Merge branch 'NOAA-EMC:develop' into feature/iaucycling_marineda

jobs/JGDAS_ATMOS_VERFOZN

@@ -4,7 +4,7 @@
 # Set up environment for GDAS Ozone Monitor job
 #############################################################
 source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "verfozn" -c "base verfozn"
 
 export OZNMON_SUFFIX=${OZNMON_SUFFIX:-${NET}}
 
@@ -42,15 +42,12 @@ export p_cyc=${pdate:8:2}
 #---------------------------------------------
 # OZN_TANKDIR - WHERE OUTPUT DATA WILL RESIDE
 #
-export OZN_TANKDIR=${OZN_TANKDIR:-$(compath.py ${envir}/${NET}/${gfs_ver})}
-export TANKverf_ozn=${TANKverf_ozn:-${OZN_TANKDIR}/${RUN}.${PDY}/${cyc}/atmos/oznmon}
-export TANKverf_oznM1=${TANKverf_oznM1:-${OZN_TANKDIR}/${RUN}.${P_PDY}/${p_cyc}/atmos/oznmon}
-
 YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS
+YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_OZNMON
 
-if [[ ! -d ${TANKverf_ozn} ]]; then
-   mkdir -p -m 775 ${TANKverf_ozn}
-fi
+export TANKverf_ozn=${TANKverf_ozn:-${COM_ATMOS_OZNMON}}
+
+if [[ ! -d ${TANKverf_ozn} ]]; then mkdir -p -m 775 ${TANKverf_ozn} ; fi
 
 #---------------------------------------
 #  set up validation file
@@ -77,10 +74,6 @@ err=$?
 ################################
 # Remove the Working Directory
 ################################
-KEEPDATA=${KEEPDATA:-NO}
-cd ${DATAROOT}
-if [ ${KEEPDATA} = NO ] ; then
-  rm -rf ${DATA}
-fi
+[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
 
 exit 0

jobs/JGDAS_ATMOS_VERFRAD

@@ -4,18 +4,13 @@
 # Set up environment for GDAS Radiance Monitor job
 #############################################################
 source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "verfrad" -c "base verfrad"
 
 export COMPONENT="atmos"
 
-export RAD_DATA_IN=${DATA}
-
 export RADMON_SUFFIX=${RADMON_SUFFIX:-${RUN}}
 export CYCLE_INTERVAL=${CYCLE_INTERVAL:-6}
 
-mkdir -p ${RAD_DATA_IN}
-cd ${RAD_DATA_IN}
-
 ##############################################
 # Specify Execution Areas
 ##############################################
@@ -52,13 +47,15 @@ export p_cyc=${pdate:8:2}
 # COMOUT - WHERE GSI OUTPUT RESIDES
 # TANKverf - WHERE OUTPUT DATA WILL RESIDE
 #############################################
-export TANKverf=${TANKverf:-$(compath.py ${envir}/${NET}/${gfs_ver})}
-export TANKverf_rad=${TANKverf_rad:-${TANKverf}/${RUN}.${PDY}/${cyc}/atmos/radmon}
-export TANKverf_radM1=${TANKverf_radM1:-${TANKverf}/${RUN}.${P_PDY}/${p_cyc}/atmos/radmon}
-
 YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS
+YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_RADMON
+YMD=${P_PDY} HH=${p_cyc} generate_com -rx COM_ATMOS_RADMON_PREV:COM_ATMOS_RADMON_TMPL
 
-mkdir -p -m 775 ${TANKverf_rad}
+export TANKverf_rad=${TANKverf_rad:-${COM_ATMOS_RADMON}}
+export TANKverf_radM1=${TANKverf_radM1:-${COM_ATMOS_RADMON_PREV}}
+
+if [[ ! -d ${TANKverf_rad} ]]; then mkdir -p -m 775 ${TANKverf_rad} ; fi
+if [[ ! -d ${TANKverf_radM1} ]]; then mkdir -p -m 775 ${TANKverf_radM1} ; fi
 
 ########################################
 # Set necessary environment variables
@@ -89,9 +86,6 @@ fi
 ################################
 # Remove the Working Directory
 ################################
-KEEPDATA=${KEEPDATA:-YES}
-cd ${DATAROOT}
-if [ ${KEEPDATA} = NO ] ; then
-  rm -rf ${RAD_DATA_IN}
-fi
+[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
 
+exit 0

jobs/JGDAS_ATMOS_VMINMON

@@ -4,7 +4,7 @@
 # GDAS Minimization Monitor (MinMon) job
 ###########################################################
 source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "vminmon" -c "base vminmon"
 
