Add bash linting to CI. Cleanup .sh scripts a bit. Address .sh bugs. …

…Adds -v Verbose option. (#2218)  Remove nowarn Intel compiler flag (#2225)

* UFSWM
- Add bash linting to CI:
  - uses superlinter to check for consistent bash code writing
- Cleans up .sh scripts to comply with superlinter
- Cleans up .sh scripts to be more consistent, easier to read.
- Add's -v verbose option if debugging outputs needed, otherwise simplifies rt.sh run echo's.
- Addresses smaller bugs
  - quota/timeout search logic adjusted.
  - check for dirs existing (DISKNM, STMP, PTMP) before starting.
  - adjustments/cleanup to ecflow/rocoto sections
  - rt.sh will attempt to start ecflow, and only stop ecflow if it started from rt.sh.
  - fix for issue where run_dir will not delete properly.
* FV3: Address compiler warnings
  * atmos_cubed_sphere: Address compiler warnings.

.github/workflows/superlinter.yml

@@ -0,0 +1,37 @@
+---
+name: Super-Linter
+
+on:
+  push: null
+  pull_request: null
+
+jobs:
+  build:
+    name: Lint
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: read
+      statuses: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Super-Linter
+        uses: super-linter/super-linter@v6.3.0
+        env:
+          LINTER_RULES_PATH: /
+          DEFAULT_BRANCH: origin/develop
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          FILTER_REGEX_EXCLUDE: .*(tests/fv3_conf/.*|tests/ci/.*|tests/auto/.*|tests/auto-jenkins/.*|tests/opnReqTests/.*|tests/opnReqTest|tests/atparse.bash).*
+          VALIDATE_BASH: true
+          BASH_SEVERITY: style
+          #VALIDATE_GITHUB_ACTIONS: true
+          #VALIDATE_LUA: true
+          #VALIDATE_MARKDOWN: true
+          #VALIDATE_PYTHON_PYLINT: true
+          #VALIDATE_YAML: true

.shellcheckrc

@@ -0,0 +1,16 @@
+# Global settings for Shellcheck (https://github.com/koalaman/shellcheck)
+enable=all
+
+external-sources=true
+
+# Disable variable referenced but not assigned
+disable=SC2154
+
+# Disable following non-constant source
+disable=SC1090
+
+# Disable non-existent binary
+disable=SC1091
+
+# Disable -p -m only applies to deepest directory
+disable=SC2174

build.sh

@@ -1,21 +1,29 @@
 #!/bin/bash
 set -eu
-
-if [[ $(uname -s) == Darwin ]]; then
-  readonly UFS_MODEL_DIR=$(cd "$(dirname "$(greadlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+uname_s=$(uname -s)
+if [[ ${uname_s} == Darwin ]]; then
+  UFS_MODEL_DIR=$(greadlink -f -n "${BASH_SOURCE[0]}")
+  UFS_MODEL_DIR=$(dirname "${UFS_MODEL_DIR}")
+  UFS_MODEL_DIR=$(cd "${UFS_MODEL_DIR}" && pwd -P)
 else
-  readonly UFS_MODEL_DIR=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+  UFS_MODEL_DIR=$(readlink -f -n "${BASH_SOURCE[0]}")
+  UFS_MODEL_DIR=$(dirname "${UFS_MODEL_DIR}")
+  UFS_MODEL_DIR=$(cd "${UFS_MODEL_DIR}" && pwd -P)
 fi
+echo "UFS MODEL DIR: ${UFS_MODEL_DIR}"
+readonly UFS_MODEL_DIR
 
 export CC=${CC:-mpicc}
 export CXX=${CXX:-mpicxx}
 export FC=${FC:-mpif90}
 
 BUILD_DIR=${BUILD_DIR:-${UFS_MODEL_DIR}/build}
-mkdir -p ${BUILD_DIR}
+mkdir -p "${BUILD_DIR}"
 
-cd ${BUILD_DIR}
-cmake ${UFS_MODEL_DIR} ${CMAKE_FLAGS}
+cd "${BUILD_DIR}"
+ARR_CMAKE_FLAGS=()
+for i in ${CMAKE_FLAGS}; do ARR_CMAKE_FLAGS+=("${i}") ; done
+cmake "${UFS_MODEL_DIR}" "${ARR_CMAKE_FLAGS[@]}"
 # Turn off OpenMP threading for parallel builds
 # to avoid exhausting the number of user processes
-OMP_NUM_THREADS=1 make -j ${BUILD_JOBS:-4} VERBOSE=${BUILD_VERBOSE:-}
+OMP_NUM_THREADS=1 make -j "${BUILD_JOBS:-4}" "VERBOSE=${BUILD_VERBOSE:-1}"

cmake/Intel.cmake

@@ -1,6 +1,12 @@
-set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback -fpp -fno-alias -auto -safe-cray-ptr -ftz -assume byterecl -nowarn -sox -align array64byte -qno-opt-dynamic-align")
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback -fpp -fno-alias -auto -safe-cray-ptr -ftz -assume byterecl -sox -align array64byte -qno-opt-dynamic-align")
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -qno-opt-dynamic-align -sox -fp-model source")
 
