[develop] Update weather model hash and correct behavior in Functiona…

…l WorkflowTaskTests Jenkins stage (ufs-community#1068)

* The ufs-weather-model hash has been updated to 1411b90 (April 1, 2024).
* Updated build_hera_gnu.lua file to allow it to work with updates to the ufs-weather-model.
* Updated behavior of the Functional WorkflowTaskTests Jenkins stage to allow the test to properly finish, rather than waiting in queue for all jobs associated with the EPIC role account to finish first (modification to .cicd/scripts/wrapper_srw_ftest.sh).
* Corrected the hang encountered while running the Functional WorkflowTaskTests stage on Gaea.
* Applied Mike Kavulich's modification to ush/bash_utils/create_symlink_to_file.sh and converted calls to the create_symlink_to_file function from using named arguments to positional arguments (Issue ufs-community#1066).

.cicd/scripts/wrapper_srw_ftest.sh

@@ -15,17 +15,16 @@ declare arg_1
 if [[ "${SRW_PLATFORM}" == cheyenne ]] || [[ "${SRW_PLATFORM}" == derecho ]]; then
  workflow_cmd=qsub
  arg_1=""
- check_job="qstat -u ${USER} -r ${job_id}"
 else
  workflow_cmd=sbatch
  arg_1="--parsable"
- check_job="squeue -u ${USER} -j ${job_id} --noheader"
 fi
 
 # Customize wrapper scripts
 if [[ "${SRW_PLATFORM}" == gaea ]]; then
  sed -i '15i #SBATCH --clusters=c5' ${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/${workflow_cmd}_srw_ftest.sh
  sed -i 's|qos=batch|qos=normal|g' ${WORKSPACE}/${SRW_PLATFORM}/.cicd/scripts/${workflow_cmd}_srw_ftest.sh
+ sed -i 's|${JOBSdir}/JREGIONAL_RUN_POST|$USHdir/load_modules_run_task.sh "run_post" ${JOBSdir}/JREGIONAL_RUN_POST|g' ${WORKSPACE}/${SRW_PLATFORM}/ush/wrappers/run_post.sh
 fi
 
 if [[ "${SRW_PLATFORM}" == hera ]]; then
@@ -52,6 +51,11 @@ sleep 10
 # Check for job and exit when done
 while true
 do
+ if [[ "${SRW_PLATFORM}" == derecho ]]; then
+ check_job="qstat -u ${USER} -r ${job_id}"
+ else
+ check_job="squeue -u ${USER} -j ${job_id} --noheader"
+ fi
  job_id_info=$($check_job)
  if [ ! -z "$job_id_info" ]; then
  echo "Job is still running. Check again in two minutes"

Externals.cfg

@@ -12,7 +12,7 @@ protocol = git
 repo_url = https://github.com/ufs-community/ufs-weather-model
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = 8518c2c
+hash = 1411b90
 local_path = sorc/ufs-weather-model
 required = True
 

modulefiles/build_hera_gnu.lua

@@ -19,7 +19,7 @@ load(pathJoin("nccmp", os.getenv("nccmp_ver") or "1.9.0.1"))
 load(pathJoin("nco", os.getenv("nco_ver") or "5.0.6"))
 load(pathJoin("openblas", os.getenv("openblas_ver") or "0.3.19"))
 
-setenv("CMAKE_C_COMPILER","mpicc")
-setenv("CMAKE_CXX_COMPILER","mpicxx")
-setenv("CMAKE_Fortran_COMPILER","mpif90")
-setenv("CMAKE_Platform","hera.gnu")
+setenv("CC", "mpicc")
+setenv("CXX", "mpic++")
+setenv("FC", "mpif90")
+setenv("CMAKE_Platform", "hera.gnu")

scripts/exregional_make_orog.sh

@@ -258,12 +258,9 @@ if [[ ${suites[@]} =~ "${CCPP_PHYS_SUITE}" ]] ; then
  grid_fp_gwd="${FIXlam}/${grid_fn_gwd}"
  ls_fn="geo_em.d01.lat-lon.2.5m.HGT_M.nc"
  ss_fn="HGT.Beljaars_filtered.lat-lon.30s_res.nc"
- create_symlink_to_file target="${grid_fp_gwd}" symlink="${DATA}/${grid_fn_gwd}" \
- relative="TRUE"
- create_symlink_to_file target="${FIXam}/${ls_fn}" symlink="${DATA}/${ls_fn}" \
- relative="TRUE"
- create_symlink_to_file target="${FIXam}/${ss_fn}" symlink="${DATA}/${ss_fn}" \
- relative="TRUE"
+ create_symlink_to_file ${grid_fp_gwd} ${DATA}/${grid_fn_gwd} TRUE
+ create_symlink_to_file ${FIXam}/${ls_fn} ${DATA}/${ls_fn} TRUE
+ create_symlink_to_file ${FIXam}/${ss_fn} ${DATA}/${ss_fn} TRUE
 
