compile with a matrix of options and cleanup arument parsing

.github/.parallelworks/checkout.sh

@@ -11,32 +11,34 @@ intelVersion=2023.2.0
 container=/contrib/containers/noaa-intel-prototype_2023.09.25.sif
 container_env_script=/contrib/containers/load_spack_noaa-intel.sh
 ##############################################################################
-## Set up the directories
-# First argument should be $GITHUB_REF which is the reference to the PR/branch
-# to be checked out for SHiELD_build
-if [ -z "$1" ]
-  then
-    echo "No branch/PR supplied; using main"
-    branch=main
-  else
-    echo Branch is ${1}
-    branch=${1}
-fi
-# Second Argument should be $GITHUB_SHA which  is the commit hash of the
-# branch or PR to trigger the CI, if run manually, you do not need a 2nd
-# argument.  This is needed in the circumstance where a PR is created, 
-# then the CI triggers, and before that CI has finished, the developer
-# pushes a newer commit which triggers a second round of CI.  We would
-# like unique directories so that both CI runs do not interfere.
-if [ -z "$2" ]
-  then
-    echo "No second argument"
-    commit=""
-  else
-    echo Commit is ${2}
-    commit=${2}
-fi
 
+#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

.github/.parallelworks/compile.sh

@@ -0,0 +1,75 @@
+#!/bin/sh -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
+    -hy|--hydro)
+      hydro="$2"
+      shift # past argument
+      shift # past value
+    -b|--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 | -b $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 $config"
+
+## Set up the directories
+testDir=${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"

.github/.parallelworks/run_test.sh

@@ -10,36 +10,45 @@ 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
-#first argument should be the name of the test and is mandatory
-if [ -z "$1" ]
-  then
-    echo "Please run this script with an argument indicating what test to run.  For example:"
-    echo "./run_test.sh C128r20.solo.superC"
-  else
-    echo Test is ${1}
-    test=${1}
-fi
-#second argument is the branch name. This is optional. Default is main branch if none supplied
-if [ -z "$2" ]
-  then
-    echo "No branch supplied; using main"
-    branch=main
-  else
-    echo Branch is ${2}
-    branch=${2}
-fi
-#third argument is the commit hash if running from CI.  This is optional
-if [ -z "$3" ]
+#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 "No commit being used in file path"
-    commit=""
-  else
-    echo Commit is ${3}
-    commit=${3}
+    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}/${commit}
@@ -57,24 +66,24 @@ runDir=${BUILDDIR}/CI/BATCH-CI
 cd ${testscriptDir}
 set -o pipefail
 # Execute the test piping output to log file
-./${test} " --partition=p2 --mpi=pmi2 --job-name=${commit}_${test} singularity exec -B /contrib ${container} ${container_env_script}" |& tee ${logDir}/run_${test}.log
+./${testname} " --partition=p2 --mpi=pmi2 --job-name=${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 [[ ${test} == "d96_2k.solo.bubble" || ${test} == "d96_2k.solo.bubble.n0" || ${test} == "d96_2k.solo.bubble.nhK" ]]
+if [[ ${testname} == "d96_2k.solo.bubble" || ${testname} == "d96_2k.solo.bubble.n0" || ${testname} == "d96_2k.solo.bubble.nhK" ]]
   then
-    echo "${test} is not expected to reproduce so answers were not compared"
+    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 ${baselineDir}/${test}`
+    for resFile in `ls ${baselineDir}/${testname}`
     do
-      nccmp -d ${baselineDir}/${test}/${resFile} ${runDir}/${test}/RESTART/${resFile}
+      nccmp -d ${baselineDir}/${testname}/${resFile} ${runDir}/${testname}/RESTART/${resFile}
     done
 fi