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Sync STOFS-3D-ATL with operational v3.1.1 #78

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181 changes: 181 additions & 0 deletions parm/stofs_3d_atl/grib2_stofs_3d_atl_conus.east_cwl
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181 changes: 181 additions & 0 deletions parm/stofs_3d_atl/grib2_stofs_3d_atl_puertori_cwl
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97 changes: 69 additions & 28 deletions scripts/stofs_3d_atl/exstofs_3d_atl_hot_restart_prep.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
# (2) save the newly created file as stofs_3d_atl.t12z.hotstart.stofs3d.nc #
# #
# Remarks: #
# May 2023 #
# September 2025 #
#################################################################################################################

seton='-xa'
Expand Down Expand Up @@ -35,14 +35,19 @@
echo "Current dir=`pwd`"; echo


# NCPU_PBS==4320; minus N_scribe=6, hence, 4316;
# note: count (0, ..., 4316-1)
NCPU_PBS_hot_restart=4314
# NCPU_PBS==4320; minus N_scribe=8, hence, 4312;
# note: count (0, ..., 4312-1)
#NCPU_PBS_hot_restart=4314

let n_scribes=8
let NCPU_PBS_hot_restart=${NCPU_PBS}-${n_scribes}
echo "NCPU_PBS_hot_restart=${NCPU_PBS_hot_restart}"

sz_cr_ht_subdmn_MB=100000 # bytes

# list_steps_OI=(288 576 864 1152 1440 1728 2016 2304 2592 2880)
list_steps_OI=(2880 2592 2304 2016 1728 1440 1152 864 576 288)
# list_steps_OI=(2880 2592 2304 2016 1728 1440 1152 864 576 288)
list_steps_OI=(2592 2304 2016 1728 1440 1152 864 576 288)

dt_timestep=150

# str_ht_fn_prefix=
Expand All @@ -52,16 +57,28 @@

rm -f tmp_chk_hotstart_file


dir_nco_tmp_archive=${COMOUT}/outputs_watchdog


echo
echo "In exstofs_3d_atl_hot_restart_prep.sh: `pwd`: dir_nco_tmp_archive=${dir_nco_tmp_archive}"
echo


# mkdir -p ${dir_nco_tmp_archive}


cd ${dir_nco_tmp_archive}

for k_OI in ${list_steps_OI[@]}
do


# list_fn_ht_OI=`ls ${DATA}/outputs/hotstart_0?????_${k_OI}.nc`
list_fn_ht_OI=`ls ./outputs/hotstart_0?????_${k_OI}.nc 2> tmp_chk_hotstart_file`
list_fn_ht_OI=`ls hotstart_0?????_${k_OI}.nc 2> tmp_chk_hotstart_file`

echo "checking hotstart file of step=${k_OI}"

N_file_hotstart_default=`ls -lr ./outputs/hotstart_0?????_*${k_OI}.nc 2>> tmp_chk_hotstart_file | wc -l`
N_file_hotstart_default=`ls -lr ./hotstart_0?????_*${k_OI}.nc 2>> tmp_chk_hotstart_file | wc -l`

echo
echo checking hotstart file of step=${k_OI}
Expand Down Expand Up @@ -117,18 +134,21 @@ if [[ ${time_sec_merge_hotstart} -ne 0 ]]; then

cd ${DATA}

mv param.nml param.nml_cold_restart
fn_src_nml_rerun_ihot1=${COMOUTrerun}/${RUN}.${cycle}.param.nml
mv ${fn_src_nml_rerun_ihot1} ${fn_src_nml_rerun_ihot1}_backup_ihot1

cat param.nml_cold_restart | sed "s/ihot = 1/ihot = 2/" > param.nml
cpreq -f ${fn_src_nml_rerun_ihot1}_backup_ihot1 param.nml_ihot1_tmp
rm -f param.nml
cat param.nml_ihot1_tmp | sed "s/ihot = 1/ihot = 2/" > param.nml

# backup param.nml of cold restart
fn_param_modelRun_std=${RUN}.${cycle}.param.nml
cpreq -f param.nml ${COMOUT}/rerun/${fn_param_modelRun_std}_hot_restart
cpreq -f param.nml ${COMOUT}/rerun/${fn_param_modelRun_std}
cpreq -f param.nml ${COMOUT}/rerun/${fn_param_modelRun_std}_backup_ihot2

