Add CI to repo

.github/.parallelworks/README.md

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+# .parallelworks Directory
+
+The .parallelworks directory stores the CI scripts that reside on Parallelworks
+These scripts are executed via the GitHub Actions Workflows in .github/workflows
+
+On Parallelworks these scripts are installed at: /contrib/fv3/SHiELD_build_CI

.github/.parallelworks/checkout.sh

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+#!/bin/bash -xe
+
+##############################################################################
+## User set up variables
+## Root directory for CI
+dirRoot=/contrib/fv3
+## Intel version to be used
+intelVersion=2023.2.0
+##############################################################################
+## HPC-ME container
+container=/contrib/containers/noaa-intel-prototype_2023.09.25.sif
+container_env_script=/contrib/containers/load_spack_noaa-intel.sh
+##############################################################################
+
+#Parse Arguments
+branch=main
+commit=""
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    -b|--branch)
+      branch="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    -h|--hash)
+      commit="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    *)
+      echo "unknown argument"
+      exit 1
+      ;;
+  esac
+done
+
+echo "branch is $branch"
+echo "commit is $commit"
+
+
+## Set up the directories
+testDir=${dirRoot}/${intelVersion}/SHiELD_build/${branch}/${commit}
+logDir=${testDir}/log
+export MODULESHOME=/usr/share/lmod/lmod
+#Define External Libs path
+export EXTERNAL_LIBS=${dirRoot}/${intelVersion}/SHiELD_build/externallibs
+mkdir -p ${EXTERNAL_LIBS}
+## create directories
+rm -rf ${testDir}
+mkdir -p ${logDir}
+# salloc commands to start up 
+#2 tests layout 8,8 (16 nodes)
+#2 tests layout 4,8 (8 nodes)
+#9 tests layout 4,4 (18 nodes)
+#5 tests layout 4,1 (5 nodes)
+#17 tests layout 2,2 (17 nodes)
+#salloc --partition=p2 -N 64 -J ${branch} sleep 20m &
+
+## clone code
+cd ${testDir}
+git clone --recursive https://github.com/NOAA-GFDL/SHiELD_build.git  
+## Check out the PR
+cd ${testDir}/SHiELD_build && git fetch origin ${branch}:toMerge && git merge toMerge
+
+##checkout components
+cd ${testDir}/SHiELD_build && ./CHECKOUT_code
+#Check if we already have FMS compiled
+grep -m 1 "fms_release" ${testDir}/SHiELD_build/CHECKOUT_code > ${logDir}/release.txt
+source ${logDir}/release.txt
+echo ${fms_release}
+echo `cat ${EXTERNAL_LIBS}/FMSversion`
+if [[ ${fms_release} != `cat ${EXTERNAL_LIBS}/FMSversion` ]]
+  then
+    #remove libFMS if it exists
+    if [ -d $EXTERNAL_LIBS/libFMS ]
+      then
+        rm -rf $EXTERNAL_LIBS/libFMS
+    fi
+    if [ -e $EXTERNAL_LIBS/FMSversion ]
+      then
+        rm $EXTERNAL_LIBS/FMSversion
+    fi
+    echo $fms_release > $EXTERNAL_LIBS/FMSversion
+    echo $container > $EXTERNAL_LIBS/FMScontainerversion
+    echo $container_env_script >> $EXTERNAL_LIBS/FMScontainerversion
+    # Build FMS
+    cd ${testDir}/SHiELD_build/Build
+    set -o pipefail
+    singularity exec -B /contrib ${container} ${container_env_script} "./BUILDlibfms intel"
+ fi

.github/.parallelworks/compile.sh

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+#!/bin/bash -xe
+
+##############################################################################
+## User set up variables
+## Root directory for CI
+dirRoot=/contrib/fv3
+## Intel version to be used
+intelVersion=2023.2.0
+##############################################################################
+## HPC-ME container
+container=/contrib/containers/noaa-intel-prototype_2023.09.25.sif
+container_env_script=/contrib/containers/load_spack_noaa-intel.sh
+##############################################################################
+
+#Parse Arguments
+branch=main
+commit=""
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    -b|--branch)
+      branch="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    -h|--hash)
+      commit="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    -c|--config)
+      config="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    --hydro)
+      hydro="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    --bit)
+      bit="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    -m|--mode)
+      mode="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    *)
+      echo "unknown argument"
+      exit 1
+      ;;
+  esac
+done
+
+if [ -z $mode ] || [ -z $bit ] || [ -z $hydro ] || [ -z $config ]
+  then
+    echo "must specify config, hydro, bit, and mode options for compile"
+    exit 1
+fi
+
+echo "branch is $branch"
+echo "commit is $commit"
+echo "mode is $mode"
+echo "bit is $bit"
+echo "hydro is $hydro"
+echo "config is $config"
+
+if [ $hydro = "sw" ] && [ $config = "shield" ]
+  then
+    echo "this combination should not be tested"
+  else
+    ## Set up the directories
+    testDir=${dirRoot}/${intelVersion}/SHiELD_build/${branch}/${commit}
+    logDir=${testDir}/log
+    # Set up build
+    cd ${testDir}/SHiELD_build/Build
+    #Define External Libs path
+    export EXTERNAL_LIBS=${dirRoot}/${intelVersion}/SHiELD_build/externallibs
+    # Build SHiELD
+    set -o pipefail
+    singularity exec -B /contrib ${container} ${container_env_script} "./COMPILE ${config} ${hydro} ${bit} ${mode} intel clean"
+fi

