[develop] Bring change of production/AQM.v7 back to develop (ufs-comm…

…unity#828)

Multiple scripts relevant to AQM are updated to meet the NCO standards and EE2 reviewer's comments based on the production/AQM.v7 branch:
* The NCO variables such as NET, RUN, envir are renamed with the suffix _default meaning the default value. This is because they should be defined in job cards as can be seen in the NCO standards (pp.4, Table 1). In the current rocoto-based workflow, the job cards do not exist (instead, it uses the XML file). Therefore, they can be set in the configuration file and ush/machine/ file. However, for ecFlow, these variables should be replaced with those in the job cards. (The ecFlow option will be added in a separate PR later). This is done in the ush/job_preamble.sh script which is sourced in the J-job scripts.
* NCO wants to define COMIN/COMOUT, COMINmodel, DATAROOT using the compath call available in prod_util.
* NCO does not want to add a new directory (COMINext) to COM. The use of COMINext is removed.
* NCO wants to use the error handling calls such as 'err_chk' and 'err_exit' in 'prod_util' which is available only on WCOSS2.
* NCO uses the YES/NO flags while SRW App uses TRUE/FALSE. To resolve this mismatch, the boolify calls for the NCO variables are added to job_preamble.sh.
* The 'pgmerr' function is added to POST_STEP.
* The forecast hour in some output file names is changed to 3 digit.
* The working directory DATA is defined and created in job_preamble.sh for the NCO mode. Therefore, if-statement for the 'community' mode is added to the J-job scripts.
* The KEEPDATA capability does not work correctly for the shared tasks
* The input data directories are renamed to DCOMINdata.

.gitignore

@@ -5,7 +5,6 @@ fix/
 include/
 lib/
 share/
-modulefiles/extrn_comp_build/
 sorc/*/
 tests/WE2E/WE2E_tests_*.yaml
 tests/WE2E/*.txt

Externals.cfg

@@ -49,7 +49,7 @@ protocol = git
 repo_url = https://github.com/noaa-oar-arl/NEXUS
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = 3842818
+hash = 6a7a994
 local_path = sorc/arl_nexus
 required = True
 
@@ -58,7 +58,7 @@ protocol = git
 repo_url = https://github.com/NOAA-EMC/AQM-utils
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = 0a86f73
+hash = 694a139
 local_path = sorc/AQM-utils
 required = True
 

jobs/JREGIONAL_AQM_ICS

@@ -77,8 +77,12 @@ mkdir_vrfy -p "${INPUT_DATA}"
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
-mkdir_vrfy -p "${DATA}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_AQM_ICS}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_AQM_LBCS

@@ -77,8 +77,13 @@ mkdir_vrfy -p "${INPUT_DATA}"
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
-mkdir_vrfy -p "${DATA}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_AQM_LBCS}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
+
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_BIAS_CORRECTION_O3

@@ -60,7 +60,14 @@ This is the J-job script for the task that runs BIAS-CORRECTION-O3.
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_BIAS_CORRECTION_O3}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
+
+mkdir_vrfy -p ${COMOUTwmo}
 
 export PARMaqm_utils="${PARMaqm_utils:-${HOMEdir}/sorc/AQM-utils/parm}"
 

jobs/JREGIONAL_BIAS_CORRECTION_PM25

@@ -60,7 +60,14 @@ This is the J-job script for the task that runs BIAS-CORRECTION-PM25.
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_BIAS_CORRECTION_PM25}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
+
+mkdir_vrfy -p ${COMOUTwmo}
 
 export PARMaqm_utils="${PARMaqm_utils:-${HOMEdir}/sorc/AQM-utils/parm}"
 

jobs/JREGIONAL_FIRE_EMISSION

@@ -90,16 +90,20 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
-mkdir_vrfy -p "${DATA}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_FIRE_EMISSION}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
 #
 #-----------------------------------------------------------------------
 #
 # Create the directory where the RAVE fire emission files should be stored
 #
 #-----------------------------------------------------------------------
 #
-export FIRE_EMISSION_STAGING_DIR="${COMINext}/FIRE_EMISSION"
+export FIRE_EMISSION_STAGING_DIR="${FIRE_EMISSION_STAGING_DIR:-${COMIN}/FIRE_EMISSION}"
 mkdir_vrfy -p "${FIRE_EMISSION_STAGING_DIR}"
 #
 #-----------------------------------------------------------------------

