Merge pull request #3 from esmf-org/feature/v1.2

bring new features

README.md

@@ -22,12 +22,14 @@ The action mainly includes following features:
 
 ## What's New
 
-### v1.1
+### v1.2
 
-* Artifacts name can be given as an argument. This is expecially useful for settin up GitHub Action matrix.
-* Minor fix is applied to `get_input.py` script to find `botocore.exceptions`.
-* The run step is modified to output ESMF PET logs in case of error in the component testing.
-* Default `architecture` is changed from `x86_64_v4` to `x86_64` to make it more generic.
+* The extra `mpirun` arguments now need to be passed with `mpirun_arg` input argument.
+* A new `debug` argument is added to the action that allow to create ssh connection to the runner for debugging (uses mxschmitt/action-tmate@v3).
+* Now uses authoritative [Spack repository](https://github.com/spack/spack.git).
+* Spack now uses `curl` to download packages and timeout limit is increased to 60 s to prevent fetching issues
+* Spack now could use system installed packages (`spack external find`).
+* Fixed following issue/s: https://github.com/esmf-org/nuopc-comp-testing/issues/2
 
 ## Usage
 
@@ -52,8 +54,10 @@ Create components `.yml` file in your repositories under `.github/workflows/test
 * `component_build` - The list of shell commands to build the component. This is required since the GitHub Action do not know anything about the component build system and requirements.
 * `component_module_name` - The Fortran module name of the component that will be tested. This argument is currently required but it would be a part of the user provided YAML files.
 * `data_component_name` - The optional name of data component that will be used to force the component. The valid values are `datm` (default), `dice`, `dlnd`, `docn`, `drof` and `dwav`. It would be a part of the user provided YAML files in the future.
+* `debug` - The optional argument for debugging purpose. It triggers extra output and also create ssh connection to the runner for debugging (uses [mxschmitt/action-tmate@v3](https://github.com/mxschmitt/action-tmate)).
 * `dependencies` - The list of dependencies that are used to build the application. Since Spack is used to install dependencies, the given packages need to be part of the Spack distribution. The list of packages can be seen in [here](https://packages.spack.io). The ESMF package (`[email protected]+parallelio`) needs to be added to the list. 
 * `dependencies_install_dir` - An optional path of installation directory for dependencies. The default value is set to `~/.spack-ci`.
+* `mpirun_arg` - The required argument to be passed to `mpirun` command. For example `--oversubscribe -np 6 --mca btl_tcp_if_include eth0` can be passed to run test case on 6 processor (`--oversubscribe` is required for the jobs that needs to be run more then 2 processor and `--mca btl_tcp_if_include eth0` is required to overcome hanging issue of collective communication under GitHub runners).
 * `test_definition` - The top level YAML file that describes the test. This is required.
 
