Merge branch 'develop' into omega/wind-forcing-and-bottom-drag

Author: philipwjones

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

@@ -20,7 +20,7 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
-    - uses: tj-actions/changed-files@v45
+    - uses: tj-actions/changed-files@v46
       id: changed-files
       with:
         files: '**/*.md'

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

@@ -34,6 +34,9 @@ concurrency:
 jobs:
   Build-and-Deploy-docs:
     if: ${{ github.repository == 'E3SM-Project/E3SM' }}
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -48,19 +51,28 @@ jobs:
           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 3.11
-        uses: actions/setup-python@v5
+      - name: Install Python deps
+        uses: mamba-org/setup-micromamba@v2
         with:
-          python-version: "3.11"
-      - name: Install python deps
-        # TODO: move to a requirements.txt file
-        # TODO: pin all versions?
-        run: python3 -m pip install mkdocs-material pymdown-extensions mkdocs-monorepo-plugin mdutils mkdocs-bibtex==2.18.0
+          init-shell: bash
+          environment-name: docs
+          create-args: >-
+            python=3.12
+            mkdocs-material
+            pymdown-extensions
+            mkdocs-monorepo-plugin
+            mdutils
+            mkdocs-bibtex==2.18.0
+            marp-cli
       # build every time (PR or push to master)
       - name: Generate EAMxx params docs
         working-directory: components/eamxx/scripts
         run: |
           ./eamxx-params-docs-autogen
+      - name: Generate presentations
+        run: |
+          marp -I components/eamxx/docs/_presentations_srcs -o components/eamxx/docs/_presentations_html
+          cp components/eamxx/docs/_presentations_srcs/*.png components/eamxx/docs/_presentations_html/
       - name: Build
         run: mkdocs build --strict --verbose
       # Only deploy to the main github page when there is a push to master

.github/workflows/eamxx-sa-sanitizer.yml

@@ -94,4 +94,4 @@ jobs:
           machine: ghci-snl-cuda
           generate: false
           submit: ${{ env.submit }}
-          cmake-configs: Kokkos_ARCH_HOPPER90=${{ env.Hopper }};Kokkos_ARCH_AMPERE80=${{ env.Ampere }};Kokkos_ARCH_VOLTA70=${{ env.Volta }};CMAKE_CUDA_ARCHITECTURES=${{ env.CUDA_ARCH }}
+          cmake-configs: Kokkos_ARCH_HOPPER90=${{ env.Hopper }};Kokkos_ARCH_AMPERE80=${{ env.Ampere }};Kokkos_ARCH_VOLTA70=${{ env.Volta }};CMAKE_CUDA_ARCHITECTURES=${{ env.CUDA_ARCH }};SCREAM_SMALL_KERNELS=ON

.github/workflows/eamxx-sa-testing.yml

@@ -12,6 +12,7 @@ on:
       - 'cime_config/machine/config_machines.xml'
       - 'components/eamxx/**'
       - 'components/homme/**'
+      - 'components/eam/src/physics/rrtmgp/**'
       - 'externals/ekat'
       - 'externals/mam4xx'
       - 'externals/haero'
@@ -105,8 +106,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        build_type: [sp, dbg, opt]
-    name: gcc-cuda / ${{ matrix.build_type }}
+        test:
+          - build_type: sp
+            SK: OFF
+          - build_type: dbg
+            SK: ON
+          - build_type: opt
+            SK: OFF
+    name: gcc-cuda / ${{ matrix.test.build_type }}
     steps:
       - name: Check out the repository
         uses: actions/checkout@v4
@@ -148,9 +155,9 @@ jobs:
       - name: Run tests
         uses: ./.github/actions/test-all-eamxx
         with:
-          build_type: ${{ matrix.build_type }}
+          build_type: ${{ matrix.test.build_type }}
           machine: ghci-snl-cuda
           generate: ${{ env.generate }}
           submit: ${{ env.submit }}
-          cmake-configs: Kokkos_ARCH_HOPPER90=${{ env.Hopper }};Kokkos_ARCH_AMPERE80=${{ env.Ampere }};Kokkos_ARCH_VOLTA70=${{ env.Volta }};CMAKE_CUDA_ARCHITECTURES=${{ env.CUDA_ARCH }}
+          cmake-configs: Kokkos_ARCH_HOPPER90=${{ env.Hopper }};Kokkos_ARCH_AMPERE80=${{ env.Ampere }};Kokkos_ARCH_VOLTA70=${{ env.Volta }};CMAKE_CUDA_ARCHITECTURES=${{ env.CUDA_ARCH }};SCREAM_SMALL_KERNELS=${{ matrix.test.SK }}
           ekat: ${{ env.ekat }}

