From 2bc180b8424adaf5738974f5d3597da0f3560868 Mon Sep 17 00:00:00 2001
From: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed, 26 Oct 2022 10:00:48 -0400
Subject: [PATCH] Fix build scripts and bring into compliance (#1096)

Adds module-setup calls and updates gfs-utils to reset modules when building. The gfs-utils update also fixes the build issue on Orion by updating the stack version to 1.2.

Brings all build scripts into full shellcheck compliance.

Also removes the workflow utils modulefiles since they are no longer needed after moving those programs to gfs-utils.

Fixes #1093
---
 Externals.cfg                         |   2 +-
 modulefiles/workflow_utils.hera.lua   |  34 -----
 modulefiles/workflow_utils.jet.lua    |  34 -----
 modulefiles/workflow_utils.orion.lua  |  34 -----
 modulefiles/workflow_utils.s4.lua     |  35 -----
 modulefiles/workflow_utils.wcoss2.lua |  32 -----
 sorc/build_all.sh                     | 200 +++++++++++++++-----------
 sorc/build_gdas.sh                    |  15 +-
 sorc/build_gfs_wafs.sh                |   2 +-
 sorc/build_gldas.sh                   |   2 +-
 sorc/build_gsi_enkf.sh                |  10 +-
 sorc/build_gsi_monitor.sh             |  10 +-
 sorc/build_gsi_utils.sh               |  10 +-
 sorc/build_ufs.sh                     |  21 +--
 sorc/build_upp.sh                     |  11 +-
 sorc/build_ww3prepost.sh              |  44 +++---
 sorc/checkout.sh                      |   2 +-
 17 files changed, 179 insertions(+), 319 deletions(-)
 delete mode 100644 modulefiles/workflow_utils.hera.lua
 delete mode 100644 modulefiles/workflow_utils.jet.lua
 delete mode 100644 modulefiles/workflow_utils.orion.lua
 delete mode 100644 modulefiles/workflow_utils.s4.lua
 delete mode 100644 modulefiles/workflow_utils.wcoss2.lua

diff --git a/Externals.cfg b/Externals.cfg
index 948447a758..9eaf7ce577 100644
--- a/Externals.cfg
+++ b/Externals.cfg
@@ -8,7 +8,7 @@ protocol = git
 required = True
 
