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More marine DA j-jobs (#1270)
Addition of 2 j-jobs: - jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT_VRFY This job currently dumps a few files of the impulse response of B. Not meant to ever go in ops. - jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY This job will eventually generate relevant figures from the marine DA cycle. It currently points to a script that does not yet exist. I also took this PR opportunity to: - update how we load the modules, following what was done for the atmosphere. - modify ```ush/load_ufsda_modules.sh``` so we could optionally specify what to load (GDAS or EVA), default is GDAS when no argument is present - Use POST to copy what's needed in `COM` Fixes #1273
1 parent fb54bb6 commit f78afeb

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‎jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT_VRFY‎

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#!/bin/bash
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export STRICT="NO"
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source "${HOMEgfs}/ush/preamble.sh"
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export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
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source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalrun"
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##############################################
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# Set variables used in the script
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##############################################
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##############################################
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# Begin JOB SPECIFIC work
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##############################################
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export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
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###############################################################
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# Run relevant script
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EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_bmat_vrfy.sh}
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${EXSCRIPT}
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status=$?
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[[ ${status} -ne 0 ]] && exit "${status}"
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##############################################
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# End JOB SPECIFIC work
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##############################################
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##############################################
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# Final processing
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##############################################
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if [[ -e "${pgmout}" ]] ; then
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cat "${pgmout}"
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fi
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##########################################
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# Do not remove the Temporary working directory (do this in POST)
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##########################################
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cd "${DATAROOT}" || exit 1
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exit 0

‎jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST‎

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@@ -6,13 +6,49 @@ DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
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source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalpost" -c "base ocnanalpost"
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##############################################
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# Begin JOB SPECIFIC work
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##############################################
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export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
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export CDATE=${CDATE:-${PDY}${cyc}}
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mkdir -p "${COMOUT}"
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###############################################################
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# Run relevant script
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###############################################################
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# Save some of the DA cycle output to COMOUT
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# TODO: Move to a dedicated script
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# Make a copy the IAU increment
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cp "${DATA}/inc.nc" "${COMOUT}/${CDUMP}.t${cyc}z.ocninc.nc"
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# TODO: Dump-splash of the sea-ice restart not done yet
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# Copy of the ioda output files, as is for now
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cp -r "${DATA}/diags" "${COMOUT}"
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# Copy of the diagonal of the background error for the cycle
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bdate=$(date -d "${CDATE:0:8} ${CDATE:8:2} - 3 hours" +"%Y-%m-%dT%H:00:00Z")
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cp "${DATA}/ocn.bkgerr_stddev.incr.${bdate}.nc" "${COMOUT}/${CDUMP}.t${cyc}z.ocn.bkgerr_stddev.nc"
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cp "${DATA}/ice.bkgerr_stddev.incr.${bdate}.nc" "${COMOUT}/${CDUMP}.t${cyc}z.ice.bkgerr_stddev.nc"
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# Copy the loacalization and correlation operators
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cp -rL "${DATA}/bump" "${COMOUT}/bump"
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# Copy the analysis in the middle of the window
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cdate=$(date -d "${CDATE:0:8} ${CDATE:8:2}" +"%Y-%m-%dT%H:00:00Z")
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cp "${DATA}/Data/ocn.3dvarfgat_pseudo.an.${cdate}.nc" "${COMOUT}/${CDUMP}.t${cyc}z.ocnana.nc"
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# TODO (#982)
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# Copy DA grid (computed for the start of the window)
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bcyc=$(((cyc - 3 + 24) % 24))
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cp "${DATA}/soca_gridspec.nc" "${COMOUT}/${CDUMP}.t${bcyc}z.ocngrid.nc"
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# Copy logs
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mkdir -p "${COMOUT}/logs"
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cp "${DATA}/*.out" "${COMOUT}/logs"
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##########################################
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# Remove the Temporary working directory

‎jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN‎

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@@ -2,22 +2,15 @@
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export STRICT="NO"
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source "${HOMEgfs}/ush/preamble.sh"
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WIPE_DATA="NO"
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DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
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export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
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source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalrun"
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##############################################
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# Set variables used in the script
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##############################################
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export CDUMP=${CDUMP:-${RUN:-"gfs"}}
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export COMPONENT="ocean"
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##############################################
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# Begin JOB SPECIFIC work
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##############################################
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export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
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export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
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###############################################################
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# Run relevant script

