Merge branch 'esmf-org:develop' into test

.github/workflows/api-change.yml

@@ -6,7 +6,7 @@ on:
       tag1:
         description: 'First ESMF Tag'
         required: true
-        default: 'v8.3.0'
+        default: 'v8.6.0'
       tag2:
         description: 'Second ESMF Tag'
         required: true

.github/workflows/build-esmf-docs.yml

@@ -46,8 +46,8 @@ jobs:
       uses: actions/checkout@v3
       with:
           repository: esmf-org/esmf-org.github.io
-          path: esmf-org.github.io
-          token: ${{ secrets.ESMF_WEB_TOKEN }}
+          path: ${{github.workspace}}/esmf-org.github.io
+          ssh-key: ${{secrets.ESMF_WEB_DEPLOY_KEY}}
 
     - name: Copy docs
       run: | 
@@ -66,10 +66,10 @@ jobs:
         cp -rf ./dev_guide/dev_guide/* ${{ github.workspace }}/esmf-org.github.io/docs/nightly/${{ github.ref_name }}/dev_guide/
         
     - name: Commit and publish docs
-      uses: actions-js/push@master
-      with:
-        repository: esmf-org/esmf-org.github.io
-        directory: ${{ github.workspace }}/esmf-org.github.io
-        branch: master
-        github_token: ${{ secrets.ESMF_WEB_TOKEN }}
-        message: 'Publish ESMF Docs'
+      run: | 
+        cd ${{ github.workspace }}/esmf-org.github.io
+        git config user.name "github-actions[bot]"
+        git config user.email "github-actions[bot]@users.noreply.github.com"
+        git add .
+        git diff-index --quiet HEAD || git commit --message "Publish ESMF Docs"
+        git push origin

.github/workflows/build-esmpy-docs.yml

@@ -41,13 +41,13 @@ jobs:
       with:
         name: esmpy-docs
         path: ${{ github.workspace }}/artifacts
-        
+
     - name: Checkout esmpy_doc
       uses: actions/checkout@v3
       with:
           repository: esmf-org/esmpy_doc
-          path: esmpy_doc
-          token: ${{ secrets.ESMF_WEB_TOKEN }}
+          path: ${{github.workspace}}/esmpy_doc
+          ssh-key: ${{secrets.ESMPY_WEB_DEPLOY_KEY}}
 
     - name: Copy docs
       run: | 
@@ -60,10 +60,10 @@ jobs:
         cp -rf latex/ESMPy.pdf ${{ github.workspace }}/esmpy_doc/docs/nightly/${{ github.ref_name }}/
 
     - name: Commit and publish docs
-      uses: actions-js/push@master
-      with:
-        repository: esmf-org/esmpy_doc
-        directory: ${{ github.workspace }}/esmpy_doc
-        branch: master
-        github_token: ${{ secrets.ESMF_WEB_TOKEN }}
-        message: 'Publish ESMPy Docs'
+      run: |
+        cd ${{ github.workspace }}/esmpy_doc
+        git config user.name "github-actions[bot]"
+        git config user.email "github-actions[bot]@users.noreply.github.com"
+        git add .
+        git diff-index --quiet HEAD || git commit --message "Publish ESMPy Docs"
+        git push origin

.github/workflows/scripts/install_oneapi.sh

@@ -0,0 +1,80 @@
+#!/bin/bash
+
+# get arguments
+while getopts c: flag
+do
+  case "${flag}" in
+    c) comp=${OPTARG};;
+  esac
+done
+
+# print out arguments
+echo "Compiler: $comp"
+
+# download the key to system keyring
+echo "::group::Setup Intel oneAPI Repository"
+wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | \
+  gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+
+# add signed entry to apt sources and configure the APT client to use Intel repository
+echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] \
+  https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+
+# update packages list and repository index
+sudo apt-get -qq update
+echo "::endgroup::"
+
+# exit if it is already installed
+if [ -d "/opt/intel/oneapi" ]; then
+  echo "/opt/intel/oneapi directory exists. Skip installing Intel oneAPI Compiler ..."
+  sudo apt-get --fix-missing update
+  exit
+fi
+
+# get compiler version
+echo "::group::Check Specified Versiion"
+compiler_version=`echo "$comp" | awk -F\@ '{print $2}'`
+echo "Compiler Version: $compiler_version"
+
+# check the version is available or not
+if [ -z "$compiler_version" ]; then
+  echo "Compiler version needs to be specified! Exiting ..."
+  exit 1
+else
+  list_compiler_versions=`apt list 2>&1 | grep "intel-basekit-[1-9]" | awk -F\- '{print $3}' | awk -F\/ '{printf $1" "}'`
+  echo "List of available Intel oneAPI basekit, hpckit versions: $list_compiler_versions"
+  in_the_list=0
+  for i in $list_compiler_versions
+  do
+    if [[ "$i" == "$compiler_version" ]]; then
+      in_the_list=1
+      break
+    fi
+  done
+  if [ $in_the_list == 0 ]; then
+    echo "Specified compiler version ($compiler_version) is not available! Exiting ..."
+    exit 1
+  fi
+fi
+echo "::endgroup::"
+
+# install
+echo "::group::Install Intel oneAPI Base and HPC Kits"
+sudo apt-get install -qq intel-basekit-$compiler_version
+sudo apt-get install -qq intel-hpckit-$compiler_version
+# remove vtune since it is creating issue in cache due to permission issue in the installation files
+list_vtune_pkgs=`apt-cache search intel-oneapi-vtune | awk '{print $1}'`
+for i in $list_vtune_pkgs
+do
+  echo "Removing package - $i"
+  sudo apt-get purge $i
+done
+echo "::endgroup::"
+
+# list content of the installation folders (for debugging)
+echo "::group::List Files in Installation Folder"
+echo "> ls -al /opt/intel/oneapi/compiler/"
+ls -al /opt/intel/oneapi/compiler/
+echo "> ls -al /opt/intel/oneapi/mpi/"
+ls -al /opt/intel/oneapi/mpi/
+echo "::endgroup::"

