Update marine DA j-jobs to new format (#1149)

The new marine DA jobs were added (PR #1134) roughly concurrently with the refactoring of the j-job scripts (PR #1120), and thus didn't pick up the changes there. These new jobs are now updated.
NOAA-EMC · Dec 12, 2022 · f19d795 · f19d795
1 parent 287f52c
commit f19d795
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Showing 3 changed files with 78 additions and 60 deletions.
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
@@ -2,14 +2,37 @@
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
 
+##############################################
+# make temp directory
+##############################################
+export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
+mkdir -p "${DATA}"
+cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
+
+
+##############################################
+# Run setpdy and initialize PDY variables
+##############################################
+export cycle="t${cyc}z"
+setpdy.sh
+. ./PDY
+
+
+##############################################
+# Determine Job Output Name on System
+##############################################
+export pid=${pid:-$$}
+export pgmout="OUTPUT.${pid}"
+export pgmerr=errfile
+
+
 #############################
 # Source relevant config files
 #############################
 export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
 configs="base ocnanalpost"
-config_path=${EXPDIR:-${PACKAGEROOT}/gfs.${gfs_ver}/parm/config}
 for config in ${configs}; do
-    . "${config_path}"/config."${config}"
+    . "${EXPDIR}/config.${config}"
     status=$?
     [[ "${status}" -ne 0 ]] && exit "${status}"
 done
@@ -18,6 +41,6 @@ done
 # Remove the Temporary working directory
 ##########################################
 cd "${DATAROOT}" || exit 1
-[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
+[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
 
 exit 0
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
@@ -2,34 +2,11 @@
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
 
-#############################
-# Source relevant config files
-#############################
-export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
-configs="base ocnanal ocnanalprep"
-config_path=${EXPDIR:-${PACKAGEROOT}/gfs.${gfs_ver}/parm/config}
-for config in ${configs}; do
-    . "${config_path}"/config."${config}"
-    status=$?
-    [[ ${status} -ne 0 ]] && exit "${status}"
-done
-
-
-##########################################
-# Source machine runtime environment
-##########################################
-. "${HOMEgfs}"/env/"${machine}".env ocnanalprep
-status=$?
-[[ ${status} -ne 0 ]] && exit "${status}"
-
-
 ##############################################
-# Obtain unique process id (pid) and make temp directory
+# make temp directory
 ##############################################
-export pid=${pid:-$$}
-export outid=${outid:-"LL${job}"}
-
-export DATA=${DATA:-${DATAROOT}/ocnanal_${CDATE}}
+export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
+rm -rf "${DATA}"  # Ensure starting with a clean DATA
 mkdir -p "${DATA}"
 cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
 
@@ -45,24 +22,45 @@ setpdy.sh
 ##############################################
 # Determine Job Output Name on System
 ##############################################
+export pid=${pid:-$$}
 export pgmout="OUTPUT.${pid}"
 export pgmerr=errfile
 
 
+#############################
+# Source relevant config files
+#############################
+export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
+configs="base ocnanal ocnanalprep"
+for config in ${configs}; do
+    . "${EXPDIR}/config.${config}"
+    status=$?
+    [[ ${status} -ne 0 ]] && exit "${status}"
+done
+
+
+##########################################
+# Source machine runtime environment
+##########################################
+. "${HOMEgfs}/env/${machine}.env ocnanalprep"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+
 ##############################################
 # Set variables used in the script
 ##############################################
 export CDATE=${CDATE:-${PDY}${cyc}}
 export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-export COMPONENT=${COMPONENT:-ocean}
+export COMPONENT="ocean"
 
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 
-GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
+GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 export GDATE
-gPDY=${GDATE:0:8}
+export gPDY=${GDATE:0:8}
 export gcyc=${GDATE:8:2}
 export GDUMP=${GDUMP:-"gdas"}
 

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
@@ -2,34 +2,11 @@
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
 
-#############################
-# Source relevant config files
-#############################
-export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
-configs="base ocnanal ocnanalrun"
-config_path=${EXPDIR:-${PACKAGEROOT}/gfs.${gfs_ver}/parm/config}
-for config in ${configs}; do
-    . "${config_path}"/config."${config}"
-    status=$?
-    [[ ${status} -ne 0 ]] && exit "${status}"
-done
-
-
-##########################################
-# Source machine runtime environment
-##########################################
-. "${HOMEgfs}"/env/"${machine}".env ocnanalrun
-status=$?
-[[ ${status} -ne 0 ]] && exit "${status}"
-
 
 ##############################################
-# Obtain unique process id (pid) and make temp directory
+# make temp directory
 ##############################################
-export pid=${pid:-$$}
-export outid=${outid:-"LL${job}"}
-
-export DATA=${DATA:-${DATAROOT}/ocnanal_${CDATE}}
+export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
 mkdir -p "${DATA}"
 cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
 
@@ -45,16 +22,37 @@ setpdy.sh
 ##############################################
 # Determine Job Output Name on System
 ##############################################
+export pid=${pid:-$$}
 export pgmout="OUTPUT.${pid}"
 export pgmerr=errfile
 
 
+#############################
+# Source relevant config files
+#############################
+export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
+configs="base ocnanal ocnanalrun"
+for config in ${configs}; do
+    . "${EXPDIR}/config.${config}"
+    status=$?
+    [[ ${status} -ne 0 ]] && exit "${status}"
+done
+
+
+##########################################
+# Source machine runtime environment
+##########################################
+. "${HOMEgfs}/env/${machine}.env ocnanalrun"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+
 ##############################################
 # Set variables used in the script
 ##############################################
 
 export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-export COMPONENT=${COMPONENT:-ocean}
+export COMPONENT="ocean"
 
 ##############################################
 # Begin JOB SPECIFIC work
@@ -82,9 +80,8 @@ if [[ -e "${pgmout}" ]] ; then
 fi
 
 ##########################################
-# Remove the Temporary working directory
+# Do not remove the Temporary working directory (do this in POST)
 ##########################################
 cd "${DATAROOT}" || exit 1
-[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
 
 exit 0