  input_redirect_fn="grid_info.dat"
  cat > "${input_redirect_fn}" <<EOF
@@ -405,8 +402,7 @@ cp_vrfy "${raw_orog_fp}" "${filtered_orog_fp}"
 # filtering executable will run) with the same name as the grid file and
 # point it to the actual grid file specified by grid_fp.
 #
-create_symlink_to_file target="${grid_fp}" symlink="${filter_dir}/${grid_fn}" \
- relative="TRUE"
+create_symlink_to_file ${grid_fp} ${filter_dir}/${grid_fn} TRUE
 #
 # Create the namelist file (in the filter_dir directory) that the orography
 # filtering executable will read in.

scripts/exregional_run_fcst.sh

@@ -121,17 +121,15 @@ fi
 #target="${FIXlam}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc" # Should this point to this halo4 file or a halo3 file???
 target="${FIXlam}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH3}.nc" # Should this point to this halo4 file or a halo3 file???
 symlink="grid_spec.nc"
-create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+create_symlink_to_file $target $symlink ${relative_link_flag}
 
 # Symlink to halo-3 grid file with "halo3" stripped from name.
 mosaic_fn="grid_spec.nc"
 grid_fn=$( get_charvar_from_netcdf "${mosaic_fn}" "gridfiles" )
 
 target="${FIXlam}/${grid_fn}"
 symlink="${grid_fn}"
-create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+create_symlink_to_file $target $symlink ${relative_link_flag}
 
 # Symlink to halo-4 grid file with "${CRES}_" stripped from name.
 #
@@ -147,8 +145,7 @@ create_symlink_to_file target="$target" symlink="$symlink" \
 #
 target="${FIXlam}/${CRES}${DOT_OR_USCORE}grid.tile${TILE_RGNL}.halo${NH4}.nc"
 symlink="grid.tile${TILE_RGNL}.halo${NH4}.nc"
-create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+create_symlink_to_file $target $symlink ${relative_link_flag}
 
 
 #
@@ -165,8 +162,7 @@ fi
 # Symlink to halo-0 orography file with "${CRES}_" and "halo0" stripped from name.
 target="${FIXlam}/${CRES}${DOT_OR_USCORE}oro_data.tile${TILE_RGNL}.halo${NH0}.nc"
 symlink="oro_data.nc"
-create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+create_symlink_to_file $target $symlink ${relative_link_flag}
 #
 # Symlink to halo-4 orography file with "${CRES}_" stripped from name.
 #
@@ -182,8 +178,7 @@ create_symlink_to_file target="$target" symlink="$symlink" \
 #
 target="${FIXlam}/${CRES}${DOT_OR_USCORE}oro_data.tile${TILE_RGNL}.halo${NH4}.nc"
 symlink="oro_data.tile${TILE_RGNL}.halo${NH4}.nc"
-create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+create_symlink_to_file $target $symlink ${relative_link_flag}
 #
 # If using the FV3_HRRR physics suite, there are two files (that contain 
 # statistics of the orography) that are needed by the gravity wave drag 
@@ -198,8 +193,7 @@ if [[ ${suites[@]} =~ "${CCPP_PHYS_SUITE}" ]] ; then
  for file_id in "${file_ids[@]}"; do
  target="${FIXlam}/${CRES}${DOT_OR_USCORE}oro_data_${file_id}.tile${TILE_RGNL}.halo${NH0}.nc"
  symlink="oro_data_${file_id}.nc"
- create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
  done
 fi
 #
@@ -238,53 +232,49 @@ if [ "${CPL_AQM}" = "TRUE" ]; then
 
  target="${COMIN}/${NET}.${cycle}${dot_ensmem}.gfs_data.tile${TILE_RGNL}.halo${NH0}.nc"
  symlink="gfs_data.nc"
- create_symlink_to_file target="$target" symlink="$symlink" relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
 
  target="${COMIN}/${NET}.${cycle}${dot_ensmem}.sfc_data.tile${TILE_RGNL}.halo${NH0}.nc"
  symlink="sfc_data.nc"
- create_symlink_to_file target="$target" symlink="$symlink" relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
 
  target="${COMIN}/${NET}.${cycle}${dot_ensmem}.gfs_ctrl.nc"
  symlink="gfs_ctrl.nc"
- create_symlink_to_file target="$target" symlink="$symlink" relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
 
