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neccton requirements #21

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2435ef2
Update pack.py: add logging to check mpi4py
plazzari Jul 2, 2025
84ad20a
Update script for NECCTON project requirements
CarolinaAmadio Jul 4, 2025
6454e83
Merge branch 'main' into 20-neccton-requirements
Jul 18, 2025
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192 changes: 146 additions & 46 deletions MY_optics/job.POST.singleyear.slurm
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#! /bin/bash

#SBATCH --job-name=POST
#SBATCH -N5
#SBATCH --ntasks-per-node=24
#SBATCH --time=01:30:00
#SBATCH --job-name=Nec20pOST
#SBATCH -N20
#SBATCH --ntasks-per-node=48
#SBATCH --time=02:20:00
#SBATCH --mem=300gb
#SBATCH --account=OGS_devC
#SBATCH --account=OGS_test2528
#SBATCH --partition=g100_meteo_prod
#SBATCH --qos=qos_meteo

Expand All @@ -27,11 +27,12 @@ case $1 in
esac
shift 2

cd $SLURM_SUBMIT_DIR

. ../profile.inc
. ./config.sh -y ${YEAR}

SLURM_POSTPROC_SUBMIT_DIR=/g100_scratch/userexternal/camadio0/$OPA_HOME/wrkdir/POSTPROC/ogstm_postproc/MY_optics
cd $SLURM_POSTPROC_SUBMIT_DIR

unset I_MPI_PMI_LIBRARY
export UCX_TLS=ib
export SLURM_PMIX_DIRECT_CONN_UCX=false
Expand All @@ -42,38 +43,44 @@ export KCOASTFILE=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/mapser.npy

export PATH=$PATH:..



####### moving in year/ directories ################
MODEL_AVEDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/
cd $MODEL_AVEDIR
rm -f AVE_FREQ_1/*nc
mkdir -p AVE_FREQ_2/${YEAR} AVE_FREQ_3/${YEAR} RESTARTS/${YEAR}
cd AVE_FREQ_2
mkdir -p AVE_FREQ_1/${YEAR} AVE_FREQ_2/${YEAR} AVE_FREQ_3/${YEAR} AVE_FREQ_4/${YEAR}

cd $MODEL_AVEDIR/AVE_FREQ_1/
my_prex "mv ave.${YEAR}*.nc ${YEAR}/ "

cd $MODEL_AVEDIR/AVE_FREQ_2/
my_prex "mv ave.${YEAR}*.nc ${YEAR}/ "
rm -f ave.${YEAR}.nc.bkp

cd $MODEL_AVEDIR/AVE_FREQ_3
my_prex "mv ave.${YEAR}*.nc ${YEAR}/"

cd $MODEL_AVEDIR/RESTARTS
my_prex "mv RST.${YEAR}*.nc ${YEAR}/"


######## LOW FREQUENCY ######################################################

cd $SLURM_SUBMIT_DIR
######## DAILY FREQUENCY AVE_FREQ_1 ######################################################
cd $SLURM_POSTPROC_SUBMIT_DIR

MODEL_AVEDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_2/${YEAR}
OUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_2/

MODEL_AVEDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_1/${YEAR}
OUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_1/


TMPS=$OUTDIR/TMPS/${YEAR}
CHLSUP_DIR=$OUTDIR/CHL_SUP
CHL_WEEKLY=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_4/${YEAR}
BOTTOMDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_1/BOTTOM/${YEAR}

my_prex_or_die_with_tries "mpirun -np 120 python ../var_aggregator.py -l ave*N1p.nc -i $MODEL_AVEDIR -d VarDescriptor_2.xml -t $MODEL_AVEDIR -c $CHLSUP_DIR -m $MASKFILE"
my_prex_or_die_with_tries "mpirun -np 120 python ../metrics_2d.py -i $MODEL_AVEDIR -m $MASKFILE -o $MODEL_AVEDIR"
mkdir -p $CHL_WEEKLY
mkdir -p $BOTTOMDIR