 [gfs-utils]
-hash = af933d3
+hash = 0b8ff56
 local_path = sorc/gfs_utils.fd
 repo_url = https://github.com/NOAA-EMC/gfs-utils
 protocol = git
diff --git a/modulefiles/workflow_utils.hera.lua b/modulefiles/workflow_utils.hera.lua
deleted file mode 100644
index e0838b2c16..0000000000
--- a/modulefiles/workflow_utils.hera.lua
+++ /dev/null
@@ -1,34 +0,0 @@
-help([[
-Build environment for workflow utilities on Hera
-]])
-
-prepend_path("MODULEPATH", "/scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack")
-
-load(pathJoin("hpc", "1.1.0"))
-load(pathJoin("hpc-intel", "18.0.5.274"))
-load(pathJoin("hpc-impi", "2018.0.4"))
-
-load(pathJoin("cmake", "3.20.0"))
-
-load(pathJoin("jasper", "2.0.25"))
-load(pathJoin("zlib", "1.2.11"))
-load(pathJoin("png", "1.6.35"))
-
-load(pathJoin("hdf5", "1.10.6"))
-load(pathJoin("netcdf", "4.7.4"))
-
-load(pathJoin("bacio", "2.4.1"))
-load(pathJoin("g2", "3.4.1"))
-load(pathJoin("ip", "3.3.3"))
-load(pathJoin("nemsio", "2.5.2"))
-load(pathJoin("sp", "2.3.3"))
-load(pathJoin("w3emc", "2.7.3"))
-load(pathJoin("w3nco", "2.4.1"))
-load(pathJoin("nemsiogfs", "2.5.3"))
-load(pathJoin("ncio", "1.0.0"))
-load(pathJoin("landsfcutil", "2.4.1"))
-load(pathJoin("sigio", "2.3.2"))
-load(pathJoin("bufr", "11.4.0"))
-
-load(pathJoin("wgrib2", "2.0.8"))
-setenv("WGRIB2","wgrib2")
diff --git a/modulefiles/workflow_utils.jet.lua b/modulefiles/workflow_utils.jet.lua
deleted file mode 100644
index 27f8ab5db5..0000000000
--- a/modulefiles/workflow_utils.jet.lua
+++ /dev/null
@@ -1,34 +0,0 @@
-help([[
-Build environment for workflow utilities on Jet
-]])
-
-prepend_path("MODULEPATH", "/lfs4/HFIP/hfv3gfs/nwprod/hpc-stack/libs/modulefiles/stack")
-
-load(pathJoin("hpc", "1.1.0"))
-load(pathJoin("hpc-intel", "18.0.5.274"))
-load(pathJoin("hpc-impi", "2018.4.274"))
-
-load(pathJoin("cmake", "3.16.1"))
-
-load(pathJoin("jasper", "2.0.25"))
-load(pathJoin("zlib", "1.2.11"))
-load(pathJoin("png", "1.6.35"))
-
-load(pathJoin("hdf5", "1.10.6"))
-load(pathJoin("netcdf", "4.7.4"))
-
-load(pathJoin("bacio", "2.4.1"))
-load(pathJoin("g2", "3.4.1"))
-load(pathJoin("w3nco", "2.4.1"))
-load(pathJoin("w3emc", "2.7.3"))
-load(pathJoin("sp", "2.3.3"))
-load(pathJoin("ip", "3.3.3"))
-load(pathJoin("nemsio", "2.5.2"))
-load(pathJoin("nemsiogfs", "2.5.3"))
-load(pathJoin("ncio", "1.0.0"))
-load(pathJoin("landsfcutil", "2.4.1"))
-load(pathJoin("sigio", "2.3.2"))
-load(pathJoin("bufr", "11.4.0"))
-
-load(pathJoin("wgrib2", "2.0.8"))
-setenv("WGRIB2","wgrib2")
diff --git a/modulefiles/workflow_utils.orion.lua b/modulefiles/workflow_utils.orion.lua
deleted file mode 100644
index 4d788725c9..0000000000
--- a/modulefiles/workflow_utils.orion.lua
+++ /dev/null
@@ -1,34 +0,0 @@
-help([[
-Build environment for workflow utilities on Orion
-]])
-
-prepend_path("MODULEPATH", "/apps/contrib/NCEP/libs/hpc-stack/modulefiles/stack")
-
-load(pathJoin("hpc", "1.1.0"))
-load(pathJoin("hpc-intel", "2018.4"))
-load(pathJoin("hpc-impi", "2018.4"))
-
-load(pathJoin("cmake", "3.17.3"))
-
-load(pathJoin("jasper", "2.0.25"))
-load(pathJoin("zlib", "1.2.11"))
-load(pathJoin("png", "1.6.35"))
-
-load(pathJoin("hdf5", "1.10.6"))
-load(pathJoin("netcdf", "4.7.4"))
-
-load(pathJoin("bacio", "2.4.1"))
-load(pathJoin("g2", "3.4.1"))
-load(pathJoin("w3nco", "2.4.1"))
-load(pathJoin("w3emc", "2.7.3"))
-load(pathJoin("sp", "2.3.3"))
-load(pathJoin("ip", "3.3.3"))
-load(pathJoin("nemsio", "2.5.2"))
-load(pathJoin("nemsiogfs", "2.5.3"))
-load(pathJoin("ncio", "1.0.0"))
-load(pathJoin("landsfcutil", "2.4.1"))
-load(pathJoin("sigio", "2.3.2"))
-load(pathJoin("bufr", "11.4.0"))
-
-load(pathJoin("wgrib2", "2.0.8"))
-setenv("WGRIB2","wgrib2")
diff --git a/modulefiles/workflow_utils.s4.lua b/modulefiles/workflow_utils.s4.lua
deleted file mode 100644
index 5770ff3cba..0000000000
--- a/modulefiles/workflow_utils.s4.lua
+++ /dev/null
@@ -1,35 +0,0 @@
-help([[
-Build environment for workflow utilities on Hera
-]])
-
-load("license_intel")
-prepend_path("MODULEPATH", "/data/prod/hpc-stack/modulefiles/stack")
-
-load(pathJoin("hpc", "1.1.0"))
-load(pathJoin("hpc-intel", "18.0.4"))
-load(pathJoin("hpc-impi", "18.0.4"))
-
-load(pathJoin("jasper", "2.0.25"))
-load(pathJoin("zlib", "1.2.11"))
-load(pathJoin("png", "1.6.35"))
-
-load(pathJoin("hdf5", "1.10.6"))
-load(pathJoin("netcdf", "4.7.4"))
-
-load(pathJoin("bacio", "2.4.1"))
-load(pathJoin("g2", "3.4.1"))
-load(pathJoin("ip", "3.3.3"))
-load(pathJoin("nemsio", "2.5.2"))
-load(pathJoin("sp", "2.3.3"))
-load(pathJoin("w3emc", "2.7.3"))
-load(pathJoin("w3nco", "2.4.1"))
-load(pathJoin("nemsiogfs", "2.5.3"))
-load(pathJoin("ncio", "1.1.2"))
-load(pathJoin("landsfcutil", "2.4.1"))
-load(pathJoin("sigio", "2.3.2"))
-load(pathJoin("bufr", "11.4.0"))
-
-load(pathJoin("wgrib2", "2.0.8"))
-setenv("WGRIB2","wgrib2")
-
-setenv("FFLAGS","-march=ivybridge")
diff --git a/modulefiles/workflow_utils.wcoss2.lua b/modulefiles/workflow_utils.wcoss2.lua
deleted file mode 100644
index 34b54a69c5..0000000000
--- a/modulefiles/workflow_utils.wcoss2.lua
+++ /dev/null
@@ -1,32 +0,0 @@
-help([[
-Build environment for workflow utilities on WCOSS2
-]])
-
-load(pathJoin("PrgEnv-intel", "8.1.0"))
-load(pathJoin("craype", "2.7.10"))
-load(pathJoin("intel", "19.1.3.304"))
-load(pathJoin("cray-mpich", "8.1.9"))
-
-load(pathJoin("cmake", "3.20.2"))
-
-load(pathJoin("jasper", "2.0.25"))
-load(pathJoin("zlib", "1.2.11"))
-load(pathJoin("libpng", "1.6.37"))
-
-load(pathJoin("hdf5", "1.10.6"))
-load(pathJoin("netcdf", "4.7.4"))
-
-load(pathJoin("bacio", "2.4.1"))
-load(pathJoin("g2", "3.4.5"))
-load(pathJoin("ip", "3.3.3"))
-load(pathJoin("nemsio", "2.5.2"))
-load(pathJoin("sp", "2.3.3"))
-load(pathJoin("w3emc", "2.9.2"))
-load(pathJoin("w3nco", "2.4.1"))
-load(pathJoin("nemsiogfs", "2.5.3"))
-load(pathJoin("ncio", "1.0.0"))
-load(pathJoin("landsfcutil", "2.4.1"))
-load(pathJoin("sigio", "2.3.2"))
-load(pathJoin("bufr", "11.5.0"))
-
-load(pathJoin("wgrib2", "2.0.8"))
diff --git a/sorc/build_all.sh b/sorc/build_all.sh
index 3acebb7347..f3cad05ffd 100755
--- a/sorc/build_all.sh
+++ b/sorc/build_all.sh
@@ -35,6 +35,7 @@ cd "${script_dir}" || exit 1
 _build_ufs_opt=""
 _ops_opt=""
 _verbose_opt=""
+_partial_opt=""
 # Reset option counter in case this script is sourced
 OPTIND=1
 while getopts ":a:c:hov" option; do
@@ -43,7 +44,6 @@ while getopts ":a:c:hov" option; do
     c) _partial_opt+="-c ${OPTARG} ";;
     h) _usage;;
     o) _ops_opt+="-o";;
-    # s) _build_ufs_opt+="-s ${OPTARG} ";;
     v) _verbose_opt="-v";;
     :)
       echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
@@ -59,13 +59,13 @@ done
 shift $((OPTIND-1))
 
