AwS setup

.github/workflows/build_parallelWorks_intel_tag.yml

@@ -0,0 +1,43 @@
+name: Tag CI libFMS and AM4 regression
+
+on:
+   push:
+        tags:
+             - '*alpha*'
+             - '*beta*'
+   workflow_dispatch:
+jobs:
+   parallelWorks:
+    runs-on: [self-hosted, pw-platform]
+    strategy:
+      fail-fast: false
+      max-parallel: 3
+      matrix:
+        include:
+                - runname: FMS with intel 18
+                  runscript: python3 /home/Thomas.Robinson/pw/storage/pw_api_python/FMStestStartClusters.py azcluster_noaa
+                - runname: FMS with intel 2021 container
+                  runscript: python3 /home/Thomas.Robinson/pw/storage/pw_api_python/FMSintel21StartClusters.py azcluster_noaa_two
+                - runname: AM4 regression
+                  runscript: python3 /home/Thomas.Robinson/pw/storage/pw_api_python/AM4_intel21StartClusters.py azcluster_noaa
+
+    steps:
+                - name: FMS make check on paralellWorks
+                  env:
+                          RUNNAME: ${{ matrix.runname }}
+                          RUNSCRIPT: ${{ matrix.runscript }}
+                  run: $RUNSCRIPT
+   ShutDownCluster:
+    runs-on: [self-hosted, pw-platform]
+    if: always()
+    needs: [parallelWorks]
+    strategy:
+      matrix:
+        include:
+                - cluster: azcluster_noaa
+                - cluster: azcluster_noaa_two
+    steps:
+                - name: Turn off cluster
+                  env:
+                          CLUSTER: ${{ matrix.cluster }}
+                  run: python3 /home/Thomas.Robinson/pw/storage/pw_api_python/stopClusters.py $CLUSTER

.github/workflows/build_ubuntu_gnu.yml

@@ -30,3 +30,5 @@ jobs:
         DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.distcheck-conf-flags }}"
     - name: Build the library
       run: make -j distcheck
+      env:
+        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.distcheck-conf-flags }}"

.github/workflows/do-the-job.yml

@@ -0,0 +1,74 @@
+name: do-the-job
+on: pull_request
+jobs:
+  start-runner:
+    name: Start self-hosted EC2 runner
+    runs-on: ubuntu-latest
+    outputs:
+      label: ${{ steps.start-ec2-runner.outputs.label }}
+      ec2-instance-id: ${{ steps.start-ec2-runner.outputs.ec2-instance-id }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+      - name: Start EC2 runner
+        id: start-ec2-runner
+        uses: machulav/ec2-github-runner@v2
+        with:
+          mode: start
+          github-token: ${{ secrets.GH_PERSONAL_ACCESS_TOKEN }}
+          #ec2-image-id: ami-092a9e946def5be32
+          ec2-image-id: ami-02e136e904f3da870
+          ec2-instance-type: m5.4xlarge
+          subnet-id: subnet-02829d7b8c3522644
+          security-group-id: sg-09f60dd1eeea6d55f
+          #subnet-id: subnet-003faaf9f1e386979
+          #security-group-id: sg-05735797b251348e2
+       ##   iam-role-name: arn:aws:iam::430073024411:user/fms_test
+  do-the-job:
+    name: Do the job on the runner
+    needs: start-runner # required to start the main job when the runner is ready
+    runs-on: ${{ needs.start-runner.outputs.label }} # run the job on the newly created runner
+    steps:
+      - name: Install epel 
+        run:  sudo amazon-linux-extras install epel -y
+      - name: config epel 
+        run:  sudo yum-config-manager --enable epel
+      - name: Install singularity
+        run:  sudo yum install -y singularity git
+      - name: Clone from git
+        run: git clone https://github.com/thomas-robinson/build_fms_script.git
+      - name: Pull the container
+        run:  singularity pull docker://thomasrobinson/model_environment:i2021.2
+      - name: Build FMS in the container
+        run:  singularity exec model_environment_i2021.2.sif ./build_fms.sh
+  stop-runner:
+    name: Stop self-hosted EC2 runner
+    needs:
+      - start-runner # required to get output from the start-runner job
+      - do-the-job # required to wait when the main job is done
+    runs-on: ubuntu-latest
+    if: ${{ always() }} # required to stop the runner even if the error happened in the previous jobs
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: ${{ secrets.AWS_REGION }}
+      - name: Stop EC2 runner
+        uses: machulav/ec2-github-runner@v2
+        with:
+          mode: stop
+          github-token: ${{ secrets.GH_PERSONAL_ACCESS_TOKEN }}
+          label: ${{ needs.start-runner.outputs.label }}
+          ec2-instance-id: ${{ needs.start-runner.outputs.ec2-instance-id }}
+ ## optional, requires additional permissions
+  #        aws-resource-tags: > # optional, requires additional permissions
+   #         [
+    #          {"Key": "Name", "Value": "ec2-github-runner"},
+     #         {"Key": "GitHubRepository", "Value": "${{ github.repository }}"}
+      #      ]

