Merge branch 'E3SM-Project:master' into develop

.circleci/checkout.sh

@@ -2,5 +2,4 @@
 
 # Replace all ssh URLs to submodules with HTTP URLs
 sed -i 's/[email protected]:/https:\/\/github.com\//' .gitmodules
-sed -i 's/[email protected]:/https:\/\/github.com\//' cime/.gitmodules
 git submodule update --init --recursive

.circleci/container.sh

@@ -1,7 +1,8 @@
 #!/bin/bash
 
-wget -t 3 -O e3sm.sif http://portal.nersc.gov/project/e3sm/lukasz/e3sm.sif || \
-    wget -t 3 -O e3sm.sif https://dabdceba-6d04-11e5-ba46-22000b92c6ec.e.globus.org/containers/public/e3sm.sif
+singularity pull e3sm.sif \
+    docker://ghcr.io/mahf708/e3sm-imgs@sha256:d1030a6f4e3a53f682859436a26b30a9477d69423829ae1d9c1b5ab4e255430d
+
 if [ $? -ne 0 ]; then
     exit -1
 fi

.circleci/run.sh

@@ -57,7 +57,7 @@ rc=$?
 if [ $rc -ne 0 ]; then
     print_bldlog "e3sm"
     print_bldlog "csm_share"
-    print_bldlog "pio"
+    print_bldlog "spio"
     print_bldlog "mct"
     print_bldlog "gptl"
     exit $rc

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

@@ -0,0 +1,50 @@
+name: Build and deploy gh-pages branch with Mkdocs
+
+on:
+  # Runs every time master branch is updated
+  push:
+    branches: ["master"]
+  # Runs every time a PR is open against master
+  pull_request:
+    branches: ["master"]
+  workflow_dispatch:
+
+concurrency:
+  # Prevent 2+ copies of this workflow from running concurrently
+  group: e3sm-docs-action
+
+jobs:
+  Build-and-Deploy-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          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
+      - name: Show action trigger
+        run: echo "= The job was automatically triggered by a ${{github.event_name}} event."
+      - name: Set up Python 3.10
+        uses: actions/[email protected]
+        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: Build
+        run: mkdocs build --strict --verbose
+      # Only deploy to the main github page when there is a push to master
+      - if: ${{ github.event_name == 'push' }}
+        name: GitHub Pages action
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          # Do not remove existing pr-preview pages
+          clean-exclude: pr-preview
+          folder: ./site/
+      # If it's a PR from within the same repo, deploy to a preview page
+      # For security reasons, PRs from forks cannot write into gh-pages for now
+      - if: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository }}
+        name: Preview docs
+        uses: rossjrw/pr-preview-action@v1
+        with:
+          source-dir: ./site/

.gitignore

@@ -24,5 +24,8 @@ buildnmlc
 buildlibc
 buildlib_cmakec
 
+#the site directory
+site
+
 # Ignore emacs backup files
 *~

.gitmodules

@@ -70,9 +70,16 @@
 	path = components/ww3/src/WW3
 	url = [email protected]:E3SM-Project/WW3.git
 	branch = e3sm
+[submodule "components/eam/src/physics/crm/pam/external"]
+	path = components/eam/src/physics/crm/pam/external
+	url = [email protected]:E3SM-Project/PAM.git
+[submodule "components/mpas-seaice/src/icepack"]
+	path = components/mpas-seaice/src/icepack
+	url = [email protected]:E3SM-Project/Icepack.git
 [submodule "externals/haero"]
 	path = externals/haero
 	url = [email protected]:eagles-project/haero.git
 [submodule "externals/mam4xx"]
 	path = externals/mam4xx
 	url = [email protected]:eagles-project/mam4xx.git
+

cime_config/allactive/config_compsets.xml

@@ -49,6 +49,11 @@
   <lname>1850SOI_EAM%CHEMUCI-LINOZV3_ELM%SPBC_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>
+</compset>
+
 <compset>
   <alias>WCYCL1850-1pctCO2</alias>
   <lname>1850SOI_EAM%CMIP6-1pctCO2_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
@@ -101,6 +106,11 @@
   <lname>20TRSOI_EAM%CHEMUCI-LINOZV3_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>
 
+<compset>
+  <alias>WCYCL20TR_chemUCI-Linozv3-mam5</alias>
+  <lname>20TRSOI_EAM%CHEMUCI-LINOZV3-MAM5_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+</compset>
+
 <compset>
   <alias>WCYCLSSP585</alias>
   <lname>SSP585SOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
@@ -320,32 +330,42 @@
 
 <compset>
   <alias>CRYO1850</alias>
-  <lname>1850SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBISMF_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYO1850-4xCO2</alias>
-  <lname>1850SOI_EAM%CMIP6-4xCO2_ELM%SPBC_MPASSI%DIB_MPASO%IBISMF_MOSART_SGLC_SWAV</lname>
+  <lname>1850SOI_EAM%CMIP6-4xCO2_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYO1950</alias>
-  <lname>1950SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBISMF_MOSART_SGLC_SWAV</lname>
+  <lname>1950SOI_EAM%CMIP6_ELM%SPBC_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>
+</compset>
+
+<compset>
+  <alias>CRYO1950-DISMF</alias>
+  <lname>1950SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBDISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYO20TR</alias>
-  <lname>20TRSOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBISMF_MOSART_SGLC_SWAV</lname>
+  <lname>20TRSOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYOSSP585</alias>
-  <lname>SSP585SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBISMF_MOSART_SGLC_SWAV</lname>
+  <lname>SSP585SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>
   <alias>CRYOSSP370</alias>
-  <lname>SSP370SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBISMF_MOSART_SGLC_SWAV</lname>
+  <lname>SSP370SOI_EAM%CMIP6_ELM%SPBC_MPASSI%DIB_MPASO%IBPISMF_MOSART_SGLC_SWAV</lname>
 </compset>
 
 <compset>