merge GFDL main

.github/workflows/SHiELD_parallelworks_intel.yml

@@ -0,0 +1,163 @@
+name: Compile SHiELD SOLO and run tests
+
+# This GitHub Action Workflow is running on the cloud devcimultiintel cluster
+# The tests are run inside of a container with the following software/libraries:
+# -intel: 2023.2.0
+# -hdf5: 1.14.0
+# -netcdf-c: 4.9.2
+# -netcdf-fortran: 4.6.0
+# -cmake
+# -libyaml
+
+on:
+  pull_request:
+    branches:
+      - main
+  # run weekly on Sunday
+  schedule:
+    - cron: '0 0 * * 0'
+
+#this should cancel in progress ci runs for the same PR 
+#(e.g. a second commit on the same PR comes in while CI is still running)
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  checkout:
+    if: github.repository == 'NOAA-GFDL/GFDL_atmos_cubed_sphere'
+    runs-on: [gfdlacsciintel]
+    name: Checkout Code
+    steps:
+    # It can take a long time (5-15 minutes) to spinup nodes
+    # so this salloc will prompt 46 nodes to startup and stay active for 20 min
+    # this is enough nodes for the first 17 tests to run in parallel, and we
+    # have 17 runners configured.
+    - run: salloc --partition=p2 -N 46 -J $GITHUB_SHA sleep 20m &
+    - run: /contrib/fv3/GFDL_atmos_cubed_sphere_CI/checkout.sh $GITHUB_REF $GITHUB_SHA
+
+  build:
+    if: github.repository == 'NOAA-GFDL/GFDL_atmos_cubed_sphere'
+    runs-on: [gfdlacsciintel]
+    name: SOLO SHiELD build
+    needs: [checkout]
+    strategy:
+      fail-fast: true
+      max-parallel: 3
+      matrix:
+        runpath: [/contrib/fv3/GFDL_atmos_cubed_sphere_CI/]
+        runscript: [swcompile.sh, nhcompile.sh, hydrocompile.sh]
+    steps:
+      - env:
+          RUNPATH: ${{ matrix.runpath }}
+          RUNSCRIPT: ${{ matrix.runscript }}
+        run: $RUNPATH/$RUNSCRIPT $GITHUB_REF $GITHUB_SHA
+
+  test:
+    if: github.repository == 'NOAA-GFDL/GFDL_atmos_cubed_sphere'
+    runs-on: [gfdlacsciintel]
+    name: SOLO SHiELD test suite
+    needs: [checkout, build]
+    strategy:
+      fail-fast: false
+      max-parallel: 17
+      matrix:
+        runpath: [/contrib/fv3/GFDL_atmos_cubed_sphere_CI/]
+        runscript:
+          # These are placed in order of largest to smallest jobs
+          #layout 8,8 needs 8 nodes on dvcimultiintel cluster
+          - C512r20.solo.superC.sh
+          - C768.sw.BTwave.sh
+          #layout 4,8 needs 4 nodes on dvcimultiintel cluster
+          - C256r20.solo.superC.sh
+          - C384.sw.BLvortex.sh
+          #layout 4,4 needs 2 nodes on dvcimultiintel cluster
+          - C128r20.solo.superC.sh
+          - C128r3.solo.TC.d1.sh
+          - C128r3.solo.TC.h6.sh
+          - C128r3.solo.TC.sh
+          - C128r3.solo.TC.tr8.sh
+          - C192.sw.BLvortex.sh
+          - C192.sw.BTwave.sh
+          - C192.sw.modon.sh
+          - C384.sw.BTwave.sh
+          #layout 4,1 and 2,2 need 1 node on dvcimultiintel cluster
+          - C96.solo.BCdry.hyd.sh
+          - C96.solo.BCdry.sh
+          - C96.solo.BCmoist.hyd.d3.sh
+          - C96.solo.BCmoist.hyd.sh
+          - C96.solo.BCmoist.nhK.sh
+          - C96.solo.BCmoist.sh
+          - C96.solo.mtn_rest.hyd.diff2.sh
+          - C96.solo.mtn_rest.hyd.sh
+          - C96.solo.mtn_rest.nonmono.diff2.sh
+          - C96.solo.mtn_rest.sh
+          - C96.sw.BLvortex.sh
+          - C96.sw.BTwave.sh
+          - C96.sw.modon.sh
+          - C96.sw.RHwave.sh
+          - d96_1k.solo.mtn_rest_shear.olddamp.sh
+          - d96_1k.solo.mtn_rest_shear.sh
+          - d96_1k.solo.mtn_schar.mono.sh
+          - d96_1k.solo.mtn_schar.sh
+          - d96_2k.solo.bubble.n0.sh
+          - d96_2k.solo.bubble.nhK.sh
+          - d96_2k.solo.bubble.sh
+          - d96_500m.solo.mtn_schar.sh
+    steps:
+      # This will end the slurm job started in the checkout job
+      - run: scancel -n $GITHUB_SHA
+      - env:
+          RUNPATH: ${{ matrix.runpath }}
+          RUNSCRIPT: ${{ matrix.runscript }}
+        run: $RUNPATH/$RUNSCRIPT $GITHUB_REF $GITHUB_SHA
+  shutdown:
+    if: always() && github.repository == 'NOAA-GFDL/GFDL_atmos_cubed_sphere'
+    runs-on: [gfdlacsciintel]
+    name: Shutdown Processes
+    needs: [checkout, build, test]
+    strategy:
+      fail-fast: false
+      max-parallel: 17
+      matrix:
+        test:
+          - C512r20.solo.superC
+          - C768.sw.BTwave
+          - C256r20.solo.superC
+          - C384.sw.BLvortex
+          - C128r20.solo.superC
+          - C128r3.solo.TC.d1
+          - C128r3.solo.TC.h6
+          - C128r3.solo.TC
+          - C128r3.solo.TC.tr8
+          - C192.sw.BLvortex
+          - C192.sw.BTwave
+          - C192.sw.modon
+          - C384.sw.BTwave
+          - C96.solo.BCdry.hyd
+          - C96.solo.BCdry
+          - C96.solo.BCmoist.hyd.d3
+          - C96.solo.BCmoist.hyd
+          - C96.solo.BCmoist.nhK
+          - C96.solo.BCmoist
+          - C96.solo.mtn_rest.hyd.diff2
+          - C96.solo.mtn_rest.hyd
+          - C96.solo.mtn_rest.nonmono.diff2
+          - C96.solo.mtn_rest
+          - C96.sw.BLvortex
+          - C96.sw.BTwave
+          - C96.sw.modon
+          - C96.sw.RHwave
+          - d96_1k.solo.mtn_rest_shear.olddamp
+          - d96_1k.solo.mtn_rest_shear
+          - d96_1k.solo.mtn_schar.mono
+          - d96_1k.solo.mtn_schar
+          - d96_2k.solo.bubble.n0
+          - d96_2k.solo.bubble.nhK
+          - d96_2k.solo.bubble
+          - d96_500m.solo.mtn_schar
+    steps:
+      - run: scancel -n $GITHUB_SHA
+      - env:
+          JOB: ${{ github.sha }}_${{ matrix.test }}
+        run: scancel -n $JOB