‎jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY‎

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#!/bin/bash
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export STRICT="NO"
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source "${HOMEgfs}/ush/preamble.sh"
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source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalprep" -c "base ocnanal ocnanalprep"
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##############################################
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# Set variables used in the script
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##############################################
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##############################################
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# Begin JOB SPECIFIC work
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##############################################
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export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
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# Add UFSDA to PYTHONPATH
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export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/:${PYTHONPATH}
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###############################################################
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# Run relevant script
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EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_vrfy.py}
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${EXSCRIPT}
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status=$?
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[[ ${status} -ne 0 ]] && exit "${status}"
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##############################################
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# End JOB SPECIFIC work
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##############################################
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##############################################
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# Final processing
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##############################################
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if [[ -e "${pgmout}" ]] ; then
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cat "${pgmout}"
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fi
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##########################################
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# Do not remove the Temporary working directory (do this in POST)
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##########################################
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cd "${DATAROOT}" || exit 1
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exit 0

‎jobs/rocoto/ocnanalpost.sh‎

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source "${HOMEgfs}/ush/preamble.sh"
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###############################################################
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# Source GDASApp modules
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module purge
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module use "${HOMEgfs}/sorc/gdas.cd/modulefiles"
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module load GDAS/"${machine,,}"
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# Source UFSDA workflow modules
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. "${HOMEgfs}/ush/load_ufsda_modules.sh"
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status=$?
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[[ ${status} -ne 0 ]] && exit "${status}"
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export job="ocnanalpost"
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export jobid="${job}.$$"

‎jobs/rocoto/ocnanalprep.sh‎

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#! /usr/bin/env bash
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export STRICT="NO"
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source "${HOMEgfs}/ush/preamble.sh"
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###############################################################
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# Source GDASApp modules
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module purge
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module use "${HOMEgfs}/sorc/gdas.cd/modulefiles"
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module load "GDAS/${machine,,}"
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# Source UFSDA workflow modules
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. "${HOMEgfs}/ush/load_ufsda_modules.sh"
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status=$?
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[[ ${status} -ne 0 ]] && exit "${status}"
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export job="ocnanalprep"
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export jobid="${job}.$$"

‎jobs/rocoto/ocnanalrun.sh‎

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source "${HOMEgfs}/ush/preamble.sh"
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###############################################################
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# Source GDASApp modules
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module purge
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module use "${HOMEgfs}/sorc/gdas.cd/modulefiles"
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module load GDAS/"${machine,,}"
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# Source UFSDA workflow modules
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. "${HOMEgfs}/ush/load_ufsda_modules.sh"
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status=$?
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[[ ${status} -ne 0 ]] && exit "${status}"
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export job="ocnanalrun"
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export jobid="${job}.$$"

‎jobs/rocoto/ocnanalvrfy.sh‎

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#! /usr/bin/env bash
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export STRICT="NO"
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source "${HOMEgfs}/ush/preamble.sh"
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###############################################################
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# Source UFSDA workflow modules
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. "${HOMEgfs}/ush/load_ufsda_modules.sh" --eva
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status=$?
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[[ ${status} -ne 0 ]] && exit "${status}"
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export job="ocnanalvrfy"
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export jobid="${job}.$$"
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###############################################################
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# Execute the JJOB
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"${HOMEgfs}/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY"
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status=$?
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exit "${status}"

‎ush/load_ufsda_modules.sh‎

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@@ -6,6 +6,23 @@ if [[ "${DEBUG_WORKFLOW:-NO}" == "NO" ]]; then
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set +x
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fi
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# Read optional module argument, default is to use GDAS
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MODS="GDAS"
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if [[ $# -gt 0 ]]; then
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case "$1" in
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--eva)
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MODS="EVA"
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;;
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--gdas)
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MODS="GDAS"
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;;
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*)
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echo "Invalid option: $1" >&2
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exit 1
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;;
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esac
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fi
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# Setup runtime environment by loading modules
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ulimit_s=$( ulimit -S -s )
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echo WARNING: UFSDA NOT SUPPORTED ON THIS PLATFORM
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elif [[ -d /scratch1 ]] ; then
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# We are on NOAA Hera
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module load GDAS/hera
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module load "${MODS}/hera"
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if [[ "${DEBUG_WORKFLOW}" == "YES" ]] ; then
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module list
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pip list
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fi
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elif [[ -d /work ]] ; then
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# We are on MSU Orion
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module load GDAS/orion
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module load "${MODS}/orion"
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if [[ "${DEBUG_WORKFLOW}" == "YES" ]] ; then
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module list
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pip list

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