  for fhr in $(seq -f "%03g" 0 ${LBC_SPEC_INTVL_HRS} ${FCST_LEN_HRS}); do
  target="${COMIN}/${NET}.${cycle}${dot_ensmem}.gfs_bndy.tile${TILE_RGNL}.f${fhr}.nc"
  symlink="gfs_bndy.tile${TILE_RGNL}.${fhr}.nc"
- create_symlink_to_file target="$target" symlink="$symlink" relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
  done
  target="${COMIN}/${NET}.${cycle}${dot_ensmem}.NEXUS_Expt.nc"
  symlink="NEXUS_Expt.nc"
- create_symlink_to_file target="$target" symlink="$symlink" relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
 
  # create symlink to PT for point source in SRW-AQM
  target="${COMIN}/${NET}.${cycle}${dot_ensmem}.PT.nc"
  if [ -f ${target} ]; then
  symlink="PT.nc"
- create_symlink_to_file target="$target" symlink="$symlink" relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
  fi
 
 else
  target="${INPUT_DATA}/${NET}.${cycle}${dot_ensmem}.gfs_data.tile${TILE_RGNL}.halo${NH0}.nc"
  symlink="gfs_data.nc"
- create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
 
  target="${INPUT_DATA}/${NET}.${cycle}${dot_ensmem}.sfc_data.tile${TILE_RGNL}.halo${NH0}.nc"
  symlink="sfc_data.nc"
- create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
 
  target="${INPUT_DATA}/${NET}.${cycle}${dot_ensmem}.gfs_ctrl.nc"
  symlink="gfs_ctrl.nc"
- create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
 
  for fhr in $(seq -f "%03g" 0 ${LBC_SPEC_INTVL_HRS} ${FCST_LEN_HRS}); do
  target="${INPUT_DATA}/${NET}.${cycle}${dot_ensmem}.gfs_bndy.tile${TILE_RGNL}.f${fhr}.nc"
  symlink="gfs_bndy.tile${TILE_RGNL}.${fhr}.nc"
- create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
  done
 fi
 #
@@ -335,8 +325,7 @@ for (( i=0; i<${num_symlinks}; i++ )); do
 
  symlink="${DATA}/$symlink"
  target="$FIXam/$target"
- create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
 
 done
 #
@@ -359,8 +348,7 @@ if [ "${USE_MERRA_CLIMO}" = "TRUE" ]; then
  symlink="${DATA}/${pre_f}.dat"
  fi
  target="${f_nm_path}"
- create_symlink_to_file target="$target" symlink="$symlink" \
- relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
  done
 fi
 #
@@ -403,17 +391,11 @@ else
  relative_link_flag="FALSE"
 fi
 
-create_symlink_to_file target="${DATA_TABLE_FP}" \
- symlink="${DATA}/${DATA_TABLE_FN}" \
- relative="${relative_link_flag}"
+create_symlink_to_file ${DATA_TABLE_FP} ${DATA}/${DATA_TABLE_FN} ${relative_link_flag}
 
-create_symlink_to_file target="${FIELD_TABLE_FP}" \
- symlink="${DATA}/${FIELD_TABLE_FN}" \
- relative="${relative_link_flag}"
+create_symlink_to_file ${FIELD_TABLE_FP} ${DATA}/${FIELD_TABLE_FN} ${relative_link_flag}
 
-create_symlink_to_file target="${FIELD_DICT_FP}" \
- symlink="${DATA}/${FIELD_DICT_FN}" \
- relative="${relative_link_flag}"
+create_symlink_to_file ${FIELD_DICT_FP} ${DATA}/${FIELD_DICT_FN} ${relative_link_flag}
 
 if [ ${WRITE_DOPOST} = "TRUE" ]; then
  cp_vrfy ${PARMdir}/upp/nam_micro_lookup.dat ./eta_micro_lookup.dat
@@ -581,7 +563,7 @@ for the current cycle's (cdate) run directory (DATA) failed:
  rm_vrfy "${file_id}"
  target="${DATA}/RESTART/${rst_yyyymmdd}.${rst_hh}0000.${file_id}"
  symlink="${file_id}"
- create_symlink_to_file target="$target" symlink="$symlink" relative="${relative_link_flag}"
+ create_symlink_to_file $target $symlink ${relative_link_flag}
  done
  cd_vrfy ${DATA} 
 fi
@@ -818,9 +800,7 @@ if [ ${WRITE_DOPOST} = "TRUE" ]; then
  if [ $RUN_ENVIR != "nco" ]; then
  basetime=$( $DATE_UTIL --date "$yyyymmdd $hh" +%y%j%H%M )
  symlink_suffix="_${basetime}f${fhr}${post_mn}"
- create_symlink_to_file target="${post_renamed_fn}" \
- symlink="${FID}${symlink_suffix}" \
- relative="TRUE"
+ create_symlink_to_file ${post_renamed_fn} ${FID}${symlink_suffix} TRUE
  fi
  # DBN alert
  if [ $SENDDBN = "TRUE" ]; then

