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Fix some bugs and make other changes so ctest in GDASApp works #1172

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Merged
WalterKolczynski-NOAA merged 11 commits into from
Dec 13, 2022
Merged

Fix some bugs and make other changes so ctest in GDASApp works #1172

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9d9a43c
wip
guillaumevernieres Dec 6, 2022
8ea33b5
container support & defaults for ocnanal
guillaumevernieres Dec 7, 2022
44b00a1
push hpc2local
guillaumevernieres Dec 10, 2022
43a247a
Merge branch 'develop' into bugfix/gdasapp-marine-ctest
guillaumevernieres Dec 10, 2022
a775a9a
Merge branch 'develop' into bugfix/gdasapp-marine-ctest
guillaumevernieres Dec 12, 2022
afc4ccc
msw
guillaumevernieres Dec 12, 2022
b60a2e8
tidy jjob run
guillaumevernieres Dec 12, 2022
6dccc6c
Merge branch 'develop' into bugfix/gdasapp-marine-ctest
guillaumevernieres Dec 12, 2022
7eddf39
revert cyc for now
guillaumevernieres Dec 12, 2022
5c1fb83
a few more typos
guillaumevernieres Dec 12, 2022
23426bc
... last one?
guillaumevernieres Dec 13, 2022
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2 changes: 1 addition & 1 deletion env/ORION.env
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Expand Up @@ -91,7 +91,7 @@ elif [ ${step} = "ocnanalrun" ]; then

export NTHREADS_OCNANAL=${nth_ocnanalrun:-${nth_max}}
[[ $NTHREADS_OCNANAL -gt ${nth_max} ]] && export NTHREADS_OCNANAL=${nth_max}
export APRUN_OCNANAL="${launcher} -n ${npe_aeroanlrun}"
export APRUN_OCNANAL="${launcher} -n ${npe_ocnanalrun}"

elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then

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2 changes: 1 addition & 1 deletion jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
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Expand Up @@ -5,7 +5,7 @@ source "${HOMEgfs}/ush/preamble.sh"
##############################################
# make temp directory
##############################################
export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
export DATA=${DATA:-${DATAROOT}/ocnanal_${CDATE}} # TODO (G): Switch to {cyc} when the downstream code is ready
mkdir -p "${DATA}"
cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)

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4 changes: 2 additions & 2 deletions jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
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Expand Up @@ -5,7 +5,7 @@ source "${HOMEgfs}/ush/preamble.sh"
##############################################
# make temp directory
##############################################
export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
export DATA=${DATA:-${DATAROOT}/ocnanal_${CDATE}} # TODO (G): Switch to {cyc} when the downstream code is ready
rm -rf "${DATA}" # Ensure starting with a clean DATA
mkdir -p "${DATA}"
cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)
Expand Down Expand Up @@ -42,7 +42,7 @@ done
##########################################
# Source machine runtime environment
##########################################
. "${HOMEgfs}/env/${machine}.env ocnanalprep"
. "${HOMEgfs}/env/${machine}.env" ocnanalprep
status=$?
[[ ${status} -ne 0 ]] && exit "${status}"

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4 changes: 2 additions & 2 deletions jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
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Expand Up @@ -6,7 +6,7 @@ source "${HOMEgfs}/ush/preamble.sh"
##############################################
# make temp directory
##############################################
export DATA=${DATA:-${DATAROOT}/ocnanal_${cyc}}
export DATA=${DATA:-${DATAROOT}/ocnanal_${CDATE}} # TODO (G): Switch to {cyc} when the downstream code is ready
mkdir -p "${DATA}"
cd "${DATA}" || (echo "${DATA} does not exist. ABORT!"; exit 1)

Expand Down Expand Up @@ -42,7 +42,7 @@ done
##########################################
# Source machine runtime environment
##########################################
. "${HOMEgfs}/env/${machine}.env ocnanalrun"
. "${HOMEgfs}/env/${machine}.env" ocnanalrun
status=$?
[[ ${status} -ne 0 ]] && exit "${status}"

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12 changes: 6 additions & 6 deletions parm/config/config.ocnanal
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Expand Up @@ -9,17 +9,17 @@ export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
export OBS_YAML=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
export OBS_LIST=${OBS_YAML_DIR}/obs_list.yaml
export FV3JEDI_STAGE_YAML=${HOMEgfs}/sorc/gdas.cd/test/soca/testinput/dumy.yaml
export SOCA_INPUT_FIX_DIR=/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/72x35x25/soca # TODO: Should be moved somewhere else
export SOCA_INPUT_FIX_DIR=@SOCA_INPUT_FIX_DIR@
export SOCA_VARS=tocn,socn,ssh
export SOCA_NINNER=50
export CASE_ANL="C48"
export SOCA_NINNER=@SOCA_NINNER@
export CASE_ANL=@CASE_ANL@
export DOMAIN_STACK_SIZE=2000000
export JEDI_BIN=${HOMEgfs}/sorc/gdas.cd/build/bin

# TODO: Move the R2D2 configuration to a common space
export R2D2_OBS_DB=shared
export R2D2_OBS_DUMP=s2s_v1
export R2D2_OBS_SRC=gdas_marine
export R2D2_OBS_DUMP=@R2D2_OBS_DUMP@
export R2D2_OBS_SRC=@R2D2_OBS_SRC@
export R2D2_OBS_WINDOW=24 # TODO: Check if the R2D2 sampling DB window is still needed
export COMIN_OBS=/scratch2/NCEPDEV/marineda/r2d2
export COMIN_OBS=@COMIN_OBS@
echo "END: config.ocnanal"
2 changes: 1 addition & 1 deletion parm/config/config.ocnanalpost
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Expand Up @@ -6,5 +6,5 @@
echo "BEGIN: config.ocnanalpost"

# Get task specific resources
. "${EXPDIR}/config.resources ocnanalpost"
. "${EXPDIR}/config.resources" ocnanalpost
echo "END: config.ocnanalpost"
2 changes: 1 addition & 1 deletion parm/config/config.ocnanalprep
100644 → 100755
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Expand Up @@ -6,5 +6,5 @@
echo "BEGIN: config.ocnanalprep"

# Get task specific resources
. "${EXPDIR}/config.resources ocnanalprep"
. "${EXPDIR}/config.resources" ocnanalprep
echo "END: config.ocnanalprep"
2 changes: 1 addition & 1 deletion parm/config/config.ocnanalrun
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Expand Up @@ -6,6 +6,6 @@
echo "BEGIN: config.ocnanalrun"

# Get task specific resources
. "${EXPDIR}/config.resources ocnanalrun"
. "${EXPDIR}/config.resources" ocnanalrun

echo "END: config.ocnanalrun"
8 changes: 8 additions & 0 deletions parm/config/yaml/defaults.yaml
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@@ -1,3 +1,11 @@
aeroanl:
IO_LAYOUT_X: 1
IO_LAYOUT_Y: 1

ocnanal:
SOCA_INPUT_FIX_DIR: '/scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/72x35x25'
CASE_ANL: 'C48'
COMIN_OBS: '/scratch2/NCEPDEV/marineda/r2d2'
SOCA_NINNER: 50
R2D2_OBS_SRC: 'gdas_marine'
R2D2_OBS_DUMP: 's2s_v1'