Add GCHP ctmEnv-only simulation option

.github/workflows/cloud-benchmarking-workflow.yml

@@ -1,57 +1,65 @@
 # Release pipeline:
-# 
+#
 # This pipeline triggers the cloud-based benchmarking workflow
-# upon pushes to the dev environment. The benchmarking workflow 
+# upon pushes to the dev environment. The benchmarking workflow
 # infrastructure code can be found in the following repository:
 # https://github.com/geoschem/gc-cloud-infrastructure
 #
-# This pipeline is triggered by pushes to dev
+# This pipeline is triggered by pushes to dev/* branches.
 #
 # Notes:
 #   - This workflow requires aws credentials necessary to
-#     trigger the benchmarking step function via the aws cli. 
-#     The credentials need step function permissions and can 
-#     be added to the repo as an action secret called 
+#     trigger the benchmarking step function via the aws cli.
+#     The credentials need step function permissions and can
+#     be added to the repo as an action secret called
 #     AWS_SECRET_ACCESS_KEY and AWS_ACCESS_KEY_ID.
 
 name: cloud_benchmarking
 on:
   push:
     branches:
-      - dev**
+      - dev/*
     tags:
       - '*'
   pull_request:
     branches:
-      - dev**
+      - dev/*
 
 jobs:
   trigger_step_function:
     runs-on: ubuntu-latest # aws cli comes pre-installed
     steps:
+
       # for now both use Spot instances -- may need to update to use on demand
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          persist-credentials: false
+
+      # By default we use 1Hr benchmarks
       - name: Set Initial Variables
-        # By default we use 1Hr benchmarks
         run: |
           echo "TIME_PERIOD=1Hr" >> $GITHUB_ENV
           echo "RESOLUTION=24" >> $GITHUB_ENV
-          echo "GITHUB_SHA_SHORT=`echo ${GITHUB_SHA} | cut -c1-7`" >> $GITHUB_ENV
-          echo "COMMIT_NAME=`echo ${GITHUB_SHA} | cut -c1-7`" >> $GITHUB_ENV
-      # conditionally overwrite variables if a tag was the triggering event
+          echo "GITHUB_SHA_SHORT=${GITHUB_SHA:0:7}" >> $GITHUB_ENV
+          echo "COMMIT_NAME=${GITHUB_SHA:0:7}" >> $GITHUB_ENV
+
+      # Conditionally overwrite variables if a tag was the triggering event
       - name: Reset Initial Variables for pull request
-        run: |
-          echo "GITHUB_SHA_SHORT=`echo ${{ github.event.pull_request.head.sha }} | cut -c1-7`" >> $GITHUB_ENV
-          echo "COMMIT_NAME=`echo ${{ github.event.pull_request.head.sha }} | cut -c1-7`" >> $GITHUB_ENV
         if: github.event_name == 'pull_request'
+        env:
+          GITHUB_SHA_SHORT: ${{ github.event.pull_request.head.sha }}
+        run: |
+          echo "GITHUB_SHA_SHORT=${GITHUB_SHA_SHORT:0:7}" >> $GITHUB_ENV
+          echo "COMMIT_NAME=${GITHUB_SHA_SHORT:0:7}" >> $GITHUB_ENV
+
+      # We do a 1Month benchmark for tags
       - name: Reset Variables For Tags
-        # We do a 1Month benchmark for tags
+        if: startsWith(github.ref, 'refs/tags/')
         run: |
           echo "TIME_PERIOD=1Mon" >> $GITHUB_ENV
           echo "COMMIT_NAME=${GITHUB_REF##*/}" >> $GITHUB_ENV
-        if: startsWith(github.ref, 'refs/tags/')
+
       - name: Generate Primary Key
         env:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
@@ -62,6 +70,7 @@ jobs:
           cd ${{ github.workspace }}
           echo "DEV_PRIMARY_KEY=gchp-c${RESOLUTION}-${TIME_PERIOD}-`git describe --tags`" >> $GITHUB_ENV
           echo "REF_PRIMARY_KEY=`./.github/workflows/findRefKey.sh ${RESOLUTION} ${TIME_PERIOD} ${GITHUB_SHA}`" >> $GITHUB_ENV
+
       - name: Trigger Step Function
         env:
           # Set config options for aws cli

