github actions utest (#169)

.dockerignore

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

.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 '/ci-test-base/ { 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 ${GITHUB_EVENT_PATH} | ./json_helper.py check_skip)
+          echo "::set-env name=TRIGGER_ID::${tr_id}"
+          echo "::set-env name=TRIGGER_BR::${tr_br}"
+          echo "skip-ci: ${check}"
+          if [[ $check == yes ]]; then
+            echo "skip-ci is requested"
+            echo '::set-env name=CURR_JOB::cancelled'
+            curl -X POST -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -H "Accept: application/vnd.github.v3+json" ${repo}/$tr_id/cancel
+          else
+            echo '::set-env name=CURR_JOB::running'
+          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' }}

modulefiles/linux.gnu/fv3

@@ -15,6 +15,19 @@ export F77=${F77:-mpif77}
 export F90=${F90:-mpif90}
 export FC=${FC:-mpif90}
 
+##
+## set up variables for ../cmake/configure_linux.gnu.cmake
+##
+export CMAKE_Platform=linux.gnu
+export CMAKE_C_COMPILER=${CC}
+export CMAKE_CXX_COMPILER=${CXX}
+export CMAKE_Fortran_COMPILER=${FC}
+
+##
+## use own NetCDF library
+##
+export NETCDF=${NETCDF:-/usr/local}
+
 ##
 ## use SIONlib library if installed and environment variable is set
 ##
@@ -24,3 +37,19 @@ if [ ! "x$SIONLIB" == "x" ]; then
   export SIONLIB_INC="-I${SIONLIB}/include -I${SIONLIB}/include/mod_64"
   export SIONLIB_LIB="-L${SIONLIB}/lib -lsionmpi_f90_64 -lsionser_f90_64 -lsionmpi_64 -lsiongen_64 -lsionser_64 -lsioncom_64 -lsioncom_64_lock_none"
 fi
+
+##
+## use pre-compiled EMSF library for above compiler / MPI combination
+##
+export ESMFMKFILE=${ESMFMKFILE:-/usr/local/lib/esmf.mk}
+
+##
+## NCEP libraries (need to download and build manually, see doc/README_{UBUNTU,CENTOS,...}.txt and https://github.com/NCAR/NCEPlibs)
+##
+export NCEPLIBS_DIR=${NCEPLIBS_DIR:-/usr/local/NCEPlibs}
+export bacio_DIR=${NCEPLIBS_DIR}/bacio-2.4.0
+export nemsio_DIR=${NCEPLIBS_DIR}/nemsio-2.5.1
+export w3nco_DIR=${NCEPLIBS_DIR}/w3nco-2.4.0
+export sp_DIR=${NCEPLIBS_DIR}/sp-2.3.0
+export w3emc_DIR=${NCEPLIBS_DIR}/w3emc-2.7.0
+export sigio_DIR=${NCEPLIBS_DIR}/sigio-2.3.0