pace container CI (#68)

* edited yaml * fix spacing in yaml * add run * fix container address * fix container address * try again * try again * testing * change checkout version * fix checkout * fix checkout * oops no git in container * oops no git in container * oops github * submodule woes * home * home * remove init * dubious ownership * testing checkout * whereami * whereami * whereami * whereami * new container * change working directory * new container * git issues * git issues * git issues * omg git * omg git * new container * conda activate * use conda * conda init bash * conda again * conda inited already * try again * constraints.txt * test * pip3 * get the right python version * consolidate runs * consolidate runs * remove cd * test pace:test * fix spacing * test checkout path * test working directory * test working directory * test working directory * change ordering * update grid unit test * modify eta test * update yaml file * oops nevermind nevermind * restore yaml file * add Dockerfile * use script to run tests * fix typo s * chmod typo * change registry * add concurrency, copied from fms * typo * remove push * unmake unecessary changes * test * lint * xfail update * Update .gitmodules * edit README.md * update tests and readme * add push * fix home * fix home * add dockerfile * fix mistakes on Docerkfile * additional dockerfiles * openmpi * test * add mpich * try again * remove test_scripts dir * update to test with openmpi and mpich * finally * noaa to readme * type missed [ * update to reality --------- Co-authored-by: mlee03 <[email protected]>
NOAA-GFDL · Apr 12, 2024 · 67277dc · 67277dc
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diff --git a/.github/workflows/main_unit_tests.yml b/.github/workflows/main_unit_tests.yml
diff --git a/.github/workflows/main_unit_tests_mpich.yaml b/.github/workflows/main_unit_tests_mpich.yaml
@@ -0,0 +1,26 @@
+name: "Main unit tests with mpich"
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  main_unit_tests:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/noaa-gfdl/pace_mpich:3.8
+    steps:
+        - name: Checkout Pace repository
+          uses: actions/checkout@v4
+          with:
+            submodules: 'recursive'
+        - name: setup env and run tests (test)
+          run: |
+            cp /home/scripts/setup_env.sh . && chmod +x setup_env.sh
+            cp /home/scripts/run_tests.sh . && chmod +x run_tests.sh
+            ./setup_env.sh
+            ./run_tests.sh
diff --git a/.github/workflows/main_unit_tests_openmpi.yaml b/.github/workflows/main_unit_tests_openmpi.yaml
@@ -0,0 +1,26 @@
+name: "Main unit tests with openmpi"
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  main_unit_tests:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/noaa-gfdl/pace_openmpi:3.8
+    steps:
+        - name: Checkout Pace repository
+          uses: actions/checkout@v4
+          with:
+            submodules: 'recursive'
+        - name: setup env and run tests
+          run: |
+            cp /home/scripts/setup_env.sh . && chmod +x setup_env.sh
+            cp /home/scripts/run_tests.sh . && chmod +x run_tests.sh
+            ./setup_env.sh
+            ./run_tests.sh
diff --git a/README.md b/README.md
@@ -123,11 +123,55 @@ mpirun --mca btl_vader_single_copy_mechanism none -n 6 python3 -m pace.driver.ru
 
 This repository was first developed at [AI2](https://github.com/ai2cm/pace) and the institute conserves an archived copy with the latest state before the NOAA took over.
 
-[contributors-shield]: https://img.shields.io/github/contributors/ai2cm/pace.svg
+[contributors-shield]: https://img.shields.io/github/contributors/NOAA-GFDL/pace.svg
 [contributors-url]: https://github.com/NOAA-GFDL/pace/graphs/contributors
 [stars-shield]: https://img.shields.io/github/stars/NOAA-GFDL/pace.svg
 [stars-url]: https://github.com/NOAA-GFDL/pace/stargazers
 [issues-shield]: https://img.shields.io/github/issues/NOAA-GFDL/pace.svg
 [issues-url]: https://github.com/NOAA-GFDL/pace/issues
 [license-shield]: https://img.shields.io/github/license/NOAA-GFDL/pace.svg
 [license-url]: https://github.com/NOAA-GFDL/pace/blob/main/LICENSE.md
+
+## Running pace in containers
+Docker images exist in the Github Container Registry associated with the NOAA-GFDL organization.
+These images are publicly accessible and can be used to run a Docker container to work with pace.
+The following are directions on how to setup the pace conda environment interactively in a container.
+
+The latest images can be pulled with the Docker as shown below or
+with any other container management tools:
+
+```shell
+docker pull ghcr.io/noaa-gfdl/pace_mpich:3.8
+```
+for MPICH installation of MPI; and
+```shell
+docker pull ghcr.io/noaa-gfdl/pace_openmpi:3.8
+```
+for OpenMPI installation of MPI.
+
+If permission issues arise during the pull, a Github personal token
+may be required.  The steps to create a personal token is found
+[here](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens)
+
+Once the token has been generated, the image can be pulled for example with with:
+```shell
+docker login --username GITHUB_USERNAME --password TOKEN
+docker pull ghcr.io/noaa-gfdl/pace_mpich:3.8
+```
+
+Any container management tools compatible with Docker images can be used
+to run the container interactively from the pulled image.
+With Docker, the following command runs the container interactively.
+```shell
+docker run -it pace_mpich:3.8
+```
+
+In the container, the default `base` conda environment is already activated.
+The `pace` conda environment can be created by following the steps below:
+
+```shell
+git clone --recursive -b develop https://github.com/NOAA-GFDL/pace.git pace
+cd pace
+cp /home/scripts/setup_env.sh . && chmod +x setup_env.sh
+source ./setup_env.sh
+```