.github/workflows/lint-ci-workflows.yml

@@ -0,0 +1,77 @@
+# Workflow to run linting checks on source
+name: Lint
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on pushes to the "main" or "dev/"* branches,
+  # i.e., PR merges
+  push:
+    branches: [ "main", "dev/*" ]
+
+  # Triggers the workflow on pushes to open pull requests with code changes
+  pull_request:
+    paths:
+      - '.github/workflows/*.yml'
+
+  # Allows you to run this workflow manually from the Actions tab
+  # (usually leave it blank)
+  workflow_dispatch:
+
+# Allow the jobs to read the secret GitHub token
+permissions:
+  contents: read
+
+# Cancel jobs running if new commits are pushed
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+# Workflow run - one or more jobs that can run sequentially or in parallel
+jobs:
+
+  # This workflow contains a single job called "lint"
+  lint:
+
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Don't quit the Action at the first 
+    strategy:
+      fail-fast: false
+
+    # GitHub secret token
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    # Steps represent a sequence of tasks that will be
+    # executed as part of the job
+    steps:
+
+      # Checks-out your repository under $GITHUB_WORKSPACE,
+      # so your job can access it
+      - name: Checkout code
+        with:
+          persist-credentials: false
+        uses: actions/checkout@v4
+
+      # Installs Python 3.x
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      # Installs Python packages
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m venv ci_venv
+          . ci_venv/bin/activate
+          pip install zizmor==0.9.2
+
+      # Apply GitHub Actions linter, zizmor
+      - name: zizmor
+        if: always()
+        run: |
+          cd ${{ github.workspace }}
+          . ci_venv/bin/activate
+          zizmor .github/workflows/*.yml

.github/workflows/spack-deployment-workflow.yml

@@ -22,7 +22,11 @@ jobs:
     runs-on: ubuntu-latest
     container: continuumio/miniconda3
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
       - name: Get release tag
         id: vars
         run: |

.gitmodules

@@ -7,9 +7,6 @@
 [submodule "ESMA_cmake"]
 	path = ESMA_cmake
 	url = https://github.com/geoschem/ESMA_cmake
-[submodule "gFTL-shared"]
-	path = src/gFTL-shared
-	url = https://github.com/geoschem/gFTL-shared.git
 [submodule "FMS"]
 	path = src/FMS
 	url = https://github.com/geoschem/FMS.git
@@ -22,12 +19,6 @@
 [submodule "HEMCO"]
 	path = src/GCHP_GridComp/GEOSChem_GridComp/HEMCO/HEMCO
 	url = https://github.com/geoschem/HEMCO.git
-[submodule "yaFyaml"]
-	path = src/yaFyaml
-	url = https://github.com/geoschem/yaFyaml.git
-[submodule "pFlogger"]
-	path = src/pFlogger
-	url = https://github.com/geoschem/pFlogger.git
 [submodule "geos-chem-shared-docs"]
 	path = docs/source/geos-chem-shared-docs
 	url = https://github.com/geoschem/geos-chem-shared-docs.git
@@ -37,3 +28,6 @@
 [submodule "HETP"]
 	path = src/GCHP_GridComp/GEOSChem_GridComp/HETP
 	url = https://github.com/geoschem/HETerogeneous-vectorized-or-Parallel.git
+[submodule "src/GFE"]
+	path = src/GFE
+	url = https://github.com/Goddard-Fortran-Ecosystem/GFE

CHANGELOG.md

@@ -9,6 +9,27 @@ This file documents all notable changes to the GCHP wrapper repository starting
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased] - TBD
+### Added
+- Added R4 exports in GCHPctmEnv for diagnostics since R8 to R4 conversion in MAPL 2.55 History is broken
+- Added submodule for GFE (Goddard-Fortran-Ecosystem) which includes GMAO libraries yafYaml, pFlogger, gFTL, gFTL-shared, fArgParse, and pFUnit as its own submodules
+- Added connectivity from GEOS-Chem to FV3 dynamics to pass DELP_DRY in GEOS-Chem restart file to advection for restart file species mass conservation
+
+### Changed
+- Changed minimum CMake version from 3.13 to 3.24
+- Changed minimum ESMF version from 8.4.2 to 8.6.1
+- Updated docs to indicate timing information now printed to allPEs.log
+- Updated docs to include library requirement udunits2 and additional information about stretched grid parameters
+- Updated `lint-ci-workflows` to run on `main` and `dev/*` branches
+- Updated badges on `README.md` and `docs/source/index.rst`
+- Updated submodule ESMA_cmake for GNU Fortran compiler compatibility with CPUs returning processor description INTEL
+
+### Fixed
+- Fixed security issues in GitHub Actions that caused the `lint-ci-workflows` action to fail
+
+### Removed
+- Removed individual submodules for yafYaml, pFlogger, and gFTL-shared since now located in new submodule GFE
+
 ## [14.6.3] - 2025-07-28
 ### Added
 - Added `-DSANITIZE` option for use with GNU Fortran compiler to check for memory leaks

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.13)
+cmake_minimum_required (VERSION 3.24)
 project (gchp_ctm
   VERSION 14.6.3
   LANGUAGES Fortran CXX C

README.md

@@ -1,14 +1,10 @@
 <img src="https://geoschem.github.io/img/GEOS-Chem_Logo_Light_Background.png" height="60%" width="60%" alt="GEOS-Chem Logo">
 