 logs_dir="${script_dir}/logs"
-if [ ! -d "${logs_dir}"  ]; then
+if [[ ! -d "${logs_dir}" ]]; then
   echo "Creating logs folder"
   mkdir "${logs_dir}" || exit 1
 fi
 
 # Check final exec folder exists
-if [ ! -d "../exec" ]; then
+if [[ ! -d "../exec" ]]; then
   echo "Creating ../exec folder"
   mkdir ../exec
 fi
@@ -74,9 +74,8 @@ fi
 # GET MACHINE
 #------------------------------------
 export COMPILER="intel"
-# shellcheck disable=SC1091
 source gfs_utils.fd/ush/detect_machine.sh
-# shellcheck disable=
+source gfs_utils.fd/ush/module-setup.sh
 if [[ -z "${MACHINE_ID}" ]]; then
   echo "FATAL: Unable to determine target machine"
   exit 1
@@ -85,8 +84,11 @@ fi
 #------------------------------------
 # INCLUDE PARTIAL BUILD
 #------------------------------------
-# shellcheck source-path=sorc
-source ./partial_build.sh $_verbose_opt $_partial_opt
+# Turn off some shellcheck warnings because we want to have
+#   variables with multiple arguments.
+# shellcheck disable=SC2086,SC2248
+source ./partial_build.sh ${_verbose_opt} ${_partial_opt}
+# shellcheck disable=
 
 if [[ ${MACHINE_ID} =~ jet.* ]]; then
   Build_gldas="false"
@@ -96,51 +98,76 @@ fi
 #------------------------------------
 # Exception Handling Init
 #------------------------------------
+# Disable shellcheck warning about single quotes not being substituted.
+# shellcheck disable=SC2016
 ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
+# shellcheck disable=
 err=0
 
+#------------------------------------
+# build gfs_utils
+#------------------------------------
+if [[ ${Build_gfs_utils} == 'true' ]]; then
+  echo " .... Building gfs_utils .... "
+    # shellcheck disable=SC2086,SC2248
+  ./build_gfs_utils.sh ${_verbose_opt} > "${logs_dir}/build_gfs_utils.log" 2>&1
+    # shellcheck disable=
+  rc=$?
+  if (( rc != 0 )) ; then
+    echo "Fatal error in building gfs_utils."
+    echo "The log file is in ${logs_dir}/build_gfs_utils.log"
+  fi
+  err=$((err + rc))
+fi
+
 #------------------------------------
 # build WW3 pre & post execs
 #------------------------------------
-${Build_ww3_prepost:?} && {
+if [[ ${Build_ww3_prepost} == "true" ]]; then
   echo " .... Building WW3 pre and post execs .... "
-  ./build_ww3prepost.sh ${_verbose_opt} ${_build_ufs_opt} > ${logs_dir}/build_ww3_prepost.log 2>&1
+  # shellcheck disable=SC2086,SC2248
+  ./build_ww3prepost.sh ${_verbose_opt} ${_build_ufs_opt} > "${logs_dir}/build_ww3_prepost.log" 2>&1
+  # shellcheck disable=
   rc=$?
-  if [[ ${rc} -ne 0 ]] ; then
+  if (( rc != 0 )) ; then
     echo "Fatal error in building WW3 pre/post processing."
     echo "The log file is in ${logs_dir}/build_ww3_prepost.log"
   fi
   err=$((err + rc))
-}
+fi
 