+# warning #5462: Global name too long.
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -diag-disable 5462")
+
+# remark #7712: This variable has not been used.
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -diag-disable 7712")
+
 if(CMAKE_Platform STREQUAL "derecho.intel")
   set(CMAKE_Fortran_LINK_FLAGS "-Wl,--copy-dt-needed-entries")
 endif()

tests/compile.sh

@@ -7,73 +7,82 @@ function trim {
     var="${var#"${var%%[![:space:]]*}"}"
     # remove trailing whitespace characters
     var="${var%"${var##*[![:space:]]}"}"
-    echo -n "$var"
+    echo -n "${var}"
 }
 
 SECONDS=0
 
-if [[ $(uname -s) == Darwin ]]; then
-  readonly MYDIR=$(cd "$(dirname "$(greadlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+uname_s=$(uname -s)
+if [[ ${uname_s} == Darwin ]]; then
+  greadlnk=$(greadlink -f -n "${BASH_SOURCE[0]}" )
+  MYDIR=$(cd "$(dirname "${greadlnk}" )" && pwd -P)
 else
-  readonly MYDIR=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+  readlnk=$(readlink -f -n "${BASH_SOURCE[0]}" )
+  MYDIR=$(cd "$(dirname "${readlnk}" )" && pwd -P)
 fi
+readonly MYDIR
 
 # ----------------------------------------------------------------------
 # Parse arguments.
 
 readonly ARGC=$#
 
-if [[ $ARGC -lt 2 ]]; then
-  echo "Usage: $0 MACHINE_ID [ MAKE_OPT [ COMPILE_ID ] [ RT_COMPILER ] [ clean_before ] [ clean_after ] ]"
+if [[ ${ARGC} -lt 2 ]]; then
+  echo "Usage: $0 MACHINE_ID [ MAKE_OPT ] [ COMPILE_ID ] [ RT_COMPILER ] [ clean_before ] [ clean_after ]"
   echo Valid MACHINE_IDs:
-  echo $( ls -1 ../cmake/configure_* | sed s:.*configure_::g | sed s:\.cmake:: ) | fold -sw72
+  echostuff=$( ls -1 ../cmake/configure_* )
+  echostuff=${echostuff/:.*configure_::g}
+  echostuff=${echostuff/:\.cmake::}
+  echostuff=$( fold -sw72 <<< "${echostuff}" )
   exit 1
 else
   MACHINE_ID=$1
   MAKE_OPT=${2:-}
-  COMPILE_ID=${3:+_$3}
+  COMPILE_ID=${3:+$3}
   RT_COMPILER=${4:-intel}
   clean_before=${5:-YES}
   clean_after=${6:-YES}
 fi
 
-BUILD_NAME=fv3${COMPILE_ID}
+BUILD_NAME=fv3_${COMPILE_ID}
 
-PATHTR=${PATHTR:-$( cd ${MYDIR}/.. && pwd )}
+PATHTR=${PATHTR:-$( cd "${MYDIR}/.." && pwd )}
 BUILD_DIR=${BUILD_DIR:-$(pwd)/build_${BUILD_NAME}}
 
 # ----------------------------------------------------------------------
 # Make sure we have reasonable number of threads.
 
-if [[ $MACHINE_ID == derecho ]]; then
+if [[ ${MACHINE_ID} == derecho ]]; then
     BUILD_JOBS=${BUILD_JOBS:-3}
 fi
 
 BUILD_JOBS=${BUILD_JOBS:-8}
 
-hostname
+#hostname
 
 set +x
-if [[ $MACHINE_ID == macosx ]] || [[ $MACHINE_ID == linux ]]; then
-  source $PATHTR/modulefiles/ufs_${MACHINE_ID}.${RT_COMPILER}
-else
-  # Activate lua environment for gaea c5
-  if [[ $MACHINE_ID == gaea ]]; then
-    module reset
-  fi
-  # Load fv3 module
-  module use $PATHTR/modulefiles
-  modulefile="ufs_${MACHINE_ID}.${RT_COMPILER}"
-  module load $modulefile
-  module list
-fi
+case ${MACHINE_ID} in
+  macosx|linux)
+    source "${PATHTR}/modulefiles/ufs_${MACHINE_ID}.${RT_COMPILER}"
+    ;;
+  *)
+    # Activate lua environment for gaea c5
+    if [[ ${MACHINE_ID} == gaea ]]; then
+      module reset
+    fi
+    # Load fv3 module
+    module use "${PATHTR}/modulefiles"
+    modulefile="ufs_${MACHINE_ID}.${RT_COMPILER}"
+    module load "${modulefile}"
+    module list
+esac
 set -x
 