.github/workflows/daily_cleanup_parallelworks.yml

@@ -0,0 +1,18 @@
+name: Old Build Cleanup
+
+# This GitHub Action Workflow is runing on the GFDL_ACS_CIINTEL cluster
+# This will delete all build directories older than 30 days
+# Build directories are on the cloud at /contrib/fv3/2023.2.0
+
+on:
+  schedule:
+    # run daily at midnight
+    - cron: '0 0 * * *'
+
+jobs:
+  delete:
+    if: github.repository == 'NOAA-GFDL/GFDL_atmos_cubed_sphere'
+    runs-on: [gfdlacsciintel]
+    name: Delete Builds
+    steps:
+      - run: find /contrib/fv3/2023.2.0/GFDL_atmos_cubed_sphere/refs/pull -maxdepth 1 -mindepth 1 -mtime +30 -type d -print -exec rm -rf "{}" \;

CODE_STYLE.md

@@ -70,7 +70,7 @@
 !* (at your option) any later version.
 !*
 !* The FV3 dynamical core is distributed in the hope that it will be
-!* useful, but WITHOUT ANYWARRANTY; without even the implied warranty
+!* useful, but WITHOUT ANY WARRANTY; without even the implied warranty
 !* of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 !* See the GNU General Public License for more details.
 !*

