Update the CI

.github/.parallelworks/checkout.sh

@@ -0,0 +1,92 @@
+#!/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}/${intelVersion}/SHiELD_physics/${branch}/${commit}
+logDir=${testDir}/log
+export MODULESHOME=/usr/share/lmod/lmod
+#Define External Libs path
+export EXTERNAL_LIBS=${dirRoot}/${intelVersion}/SHiELD_physics/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  
+
+##checkout components
+cd ${testDir}/SHiELD_build && ./CHECKOUT_code
+
+## Check out the PR
+cd ${testDir}/SHiELD_SRC/SHiELD_physcis && git fetch origin ${branch}:toMerge && git merge toMerge
+
+##Check if we already have FMS compiled and recompile if version doesn't match what is in SHiELD_build checkout script
+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

@@ -0,0 +1,84 @@
+#!/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}/${intelVersion}/SHiELD_physics/${branch}/${commit}
+    logDir=${testDir}/log
+    # Set up build
+    cd ${testDir}/SHiELD_build/Build
+    #Define External Libs path
+    export EXTERNAL_LIBS=${dirRoot}/${intelVersion}/SHiELD_physics/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

@@ -0,0 +1,89 @@
+#!/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}/${intelVersion}/SHiELD_physics/${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