my_prex_or_die "mpirun --map-by ppr:4:node,PE=1 -np 16 python ../var_aggregator.py -l ave*N1p.nc -i $MODEL_AVEDIR -d VarDescriptor_1.xml -t $MODEL_AVEDIR -c $CHLSUP_DIR -m $MASKFILE"

my_prex_or_die "mpirun --map-by ppr:24:node,PE=1 -np 120 python ../metrics_2d.py -i $MODEL_AVEDIR -m $MASKFILE -o $MODEL_AVEDIR"

for var in O2o pH R8c R6c; do
my_prex_or_die "mpirun python bottom.py -i $MODEL_AVEDIR -o $BOTTOMDIR -m $MASKFILE -s ave.*${var}.nc --point_position C"
done

cd $MODEL_AVEDIR
for filename in metrics*; do
Expand All @@ -83,57 +90,100 @@ for filename in metrics*; do
done
done

cd $SLURM_SUBMIT_DIR
cd $SLURM_POSTPROC_SUBMIT_DIR

for var in P_l P1l P2l P3l P4l resPPYc ruPPYc; do
my_prex_or_die "mpirun python ../weekly_averager.py --inputdir ${MODEL_AVEDIR} --maskfile ${MASKFILE} --outdir ${CHL_WEEKLY} --timeaverage thursday --var ${var}"
done

export BASINS=V2
my_prex_or_die_with_tries "mpirun python ../aveScan.py -l ave*nc -i $MODEL_AVEDIR -f N1p -a $MODEL_AVEDIR -d VarDescriptor_2.xml -o $OUTDIR -t $TMPS -s "
my_prex_or_die_with_tries "mpirun python ../aveScan.py -l ave*nc -i $MODEL_AVEDIR -f N1p -a $MODEL_AVEDIR -d VarDescriptor_1.xml -o $OUTDIR -t $TMPS -s "
rm -rf $TMPS
my_prex_or_die_with_tries "mpirun --map-by ppr:4:node,PE=1 -np 16 python ../compact_profiles.py -i $OUTDIR/STAT_PROFILES/ -o $OUTDIR/STAT_PROFILES/"

my_prex_or_die_with_tries "mpirun -np 16 python ../compact_profiles.py -i $OUTDIR/STAT_PROFILES/ -o $OUTDIR/STAT_PROFILES/"
######## MONTHLY FREQUENCY AVE_FREQ_2 ######################################################

cd $SLURM_POSTPROC_SUBMIT_DIR


MODEL_AVEDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_2/${YEAR}
OUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_2/



TMPS=$OUTDIR/TMPS/${YEAR}
CHLSUP_DIR=$OUTDIR/CHL_SUP

my_prex_or_die "mpirun --map-by ppr:4:node,PE=1 -np 16 python ../var_aggregator.py -l ave*N1p.nc -i $MODEL_AVEDIR -d VarDescriptor_2.xml -t $MODEL_AVEDIR -c $CHLSUP_DIR -m $MASKFILE"

my_prex_or_die "mpirun --map-by ppr:24:node,PE=1 -np 120 python ../metrics_2d.py -i $MODEL_AVEDIR -m $MASKFILE -o $MODEL_AVEDIR"


cd $MODEL_AVEDIR
for filename in metrics*; do
date17=${filename:8:17}
for var in dcm phosphocline nitracline; do
ln -fs $filename ave.${date17}.${var}.nc
done
done