 ###########################################################
 # obtain unique process id (pid) and make temp directories
@@ -40,12 +40,15 @@ export p_cyc=${pdate:8:2}
 #############################################
 # TANKverf - WHERE OUTPUT DATA WILL RESIDE
 #############################################
-export M_TANKverf=${M_TANKverf:-${COM_IN}/${RUN}.${PDY}/${cyc}/atmos/minmon}
-export M_TANKverfM1=${M_TANKverfM1:-${COM_IN}/${RUN}.${P_PDY}/${p_cyc}/atmos/minmon}
-
 YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS
+YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_MINMON
+YMD=${P_PDY} HH=${p_cyc} generate_com -rx COM_ATMOS_MINMON_PREV:COM_ATMOS_MINMON_TMPL
+
+export M_TANKverf=${M_TANKverf:-${COM_ATMOS_MINMON}}
+export M_TANKverfM1=${M_TANKverfM1:-${COM_ATMOS_MINMON_PREV}}
 
-mkdir -p -m 775 ${M_TANKverf}
+if [[ ! -d ${M_TANKverf} ]]; then mkdir -p -m 775 ${M_TANKverf} ; fi
+if [[ ! -d ${M_TANKverfM1} ]]; then mkdir -p -m 775 ${M_TANKverfM1} ; fi
 
 
 ########################################
@@ -65,10 +68,6 @@ err=$?
 ################################
 # Remove the Working Directory
 ################################
-KEEPDATA=${KEEPDATA:-NO}
-cd ${DATAROOT}
-if [ ${KEEPDATA} = NO ] ; then
-  rm -rf ${DATA}
-fi
+[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
 
 exit 0

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT

@@ -20,7 +20,7 @@ export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_bmat.sh}
+EXSCRIPT=${GDASOCNBMATSH:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_bmat.sh}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT_VRFY

@@ -19,7 +19,7 @@ export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_bmat_vrfy.sh}
+EXSCRIPT=${GDASOCNMBATVRFYSH:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_bmat_vrfy.sh}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT

@@ -34,7 +34,7 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_HISTORY_PREV:COM_
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_chkpt.sh}
+EXSCRIPT=${GDASOCNCHKPTSH:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_chkpt.sh}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST

@@ -31,7 +31,7 @@ export PYTHONPATH
 # Run relevant script
 ###############################################################
 
-EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_post.py}
+EXSCRIPT=${GDASOCNPOSTPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_post.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP

@@ -41,7 +41,7 @@ export PYTHONPATH
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_prep.py}
+EXSCRIPT=${GDASOCNPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_prep.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN

@@ -17,7 +17,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalr
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_run.sh}
+EXSCRIPT=${GDASOCNRUNSH:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_run.sh}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY

@@ -32,7 +32,7 @@ export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/soca:${PYTHONPATH}
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_vrfy.py}
+EXSCRIPT=${GDASOCNVRFYPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_vrfy.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"

jobs/JGFS_ATMOS_VMINMON

@@ -4,7 +4,7 @@
 # GFS Minimization Monitor (MinMon) job
 ###########################################################
 source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "vminmon" -c "base vminmon"
 
 ###########################################################
 # obtain unique process id (pid) and make temp directories
@@ -39,12 +39,15 @@ export p_cyc=${pdate:8:2}
 # TANKverf - WHERE OUTPUT DATA WILL RESIDE
 #############################################
 YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS
-YMD=${P_PDY} HH=${p_cyc} generate_com -rx COM_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL
+YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_MINMON
+YMD=${P_PDY} HH=${p_cyc} generate_com -rx COM_ATMOS_MINMON_PREV:COM_ATMOS_MINMON_TMPL
 
-M_TANKverf=${M_TANKverf:-${COM_ATMOS_ANALYSIS}/minmon}
-export M_TANKverfM1=${M_TANKverfM1:-${COM_ATMOS_ANALYSIS_PREV}/minmon}
+export M_TANKverf=${M_TANKverf:-${COM_ATMOS_MINMON}}
+export M_TANKverfM1=${M_TANKverfM1:-${COM_ATMOS_MINMON_PREV}}
+
+if [[ ! -d ${M_TANKverf} ]]; then mkdir -p -m 775 ${M_TANKverf} ; fi
+if [[ ! -d ${M_TANKverfM1} ]]; then mkdir -p -m 775 ${M_TANKverfM1} ; fi
 
-mkdir -p -m 775 ${M_TANKverf}
 
 ########################################
 # Set necessary environment variables
@@ -63,11 +66,6 @@ err=$?
 ################################
 # Remove the Working Directory
 ################################
-KEEPDATA=${KEEPDATA:-NO}
-cd ${DATAROOT}
-
-if [ ${KEEPDATA} = NO ] ; then
-  rm -rf ${DATA}
-fi
-
+[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
 