 #------------------------------------
 # build forecast model
 #------------------------------------
-${Build_ufs_model:?} && {
+if [[ ${Build_ufs_model} == 'true' ]]; then
   echo " .... Building forecast model .... "
-  ./build_ufs.sh ${_verbose_opt} ${_build_ufs_opt} > ${logs_dir}/build_ufs.log 2>&1
+  # shellcheck disable=SC2086,SC2248
+  ./build_ufs.sh ${_verbose_opt} ${_build_ufs_opt} > "${logs_dir}/build_ufs.log" 2>&1
+  # shellcheck disable=
   rc=$?
-  if [[ ${rc} -ne 0 ]] ; then
+  if (( rc != 0 )) ; then
     echo "Fatal error in building UFS model."
     echo "The log file is in ${logs_dir}/build_ufs.log"
   fi
   err=$((err + rc))
-}
+fi
 
 #------------------------------------
 # build GSI and EnKF - optional checkout
 #------------------------------------
-if [ -d gsi_enkf.fd ]; then
-  ${Build_gsi_enkf:?} && {
-  echo " .... Building gsi and enkf .... "
-  ./build_gsi_enkf.sh ${_ops_opt} ${_verbose_opt} > ${logs_dir}/build_gsi_enkf.log 2>&1
-  rc=$?
-  if [[ ${rc} -ne 0 ]] ; then
-    echo "Fatal error in building gsi_enkf."
-    echo "The log file is in ${logs_dir}/build_gsi_enkf.log"
+if [[ -d gsi_enkf.fd ]]; then
+  if [[ ${Build_gsi_enkf} == 'true' ]]; then
+    echo " .... Building gsi and enkf .... "
+    # shellcheck disable=SC2086,SC2248
+    ./build_gsi_enkf.sh ${_ops_opt} ${_verbose_opt} > "${logs_dir}/build_gsi_enkf.log" 2>&1
+    # shellcheck disable=
+    rc=$?
+    if (( rc != 0 )) ; then
+      echo "Fatal error in building gsi_enkf."
+      echo "The log file is in ${logs_dir}/build_gsi_enkf.log"
+    fi
+    err=$((err + rc))
   fi
-  err=$((err + rc))
-}
 else
   echo " .... Skip building gsi and enkf .... "
 fi
@@ -148,17 +175,19 @@ fi
 #------------------------------------
 # build gsi utilities
 #------------------------------------
-if [ -d gsi_utils.fd ]; then
-  ${Build_gsi_utils:?} && {
-  echo " .... Building gsi utilities .... "
-  ./build_gsi_utils.sh ${_ops_opt} ${_verbose_opt} > ${logs_dir}/build_gsi_utils.log 2>&1
-  rc=$?
-  if [[ ${rc} -ne 0 ]] ; then
-    echo "Fatal error in building gsi utilities."
-    echo "The log file is in ${logs_dir}/build_gsi_utils.log"
+if [[ -d gsi_utils.fd ]]; then
+  if [[ ${Build_gsi_utils} == 'true' ]]; then
+    echo " .... Building gsi utilities .... "
+    # shellcheck disable=SC2086,SC2248
+    ./build_gsi_utils.sh ${_ops_opt} ${_verbose_opt} > "${logs_dir}/build_gsi_utils.log" 2>&1
+    # shellcheck disable=
+    rc=$?
+    if (( rc != 0 )) ; then
+      echo "Fatal error in building gsi utilities."
+      echo "The log file is in ${logs_dir}/build_gsi_utils.log"
+    fi
+    err=$((err + rc))
   fi
-  err=$((err + rc))
-}
 else
   echo " .... Skip building gsi utilities .... "
 fi
@@ -166,17 +195,19 @@ fi
 #------------------------------------
 # build gdas - optional checkout
 #------------------------------------
-if [ -d gdas.cd ]; then
-  ${Build_gdas:?}  && {
-  echo " .... Building GDASApp  .... "
-  ./build_gdas.sh ${_verbose_opt} > ${logs_dir}/build_gdas.log 2>&1
-  rc=$?
-  if [[ ${rc} -ne 0 ]] ; then
-    echo "Fatal error in building GDASApp."
-    echo "The log file is in ${logs_dir}/build_gdas.log"
+if [[ -d gdas.cd ]]; then
+  if [[ ${Build_gdas} == 'true' ]]; then
+    echo " .... Building GDASApp  .... "
+    # shellcheck disable=SC2086,SC2248
+    ./build_gdas.sh ${_verbose_opt} > "${logs_dir}/build_gdas.log" 2>&1
+    # shellcheck disable=
+    rc=$?
+    if (( rc != 0 )) ; then
+      echo "Fatal error in building GDASApp."
+      echo "The log file is in ${logs_dir}/build_gdas.log"
+    fi
+    err=$((err + rc))
   fi
-  err=$((err + rc))
-}
 else
   echo " .... Skip building GDASApp  .... "
 fi
@@ -184,17 +215,19 @@ fi
 #------------------------------------
 # build gsi monitor
 #------------------------------------
-if [ -d gsi_monitor.fd ]; then
-  ${Build_gsi_monitor:?} && {
+if [[ -d gsi_monitor.fd ]]; then
+  if [[ ${Build_gsi_monitor} == 'true' ]]; then
     echo " .... Building gsi monitor .... "
-    ./build_gsi_monitor.sh ${_ops_opt} ${_verbose_opt} > ${logs_dir}/build_gsi_monitor.log 2>&1
+    # shellcheck disable=SC2086,SC2248
+    ./build_gsi_monitor.sh ${_ops_opt} ${_verbose_opt} > "${logs_dir}/build_gsi_monitor.log" 2>&1
+    # shellcheck disable=
     rc=$?
-    if [[ ${rc} -ne 0 ]] ; then
+    if (( rc != 0 )) ; then
       echo "Fatal error in building gsi monitor."
       echo "The log file is in ${logs_dir}/build_gsi_monitor.log"
     fi
     err=$((err + rc))
-  }
+  fi
 else
   echo " .... Skip building gsi monitor .... "
 fi
@@ -202,45 +235,51 @@ fi
 #------------------------------------
 # build UPP
 #------------------------------------
-${Build_upp:?} && {
+if [[ ${Build_upp} == 'true' ]]; then
   echo " .... Building UPP .... "
-  ./build_upp.sh ${_ops_opt} ${_verbose_opt} > ${logs_dir}/build_upp.log 2>&1
+  # shellcheck disable=SC2086,SC2248
+  ./build_upp.sh ${_ops_opt} ${_verbose_opt} > "${logs_dir}/build_upp.log" 2>&1
+  # shellcheck disable=
   rc=$?
-  if [[ ${rc} -ne 0 ]] ; then
+  if (( rc != 0 )) ; then
     echo "Fatal error in building UPP."
     echo "The log file is in ${logs_dir}/build_upp.log"
   fi
   err=$((err + rc))
-}
+fi
 