################## end of integrals/profiles stuff ##############

################ Kd #########################

cd $SLURM_POSTPROC_SUBMIT_DIR

INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_3/${YEAR}
KD__DAILY=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_3/KD_DAILY/${YEAR}
KD_WEEKLY=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_2/${YEAR}
KD_WEEKLY=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_4/${YEAR}
BOTTOMDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_3/BOTTOM/${YEAR}
SURF__DIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_3/SURF/{$YEAR}
SURF__DIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_3/SURF/${YEAR}

mkdir -p $BOTTOMDIR
mkdir -p $SURF__DIR
mkdir -p $KD__DAILY
mkdir -p $KD_WEEKLY
my_prex_or_die "mpirun python ../kd.py -i $INPUTDIR -m $MASKFILE -o $KD__DAILY -l ave*.nc"
my_prex_or_die "mpirun python ../weekly_averager.py -i $KD__DAILY -o $KD_WEEKLY -m $MASKFILE -v kd490 -t thursday"

my_prex_or_die "mpirun --map-by ppr:24:node,PE=1 -np 48 python ../kd.py -i $INPUTDIR -m $MASKFILE -o $KD__DAILY -l ave*.nc"

my_prex_or_die "mpirun python ../weekly_averager.py -i $KD__DAILY -o $KD_WEEKLY -m $MASKFILE -v kd490 -t thursday"
################ end Kd #########################
export BASINS=V2
my_prex_or_die_with_tries "mpirun python ../aveScan.py -l ave*nc -i $MODEL_AVEDIR -f N1p -a $MODEL_AVEDIR -d VarDescriptor_2.xml -o $OUTDIR -t $TMPS -s "
rm -rf $TMPS
my_prex_or_die_with_tries "mpirun --map-by ppr:4:node,PE=1 -np 16 python ../compact_profiles.py -i $OUTDIR/STAT_PROFILES/ -o $OUTDIR/STAT_PROFILES/"
################## end of integrals/profiles stuff ##############

################ RRS #########################
RRS__DAILY=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_3/RRS_DAILY/${YEAR}
RRS_WEEKLY=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_2/${YEAR}
RRS_WEEKLY=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_4/${YEAR}

mkdir -p $RRS__DAILY
mkdir -p $RRS_WEEKLY
my_prex_or_die "mpirun python ../rrs.py -i $INPUTDIR -m $MASKFILE -o $RRS__DAILY -l ave*.nc"

my_prex_or_die "mpirun python ../rrs.py -i $INPUTDIR -m $MASKFILE -o $RRS__DAILY -qi ../Qfiles -l ave*.nc" ##### PL modified

for var in RRS412 RRS443 RRS490 RRS510 RRS555 RRS670; do
my_prex_or_die "mpirun python ../weekly_averager.py --inputdir ${RRS__DAILY} --maskfile ${MASKFILE} --outdir ${RRS_WEEKLY} --timeaverage thursday --var ${var}"
done


my_prex_or_die "mpirun python ../bottom.py -i $INPUTDIR -o $BOTTOMDIR -m $MASKFILE -s ave*nc"
INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_3/${YEAR}
my_prex_or_die "mpirun python bottom.py -i $INPUTDIR -o $BOTTOMDIR -m $MASKFILE -s ave.*E[ds]_*.nc --point_position W"
my_prex_or_die "mpirun python ../surf.py -i $INPUTDIR -o $SURF__DIR -m $MASKFILE -s ave*nc"


OUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_3/bottom/
TMPS=$OUTDIR/TMPS/${YEAR}
my_prex_or_die_with_tries "mpirun python ../aveScan.py -l ave*nc -i $BOTTOMDIR -f Eu_0475 -a $BOTTOMDIR -d VarDescriptor_3.xml -o $OUTDIR -t $TMPS -s "
my_prex_or_die_with_tries "mpirun python ../aveScan.py -l ave*nc -i $BOTTOMDIR -f Ed_0475 -a $BOTTOMDIR -d VarDescriptor_BOTTOM_3.xml -o $OUTDIR -t $TMPS -s "
rm -rf $TMPS
my_prex_or_die_with_tries "mpirun -np 100 python ../compact_profiles.py -i $OUTDIR/STAT_PROFILES/ -o $OUTDIR/STAT_PROFILES/"
my_prex_or_die_with_tries "mpirun --map-by ppr:4:node -np 16 python ../compact_profiles.py -i $OUTDIR/STAT_PROFILES/ -o $OUTDIR/STAT_PROFILES/"


OUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_3/surf/
TMPS=$OUTDIR/TMPS/${YEAR}
my_prex_or_die_with_tries "mpirun python ../aveScan.py -l ave*nc -i $SURF__DIR -f Eu_0475 -a $SURF__DIR -d VarDescriptor_3.xml -o $OUTDIR -t $TMPS -s "
rm -rf $TMPS
my_prex_or_die_with_tries "mpirun -np 100 python ../compact_profiles.py -i $OUTDIR/STAT_PROFILES/ -o $OUTDIR/STAT_PROFILES/"
my_prex_or_die_with_tries "mpirun --map-by ppr:4:node -np 16 python ../compact_profiles.py -i $OUTDIR/STAT_PROFILES/ -o $OUTDIR/STAT_PROFILES/"


# cleaning setup
INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_3/${YEAR}
Expand All @@ -145,23 +195,42 @@ for nanom in 375 400 425 475 500; do
my_prex "mv ave.*.Eu_0${nanom}.nc tosave/ "
done

######## WEEKLY FREQUENCY AVE_FREQ_4 ######################################################
cd $SLURM_POSTPROC_SUBMIT_DIR


MODEL_AVEDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_4/${YEAR}
OUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_4/


TMPS=$OUTDIR/TMPS/${YEAR}
CHLSUP_DIR=$OUTDIR/CHL_SUP

export BASINS=V2

my_prex_or_die "mpirun --map-by ppr:4:node,PE=1 -np 16 python ../var_aggregator.py -l ave*P_l.nc -i $MODEL_AVEDIR -d VarDescriptor_4.xml -t $MODEL_AVEDIR -c $CHLSUP_DIR -m $MASKFILE"
my_prex_or_die_with_tries "mpirun python ../aveScan.py -l ave*nc -i $MODEL_AVEDIR -f P_l -a $MODEL_AVEDIR -d VarDescriptor_4.xml -o $OUTDIR -t $TMPS -s "
rm -rf $TMPS
my_prex_or_die_with_tries "mpirun --map-by ppr:4:node,PE=1 -np 16 python ../compact_profiles.py -i $OUTDIR/STAT_PROFILES/ -o $OUTDIR/STAT_PROFILES/"

###### Sat Validation ############

# SAT_CHLWEEKLY_DIR and SAT_VALID_DIR come from config.sh
INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_2/${YEAR}
INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_4/${YEAR}
SAT_DIR=$SAT_CHLWEEKLY_DIR
LAYER=10

mkdir -p $SAT_VALID_DIR
YEAR2=$(( YEAR + 1 ))
PERIOD="-t ${YEAR}0101 -e ${YEAR2}0101"
command="mpirun python $BITSEA/src/bitsea/validation/deliverables/ScMYvalidation_plan.py"

for VAR in P_l P1l P2l P3l P4l; do
my_prex_or_die "$command -s $SAT_DIR -i $INPUTDIR -l $LAYER -o $SAT_VALID_DIR -c coast,open_sea $PERIOD -v $VAR -m $MASKFILE"
done

SAT_DIR=$SAT_KD_WEEKLY_DIR
for var in kd490 ; do
for VAR in kd490 ; do
my_prex_or_die "$command -s $SAT_DIR -i $INPUTDIR -l $LAYER -o $SAT_VALID_DIR -c coast,open_sea $PERIOD -v $VAR -m $MASKFILE"
done

Expand All @@ -171,9 +240,29 @@ for VAR in RRS412 RRS443 RRS490 RRS510 RRS555 RRS670; do
done


