From 8ed01d3376194945b1cbf4c45b8f998b5e4844c0 Mon Sep 17 00:00:00 2001
From: Lauren Chilutti <lauren.chilutti@noaa.gov>
Date: Tue, 18 Jun 2024 13:23:10 +0000
Subject: [PATCH 1/2] runscripts for CI being stored in .github/.parallelworks.
 These runscripts need to be stored on parallelworks SHiELD_physics_CI cluster
 at /contrib/fv3/SHiELD_physics_CI

---
 .github/.parallelworks/checkout.sh | 92 ++++++++++++++++++++++++++++++
 .github/.parallelworks/compile.sh  | 84 +++++++++++++++++++++++++++
 .github/.parallelworks/run_test.sh | 89 +++++++++++++++++++++++++++++
 3 files changed, 265 insertions(+)
 create mode 100755 .github/.parallelworks/checkout.sh
 create mode 100755 .github/.parallelworks/compile.sh
 create mode 100755 .github/.parallelworks/run_test.sh

diff --git a/.github/.parallelworks/checkout.sh b/.github/.parallelworks/checkout.sh
new file mode 100755
index 00000000..9749ab8c
--- /dev/null
+++ b/.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
diff --git a/.github/.parallelworks/compile.sh b/.github/.parallelworks/compile.sh
new file mode 100755
index 00000000..39017366
--- /dev/null
+++ b/.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
diff --git a/.github/.parallelworks/run_test.sh b/.github/.parallelworks/run_test.sh
new file mode 100755
index 00000000..355f9ee2
--- /dev/null
+++ b/.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

From 4b5fd232478a712d1df056c35af7648c1c7be7ca Mon Sep 17 00:00:00 2001
From: Lauren Chilutti <60401591+laurenchilutti@users.noreply.github.com>
Date: Tue, 18 Jun 2024 09:35:50 -0400
Subject: [PATCH 2/2] Update Intel_Parallelworks_CI.yaml to now build full
 shield and not solo shield. Still to do: add a full shield test run.  Right
 now it only checks out code and builds shield

---
 .github/workflows/Intel_Parallelworks_CI.yaml | 170 ++++++------------
 1 file changed, 53 insertions(+), 117 deletions(-)

diff --git a/.github/workflows/Intel_Parallelworks_CI.yaml b/.github/workflows/Intel_Parallelworks_CI.yaml
index f814b114..4c08d8bf 100644
--- a/.github/workflows/Intel_Parallelworks_CI.yaml
+++ b/.github/workflows/Intel_Parallelworks_CI.yaml
@@ -1,4 +1,4 @@
-name: Compile SHiELD SOLO and run tests
+name: Compile SHiELD and run tests
 
 # This GitHub Action Workflow is running on the cloud shieldphysicsciintel cluster
 # The tests are run inside of a container with the following software/libraries:
@@ -30,131 +30,67 @@ jobs:
     # so this salloc will prompt 46 nodes to startup and stay active for 20 min
     # this is enough nodes for the first 17 tests to run in parallel, and we
     # have 17 runners configured.
-    - run: salloc --partition=p2 -N 46 -J $GITHUB_SHA sleep 20m &
-    - run: /contrib/fv3/SHiELD_physics_CI/checkout.sh $GITHUB_REF $GITHUB_SHA
+#    - run: salloc --partition=p2 -N 46 -J $GITHUB_SHA sleep 20m &
+    - run: /contrib/fv3/SHiELD_physics_CI/checkout.sh -b $GITHUB_REF -h $GITHUB_SHA
     
