Merge branch 'develop' into cpld_s2sw_wavice

.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/[email protected]
+ 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=https://' | 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"