# files for ihot=2:
mv outputs/mirror.out outputs/mirror.out_cold_restart
touch outputs/mirror.out
touch outputs/flux.out
# post-crash run started 'new' dir: mv outputs/mirror.out outputs/mirror.out_cold_restart
touch outputs/mirror.out
touch outputs/flux.out

if [[ ! -f "outputs/staout_1" ]]; then
for i in {1,2,3,4,5,6,7,8,9}; do
Expand All @@ -143,33 +163,51 @@ fi

if [[ ${time_sec_merge_hotstart} -eq 0 ]];
then
# cold restart file
# use rerun/_restart.nc (at beginning time of nowcast)
fn_restart_rerun=${COMOUTrerun}/${RUN}.${cycle}.restart.nc

if [[ $(find ${fn_restart_rerun} -type f -size +20G 2>/dev/null) ]]; then
msg="restart.nc: ${fn_restart_rerun}"
ln -sf ${fn_restart_rerun} ${DATA}/hotstart.nc
# cpreq -pf ${fn_restart_rerun} ${DATA}/hotstart.nc

list_fn_avail_input_forcing+=(" \n " $fn_restart_rerun)
msg="restart.nc=${fn_restart_rerun}"

else
else
fn_restart_hotstart="${fn_restart_rerun}"
FLAG_all_exist_model_input_files=0
list_fn_missed_input_forcing+=(" \n " ${fn_restart_rerun})

echo -e "\n ${fn_restart_rerun}/hotstart file is not found in ${COMOUTrerun}"
msg="\n WARNING: None existing: ${COMOUTrerun} - WARNING"
fi
msg="\n To use the cold restart nc"

msg="\n To use the rerun/_restart.nc at beginning time of nowcast"
echo -e $msg; echo $msg >> $pgmout

else
# hot restart file

else

# Generate new global domain _restart.nc: to continue the unfinished run of the current cycle
mkdir -p ${DATA}/outputs/
cd ${DATA}/outputs/

# cp local_global & hotstart nc to $DATA/outputs/
touch ../log_cp_watchdog_hot_local2glb_timing.txt
postmsg ../log_cp_watchdog_hot_local2glb_timing.txt "Before cp dir_nco_tmp_archive"

if [ -d ${dir_nco_tmp_archive} ]; then
echo; echo dir_nco_tmp_archive=${dir_nco_tmp_archive} exists; echo
cp -fp ${dir_nco_tmp_archive}/local_to_global_* ${DATA}/outputs
cp -fp ${dir_nco_tmp_archive}/hotstart_*_${idx_time_step_merge_hotstart}.nc ${DATA}/outputs
cp -fp ${dir_nco_tmp_archive}/staout* ${DATA}/outputs

fi

postmsg ../log_cp_watchdog_hot_local2glb_timing.txt "Done cp dir_nco_tmp_archive"


#idx_time_step_merge_hotstart=576
fn_merged_hotstart_ftn=hotstart_it\=${idx_time_step_merge_hotstart}.nc
fn_hotstart_stofs3d_merged_std=${RUN}.${cycle}.restart.nc
Expand All @@ -191,11 +229,14 @@ else
msg="echo ${fn_merged_hotstart_ftn} has been created";
echo $msg; echo $msg >> $pgmout

cpreq -pf ${fn_merged_hotstart_ftn} ${COMOUT}/rerun/${fn_hotstart_stofs3d_merged_std}_hot_restart

cd ${DATA};
mv hotstart.nc hotstart.nc_cold_restart 2> tmp_rename_cold_restart_file
ln -sf ${COMOUT}/rerun/${fn_hotstart_stofs3d_merged_std}_hot_restart hotstart.nc
mv ${COMOUT}/rerun/${fn_hotstart_stofs3d_merged_std} ${COMOUT}/rerun/${fn_hotstart_stofs3d_merged_std}_ihot1
cpreq -pf ${fn_merged_hotstart_ftn} ${COMOUT}/rerun/${fn_hotstart_stofs3d_merged_std}
ln -sf ${COMOUT}/rerun/${fn_hotstart_stofs3d_merged_std} ${COMOUT}/rerun/${fn_hotstart_stofs3d_merged_std}_back_ihot2

cd ${DATA};
rm -f mv hotstart.nc
ln -sf ${COMOUT}/rerun/${fn_hotstart_stofs3d_merged_std} hotstart.nc

else
msg=`echo ${fn_merged_hotstart_ftn}} was not created`
Expand Down
18 changes: 17 additions & 1 deletion scripts/stofs_3d_atl/exstofs_3d_atl_post_1.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@