 #### Environment Variables
@@ -110,7 +114,7 @@ jobs:
     steps:
       # test component
       - name: Test Component
-        uses: esmf-org/nuopc-comp-testing@v1.1.0
+        uses: esmf-org/nuopc-comp-testing@v1.2.0
         with:
           app_install_dir: ${{ env.APP_INSTALL_DIR }}
           artifacts_name: artifacts for ${{ matrix.test }} ${{ matrix.os }} esmf@${{ matrix.esmf }}
@@ -138,10 +142,9 @@ jobs:
           component_module_name: lnd_comp_nuopc
           data_component_name: datm
           dependencies: |
-            [email protected]
-            esmf@${{ matrix.esmf }}+parallelio~xerces~pnetcdf
-            [email protected]+pnetcdf
+            esmf@${{ matrix.esmf }}+external-parallelio
           dependencies_install_dir: ${{ env.DEP_INSTALL_DIR }}
+          mpirun_args: --oversubscribe -np 6 --mca btl_tcp_if_include eth0
           test_definition: ${{ env.APP_INSTALL_DIR }}/noahmp/.github/workflows/tests/${{ matrix.test }}.yaml
 ```
 

action.yaml

@@ -29,6 +29,10 @@ inputs:
   cache_input_file_list:
     description: list of input files that needs to be cached
     required: false
+  compiler:
+    description: compiler that will be used
+    required: false
+    default: [email protected]
   component_name:
     description: component name
     required: false
@@ -43,13 +47,20 @@ inputs:
     description: data component name
     required: false
     default: datm
+  debug:
+    description: enable debug capability
+    required: false
+    default: OFF
   dependencies:
     description: list of packages to install
     required: true
   dependencies_install_dir:
     description: spack dependency installation directory
     required: false
     default: ~/.spack-ci
+  mpirun_args:
+    description: atguments that will be used in mpirun command
+    required: true
   test_definition:
     description: YAML file that describes the test
     required: true
@@ -77,9 +88,11 @@ runs:
     # concretize dependencies
     - name: Concretize Spack Environment Using YAML Specification
       run: |
+        echo "${{ inputs.dependencies }}"
         $GITHUB_ACTION_PATH/scripts/concretize_deps.sh \
           -a ${{ inputs.architecture }} \
-          -d $(echo "${{ inputs.dependencies }}" | awk '$1=$1' RS= OFS=,) \
+          -c ${{ inputs.compiler }} \
+          -d "$(echo "${{ inputs.dependencies }}" | sed -z 's/\n/:/g' | sed 's/:$//')" \
           -i ${{ inputs.dependencies_install_dir }} \
           -r $GITHUB_WORKSPACE
       shell: bash
@@ -97,7 +110,8 @@ runs:
     - name: Install Dependencies with Spack 
       run: |
         $GITHUB_ACTION_PATH/scripts/install_deps.sh \
-          -r $GITHUB_WORKSPACE
+          -i "${{ inputs.dependencies_install_dir }}" \
+          -r "$GITHUB_WORKSPACE"
       shell: bash
 
     # checkout data models
@@ -179,21 +193,30 @@ runs:
         python3 $GITHUB_ACTION_PATH/scripts/gen_config.py --ifile ${{ inputs.test_definition }}
       shell: bash
 
+    # used to debug run and allow ssh just before running the model
+    - name: Setup tmate session to allow ssh connection
+      if: ${{ inputs.debug == 'ON' }}
+      uses: mxschmitt/action-tmate@v3
+
     # run application
     - name: Run Application
       run: |
         export PATH=${{ inputs.dependencies_install_dir }}/view/bin:$PATH
         cd ${{ inputs.app_install_dir }}/run
-        mpirun --oversubscribe -np 6 --allow-run-as-root ${{ inputs.app_install_dir }}/build/esmx 2>&1 | tee out_err.txt
-        if [ $? -ne 0 ]; then
+        mpirun ${{ inputs.mpirun_args }} ${{ inputs.app_install_dir }}/build/esmx >& out_err.txt
+        cat out_err.txt
+        exc=$?
+        if [ $exc -ne 0 ]; then
           echo "Component did not run successfully! Partial output from PET log files: "
           tail -n 50 PET*
+          exit $exc
         fi
       shell: bash {0}
 
     # upload model artifacts to check it later
     - name: Upload Artifacts
       uses: actions/upload-artifact@v3
+      if: ${{ always() }}
       with:
         name: ${{ inputs.artifacts_name }}
         path: ${{ inputs.artifacts_files }}

scripts/concretize_deps.sh

@@ -1,11 +1,12 @@
 #!/bin/bash
 
 # get arguments
-while getopts a:d:i:r: flag
+while getopts a:c:d:i:r: flag
 do
   case "${flag}" in
     a) arch=${OPTARG};;
-    d) deps=${OPTARG};;
+    c) comp=${OPTARG};;
+    d) deps="${OPTARG}";;
     i) install_dir=${OPTARG};;
     r) run_dir=${OPTARG};;
   esac
@@ -30,21 +31,32 @@ if [[ -z "$run_dir" || ! -z `echo $run_dir | grep '^-'` ]]; then
 fi
 