   build:
     if: github.repository == 'NOAA-GFDL/SHiELD_physics'
     runs-on: [shieldphysicsciintel]
-    name: SOLO SHiELD build
+    name: SHiELD build
     needs: [checkout]
     strategy:
       fail-fast: true
-      max-parallel: 3
-      matrix:
-        runpath: [/contrib/fv3/SHiELD_physics_CI/]
-        runscript: [swcompile.sh, nhcompile.sh, hydrocompile.sh]
-    steps:
-      - env:
-          RUNPATH: ${{ matrix.runpath }}
-          RUNSCRIPT: ${{ matrix.runscript }}
-        run: $RUNPATH/$RUNSCRIPT $GITHUB_REF $GITHUB_SHA
-        
-  test:
-    if: github.repository == 'NOAA-GFDL/SHiELD_physics'
-    runs-on: [shieldphysicsciintel]
-    name: SOLO SHiELD test suite
-    needs: [checkout, build]
-    strategy:
-      fail-fast: false
       max-parallel: 17
       matrix:
-        runpath: [/contrib/fv3/SHiELD_physics_CI/]
-        runscript:
-          # These are placed in order of largest to smallest jobs
-          #layout 8,8 needs 8 nodes on dvcimultiintel cluster
-          - C512r20.solo.superC.sh
-          - C768.sw.BTwave.sh
-          #layout 4,8 needs 4 nodes on dvcimultiintel cluster
-          - C256r20.solo.superC.sh
-          - C384.sw.BLvortex.sh
-          #layout 4,4 needs 2 nodes on dvcimultiintel cluster
-          - C128r20.solo.superC.sh
-          - C128r3.solo.TC.d1.sh
-          - C128r3.solo.TC.h6.sh
-          - C128r3.solo.TC.sh
-          - C128r3.solo.TC.tr8.sh
-          - C192.sw.BLvortex.sh
-          - C192.sw.BTwave.sh
-          - C192.sw.modon.sh
-          - C384.sw.BTwave.sh
-          #layout 4,1 and 2,2 need 1 node on dvcimultiintel cluster
-          - C96.solo.BCdry.hyd.sh
-          - C96.solo.BCdry.sh
-          - C96.solo.BCmoist.hyd.d3.sh
-          - C96.solo.BCmoist.hyd.sh
-          - C96.solo.BCmoist.nhK.sh
-          - C96.solo.BCmoist.sh
-          - C96.solo.mtn_rest.hyd.diff2.sh
-          - C96.solo.mtn_rest.hyd.sh
-          - C96.solo.mtn_rest.nonmono.diff2.sh
-          - C96.solo.mtn_rest.sh
-          - C96.sw.BLvortex.sh
-          - C96.sw.BTwave.sh
-          - C96.sw.modon.sh
-          - C96.sw.RHwave.sh
-          - d96_1k.solo.mtn_rest_shear.olddamp.sh
-          - d96_1k.solo.mtn_rest_shear.sh
-          - d96_1k.solo.mtn_schar.mono.sh
-          - d96_1k.solo.mtn_schar.sh
-          - d96_2k.solo.bubble.n0.sh
-          - d96_2k.solo.bubble.nhK.sh
-          - d96_2k.solo.bubble.sh
-          - d96_500m.solo.mtn_schar.sh
+        runscript: [/contrib/fv3/SHiELD_physics_CI/compile.sh]
+        config: [shield]
+        hydro: [nh]
+        bit: [32bit]
+        mode: [repro]
     steps:
-      # This will end the slurm job started in the checkout job
-      - run: scancel -n $GITHUB_SHA
       - env:
-          RUNPATH: ${{ matrix.runpath }}
           RUNSCRIPT: ${{ matrix.runscript }}
-        run: $RUNPATH/$RUNSCRIPT $GITHUB_REF $GITHUB_SHA
-  shutdown:
-    if: always() && github.repository == 'NOAA-GFDL/SHiELD_physics'
-    runs-on: [shieldphysicsciintel]
-    name: Shutdown Processes
-    needs: [checkout, build, test]
-    strategy:
-      fail-fast: false
-      max-parallel: 17
-      matrix:
-        test:
-          - C512r20.solo.superC
-          - C768.sw.BTwave
-          - C256r20.solo.superC
-          - C384.sw.BLvortex
-          - C128r20.solo.superC
-          - C128r3.solo.TC.d1
-          - C128r3.solo.TC.h6
-          - C128r3.solo.TC
-          - C128r3.solo.TC.tr8
-          - C192.sw.BLvortex
-          - C192.sw.BTwave
-          - C192.sw.modon
-          - C384.sw.BTwave
-          - C96.solo.BCdry.hyd
-          - C96.solo.BCdry
-          - C96.solo.BCmoist.hyd.d3
-          - C96.solo.BCmoist.hyd
-          - C96.solo.BCmoist.nhK
-          - C96.solo.BCmoist
-          - C96.solo.mtn_rest.hyd.diff2
-          - C96.solo.mtn_rest.hyd
-          - C96.solo.mtn_rest.nonmono.diff2
-          - C96.solo.mtn_rest
-          - C96.sw.BLvortex
-          - C96.sw.BTwave
-          - C96.sw.modon
-          - C96.sw.RHwave
-          - d96_1k.solo.mtn_rest_shear.olddamp
-          - d96_1k.solo.mtn_rest_shear
-          - d96_1k.solo.mtn_schar.mono
-          - d96_1k.solo.mtn_schar
-          - d96_2k.solo.bubble.n0
-          - d96_2k.solo.bubble.nhK
-          - d96_2k.solo.bubble
-          - d96_500m.solo.mtn_schar
-    steps:
-      - run: scancel -n $GITHUB_SHA
-      - env:
-          JOB: ${{ github.sha }}_${{ matrix.test }}
-        run: scancel -n $JOB
+          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
+        
+#  test:
+#    if: github.repository == 'NOAA-GFDL/SHiELD_physics'
+#    runs-on: [shieldphysicsciintel]
+#    name: SHiELD test suite
+#    needs: [checkout, build]
+#    strategy:
+#      fail-fast: false
+#      max-parallel: 17
+#      matrix:
+#        runscript: [/contrib/fv3/SHiELD_physics_CI/run_test.sh]
+#        argument:
+#          - test1
+#          - test2
+#    steps:
+#      # This will end the slurm job started in the checkout job
+#      - run: scancel -n $GITHUB_SHA
+#      - env:
+#          RUNSCRIPT: ${{ matrix.runscript }}
+#          ARG1: ${{ matrix.argument }}
+#        run: $RUNSCRIPT -t $ARG1 -b $GITHUB_REF -h $GITHUB_SHA
+#  shutdown:
+#    if: always() && github.repository == 'NOAA-GFDL/SHiELD_physics'
+#    runs-on: [shieldphysicsciintel]
+#    name: Shutdown Processes
+#    needs: [checkout, build, test]
+#    needs: [checkout, build]
+#    strategy:
+#      fail-fast: false
+#      max-parallel: 17
+#      matrix:
+#        test:
+#          - test2
+#          - test2
+#    steps:
+#      - run: scancel -n $GITHUB_SHA
+#      - env:
+#          JOB: ${{ github.sha }}_${{ matrix.test }}
+#        run: scancel -n $JOB