-echo "Compiling ${MAKE_OPT} into $BUILD_NAME.exe on $MACHINE_ID"
+echo "Compiling ${MAKE_OPT} into ${BUILD_NAME}.exe on ${MACHINE_ID}"
 
 # set CMAKE_FLAGS based on $MAKE_OPT
 
-CMAKE_FLAGS=$MAKE_OPT
+CMAKE_FLAGS=${MAKE_OPT}
 CMAKE_FLAGS+=" -DMPI=ON"
 
 if [[ ${MAKE_OPT} == *-DDEBUG=ON* ]]; then
@@ -87,15 +96,11 @@ fi
 
 # Check if suites argument is provided or not
 set +ex
-TEST=$( echo $MAKE_OPT | grep -e "-DCCPP_SUITES=" )
-if [[ $? -eq 0 ]]; then
-  SUITES=$( echo $MAKE_OPT | sed 's/.*-DCCPP_SUITES=//' | sed 's/ .*//' )
-  echo "Compiling suites ${SUITES}"
-fi
+SUITES=$(grep -Po "\-DCCPP_SUITES=\K[^ ]*" <<< "${MAKE_OPT}")
+export SUITES
 set -ex
 
 # Valid applications
-
 if [[ "${MAKE_OPT}" == *"-DAPP=S2S"* ]]; then
     CMAKE_FLAGS+=" -DMOM6SOLO=ON"
 fi
@@ -104,31 +109,27 @@ if [[ "${MAKE_OPT}" == *"-DAPP=NG-GODAS"* ]]; then
     CMAKE_FLAGS+=" -DMOM6SOLO=ON"
 fi
 
-CMAKE_FLAGS=$(trim "${CMAKE_FLAGS}")
+CMAKE_FLAGS=$(set -e; trim "${CMAKE_FLAGS}")
 echo "CMAKE_FLAGS = ${CMAKE_FLAGS}"
 
-if [ $clean_before = YES ] ; then
-  rm -rf ${BUILD_DIR}
-fi
+[[ ${clean_before} = YES ]] && rm -rf "${BUILD_DIR}"
 
 export BUILD_VERBOSE=1
 export BUILD_DIR
 export BUILD_JOBS
 export CMAKE_FLAGS
 
-bash -x ${PATHTR}/build.sh
+bash -x "${PATHTR}/build.sh"
 
-mv ${BUILD_DIR}/ufs_model ${PATHTR}/tests/${BUILD_NAME}.exe
-if [[ $MACHINE_ID == linux ]]; then
-  cp ${PATHTR}/modulefiles/ufs_${MACHINE_ID}.${RT_COMPILER}       ${PATHTR}/tests/modules.${BUILD_NAME}
+mv "${BUILD_DIR}/ufs_model" "${PATHTR}/tests/${BUILD_NAME}.exe"
+if [[ ${MACHINE_ID} == linux ]]; then
+  cp "${PATHTR}/modulefiles/ufs_${MACHINE_ID}.${RT_COMPILER}" "${PATHTR}/tests/modules.${BUILD_NAME}"
 else
-  cp ${PATHTR}/modulefiles/ufs_${MACHINE_ID}.${RT_COMPILER}.lua       ${PATHTR}/tests/modules.${BUILD_NAME}.lua
+  cp "${PATHTR}/modulefiles/ufs_${MACHINE_ID}.${RT_COMPILER}.lua" "${PATHTR}/tests/modules.${BUILD_NAME}.lua"
 fi
 
-if [ $clean_after = YES ] ; then
-  rm -rf ${BUILD_DIR}
-fi
+[[ ${clean_after} == YES ]] && rm -rf "${BUILD_DIR}"
 
-elapsed=$SECONDS
-echo "Elapsed time $elapsed seconds. Compiling ${CMAKE_FLAGS} finished"
-echo "Compile ${COMPILE_ID/#_} elapsed time $elapsed seconds. ${CMAKE_FLAGS}" > compile${COMPILE_ID}_time.log
+elapsed=${SECONDS}
+echo "Elapsed time ${elapsed} seconds. Compiling ${CMAKE_FLAGS} finished"
+echo "Compile ${COMPILE_ID} elapsed time ${elapsed} seconds. ${CMAKE_FLAGS}" > "compile_${COMPILE_ID}_time.log"