 #------------------------------------
 # build ufs_utils
 #------------------------------------
-${Build_ufs_utils:?} && {
+if [[ ${Build_ufs_utils} == 'true' ]]; then
   echo " .... Building ufs_utils .... "
-  ./build_ufs_utils.sh ${_verbose_opt} > ${logs_dir}/build_ufs_utils.log 2>&1
+  # shellcheck disable=SC2086,SC2248
+  ./build_ufs_utils.sh ${_verbose_opt} > "${logs_dir}/build_ufs_utils.log" 2>&1
+  # shellcheck disable=
   rc=$?
-  if [[ ${rc} -ne 0 ]] ; then
+  if (( rc != 0 )) ; then
     echo "Fatal error in building ufs_utils."
     echo "The log file is in ${logs_dir}/build_ufs_utils.log"
   fi
   err=$((err + rc))
-}
+fi
 
 #------------------------------------
 # build gldas
 #------------------------------------
-if [ -d gldas.fd ]; then
-  ${Build_gldas:?} && {
+if [[ -d gldas.fd ]]; then
+  if [[ ${Build_gldas} == 'true' ]]; then
     echo " .... Building gldas .... "
-    ./build_gldas.sh ${_verbose_opt} > ${logs_dir}/build_gldas.log 2>&1
+    # shellcheck disable=SC2086,SC2248
+    ./build_gldas.sh ${_verbose_opt} > "${logs_dir}/build_gldas.log" 2>&1
+    # shellcheck disable=
     rc=$?
-    if [[ ${rc} -ne 0 ]] ; then
+    if (( rc != 0 )) ; then
       echo "Fatal error in building gldas."
       echo "The log file is in ${logs_dir}/build_gldas.log"
     fi
     err=$((err + rc))
-  }
+  fi
 else
   echo " .... Skip building gldas .... "
 fi
@@ -248,38 +287,31 @@ fi
 #------------------------------------
 # build gfs_wafs - optional checkout
 #------------------------------------
-if [ -d gfs_wafs.fd ]; then
-  ${Build_gfs_wafs:?}  && {
+if [[ -d gfs_wafs.fd ]]; then
+  if [[ ${Build_gfs_wafs} == 'true' ]]; then
     echo " .... Building gfs_wafs  .... "
-    ./build_gfs_wafs.sh ${_verbose_opt} > ${logs_dir}/build_gfs_wafs.log 2>&1
+    # shellcheck disable=SC2086,SC2248
+    ./build_gfs_wafs.sh ${_verbose_opt} > "${logs_dir}/build_gfs_wafs.log" 2>&1
+    # shellcheck disable=
     rc=$?
-    if [[ ${rc} -ne 0 ]] ; then
+    if (( rc != 0 )) ; then
       echo "Fatal error in building gfs_wafs."
       echo "The log file is in ${logs_dir}/build_gfs_wafs.log"
     fi
     err=$((err + rc))
-  }
-fi
-
-#------------------------------------
-# build gfs_utils
-#------------------------------------
-${Build_gfs_utils:?} && {
-  echo " .... Building gfs_utils .... "
-  target=$target ./build_gfs_utils.sh ${_verbose_opt} > ${logs_dir}/build_gfs_utils.log 2>&1
-  rc=$?
-  if [[ ${rc} -ne 0 ]] ; then
-    echo "Fatal error in building gfs_utils."
-    echo "The log file is in ${logs_dir}/build_gfs_utils.log"
   fi
-  err=$((err + rc))
-}
+fi
 