# -----------------------> check & wait for model run complete
fn_mirror=${DATA}/outputs/mirror.out
fn_mirror=${COMOUT}/outputs_watchdog/mirror.out

str_model_run_status="Run completed successfully"

Expand All @@ -79,6 +79,22 @@ if [[ ${flag_run_status} == 0 ]]; then
cd ${DATA}


echo "date/time before cp data to post_1 outputs: `date`"


cpreq -f ${COMOUT}/outputs_watchdog/{horizontalVelX,horizontalVelY,out2d,salinity,temperature,zCoordinates,verticalVelocity,diffusivity}_*.nc ${dir_outputs_local};
cpreq -f ${COMOUT}/outputs_watchdog/staout_* ${dir_outputs_local}


echo "date/time when done cp data to post_1 outputs: `date`"

# Following is done in watchdog.sh
# including: history nc & local_to_global & hotstart_*_576.nc
# cpreq -fp ${COMOUT}/outputs_hotstart/hotstart_*_576.nc ${dir_outputs_local}
# cpreq -fp ${COMOUT}/outputs_hotstart/local_to_global_?????? ${dir_outputs_local}



# ---------> Update 2d & 3d nc: adding variable attributes
cd ${DATA}; pwd
file_log_attr=log_add_attribute_2d_3d_nc.${cycle}.log
Expand Down
36 changes: 30 additions & 6 deletions scripts/stofs_3d_atl/exstofs_3d_atl_post_2.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -32,16 +32,17 @@


# -----------------------> static files
# fn_station_in=$FIXstofs3d/${RUN}_station.in
# cpreq --remove-destination -f ${fn_station_in} station.in

cd ${DATA}

fn_src_nml=${COMOUTrerun:-${COMOUT}}/${RUN}.${cycle}.param.nml
if [ -f "${fn_src_nml}" ]; then
ln -sf ${fn_src_nml} param.nml
fi
fn_src_nml=${COMOUTrerun}/${RUN}.${cycle}.param.nml
ln -sf ${fn_src_nml} param.nml


# -----------------------> check for model run complete
fn_mirror=outputs/mirror.out
# -----------------------> check & wait for model run complete
fn_mirror=${COMOUT}/outputs_watchdog/mirror.out
str_model_run_status="Run completed successfully"


Expand All @@ -56,6 +57,29 @@ if [[ ${flag_run_status} == 0 ]]; then
echo $msg
echo $msg >> $pgmout

dir_outputs_local=${DATA}/outputs

mkdir -p ${dir_outputs_local}
cd ${DATA}

# including: history nc & local_to_global & hotstart_*_576.nc
#cpreq -fp ${COMOUT}/outputs_watchdog/hotstart_*_576.nc ${dir_outputs_local}
#cpreq -fp ${COMOUT}/outputs_watchdog/local_to_global_?????? ${dir_outputs_local}
#cpreq -fp ${COMOUT}/outputs_2d3d_sta/* ${dir_outputs_local}

postmsg "before cp data to post_1 outputs"

for i in ${COMOUT}/outputs_watchdog/local_to_global*; do
cpreq -f "$i" ${dir_outputs_local};
done

cpreq -f ${COMOUT}/outputs_watchdog/{horizontalVelX,horizontalVelY,out2d,salinity,temperature,zCoordinates,verticalVelocity,diffusivity}_*.nc ${dir_outputs_local};

TIME_STEP_restart=576
cpreq -f ${COMOUT}/outputs_watchdog/hotstart_*_${TIME_STEP_restart}.nc ${dir_outputs_local};

postmsg "done cp data to post_1 outputs"

# ---------> Update 2d & 3d nc: adding variable attributes
cd ${DATA}; pwd

Expand Down
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