.github/workflows/scripts/run_nuopc_app_proto.sh

@@ -0,0 +1,96 @@
+#!/bin/bash
+
+# get arguments
+while getopts c:r:s: flag
+do
+  case "${flag}" in
+    c) comp=${OPTARG};;
+    r) run_dir=${OPTARG};;
+    s) spack_install_dir=${OPTARG};;
+  esac
+done
+
+# check for default values
+if [[ -z "$comp" || ! -z `echo $comp | grep '^-'` ]]; then
+  comp="[email protected]"
+fi
+
+if [[ -z "$run_dir" || ! -z `echo $run_dir | grep '^-'` ]]; then
+  run_dir=`pwd`
+fi
+
+if [[ -z "$spack_install_dir" || ! -z `echo $spack_install_dir | grep '^-'` ]]; then
+  spack_install_dir=`pwd`
+fi
+
+# print out arguments
+echo "Compiler               : $comp"
+echo "Run Directory          : $run_dir";
+echo "Spack Install Directory: $spack_install_dir";
+
+# go to directory
+cd $run_dir
+
+# output esmf.mk file for debugging
+echo "::group::Content of esmf.mk"
+cat $spack_install_dir/view/lib/esmf.mk
+echo "::endgroup::"
+
+# debug
+echo "::group::Prepare Environment and Debug Output for NUOPC Application Prototypes"
+export ESMFMKFILE=$spack_install_dir/view/lib/esmf.mk
+if [[ "$comp" == *"oneapi"* ]]; then
+  # this is not correct, need to be changed later
+  . /opt/intel/oneapi/setvars.sh
+  export TOOLRUN=""
+  MPI_FC=mpiifort
+else
+  export PATH=$spack_install_dir/view/bin:$PATH
+  # set it for OpenMPI to fix not enough slots issue
+  export TOOLRUN="--oversubscribe --mca btl_tcp_if_include eth0"
+  MPI_FC=mpif90
+fi
+which mpirun
+cat testProtos.sh | grep "^Test"
+echo "::endgroup::"
+
+# test installation by building and running simple MPI job
+echo "::group::Test Installation"
+echo "program test_mpi" > test_mpi.F90
+echo "  use mpi" >> test_mpi.F90
+echo "  integer :: err, p, id" >> test_mpi.F90
+echo "  call MPI_Init(err)" >> test_mpi.F90
+echo "  call MPI_Comm_size(MPI_COMM_WORLD, p, err)" >> test_mpi.F90
+echo "  call MPI_Comm_rank(MPI_COMM_WORLD, id, err)" >> test_mpi.F90
+echo "  print*, 'Hello from ', id, ' of ', p" >> test_mpi.F90
+echo "  call MPI_Finalize(err)" >> test_mpi.F90
+echo "end program test_mpi" >> test_mpi.F90
+$MPI_FC -o test_mpi.x test_mpi.F90
+mpirun -np 2 ${TOOLRUN} ./test_mpi.x
+echo "::endgroup::"
+
+# run app prototypes 
+echo "::group::Build and Run NUOPC Application Prototypes"
+# make proto script executable
+chmod 755 testProtos.sh
+# run app prototypes in the background
+./testProtos.sh 2>&1 | tee testProtos.log
+echo "::endgroup::"
+
+# process output
+echo "::group::Process Output of NUOPC Application Prototypes"
+sed -n '/== TEST SUMMARY START ==/, /== TEST SUMMARY STOP ==/p' testProtos.log >& testProtos_summary.log
+result_fail=`cat testProtos_summary.log | grep "FAIL"`
+echo "-------------"
+echo "FAILED TESTS:"
+echo "-------------"
+cat testProtos_summary.log | grep "FAIL"
+echo "-------------"
+echo "PASSED TESTS:"
+echo "-------------"
+cat testProtos_summary.log | grep "PASS"
+if [[ ! -z "$result_fail" ]]; then
+  echo "Some of NUOPC app prototypes are failed! Exiting ..."
+  exit 1
+fi
+echo "::endgroup::"