 #------------------------------------
 # Exception Handling
 #------------------------------------
-[[ ${err} -ne 0 ]] && echo "FATAL BUILD ERROR: Please check the log file for detail, ABORT!"
-${ERRSCRIPT} || exit ${err}
+if (( err != 0 )); then
+  cat << EOF
+BUILD ERROR: One or more components failed to build
+  Check the associated build log(s) for details.
+EOF
+  ${ERRSCRIPT} || exit "${err}"
+fi
 
 echo;echo " .... Build system finished .... "
 
diff --git a/sorc/build_gdas.sh b/sorc/build_gdas.sh
index 468516ff43..9c7e024753 100755
--- a/sorc/build_gdas.sh
+++ b/sorc/build_gdas.sh
@@ -4,29 +4,26 @@ set -eux
 script_dir=$(dirname "${BASH_SOURCE[0]}")
 cd "${script_dir}" || exit 1
 
-# shellcheck disable=SC1091
 source gfs_utils.fd/ush/detect_machine.sh
-# shellcheck disable=
+source gfs_utils.fd/ush/module-setup.sh
 
 # detect_machine now includes the compiler on some machines
 #   but the GDAS build script does not want it
 MACHINE_ID=$(echo "${MACHINE_ID}" | cut -d "." -f 1)
 
-# use more build jobs if on NOAA HPC
-build_jobs=4
 case "${MACHINE_ID}" in
-  hera|orion)
-    build_jobs=10
-    ;;
+    hera|orion) build_jobs=10 ;;
+    *)          build_jobs=4 ;;
 esac
 
 # Check final exec folder exists
-if [ ! -d "../exec" ]; then
+if [[ ! -d "../exec" ]]; then
   mkdir ../exec
 fi
 
 cd gdas.cd
+
 BUILD_JOBS="${build_jobs}" ./build.sh -t "${MACHINE_ID}"
 
-exit
+exit $?
 
diff --git a/sorc/build_gfs_wafs.sh b/sorc/build_gfs_wafs.sh
index 8e36affd49..cbbf6ec950 100755
--- a/sorc/build_gfs_wafs.sh
+++ b/sorc/build_gfs_wafs.sh
@@ -5,7 +5,7 @@ script_dir=$(dirname "${BASH_SOURCE[0]}")
 cd "${script_dir}" || exit 1
 
 # Check final exec folder exists
-if [ ! -d "../exec" ]; then
+if [[ ! -d "../exec" ]]; then
   mkdir ../exec
 fi
 
diff --git a/sorc/build_gldas.sh b/sorc/build_gldas.sh
index 2b9a9ef5b1..05963b9348 100755
--- a/sorc/build_gldas.sh
+++ b/sorc/build_gldas.sh
@@ -5,7 +5,7 @@ script_dir=$(dirname "${BASH_SOURCE[0]}")
 cd "${script_dir}" || exit 1
 
 # Check final exec folder exists
-if [ ! -d "../exec" ]; then
+if [[ ! -d "../exec" ]]; then
   mkdir ../exec
 fi
 
diff --git a/sorc/build_gsi_enkf.sh b/sorc/build_gsi_enkf.sh
index 1adb80061b..671c3d6205 100755
--- a/sorc/build_gsi_enkf.sh
+++ b/sorc/build_gsi_enkf.sh
@@ -1,20 +1,18 @@
 #! /usr/bin/env bash
 set -eux
 
-cwd=$(pwd)
-
 OPTIND=1
 while getopts ":dov" option; do
   case "${option}" in
     d) export BUILD_TYPE="DEBUG";;
     o) _ops="YES";;
     v) export BUILD_VERBOSE="YES";;
-    \?)
-      echo "[$BASH_SOURCE]: Unrecognized option: ${option}"
+    :)
+      echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
       usage
       ;;
-    :)
-      echo "[$BASH_SOURCE]: ${option} requires an argument"
+    *)
+      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
       usage
       ;;
   esac
diff --git a/sorc/build_gsi_monitor.sh b/sorc/build_gsi_monitor.sh
index 0fa78044d8..ec3645e52f 100755
--- a/sorc/build_gsi_monitor.sh
+++ b/sorc/build_gsi_monitor.sh
@@ -9,12 +9,12 @@ while getopts ":dov" option; do
     d) export BUILD_TYPE="DEBUG";;
     o) _ops="YES";;
     v) export BUILD_VERBOSE="YES";;
-    \?)
-      echo "[$BASH_SOURCE]: Unrecognized option: ${option}"
+    :)
+      echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
       usage
       ;;
-    :)
-      echo "[$BASH_SOURCE]: ${option} requires an argument"
+    *)
+      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
       usage
       ;;
   esac
@@ -23,6 +23,6 @@ shift $((OPTIND-1))
 