.github/workflows/parallelWorks_intel_pr.yml

@@ -0,0 +1,37 @@
+name: Pull Request CI libFMS with intel18 and intel21
+
+on: pull_request 
+jobs:
+   parallelWorks:
+    runs-on: [self-hosted, pw-platform]
+    strategy:
+      fail-fast: false
+      max-parallel: 2
+      matrix:
+        include:
+# Turn this back on when fixed 
+                - runname: FMS with intel 18
+                  runscript: python3 /home/Thomas.Robinson/pw/storage/pw_api_python/PRFMSintel18StartClusters.py $GITHUB_REF
+# Runs on FMS_CONTAINER_CI cluster
+                - runname: FMS with intel 2021 container
+                  runscript: python3 /home/Thomas.Robinson/pw/storage/pw_api_python/PRFMSintel21StartClusters.py $GITHUB_REF
+    steps:
+                - name: FMS make check on paralellWorks
+                  env:
+                          RUNNAME: ${{ matrix.runname }}
+                          RUNSCRIPT: ${{ matrix.runscript }}
+                  run: $RUNSCRIPT
+   ShutDownCluster:
+    runs-on: [self-hosted, pw-platform]
+    if: always()
+    needs: [parallelWorks]
+    strategy:
+      matrix:
+        include:
+                - cluster: FMS_CONTAINER_CI
+                - cluster: fms_intel18_ci
+    steps:
+                - name: Turn off cluster
+                  env:
+                          CLUSTER: ${{ matrix.cluster }}
+                  run: python3 /home/Thomas.Robinson/pw/storage/pw_api_python/stopClusters.py $CLUSTER

CHANGELOG.md

@@ -6,6 +6,28 @@ and this project uses `yyyy.rr[.pp]`, where `yyyy` is the year a patch is releas
 `rr` is a sequential release number (starting from `01`), and an optional two-digit
 sequential patch number (starting from `01`).
 
+## [2021.03] - 2021-08-16
+### Known Issues
+- DIAG_MANAGER: 3D diurnal diagnostic variables are not supported in this version of FMS
+### Added
+- FMS2_IO: Documentation was added for FMS2_io to help users convert from fms_io/mpp_io
+### Changed
+- FMS2_IO: The error messages in FMS2_io were updated to give more useful information
+- TEST_FMS: The unit tests in mosaic, axis_utils, and time_interp_external were updated to use the FMS2_io version of these routines and are no longer skipped
+- DOCS: The doxygen generated documentation has been improved with more doxygen comments added and a more cohesive layout
+- TEST_FMS: Unit tests for time_manager were updated to use the new get/set_date_gregorian routines
+### Removed
+- MPP_IO: The namelist variable use_mpp_io was removed from interpolator, amip_interp, diag_manager, topography, xgrid, and data_override
+- MPP_IO: Any remaining fms_io/mpp_io calls from the source and test code were removed
+- FMS: Removes the hardcoded path for input.nml, path now may be specified in the call to `fms_init`
+### Fixed
+- MPP: Fixes algorithm used with nested grid updates to properly coalesce x-dir and y-dir pelists for vector quantities
+- CMAKE/AUTOTOOLS: Fixes for minor issues with filenames in both the CMake and autotools build systems
+- MPP: Restored deleted pset functionality needed by GFDL SCM by reinstating mpp_pset.F90
+- MPP: Fixed uninitialized variables for data domains in mpp domains broadcast routines
+- MPP: Minor memory leaks from deallocating domains
+- AXIS_UTILS: Fix PGI related error with string length sizes
+
 ## [2021.02] - 2021-05-20
 ### Added
 - FMS2_IO: Added fms2_io support for boundary condition restarts. `register_restart_region_2d` and `register_restart_region_3d` were added to fms2_io’s `register_restart_field` interface and `read_restart_bc` and `write_restart_bc` subroutines were added to read and write boundary conditions restarts. See [test_fms/fms2_io/test_bc_restart.F90](https://github.com/NOAA-GFDL/FMS/blob/9d55115a331685e4c6e01f2dfb3b770a9f80fa37/test_fms/fms2_io/test_bc_restart.F90) for sample usage.

CMakeLists.txt

@@ -19,11 +19,11 @@
 
 # Copyright (c) GFDL, @underwoo
 
-cmake_minimum_required(VERSION 3.7...3.15 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
 # Define the CMake project
 project(FMS
-  VERSION 2021.02.0
+  VERSION 2021.03.0
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)
@@ -93,11 +93,11 @@ list(APPEND fms_fortran_src_files
   block_control/block_control.F90
   column_diagnostics/column_diagnostics.F90
   constants/constants.F90
+  constants/fmsconstants.F90
   coupler/atmos_ocean_fluxes.F90
   coupler/coupler_types.F90
   coupler/ensemble_manager.F90
-  data_override/get_grid_version_fms2io.F90
-  data_override/get_grid_version_mpp.F90
+  data_override/get_grid_version.F90
   data_override/data_override.F90
   diag_integral/diag_integral.F90
   diag_manager/diag_axis.F90

Makefile.am

@@ -65,6 +65,7 @@ SUBDIRS = \
   tracer_manager \
   sat_vapor_pres \
   random_numbers \
+  . \
   libFMS \
   test_fms \
   ${DOCS}

README.md

@@ -63,6 +63,15 @@ infrastructural changes to enable such developments are within the scope of FMS.
 The collaborative software review process of contributed models is therefore an
 essential facet of FMS.
 
+## Documentation
+
+Source code documentation for the FMS code base is available at http://noaa-gfdl.github.io/FMS.
+The documentation is generated by doxygen and updated upon releases, and a copy of the site
+can be obtained through the `gh-pages` branch or generated manually with
+`./configure --enable-docs && make -C docs`. For more information on documentating the code
+with doxygen please see the
+[documentation style guide](http://noaa-gfdl.github.io/FMS/md_docs_doxygenGuide.html).
+
 # Disclaimer
 
 The United States Department of Commerce (DOC) GitHub project code is provided