CONTRIBUTING_GUIDE.md

@@ -0,0 +1,122 @@
+# Contributing Guide for the GFDL_atmos_cubed_sphere Repository
+
+This guide will walk a developer through the correct process for making a Pull Request in this repository. 
+GFDL_atmos_cubed_sphere is a repository with 4 different development branches.  It is imperitive that the developer understands the difference between each branch.
+
+## Understanding the Development Branches
+
+There are 4 different development branches being supported in this repository.
+
+| Branch | Description |
+| :--- | :--- |
+| main | This branch is the main development branch. The SHiELD model will compile with this branch. When there is a Public Release of the FV3 Dyncamical Core, updates will first be introduced to this branch. |
+| dev/gfdl | This branch is used for all AM4 based GFDL Models. |
+| dev/emc | This branch is used for the UFS Weather Model development. |
+| dev/gfdl_am5 | This branch is being used for GFDL AM5 development. |
+
+## How to contribute code changes
+
+1. Create a Fork
+    1. Click on **Fork** in the top right of the repository GitHub page
+    2. The **Owner** should be set to your GitHub username
+    3. The **Repository Name** should be GFDL_atmos_cubed_sphere
+    4. Click **Create fork**
+
+2. Create an Issue describing the change that you would like to implement.
+    1. Navigate to the **Issue** tab at the top of the repository GitHub page
+    2. Click on the **New issue** button
+    3. Choose from one of the suggested templates (Bug Report, Feature Request, or Support Request)
+    4. Fill out the Issue with specifics and submit issue
+
+3. Clone the repository locally on your machine
+
+    `git clone https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere.git`
+
+4. Add your fork locally
+
+    This guide will refer to the fork as `myFork`, but you can name this anything.
+
+    `git remote add myFork https://github.com/<username>/GFDL_atmos_cubed_sphere.git`
+
+    `git remote -v` will display all remote repositories that you have added.  The repository that you cloned will be named `origin` by default.  
+
+    The ouput of `git remote -v` should be similar to:
+
+    ```
+    myFork https://github.com/<username>/GFDL_atmos_cubed_sphere.git (fetch)
+    myFork https://github.com/<username>/GFDL_atmos_cubed_sphere.git (push)
+    origin https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere.git (fetch)
+    origin https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere.git (push)
+    ```
+
+5.  Checkout the branch that you would like your changes added to
+
+    Refer to section [Understanding the Development Branches](#Understanding-the-Development-Branches) to choose which branch to checkout
+    
+    This guide will reference this branch as `baseBranch`
+
+    `git checkout baseBranch `
+
+6. Create a feature branch to make your changes to
+
+    This guide will refer to this new branch as `newBranch`, but you should name this branch with a unique name related to the task
+
+    `git checkout -b newBranch`
+
+7. Update the code
+    1. To see the files you have modified use the command `git status`
+    2. To see exactly what you changed in each file use the command `git diff`
+    3. When you are satisfied with your changes stage them for a commit
+
+        `git add <filenames or paths of all added and modified files>`
+
+    4. Make a commit
+    
+        `git commit -m "Descriptive message describing what you have changed in this commit"`
+        
+    5. Make sure branch is up to date with the base branch (main, dev/gfdl, dev/emc, or dev/gfdl_am5)
+
+        `git fetch origin baseBranch`
+        
+        `git merge origin/baseBranch`
+
+    6. Push that commit to your fork
+
+        `git push myFork newBranch`
+        
+8. Create a Pull Request
+    1. Navigate to your fork on GitHub
+
+       The URL to get you to your fork should be `https://github.com/<username>/GFDL_atmos_cubed_sphere`
+       
+    2. Navigate to the **Pull requests** tab at the top of the repository GitHub page
+    3. Click on the **New pull request** button
+    4. The **base repository** should be *NOAA-GFDL/GFDL_atmos_cubed_sphere*
+    5. The **base** branch is the branch you would like to add your changes to
+
+        Refer to section [Understanding the Development Branches](#Understanding-the-Development-Branches)
+        
+        This is the same branch that you originally checked out in Step 5 of this guide that was referred to as `baseBranch`
+    
+    6. The **head repository** should be your fork (e.g. *\<username\>/GFDL_atmos_cubed_sphere*)
+    7. The **compare** branch is the feeature branch containing your updates.  This was referred to as `newBranch` in this guide
+ 
+        You should now see a comparison of the two branches  
+  
+    8. Click on the **Create pull request** button
+    9. Fill in the details of the Pull request, being sure to follow the template provided:
+        1. Provide a desciption: Include a summary of the change and which issue is fixed. 
+        Please also include relevant motivation and context. 
+        List any dependencies that are required for this change.
+        2. Link the Issue from Step 2 by including a line `Fixes #123` where *123* is the Issue #
+        3. Please describe the tests that you ran to verify your changes. 
+        Please also note any relevant details for your test configuration (e.g. compiler, OS). 
+        Include enough information so someone can reproduce your tests.
+        4. Ensure that all checkboxes  are populated.  If something does not apply, please check it and note that it does not apply somewhere in the PR.
+        If you have not completed an item in the checklist, the PR will not be merged.
+        
+            To check a box replace the space in `[ ]` with an x `[x]`
+        5. Click on the **Create pull request** button.
+    10.  Code managers will assign reviewers to the PR. 
+    If you would like someone specific to review your PR please leave a comment on the PR requesting that.
+    When all reviewers approve the code, a code manager will merge the code and your changes will now be in the relevant development branch.

README.md

@@ -1,7 +1,8 @@
 # GFDL_atmos_cubed_sphere
 
-This is for the FV3 dynamical core and the GFDL Microphysics for use by NCEP/EMC within GFS.
-The source in this branch reflects the codebase used by NCEP/EMC for use in GFS and UFS.
+The source contained herein reflects the 202305 release of the Finite Volume Cubed-Sphere Dynamical Core (FV3) from GFDL
+
+The GFDL Microphysics is also available within this repository.
 
 # Where to find information