF</alias>
-  <lname>1850SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBDISMF_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI%DIB_MPASO%IBDISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYO1950-DISMF</alias>
-  <lname>1950SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBDISMF_MOSART_SGLC_SWAV</lname>
+  <lname>1950SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI%DIB_MPASO%IBDISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYO20TR</alias>
-  <lname>20TRSOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
+  <lname>20TRSOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>CRYOSSP245</alias>
+  <lname>SSP245SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYOSSP585</alias>
-  <lname>SSP585SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
+  <lname>SSP585SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYOSSP370</alias>
-  <lname>SSP370SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
+  <lname>SSP370SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>

cime_config/allactive/config_pesall.xml

@@ -843,6 +843,29 @@
       </pes>
     </mach>
   </grid>
+  <grid name="a%ne30np4.pg2_l%.+_oi%SOwISC12to30E3r3">
+    <mach name="chrysalis">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="M">
+        <comment> -compset WCYCL*/CRYO* -res SOwISC12to30E3r3* on 52 nodes pure-MPI, ~8.5 sypd </comment>
+        <ntasks>
+          <ntasks_atm>1408</ntasks_atm>
+          <ntasks_lnd>384</ntasks_lnd>
+          <ntasks_rof>384</ntasks_rof>
+          <ntasks_ice>1024</ntasks_ice>
+          <ntasks_ocn>1920</ntasks_ocn>
+          <ntasks_cpl>1408</ntasks_cpl>
+        </ntasks>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_lnd>1024</rootpe_lnd>
+          <rootpe_rof>1024</rootpe_rof>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_ocn>1408</rootpe_ocn>
+          <rootpe_cpl>0</rootpe_cpl>
+        </rootpe>
+      </pes>
+    </mach>
+  </grid>
   <grid name="a%ne30np4.pg2_l%.+_oi%ECwISC30to60E2r1">
     <mach name="anvil">
       <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="M">
@@ -1774,6 +1797,21 @@
         </ntasks>
       </pes>
     </mach>
+    <mach name="pm-cpu|muller-cpu|alvarez">
+      <pes compset="any" pesize="any">
+        <comment>allactive+pm-cpu: default, 1 node, 96 tasks, 1 thread</comment>
+        <ntasks>
+          <ntasks_atm>96</ntasks_atm>
+          <ntasks_lnd>96</ntasks_lnd>
+          <ntasks_rof>96</ntasks_rof>
+          <ntasks_ice>96</ntasks_ice>
+          <ntasks_ocn>96</ntasks_ocn>
+          <ntasks_glc>96</ntasks_glc>
+          <ntasks_wav>96</ntasks_wav>
+          <ntasks_cpl>96</ntasks_cpl>
+        </ntasks>
+      </pes>
+    </mach>
   </grid>
   <grid name="a%ne30np4">
     <mach name="pm-gpu|muller-gpu">