 <p>
-  <a href="https://github.com/geoschem/GCHP/releases"><img src="https://img.shields.io/github/v/release/geoschem/GCHP?include_prereleases&label=Latest%20Pre-Release"></a>
-  <a href="https://github.com/geoschem/GCHP/releases/"><img src="https://img.shields.io/github/v/release/geoschem/GCHP?label=Latest%20Stable%20Release"></a>
-  <a href="https://github.com/geoschem/GCHP/"><img src="https://img.shields.io/github/release-date/geoschem/GCHP"></a>
-  <a href="https://github.com/geoschem/GCHP/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg"></a>
-  <br />
-  <a href="https://spack.readthedocs.io/en/latest/package_list.html#gchp"><img src="https://img.shields.io/badge/Install%20with-Spack-ff69b4"></a>
-  <a href="https://hub.docker.com/r/geoschem/gchp"><img src="https://img.shields.io/docker/v/geoschem/gchp?color=blue&label=Docker%2FSingularity"></a>
+  <a href="https://github.com/geoschem/GCHP/releases/"><img src="https://img.shields.io/github/v/release/geoschem/GCHP?label=Latest%20Stable%20Release" alt="Latest release"></a>
+  <a href="https://github.com/geoschem/GCHP/"><img src="https://img.shields.io/github/release-date/geoschem/GCHP" alt="Release date"></a><br/>
   <a href="https://doi.org/10.5281/zenodo.4428926"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4428926.svg" alt="DOI"></a>
+  <a href="https://github.com/geoschem/GCHP/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg"></a>
   <a href="https://gchp.readthedocs.io"><img src="https://img.shields.io/readthedocs/gchp?label=ReadTheDocs"></a>
 </p>
 

docs/source/getting-started/requirements.rst

@@ -15,7 +15,8 @@ following software:
 
 * Git
 * Make (or GNUMake)
-* CMake version ≥ 3.13
+* CMake version ≥ 3.24
+* UDUNITS2
 * Compilers (C, C++, and Fortran):
 
    * Intel compilers versions 2019-2021, or
@@ -31,7 +32,7 @@ following software:
 
 * HDF5
 * NetCDF (with C, C++, and Fortran support)
-* Earth System Modeling Framework (ESMF) version 8.4.2+. Problems with 8.1 and prior have been reported.
+* Earth System Modeling Framework (ESMF) version 8.6.1+. Prior versions are not compatible with the version of MAPL used in GCHP.
 
 Your system administrator should be able to tell you if this software is already available on your cluster, and if so, how to activate it.
 If it is not already available, they might be able to build it for you.

docs/source/index.rst

@@ -4,15 +4,14 @@ GEOS-Chem High Performance
 .. raw:: html
 
    <p>
-   <a href="https://github.com/geoschem/GCHP/releases"><img src="https://img.shields.io/github/v/release/geoschem/GCHP?include_prereleases&label=Latest%20Pre-Release"></a>
-   <a href="http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_versions"><img src="https://img.shields.io/github/v/release/geoschem/GCHP?label=Latest%20Stable%20Release"></a>
-   <a href="https://github.com/geoschem/GCHP/releases/"><img src="https://img.shields.io/github/release-date/geoschem/GCHP"></a><br/>
-   <a href="https://zenodo.org/badge/latestdoi/200900441"><img src="https://zenodo.org/badge/200900441.svg"></a>
-   <a href="https://github.com/geoschem/GCHP/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg"></a>
-   <a href="https://gchp.readthedocs.io/en/latest/"><img src="https://img.shields.io/readthedocs/gchp?label=ReadTheDocs"></a>
-   <a href="https://dev.azure.com/geoschem/GCHP/_build"><img src="https://img.shields.io/azure-devops/build/geoschem/GCHP/20/main?label=Build%20Matrix"></a>
+     <a href="https://github.com/geoschem/GCHP/releases/"><img src="https://img.shields.io/github/v/release/geoschem/GCHP?label=Latest%20Stable%20Release" alt="Latest release"></a>
+     <a href="https://github.com/geoschem/GCHP/"><img src="https://img.shields.io/github/release-date/geoschem/GCHP" alt="Release date"></a><br/>
+     <a href="https://doi.org/10.5281/zenodo.4428926"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4428926.svg" alt="DOI"></a>
+     <a href="https://github.com/geoschem/GCHP/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg"></a>
+     <a href="https://gchp.readthedocs.io"><img src="https://img.shields.io/readthedocs/gchp?label=ReadTheDocs"></a>
    </p>
 
+
 The `GEOS--Chem model <http://geos-chem.org/>`_ is a global 3-D model
 of atmospheric composition driven by assimilated meteorological
 observations from the Goddard Earth Observing System (GEOS) of the