scripts/exregional_run_post.sh

@@ -284,9 +284,7 @@ for fid in "${fids[@]}"; do
  post_renamed_fn="${NET}.${cycle}${dot_ensmem}.${fid}.${post_renamed_fn_suffix}"
  mv_vrfy ${DATA_FHR}/${post_orig_fn} ${post_renamed_fn}
  if [ $RUN_ENVIR != "nco" ]; then
- create_symlink_to_file target="${post_renamed_fn}" \
- symlink="${FID}${symlink_suffix}" \
- relative="TRUE"
+ create_symlink_to_file ${post_renamed_fn} ${FID}${symlink_suffix} TRUE
  fi
  # DBN alert
  if [ $SENDDBN = "TRUE" ]; then

ush/bash_utils/create_symlink_to_file.sh

@@ -16,78 +16,20 @@ function create_symlink_to_file() {
 #
 #-----------------------------------------------------------------------
 #
-# Save current shell options (in a global array). Then set new options
-# for this script/function.
-#
-#-----------------------------------------------------------------------
-#
- { save_shell_opts; . ${USHdir}/preamble.sh; } > /dev/null 2>&1
-#
-#-----------------------------------------------------------------------
-#
-# Get the full path to the file in which this script/function is located 
-# (scrfunc_fp), the name of that file (scrfunc_fn), and the directory in
-# which the file is located (scrfunc_dir).
-#
-#-----------------------------------------------------------------------
-#
- local scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
- local scrfunc_fn=$( basename "${scrfunc_fp}" )
- local scrfunc_dir=$( dirname "${scrfunc_fp}" )
-#
-#-----------------------------------------------------------------------
-#
-# Get the name of this function.
-#
-#-----------------------------------------------------------------------
-#
- local func_name="${FUNCNAME[0]}"
-#
-#-----------------------------------------------------------------------
-#
 # Specify the set of valid argument names for this script/function. Then
 # process the arguments provided to this script/function (which should
 # consist of a set of name-value pairs of the form arg1="value1", etc).
 #
 #-----------------------------------------------------------------------
 #
- local valid_args=( \
-"target" \
-"symlink" \
-"relative" \
- )
- process_args valid_args "$@"
-#
-#-----------------------------------------------------------------------
-#
-# For debugging purposes, print out values of arguments passed to this
-# script. Note that these will be printed out only if VERBOSE is set to
-# TRUE.
-#
-#-----------------------------------------------------------------------
-#
- print_input_args valid_args
-#
-#-----------------------------------------------------------------------
-#
-# Verify that the required arguments to this function have been specified.
-# If not, print out an error message and exit.
-#
-#-----------------------------------------------------------------------
-#
- if [ -z "${target}" ]; then
- print_err_msg_exit "\
-The argument \"target\" specifying the target of the symbolic link that
-this function will create was not specified in the call to this function:
- target = \"$target\""
- fi
+if [[ $# -lt 2 ]]; then
+ usage
+ print_err_msg_exit "Function create_symlink_to_file() requires at least two arguments"
+fi
 
- if [ -z "${symlink}" ]; then
- print_err_msg_exit "\
-The argument \"symlink\" specifying the symbolic link that this function
-will create was not specified in the call to this function:
- symlink = \"$symlink\""
- fi
+target=$1
+symlink=$2
+relative=${3:-TRUE}
 #
 #-----------------------------------------------------------------------
 #
@@ -106,8 +48,6 @@ will create was not specified in the call to this function:
 #
 #-----------------------------------------------------------------------
 #
- relative=${relative:-"TRUE"}
-
  valid_vals_relative=("TRUE" "true" "YES" "yes" "FALSE" "false" "NO" "no")
  check_var_valid_value "relative" "valid_vals_relative"
 #
@@ -148,16 +88,7 @@ not exist or is not a file:
 #
 #-----------------------------------------------------------------------
 #
- ln_vrfy -sf ${relative_flag} "$target" "$symlink"
-#
-#-----------------------------------------------------------------------
-#
-# Restore the shell options saved at the beginning of this script/func-
-# tion.
-#
-#-----------------------------------------------------------------------
-#
- { restore_shell_opts; } > /dev/null 2>&1
+ln -sf ${relative_flag} "$target" "$symlink"
 
 }