jobs/JREGIONAL_GET_EXTRN_MDL_FILES

@@ -30,7 +30,7 @@
 #
 . $USHdir/source_util_funcs.sh
 source_config_for_task "task_get_extrn_ics|task_get_extrn_lbcs" ${GLOBAL_VAR_DEFNS_FP}
-. $USHdir/job_preamble.sh
+. $USHdir/job_preamble.sh "TRUE"
 #
 #-----------------------------------------------------------------------
 #
@@ -221,8 +221,7 @@ esac
 #-----------------------------------------------------------------------
 #
 if [ $RUN_ENVIR = "nco" ]; then
-    export EXTRN_MDL_STAGING_DIR="${COMINext}"
-    mkdir_vrfy -p "${EXTRN_MDL_STAGING_DIR}"
+    export EXTRN_MDL_STAGING_DIR="${EXTRN_MDL_STAGING_DIR:-${DATA}}"
 else
     export EXTRN_MDL_STAGING_DIR="${COMIN}/${EXTRN_MDL_NAME}/for_${ICS_OR_LBCS}"
     mkdir_vrfy -p "${EXTRN_MDL_STAGING_DIR}"
@@ -245,7 +244,7 @@ Call to ex-script corresponding to J-job \"${scrfunc_fn}\" failed."
 #
 #-----------------------------------------------------------------------
 #
-job_postamble
+job_postamble "FALSE"
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_MAKE_ICS

@@ -72,8 +72,12 @@ mkdir_vrfy -p "${INPUT_DATA_NWGES}"
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
-mkdir_vrfy -p "${DATA}"
+if [ $RUN_ENVIR = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_MAKE_ICS}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_MAKE_LBCS

@@ -71,8 +71,12 @@ mkdir_vrfy -p "${INPUT_DATA_NWGES}"
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
-mkdir_vrfy -p "${DATA}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_MAKE_LBCS}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_NEXUS_EMISSION

@@ -75,8 +75,12 @@ mkdir_vrfy -p "${INPUT_DATA}"
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
-mkdir_vrfy -p "${DATA}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_NEXUS_EMISSION_${nspt}}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_NEXUS_GFS_SFC

@@ -17,7 +17,7 @@
 #
 . $USHdir/source_util_funcs.sh
 source_config_for_task "cpl_aqm_parm|task_nexus_gfs_sfc" ${GLOBAL_VAR_DEFNS_FP}
-. $USHdir/job_preamble.sh
+. $USHdir/job_preamble.sh "TRUE"
 #
 #-----------------------------------------------------------------------
 #
@@ -91,21 +91,16 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-# Create the directory where the RAVE fire emission files should be stored
-#
-#-----------------------------------------------------------------------
-#
-export GFS_SFC_STAGING_DIR="${COMINext}/GFS_SFC"
-mkdir_vrfy -p "${GFS_SFC_STAGING_DIR}"
-#
-#-----------------------------------------------------------------------
-#
 # Set the run directory
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
-mkdir_vrfy -p "${DATA}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_NEXUS_GFS_SFC}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
 #
 #-----------------------------------------------------------------------
 #
@@ -123,7 +118,7 @@ Call to ex-script corresponding to J-job \"${scrfunc_fn}\" failed."
 #
 #-----------------------------------------------------------------------
 #
-job_postamble
+job_postamble "FALSE"
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_NEXUS_POST_SPLIT

@@ -67,8 +67,12 @@ mkdir_vrfy -p "${INPUT_DATA}"
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
-mkdir_vrfy -p "${DATA}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_NEXUS_POST_SPLIT}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_POINT_SOURCE

@@ -66,8 +66,12 @@ mkdir_vrfy -p "${INPUT_DATA}"
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
-mkdir_vrfy -p "${DATA}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_POINT_SOURCE}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
 #
 #
 #-----------------------------------------------------------------------

jobs/JREGIONAL_POST_STAT_O3

@@ -60,7 +60,14 @@ This is the J-job script for the task that runs POST-STAT-O3.
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_POST_STAT_O3}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
+
+mkdir_vrfy -p ${COMOUTwmo}
 
 export PARMaqm_utils="${PARMaqm_utils:-${HOMEdir}/sorc/AQM-utils/parm}"
 #

jobs/JREGIONAL_POST_STAT_PM25

@@ -60,7 +60,14 @@ This is the J-job script for the task that runs POST-UPP-STAT.
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
+DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_POST_STAT_PM25}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
+
+mkdir_vrfy -p ${COMOUTwmo}
 
