Ci fix

.dockerignore

@@ -0,0 +1,5 @@
+Dockerfile
+.git
+.gitignore
+tests/*.log
+tests/log_ut_linux.gnu

.github/pull_request_template.md

@@ -4,8 +4,7 @@
 Provide a detailed description of what this PR does.
 What bug does it fix, or what feature does it add?
 Is a change of answers expected from this PR?
-
-
+Are any library updates included in this PR (modulefiles etc.)?
 
 ### Issue(s) addressed
 
@@ -14,15 +13,12 @@ Link the issues to be closed with this PR, whether in this repository, or in ano
 - fixes #<issue_number>
 - fixes noaa-emc/fv3atm/issues/<issue_number>
 
-
-
 ## Testing
 
 How were these changes tested?
 What compilers / HPCs was it tested with?
 Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)
-
-
+Have regression tests and unit tests (utests) been run? On which platforms and with which compilers? (Note that unit tests can only be run on tier-1 platforms)
 
 ## Dependencies
 

.github/workflows/main.yml

@@ -0,0 +1,121 @@
+name: Pull Request Tests
+
+on:
+  push:
+    branches:
+    - develop
+  pull_request:
+    branches:
+    - develop
+
+jobs:
+  setup:
+    name: Set up
+    runs-on: ubuntu-latest
+
+    outputs:
+      tn: ${{ steps.parse.outputs.tn }}
+      bld: ${{ steps.parse.outputs.bld }}
+      test: ${{ steps.parse.outputs.test }}
+      img: ${{ steps.parse.outputs.img }}
+
+    steps:
+    - name: Checkout codes
+      uses: actions/checkout@v2
+
+    - name: Parse cases
+      id: parse
+      run: |
+        cd ${GITHUB_WORKSPACE}/tests/ci
+        parsed_output=( $(./parse.sh) )
+        name_=${parsed_output[0]}
+        bld_=${parsed_output[1]}
+        test_=${parsed_output[2]}
+        img_=${parsed_output[3]}
+
+        echo "::set-output name=tn::$name_"
+        echo "::set-output name=bld::$bld_"
+        echo "::set-output name=test::$test_"
+        echo "::set-output name=img::$img_"
+
+        echo "test name : $name_"
+        echo "build set : $bld_"
+        echo "test set  : $test_"
+        echo "image name: $img_"
+
+  build:
+    name: Build (${{ matrix.bld_set }})
+    needs: setup
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix: ${{ fromJson(needs.setup.outputs.bld) }}
+
+    steps:
+    - name: Checkout codes
+      uses: actions/checkout@v2
+      with:
+        submodules: recursive
+
+    - name: Build
+      run: |
+        printf '{\n    "experimental": true\n}' | sudo tee /etc/docker/daemon.json >/dev/null
+        sudo systemctl restart docker
+        sleep 10
+        cd tests/ci && ./ci.sh -n ${{ needs.setup.outputs.tn }} -b ${{ matrix.bld_set }}
+
+    - name: Free up disk space
+      run: |
+        sudo docker rmi $(sudo docker image ls | grep -E -m1 '<none>' | awk '{ print $3 }')
+        sudo docker rmi $(sudo docker image ls | awk '/ubuntu-hpc/ { print $3 }')
+
+    - name: Prepare artifacts
+      run: |
+        cd tests/ci
+        sudo docker save ${{ needs.setup.outputs.img }} | gzip >${{ needs.setup.outputs.img }}.tar.gz
+        tar cvjf artifact.tar.bz2 ${{ needs.setup.outputs.img }}.tar.gz ci.sh ci.test
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v2
+      with:
+        name: ${{ matrix.bld_set }}.artifact.tar.bz2
+        path: tests/ci/artifact.tar.bz2
+
+  utest:
+    name: Unit test (${{ needs.setup.outputs.tn }}, ${{ matrix.test_set }})
+    needs: [setup,build]
+    runs-on: ubuntu-latest
+    #runs-on: self-hosted
+
+    strategy:
+      fail-fast: false
+      matrix: ${{ fromJson(needs.setup.outputs.test) }}
+
+    steps:
+    - name: Download artifacts
+      uses: actions/download-artifact@v2
+      with:
+        name: ${{ matrix.artifact }}.artifact.tar.bz2
+
+    - name: Prepare artifacts
+      run: |
+        tar xvjf artifact.tar.bz2 && rm -f artifact.tar.bz2
+        sudo docker load --input ${{ needs.setup.outputs.img }}.tar.gz && rm -f ${{ needs.setup.outputs.img }}.tar.gz
+
+    - name: Run utest
+      run: ./ci.sh -n ${{ needs.setup.outputs.tn }} -r ${{ matrix.test_set }}
+
+    - name: Upload memory usage file
+      if: ${{ always() }}
+      uses: actions/upload-artifact@v2
+      with:
+        name: memory_stat_${{ matrix.test_set }}
+        path: memory_stat
+
+    - name: Clean up
+      if: ${{ always() }}
+      run: |
+        rm -f ci.sh ci.test
+        sudo docker rm  my-container && sudo docker rmi ${{ needs.setup.outputs.img }}:latest
+        sudo docker volume rm DataVolume