+exit 0

jobs/JGLOBAL_ARCHIVE

@@ -18,7 +18,8 @@ YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS COM_ATMOS_BUFR COM_ATMO
   COM_OBS COM_TOP \
   COM_OCEAN_HISTORY COM_OCEAN_INPUT COM_OCEAN_RESTART COM_OCEAN_XSECT COM_OCEAN_2D COM_OCEAN_3D \
   COM_OCEAN_ANALYSIS \
-  COM_WAVE_GRID COM_WAVE_HISTORY COM_WAVE_STATION
+  COM_WAVE_GRID COM_WAVE_HISTORY COM_WAVE_STATION \
+  COM_ATMOS_OZNMON COM_ATMOS_RADMON COM_ATMOS_MINMON
 
 for grid in "0p25" "0p50" "1p00"; do
   YMD=${PDY} HH=${cyc} GRID=${grid} generate_com -rx "COM_ATMOS_GRIB_${grid}:COM_ATMOS_GRIB_GRID_TMPL"

jobs/JGLOBAL_ATMOS_POST

@@ -17,18 +17,6 @@ export g2tmpl_ver=${g2tmpl_ver:-v1.5.0}
 ##############################################
 export CDUMP=${RUN/enkf}
 
-
-##############################################
-# TODO: Remove this egregious HACK
-##############################################
-if [[ "${SDATE:-}" = "${PDY}${cyc}" ]]; then
-  if [[ ${post_times} = "anl" ]]; then
-    echo "No offline post-processing in the first half cycle for analysis"
-    exit 0
-  fi
-fi
-
-
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################

jobs/JGLOBAL_PREP_OCEAN_OBS

@@ -7,15 +7,23 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "prepoceanobs" -c "base prepoceanobs"
 # Set variables used in the script
 ##############################################
 
+export COMIN_OBS="${DATA}"
+
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 
+# Add prep_marine_obs.py to PYTHONPATH
+export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/soca:${PYTHONPATH}
 
 ###############################################################
 # Run relevant script
 
-# the relevant script goes here
+EXSCRIPT=${GDASPREPOCNOBSPY:-${HOMEgfs}/ush/exglobal_prep_ocean_obs.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
 
 ##############################################
 # End JOB SPECIFIC work

jobs/rocoto/post.sh

@@ -4,7 +4,6 @@ source "${HOMEgfs}/ush/preamble.sh"
 
 ###############################################################
 ## NCEP post driver script
-## FHRGRP : forecast hour group to post-process (e.g. 0, 1, 2 ...)
 ## FHRLST : forecast hourlist to be post-process (e.g. anl, f000, f000_f001_f002, ...)
 ###############################################################
 
@@ -16,11 +15,7 @@ status=$?
 export job="post"
 export jobid="${job}.$$"
 
-if [ ${FHRGRP} = 'anl' ]; then
-    fhrlst="anl"
-else
-    fhrlst=$(echo ${FHRLST} | sed -e 's/_/ /g; s/f/ /g; s/,/ /g')
-fi
+fhrlst=$(echo ${FHRLST} | sed -e 's/_/ /g; s/f/ /g; s/,/ /g')
 
 #---------------------------------------------------------------
 for fhr in ${fhrlst}; do

jobs/rocoto/postanl.sh

@@ -0,0 +1 @@
+post.sh

jobs/rocoto/verfozn.sh

@@ -0,0 +1,22 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source FV3GFS workflow modules
+source "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
+status=$?
+(( status != 0 )) && exit "${status}"
+
+export job="verfozn"
+export jobid="${job}.$$"
+
+###############################################################
+# Execute the JJOB
+echo
+echo "=============== START TO RUN OZMON DATA EXTRACTION ==============="
+
+"${HOMEgfs}/jobs/JGDAS_ATMOS_VERFOZN"
+status=$?
+
+exit "${status}"

jobs/rocoto/verfrad.sh

@@ -0,0 +1,22 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source FV3GFS workflow modules
+source "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
+status=$?
+(( status != 0 )) && exit "${status}"
+
+export job="verfrad"
+export jobid="${job}.$$"
+
+###############################################################
+# Execute the JJOB
+echo
+echo "=============== START TO RUN RADMON DATA EXTRACTION ==============="
+
+"${HOMEgfs}/jobs/JGDAS_ATMOS_VERFRAD"
+status=$?
+
+exit "${status}"

jobs/rocoto/vminmon.sh

@@ -0,0 +1,22 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source FV3GFS workflow modules
+source "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
+status=$?
+(( status != 0 )) && exit "${status}"
+
+export job="vminmon"
+export jobid="${job}.$$"
+
+###############################################################
+# Execute the JJOB
+echo
+echo "=============== START TO RUN MINMON ==============="
+
+"${HOMEgfs}/jobs/J${RUN^^}_ATMOS_VMINMON"
+status=$?
+
+exit "${status}"