 BUILD_TYPE=${BUILD_TYPE:-"Release"} \
 BUILD_VERBOSE=${BUILD_VERBOSE:-"NO"} \
-${cwd}/gsi_monitor.fd/ush/build.sh
+"${cwd}/gsi_monitor.fd/ush/build.sh"
 
 exit
diff --git a/sorc/build_gsi_utils.sh b/sorc/build_gsi_utils.sh
index bc579300d1..bcbc110cf6 100755
--- a/sorc/build_gsi_utils.sh
+++ b/sorc/build_gsi_utils.sh
@@ -9,12 +9,12 @@ while getopts ":dov" option; do
     d) export BUILD_TYPE="DEBUG";;
     o) _ops="YES";;  # TODO - unused; remove?
     v) export BUILD_VERBOSE="YES";;
-    \?)
-      echo "[$BASH_SOURCE]: Unrecognized option: ${option}"
+    :)
+      echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
       usage
       ;;
-    :)
-      echo "[$BASH_SOURCE]: ${option} requires an argument"
+    *)
+      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
       usage
       ;;
   esac
@@ -24,6 +24,6 @@ shift $((OPTIND-1))
 BUILD_TYPE=${BUILD_TYPE:-"Release"} \
 BUILD_VERBOSE=${BUILD_VERBOSE:-"NO"} \
 UTIL_OPTS="-DBUILD_UTIL_ENKF_GFS=ON -DBUILD_UTIL_NCIO=ON" \
-${cwd}/gsi_utils.fd/ush/build.sh
+"${cwd}/gsi_utils.fd/ush/build.sh"
 
 exit
diff --git a/sorc/build_ufs.sh b/sorc/build_ufs.sh
index 2d7b5abd51..c91bb07e37 100755
--- a/sorc/build_ufs.sh
+++ b/sorc/build_ufs.sh
@@ -8,7 +8,8 @@ APP="S2SWA"
 CCPP_SUITES="FV3_GFS_v16,FV3_GFS_v16_no_nsst,FV3_GFS_v16_ugwpv1,FV3_GFS_v17_p8,FV3_GFS_v16_coupled_nsstNoahmpUGWPv1,FV3_GFS_v17_coupled_p8"
 
 export RT_COMPILER="intel"
-source $cwd/ufs_model.fd/tests/detect_machine.sh
+source "${cwd}/ufs_model.fd/tests/detect_machine.sh"
+source "${cwd}/ufs_model.fd/tests/module-setup.sh"
 
 if [[ ${MACHINE_ID} =~ wcoss2.* ]]; then
 	APP='S2SW'
@@ -18,17 +19,17 @@ while getopts ":da:v" option; do
   case "${option}" in
     d) BUILD_TYPE="Debug";;
     a) APP="${OPTARG}" ;;
-    v) BUILD_VERBOSE="YES";;
-    \?)
-      echo "[$BASH_SOURCE]: Unrecognized option: ${option}"
-      ;;
+    v) export BUILD_VERBOSE="YES";;
     :)
-      echo "[$BASH_SOURCE]: ${option} requires an argument"
+      echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
+      ;;
+    *)
+      echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
       ;;
   esac
 done
 
-cd $cwd/ufs_model.fd
+cd "${cwd}/ufs_model.fd"
 
 MAKE_OPT="-DAPP=${APP} -DCCPP_SUITES=${CCPP_SUITES}"
 [[ ${BUILD_TYPE:-"Release"} = "DEBUG" ]] && MAKE_OPT+=" -DDEBUG=ON"
@@ -36,8 +37,8 @@ COMPILE_NR=0
 CLEAN_BEFORE=YES
 CLEAN_AFTER=NO
 
-./tests/compile.sh $MACHINE_ID "$MAKE_OPT" $COMPILE_NR $CLEAN_BEFORE $CLEAN_AFTER
-mv ./tests/fv3_${COMPILE_NR}.exe ./tests/ufs_model.x
-mv ./tests/modules.fv3_${COMPILE_NR}.lua ./tests/modules.ufs_model.lua
+./tests/compile.sh "${MACHINE_ID}" "${MAKE_OPT}" "${COMPILE_NR}" "${CLEAN_BEFORE}" "${CLEAN_AFTER}"
+mv "./tests/fv3_${COMPILE_NR}.exe" ./tests/ufs_model.x
+mv "./tests/modules.fv3_${COMPILE_NR}.lua" ./tests/modules.ufs_model.lua
 
 exit 0
diff --git a/sorc/build_upp.sh b/sorc/build_upp.sh
index bb9f47dafb..67460487a6 100755
--- a/sorc/build_upp.sh
+++ b/sorc/build_upp.sh
@@ -11,22 +11,23 @@ while getopts ":dov" option; do
 		d) export BUILD_TYPE="DEBUG";;
 		o) _opts+="-g ";;
 		v) _opts+="-v ";;
-		\?)
-			echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
-			usage
-			;;
 		:)
 			echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
 			usage
 			;;
+		*)
+			echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
+			usage
+			;;
 	esac
 done
 shift $((OPTIND-1))
 
 # Check final exec folder exists
-if [ ! -d "../exec" ]; then
+if [[ ! -d "../exec" ]]; then
   mkdir ../exec
 fi
 
 cd ufs_model.fd/FV3/upp/tests
+# shellcheck disable=SC2086
 ./compile_upp.sh ${_opts}
diff --git a/sorc/build_ww3prepost.sh b/sorc/build_ww3prepost.sh
index 786eeaa7cb..bf78e7b2ac 100755
--- a/sorc/build_ww3prepost.sh
+++ b/sorc/build_ww3prepost.sh
@@ -5,9 +5,8 @@ script_dir=$(dirname "${BASH_SOURCE[0]}")
 cd "${script_dir}" || exit 1
 
 export RT_COMPILER="intel"
-# shellcheck disable=SC1091
-source ${script_dir}/ufs_model.fd/tests/detect_machine.sh
-# shellcheck disable=
+source "${script_dir}/ufs_model.fd/tests/detect_machine.sh"
+source "${script_dir}/ufs_model.fd/tests/module-setup.sh"
 