####### R6_R8 in West East sub basins #########

cd $SLURM_POSTPROC_SUBMIT_DIR
export BASINS=EAST_WEST
MODEL_AVEDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_2/${YEAR}
OUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_2/R6R8/
TMPS=$OUTDIR/TMPS/${YEAR}
mkdir -p $OUTDIR $TMPS
my_prex_or_die_with_tries "mpirun python ../aveScan.py -l ave*nc -i $MODEL_AVEDIR -f N1p -a $MODEL_AVEDIR -d VarDescriptor_R6_R8.xml -o $OUTDIR -t $TMPS -s "
rm -rf $TMPS
my_prex_or_die_with_tries "mpirun --map-by ppr:24:node -np 16 python ../compact_profiles.py -i $OUTDIR/STAT_PROFILES/ -o $OUTDIR/STAT_PROFILES/"
################## end of integrals/profiles stuff ##############
####### end R6_R8 in West East sub basins #########



## COMPRESSION ##

cd $SLURM_SUBMIT_DIR/archive
cd $SLURM_POSTPROC_SUBMIT_DIR/../archive

INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_1/${YEAR}
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_1_tar/${YEAR}
my_prex_or_die "./tar_avedir.sh -i $INPUTDIR -o $TARDIR -n 120 -v N1p"

INPUTDIR=$KD__DAILY
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_3_tar/${YEAR}
Expand All @@ -183,26 +272,37 @@ INPUTDIR=$RRS__DAILY
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_3_tar/${YEAR}
my_prex_or_die "./tar_avedir.sh -i $INPUTDIR -o $TARDIR -n 120 -v RRS490"


INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_2/${YEAR}
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_2_tar/${YEAR}
my_prex_or_die "./tar_avedir.sh -i $INPUTDIR -o $TARDIR -n 120 -v N1p"


INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_3/${YEAR}/tosave
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_3_tar/${YEAR}
my_prex_or_die "./lossy_tar_avedir.sh -i $INPUTDIR -o $TARDIR -n 120 -v Ed_0250 -s 5"
my_prex_or_die "./lossy_tar_avedir.sh -i $INPUTDIR -o $TARDIR -n 120 -v Ed_0400 -s 5"

INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/RESTARTS/${YEAR}
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/RESTARTS_tar
#my_prex_or_die "./tar_rstdir.sh -i $INPUTDIR -o $TARDIR -n 120"

INPUTDIR=$BOTTOMDIR
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_3_tar/${YEAR}/bottom/
my_prex_or_die "./tar_avedir.sh -i $INPUTDIR -o $TARDIR -n 120 -v Ed_0250"

BOTTOMDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/POSTPROC/output/AVE_FREQ_1/BOTTOM/${YEAR}
INPUTDIR=$BOTTOMDIR
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_1_tar/${YEAR}/bottom/
my_prex_or_die "./tar_avedir.sh -i $INPUTDIR -o $TARDIR -n 120 -v O2o"

INPUTDIR=$SURF__DIR
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_3_tar/${YEAR}/surf/
my_prex_or_die "./tar_avedir.sh -i $INPUTDIR -o $TARDIR -n 120 -v Ed_0250"

INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_4/${YEAR}
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/AVE_FREQ_4_tar/${YEAR}
my_prex_or_die "./tar_avedir.sh -i $INPUTDIR -o $TARDIR -n 120 -v ppn"

##### removng files not compreesed


INPUTDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/RESTARTS/${YEAR}
TARDIR=$CINECA_SCRATCH/$OPA_HOME/wrkdir/MODEL/RESTARTS_tar
my_prex_or_die "./tar_rstdir.sh -i $INPUTDIR -o $TARDIR -n 120"

2 changes: 2 additions & 0 deletions archive/pack.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,9 +41,11 @@ def addsep(string):
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nranks =comm.size
print("pack: using mpi4py.", flush=True)
except:
rank = 0
nranks = 1
print("pack: mpi4py not found, using serial.", flush=True)


args = argument()
Expand Down