 if [[ -z "$arch" || ! -z `echo $arch | grep '^-'` ]]; then
-  arch="x86_64_v4"
+  arch="x86_64"
+fi
+
+if [[ -z "$comp" || ! -z `echo $comp | grep '^-'` ]]; then
+  comp="[email protected]"
 fi
 
 # print out arguments
 echo "Target Architecture: $arch"
+echo "Compiler: $comp"
 echo "Dependencies: $deps";
 echo "Install Directory: $install_dir";
 echo "Run Directory: $run_dir";
 
 # go to directory
 cd $run_dir
 
-# checkout spack
+# checkout spack and setup to use it
 echo "::group::Checkout Spack"
-git clone -b jcsda_emc_spack_stack https://github.com/NOAA-EMC/spack.git
+git clone https://github.com/spack/spack.git
+. spack/share/spack/setup-env.sh
+echo "::endgroup::"
+
+# find compilers
+spack compiler find
+cat ~/.spack/linux/compilers.yaml
 echo "::endgroup::"
 
 # create spack.yaml
@@ -56,30 +68,47 @@ echo "      granularity: generic" >> spack.yaml
 echo "      host_compatible: false" >> spack.yaml
 echo "    unify: when_possible" >> spack.yaml
 echo "  specs:" >> spack.yaml
-IFS=', ' read -r -a array <<< "$deps"
+IFS=':' read -r -a array <<< "$deps"
 for d in "${array[@]}"
 do
-  echo "  - $d target=$arch" >> spack.yaml
+  echo "  - $d %$comp target=$arch" >> spack.yaml
 done
 echo "  packages:" >> spack.yaml
 echo "    all:" >> spack.yaml
 # following is required to build same optimized spack for different github action runners
 # spack arch --known-targets command can be used to list known targets
 echo "      target: ['$arch']" >> spack.yaml
-# following fixes compiler version
-echo "      compiler: [[email protected]]" >> spack.yaml
+echo "      compiler: [$comp]" >> spack.yaml
 echo "  view: $install_dir/view" >> spack.yaml
 echo "  config:" >> spack.yaml
 echo "    source_cache: $install_dir/source_cache" >> spack.yaml
 echo "    misc_cache: $install_dir/misc_cache" >> spack.yaml
 echo "    test_cache: $install_dir/test_cache" >> spack.yaml
 echo "    install_tree:" >> spack.yaml
 echo "      root: $install_dir/opt" >> spack.yaml
+echo "    install_missing_compilers: true" >> spack.yaml
 cat spack.yaml
 echo "::endgroup::"
 
+# find external tools
+echo "::group::Find Externals"
+spack external find
+echo "::endgroup::"
+
+# create config file (to fix FetchError issue)
+echo "::group::Create config.yaml"
+echo "config:" > ~/.spack/config.yaml
+echo "  url_fetch_method: curl" >> ~/.spack/config.yaml
+echo "  connect_timeout: 60" >> ~/.spack/config.yaml
+cat ~/.spack/config.yaml
+echo "::endgroup::"
+
 # concretize spack environment
 echo "::group::Concretize Spack Environment Using YAML Specification"
-. spack/share/spack/setup-env.sh
 spack --color always -e $run_dir/. concretize -f
+exc=$?
+if [ $exc -ne 0 ]; then
+  echo "Error in concretizing dependencies! exit code is $exc ..."
+  exit $exc
+fi
 echo "::endgroup::"

scripts/create_exe.sh

@@ -72,6 +72,11 @@ cat esmxBuild.yaml
 
 # create build directory
 cmake -H$ESMF_ESMXDIR -Bbuild
+exc=$?
+if [ $exc -ne 0 ]; then
+  echo "Error when creating executable! exit code is $exc ..."
+  exit $exc
+fi
 
 # compile and create executable
 cd $app_install_dir/build

scripts/get_input.py

@@ -44,6 +44,16 @@ def recv_files(_dict, fhash, force_download):
             else:
                 sys.exit('Files are not listed for component {} and section {}!'.format(k1, k2))
 
+            if 'force' in v2:
+                force = v2['force']
+            else:
+                force = False
+
+            # overwrite force download using YAML
+            if force:
+                force_download = True
+                print('Force download of {}!'.format(files))
+
             # save current directory
             current_dir = os.getcwd()
 

scripts/install_deps.sh

@@ -1,14 +1,19 @@
 #!/bin/bash
 
 # get arguments
-while getopts r: flag
+while getopts i:r: flag
 do
   case "${flag}" in
+    i) install_dir=${OPTARG};;
     r) run_dir=${OPTARG};;
   esac
 done
 
 # check for default values
+if [[ -z "$install_dir" || ! -z `echo $install_dir | grep '^-'` ]]; then
+  install_dir="$HOME/.spack-ci"
+fi
+
 if [[ -z "$run_dir" || ! -z `echo $run_dir | grep '^-'` ]]; then
   run_dir=`pwd`
 fi
@@ -23,4 +28,14 @@ cd $run_dir
 echo "::group::Install Spack Packages"
 . spack/share/spack/setup-env.sh
 spack --color always -e $run_dir/. install -j3 --deprecated --no-checksum
+exc=$?
+if [ $exc -ne 0 ]; then
+  echo "Error in installing dependencies! exit code is $exc ..."
+  exit $exc
+fi
+echo "::endgroup::"
+
+# output esmf.mk file for debugging
+echo "::group::Content of esmf.mk"
+cat $install_dir/view/lib/esmf.mk
 echo "::endgroup::"