.github/workflows/eamxx-v1-testing.yml

@@ -11,6 +11,7 @@ on:
       - 'cime_config/machine/config_machines.xml'
       - 'components/eamxx/**'
       - 'components/homme/**'
+      - 'components/eam/src/physics/rrtmgp/**'
       - 'externals/ekat'
       - 'externals/mam4xx'
       - 'externals/haero'
@@ -43,7 +44,7 @@ concurrency:
 
 env:
   # Submit to cdash only for nightlies or if the user explicitly forced a submission via workflow dispatch
-  submit: ${{ github.event_name == 'schedule' || (github.event_name == 'workflow_dispatch' && inputs.submit) }}
+  submit: ${{ github.event_name == 'schedule' || (github.event_name == 'workflow_dispatch') }}
   # Generate only if user requested via workflow_dispatch
   generate: ${{ github.event_name == 'workflow_dispatch' && inputs.bless }}
   # Correct case folder suffix for generate/compare, used to find files to upload as artifacts
@@ -73,8 +74,6 @@ jobs:
             short_name: ERS_Ln22.ne4pg2_ne4pg2.F2010-SCREAMv1.eamxx-small_kernels--eamxx-output-preset-5
           - full_name: SMS_D_Ln5.ne4pg2_oQU480.F2010-SCREAMv1-MPASSI.ghci-snl-cpu_gnu.eamxx-mam4xx-all_mam4xx_procs
             short_name: SMS_D_Ln5.ne4pg2_oQU480.F2010-SCREAMv1-MPASSI.eamxx-mam4xx-all_mam4xx_procs
-          - full_name: SMS_Ln3.ne4pg2_oQU480.F2010-MMF2.ghci-snl-cpu_gnu
-            short_name: SMS_Ln3.ne4pg2_oQU480.F2010-MMF2
       fail-fast: false
     name: cpu-gcc / ${{ matrix.test.short_name }}
     steps:

.github/workflows/omega-build-workflow.yml

@@ -93,4 +93,4 @@ jobs:
         run: |
           conda activate omega_dev
           cd components/omega/doc
-          make html
+          make html-strict

.github/workflows/omega-docs-workflow.yml

@@ -49,6 +49,7 @@ jobs:
           conda list
 
       - name: Build Sphinx Docs
+        # Use 'make html' (not html-strict) so docs always update, even if warnings exist.
         run: |
           conda activate omega_dev
           cd components/omega/doc

.gitignore

@@ -45,6 +45,8 @@ site
 components/eamxx/site/*
 # Ignore auto-generated eamxx_params.md file
 components/eamxx/docs/user/eamxx_params.md
+# Ignore html generated for presentations in the source code
+components/eamxx/docs/_presentations_html/
 
 # Python packaging
 *.egg-info

.gitmodules

@@ -82,4 +82,6 @@
 [submodule "externals/mam4xx"]
 	path = externals/mam4xx
 	url = [email protected]:eagles-project/mam4xx.git
-
+[submodule "externals/cpptrace"]
+	path = externals/cpptrace
+	url = [email protected]:jeremy-rifkin/cpptrace