.github/.parallelworks/run_test.sh

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+#!/bin/bash -xe
+ulimit -s unlimited
+##############################################################################
+## User set up veriables
+## Root directory for CI
+dirRoot=/contrib/fv3
+## Intel version to be used
+intelVersion=2023.2.0
+##############################################################################
+## HPC-ME container
+container=/contrib/containers/noaa-intel-prototype_2023.09.25.sif
+container_env_script=/contrib/containers/load_spack_noaa-intel.sh
+##############################################################################
+
+#Parse Arguments
+branch=main
+commit=""
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    -b|--branch)
+      branch="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    -h|--hash)
+      commit="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    -t|--test)
+      testname="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    *)
+      echo "unknown argument"
+      exit 1
+      ;;
+  esac
+done
+
+if [ -z $testname ]
+  then
+    echo "must specify a test name with -t"
+    exit 1
+fi
+
+echo "branch is $branch"
+echo "commit is $commit"
+echo "test is $testname"
+
+## Set up the directories
+MODULESHOME=/usr/share/lmod/lmod
+testDir=${dirRoot}/${intelVersion}/SHiELD_build/${branch}/${commit}
+logDir=${testDir}/log
+baselineDir=${dirRoot}/baselines/intel/${intelVersion}
+
+## Run the CI Test
+# Define the builddir testscriptdir and rundir 
+# Set the BUILDDIR for the test script to use
+export BUILDDIR="${testDir}/SHiELD_build"
+testscriptDir=${BUILDDIR}/RTS/CI
+runDir=${BUILDDIR}/CI/BATCH-CI
+
+# Run CI test scripts
+cd ${testscriptDir}
+set -o pipefail
+# Execute the test piping output to log file
+./${testname} " --partition=p2 --mpi=pmi2 --job-name=${commit}_${testname} singularity exec -B /contrib ${container} ${container_env_script}" |& tee ${logDir}/run_${testname}.log
+
+## Compare Restarts to Baseline
+#The following tests are not expectred to have run-to-run reproducibility:
+#d96_2k.solo.bubble
+#d96_2k.solo.bubble.n0
+#d96_2k.solo.bubble.nhK
+if [[ ${testname} == "d96_2k.solo.bubble" || ${testname} == "d96_2k.solo.bubble.n0" || ${testname} == "d96_2k.solo.bubble.nhK" ]]
+  then
+    echo "${testname} is not expected to reproduce so answers were not compared"
+  else
+    source $MODULESHOME/init/sh
+    export MODULEPATH=/mnt/shared/manual_modules:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core:/apps/modules/modulefiles:/apps/modules/modulefamilies/intel
+    module load intel/2022.1.2
+    module load netcdf
+    module load nccmp
+    for resFile in `ls ${baselineDir}/${testname}`
+    do
+      nccmp -d ${baselineDir}/${testname}/${resFile} ${runDir}/${testname}/RESTART/${resFile}
+    done
+fi

.github/workflows/Intel_Parallelworks_CI.yaml

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+name: Build SHiELD
+
+on:
+  pull_request:
+    branches:
+      - main
+
+#this should cancel in progress ci runs for the same PR 
+#(e.g. a second commit on the same PR comes in while CI is still running)
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  checkout:
+    if: github.repository == 'NOAA-GFDL/SHiELD_build'
+    runs-on: [self-hosted]
+    name: Checkout SHiELD and Build FMS
+    steps:
+      - run: /contrib/fv3/SHiELD_build_CI/checkout_fms.sh -b $GITHUB_REF -h $GITHUB_SHA  
+  build:
+    if: github.repository == 'NOAA-GFDL/SHiELD_build'
+    runs-on: [self-hosted]
+    name: SOLO SHiELD build
+    needs: [checkout]
+    strategy:
+      fail-fast: true
+      max-parallel: 4
+      matrix:
+        runscript: [/contrib/fv3/SHiELD_build_CI/compile.sh]
+        config: [shield, solo, shiemom, shiemom_lm4]
+        hydro: [nh]
+        bit: [32bit]
+        mode: [repro]
+    steps:
+      - env:
+          RUNSCRIPT: ${{ matrix.runscript }}
+          CONFIG: ${{ matrix.config }}
+          HYDRO: ${{ matrix.hydro }}
+          BIT: ${{ matrix.bit }}
+          MODE: ${{ matrix.mode }}
+        run: $RUNSCRIPT -b $GITHUB_REF -h $GITHUB_SHA -c $CONFIG --hydro $HYDRO --bit $BIT -m $MODE

.github/workflows/daily_cleanup_parallelworks.yaml

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+name: Old Build Cleanup
+
+# This GitHub Action Workflow is runing on the devcimultiintel cluster
+# This will delete all build directories older than 30 days
+# Build directories are on the cloud at /contrib/fv3/2023.2.0
+
+on:
+  schedule:
+    # run daily at midnight
+    - cron: '0 0 * * *'
+
+jobs:
+  delete:
+    runs-on: [shieldbuild]
+    name: Delete Builds
+    steps:
+      - run: find /contrib/fv3/2023.2.0/SHiELD_build/refs/pull -maxdepth 1 -mindepth 1 -mtime +30 -type d -print -delete