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Update marine DA j-jobs to new format #1149

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merged 3 commits into from
Dec 12, 2022
Merged

Update marine DA j-jobs to new format #1149

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b67ec89
make ocean analysis j-jobs consistent
aerorahul Dec 6, 2022
c2fb077
fix SC2155
aerorahul Dec 6, 2022
72f2848
fix SC2086 in the canonical form
aerorahul Dec 6, 2022
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29 changes: 26 additions & 3 deletions jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
56 changes: 27 additions & 29 deletions jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
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Original file line number Diff line number Diff line change
Expand Up @@ -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}}
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@guillaumevernieres @CoryMartin-NOAA
Take note here in the use of ${cyc} instead of ${CDATE}.

At this stage, we only have $cyc in ops coming from ecFlow.
In our development we provide $PDY and $CDATE via the Rocoto XML.

Please take special note of this.

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@aerorahul where in ops does PDY come in then? the ex-script? I thought the setpdy was run in the j-job?

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setpdy.sh sets PDY based on a file in the ops space.
If PDY is previously set (as is the case in development), setpdy.sh uses that info (with the cycle).

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Yeah so I guess my point is that we can assume we have ${PDY}${cyc} at this point, right? Not that it really matters for this ${DATA} directory.

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@aerorahul aerorahul Dec 12, 2022 •
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In ops PDY is set by the setpdy.sh script.
setpdy.sh needs to be executed while in the DATA directory as it creates a (pesky) file ncepdate.

As you can see, in this (and other) j-job, DATA directory name contains PDY which is undefined in ops at this point in the script.

rm -rf "${DATA}" # Ensure starting with a clean DATA
mkdir -p "${DATA}"
cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)

Expand All @@ -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"}

Expand Down
53 changes: 25 additions & 28 deletions jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand All @@ -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
Expand Down Expand Up @@ -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