.github/workflows/manage.yml

@@ -0,0 +1,54 @@
+name: Manage workflows
+
+on:
+  workflow_run:
+    workflows: ["Pull Request Tests"]
+    types:
+      - requested
+
+jobs:
+  job1:
+    name: Job 1
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout codes
+        uses: actions/checkout@v2
+
+      - name: Check if skip-ci is requested
+        run: |
+          cd ${GITHUB_WORKSPACE}/tests/ci
+          repo="${GITHUB_API_URL}/repos/${GITHUB_REPOSITORY}/actions/runs"
+          tr_id=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py get_trigger_id)
+          tr_br=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py get_trigger_br)
+          check=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py check_skip)
+          echo "TRIGGER_ID=${tr_id}" >> $GITHUB_ENV
+          echo "TRIGGER_BR=${tr_br}" >> $GITHUB_ENV
+          echo "skip-ci: ${check}"
+          if [[ $check == yes ]]; then
+            echo "skip-ci is requested"
+            echo "CURR_JOB=cancelled" >> $GITHUB_ENV
+            curl -X POST -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -H "Accept: application/vnd.github.v3+json" ${repo}/$tr_id/cancel
+          else
+            echo "CURR_JOB=running" >> $GITHUB_ENV
+          fi
+
+      - name: Cancel redundant jobs
+        run: |
+          echo "CURR_JOB is $CURR_JOB"
+          echo "TRIGGER_ID is $TRIGGER_ID"
+          echo "TRIGGER_BR is $TRIGGER_BR"
+          export GITHUB_ACTOR
+          export GITHUB_RUN_ID
+          export TRIGGER_ID
+          export TRIGGER_BR
+          cd ${GITHUB_WORKSPACE}/tests/ci
+          repo="${GITHUB_API_URL}/repos/${GITHUB_REPOSITORY}/actions/runs"
+          cancel_ids=$(curl -H "Accept: application/vnd.github.v3+json" ${repo} | ./json_helper.py cancel_workflow)
+          echo "cancel ids: $cancel_ids"
+          if [[ $cancel_ids != '' ]]; then
+            for i in $cancel_ids; do
+              curl -X POST -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -H "Accept: application/vnd.github.v3+json" ${repo}/$i/cancel
+            done
+          fi
+        if: ${{ env.CURR_JOB == 'running' }}

.gitignore

@@ -1,2 +1,70 @@
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+*.x
+
+# system files
+*.swp
+*~
+.DS_Store
+
+# python files
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# CMake files and directories
+build*/
+install*/
+CMakeLists.txt.user
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
+
+# repo-specific ignorables
 coupled*.mk
 rt.conf.single
+ufs_model
+tests/modules.fv3_*
+tests/ecflow_run/
+tests/log_*/
+tests/lock/
+tests/Compile_*.log
+tests/fail_test
+log*
+build*.log*

.gitmodules

@@ -1,20 +1,42 @@
 [submodule "FV3"]
-	path = FV3
-	url = https://github.com/NOAA-EMC/fv3atm
-	branch = develop
+  path = FV3
+  #url = https://github.com/NOAA-GSL/fv3atm
+  #branch = gsl/develop
+  url = https://github.com/climbfuji/fv3atm
+  branch = update_develop_from_gsl_develop
 [submodule "NEMS"]
-	path = NEMS
-	url = https://github.com/NOAA-EMC/NEMS
-	branch = develop
+  path = NEMS
+  url = https://github.com/NOAA-EMC/NEMS
+  branch = develop
 [submodule "FMS"]
-	path = FMS
-	url = https://github.com/NOAA-GFDL/FMS
-	branch = master
+  path = FMS
+  url = https://github.com/NOAA-GFDL/FMS
+  branch = master
 [submodule "WW3"]
-	path = WW3
-	url = https://github.com/NOAA-EMC/WW3
-	branch = develop
+  path = WW3
+  url = https://github.com/NOAA-EMC/WW3
+  branch = develop
 [submodule "stochastic_physics"]
-	path = stochastic_physics
-	url = https://github.com/noaa-psd/stochastic_physics
-	branch = master
+  path = stochastic_physics
+  url = https://github.com/noaa-psd/stochastic_physics
+  branch = master
+[submodule "CMakeModules"]
+  path = CMakeModules
+  url = https://github.com/NOAA-EMC/CMakeModules
+  branch = develop
+[submodule "CMEPS"]
+  path = CMEPS-interface/CMEPS
+  url = https://github.com/NOAA-EMC/CMEPS.git
+  branch = emc/develop
+[submodule "MOM6"]
+  path = MOM6-interface/MOM6
+  url = https://github.com/NOAA-EMC/MOM6
+  branch = dev/emc
+[submodule "CICE"]
+  path = CICE-interface/CICE
+  url = https://github.com/NOAA-EMC/CICE
+  branch = emc/develop
+[submodule "DATM"]
+  path = DATM
+  url = https://github.com/NOAA-EMC/NEMSdatm
+  branch = develop