 export PARMaqm_utils="${PARMaqm_utils:-${HOMEdir}/sorc/AQM-utils/parm}"
 #

jobs/JREGIONAL_PRE_POST_STAT

@@ -60,7 +60,12 @@ This is the J-job script for the task that runs POST-UPP-STAT.
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}/tmp_PRE_POST_STAT}"
+  check_for_preexist_dir_file "$DATA" "delete"
+  mkdir_vrfy -p $DATA
+  cd_vrfy $DATA
+fi
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_FCST

@@ -66,6 +66,7 @@ the specified cycle.
 if [ $RUN_ENVIR = "nco" ]; then
     export INPUT_DATA="${COMIN}"
 else
+    DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
     export INPUT_DATA="${COMIN}${SLASH_ENSMEM_SUBDIR}/INPUT"
 fi
 #
@@ -75,7 +76,6 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
 mkdir_vrfy -p ${DATA}/INPUT
 mkdir_vrfy -p ${DATA}/RESTART
 #
@@ -96,7 +96,7 @@ Call to ex-script corresponding to J-job \"${scrfunc_fn}\" failed."
 #
 #-----------------------------------------------------------------------
 #
-job_postamble
+job_postamble "FALSE"
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_POST

@@ -56,14 +56,6 @@ This is the J-job script for the task that runs the post-processor (UPP)
 on the output files corresponding to a specified forecast hour.
 ========================================================================"
 #
-#-----------------------------------------------------------------------
-#
-# Set the run directory.
-#
-#-----------------------------------------------------------------------
-#
-DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
-#
 # If SUB_HOURLY_POST is not set to "TRUE", ensure that the forecast 
 # minutes (fmn) are set to "00".  This is necessary in order to pass
 # "fmn" into the post ex-script for the calculation of post_time.
@@ -90,10 +82,11 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-if [ "${RUN_ENVIR}" != "nco" ]; then
+if [ "${RUN_ENVIR}" = "community" ]; then
+  DATA="${DATA:-${COMIN}${SLASH_ENSMEM_SUBDIR}}"
   export COMOUT="${DATA}/postprd"
+  mkdir_vrfy -p "${COMOUT}"
 fi
-mkdir_vrfy -p "${COMOUT}"
 
 if [ "${SUB_HOURLY_POST}" = "TRUE" ]; then
   export DATA_FHR="${DATA:-$COMOUT}/$fhr$fmn"
@@ -143,9 +136,11 @@ if [ ${#FCST_LEN_CYCL[@]} -gt 1 ]; then
   CYCLE_IDX=$(( ${cyc_mod} / ${INCR_CYCL_FREQ} ))
   FCST_LEN_HRS=${FCST_LEN_CYCL[$CYCLE_IDX]}
 
-  fcst_len_hrs=$( printf "%03d" "${FCST_LEN_HRS}" )
-  if [ "${fhr}" = "${fcst_len_hrs}" ]; then
-    touch "${COMIN}/post_${PDY}${cyc}_task_complete.txt"
+  if [ "${WORKFLOW_MANAGER}" = "rocoto" ]; then 
+    fcst_len_hrs=$( printf "%03d" "${FCST_LEN_HRS}" ) 
+    if [ "${fhr}" = "${fcst_len_hrs}" ]; then
+      touch "${COMIN}/post_${PDY}${cyc}_task_complete.txt"
+    fi
   fi
 fi
 #
@@ -155,7 +150,12 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-job_postamble
+fcst_len_hrs=$( printf "%03d" "${FCST_LEN_HRS}" )
+if [ "${fhr}" = "${fcst_len_hrs}" ]; then
+    job_postamble "TRUE"
+else
+    job_postamble
+fi
 #
 #-----------------------------------------------------------------------
 #

modulefiles/tasks/wcoss2/python_srw.lua

@@ -1,3 +1,5 @@
+load(pathJoin("PrgEnv-intel", os.getenv("PrgEnv_intel_ver")))
+load(pathJoin("craype", os.getenv("craype_ver")))
 load(pathJoin("intel", os.getenv("intel_ver")))
 load(pathJoin("python", os.getenv("python_ver")))
 load(pathJoin("prod_util", os.getenv("prod_util_ver")))