 # Default settings
 APP="S2SWA"
@@ -15,7 +14,7 @@ APP="S2SWA"
 while getopts "a:v" option; do
   case "${option}" in
     a) APP="${OPTARG}" ;;
-    v) BUILD_VERBOSE="YES";;
+    v) export BUILD_VERBOSE="YES";;
     :)
       echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
       usage
@@ -37,11 +36,11 @@ fi
 
 
 # Check final exec folder exists
-if [ ! -d "../exec" ]; then
+if [[ ! -d "../exec" ]]; then
   mkdir ../exec
 fi
 
-finalexecdir=$( pwd -P )/../exec
+finalexecdir="$( pwd -P )/../exec"
 
 #Determine machine and load modules
 set +x
@@ -50,8 +49,9 @@ module load "ufs_${MACHINE_ID}"
 set -x
 
 #Set WW3 directory, switch, prep and post exes 
-cd ufs_model.fd/WW3
-export WW3_DIR=$( pwd -P )
+cd ufs_model.fd/WW3 || exit 1
+WW3_DIR=$( pwd -P )
+export WW3_DIR
 export SWITCHFILE="${WW3_DIR}/${ww3switch}"
 
 # Build exes for prep jobs and post jobs:
@@ -59,12 +59,12 @@ prep_exes="ww3_grid ww3_prep ww3_prnc ww3_grid"
 post_exes="ww3_outp ww3_outf ww3_outp ww3_gint ww3_ounf ww3_ounp ww3_grib"
 
 #create build directory: 
-path_build="$WW3_DIR/build_SHRD"
-mkdir -p "$path_build" || exit 1
-cd "$path_build" || exit 1
+path_build="${WW3_DIR}/build_SHRD"
+mkdir -p "${path_build}" || exit 1
+cd "${path_build}" || exit 1
 echo "Forcing a SHRD build" 
 
-echo $(cat "${SWITCHFILE}") > "${path_build}/tempswitch"
+cat "${SWITCHFILE}" > "${path_build}/tempswitch"
 
 sed -e "s/DIST/SHRD/g"\
     -e "s/OMPG / /g"\
@@ -77,35 +77,35 @@ sed -e "s/DIST/SHRD/g"\
        "${path_build}/tempswitch" > "${path_build}/switch"
 rm "${path_build}/tempswitch"
 
-echo "Switch file is $path_build/switch with switches:" 
-cat "${path_build}/switch "
+echo "Switch file is ${path_build}/switch with switches:" 
+cat "${path_build}/switch"
 
 #Build executables: 
 cmake "${WW3_DIR}" -DSWITCH="${path_build}/switch" -DCMAKE_INSTALL_PREFIX=install 
 rc=$?
-if [[ ${rc} -ne 0 ]] ; then
+if (( rc != 0 )); then
   echo "Fatal error in cmake."
-  exit ${rc}
+  exit "${rc}"
 fi
 make -j 8 
 rc=$?
-if [[ ${rc} -ne 0 ]] ; then
+if (( rc != 0 )); then
   echo "Fatal error in make."
-  exit ${rc}
+  exit "${rc}"
 fi
 make install 
-if [[ ${rc} -ne 0 ]] ; then
+if (( rc != 0 )); then
   echo "Fatal error in make install."
-  exit ${rc}  
+  exit "${rc}" 
 fi
 
 # Copy to top-level exe directory
 for prog in ${prep_exes} ${post_exes}; do
   cp "${path_build}/install/bin/${prog}" "${finalexecdir}/"
   rc=$?
-  if [[ ${rc} -ne 0 ]] ; then
+  if (( rc != 0 )); then
     echo "FATAL: Unable to copy ${path_build}/${prog} to ${finalexecdir} (Error code ${rc})"
-    exit ${rc}
+    exit "${rc}"
   fi
 done
 
diff --git a/sorc/checkout.sh b/sorc/checkout.sh
index abab899cc6..d414bbaade 100755
--- a/sorc/checkout.sh
+++ b/sorc/checkout.sh
@@ -151,7 +151,7 @@ mkdir -p "${logdir}"
 
 # The checkout version should always be a speciifc commit (hash or tag), not a branch
 errs=0
-checkout "gfs_utils.fd"    "https://github.com/NOAA-EMC/gfs-utils"              "af933d3"                    ; errs=$((errs + $?))
+checkout "gfs_utils.fd"    "https://github.com/NOAA-EMC/gfs-utils"              "0b8ff56"                    ; errs=$((errs + $?))
 checkout "ufs_model.fd"    "https://github.com/ufs-community/ufs-weather-model" "${ufs_model_hash:-6b73f5d}" ; errs=$((errs + $?))
 checkout "ufs_utils.fd"    "https://github.com/ufs-community/UFS_UTILS.git"     "8b990c0"                    ; errs=$((errs + $?))
 checkout "verif-global.fd" "https://github.com/NOAA-EMC/EMC_verif-global.git"   "c267780"                    ; errs=$((errs + $?))